From 2343d1a31fee4bbefa1e08c2374d100def8512e1 Mon Sep 17 00:00:00 2001 From: gvegayon Date: Fri, 22 Nov 2024 00:15:47 +0000 Subject: [PATCH] deploy: d7e04a4a5d232d254b21511690bb0caabc1e1d84 --- agent-meat-virus-sampling_8hpp_source.html | 6 +- class_l_f_m_c_m_c-members.html | 4 +- class_l_f_m_c_m_c.html | 12 +- class_model_s_e_i_r.html | 4 +- class_model_s_e_i_r_d.html | 4 +- classepiworld_1_1_l_f_m_c_m_c-members.html | 4 +- classepiworld_1_1_l_f_m_c_m_c.html | 12 +- classepiworld_1_1_model.html | 2 +- ...iworld_1_1epimodels_1_1_model_s_e_i_r.html | 4 +- ...orld_1_1epimodels_1_1_model_s_e_i_r_d.html | 4 +- diffnet_8hpp_source.html | 8 +- dir_02538684322ef550c75c27a53acd1367.html | 79 + epiworld_8hpp_source.html | 34266 ++++++++-------- include_2epiworld_2epiworld_8hpp_source.html | 4 +- init-functions_8hpp_source.html | 4 +- latex/agent-meat-state_8hpp__dep__incl.pdf | Bin 7058 -> 7058 bytes latex/agent-meat-state_8hpp__incl.pdf | Bin 6750 -> 6750 bytes latex/class_l_f_m_c_m_c.tex | 10 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misc_8hpp_source.html | 2 +- model-meat_8hpp_source.html | 2 +- namespaceepiworld_1_1sampler.html | 12 +- namespacesampler.html | 12 +- seir_8hpp_source.html | 6 +- seirconnected_8hpp_source.html | 8 +- seird_8hpp_source.html | 10 +- seirdconnected_8hpp_source.html | 10 +- seirmixing_8hpp_source.html | 8 +- sir_8hpp_source.html | 4 +- sirconnected_8hpp_source.html | 8 +- sird_8hpp_source.html | 4 +- sirdconnected_8hpp_source.html | 10 +- sirlogit_8hpp_source.html | 6 +- sirmixing_8hpp_source.html | 8 +- sis_8hpp_source.html | 4 +- sisd_8hpp_source.html | 4 +- surveillance_8hpp_source.html | 8 +- tests_8hpp_source.html | 6 +- 113 files changed, 17977 insertions(+), 17810 deletions(-) create mode 100644 dir_02538684322ef550c75c27a53acd1367.html diff --git a/agent-meat-virus-sampling_8hpp_source.html b/agent-meat-virus-sampling_8hpp_source.html index 96d01f21a..e70b2af93 100644 --- a/agent-meat-virus-sampling_8hpp_source.html +++ b/agent-meat-virus-sampling_8hpp_source.html @@ -75,7 +75,7 @@
3 
8 namespace sampler {
9 
-
23 template<typename TSeq>
+
23 template<typename TSeq = EPI_DEFAULT_TSEQ>
24 inline std::function<void(Agent<TSeq>*,Model<TSeq>*)> make_update_susceptible(
25  std::vector< epiworld_fast_uint > exclude = {}
26  )
@@ -221,7 +221,7 @@
166 
167 }
168 
-
182 template<typename TSeq = int>
+
182 template<typename TSeq = EPI_DEFAULT_TSEQ>
183 inline std::function<Virus<TSeq>*(Agent<TSeq>*,Model<TSeq>*)> make_sample_virus_neighbors(
184  std::vector< epiworld_fast_uint > exclude = {}
185 )
@@ -373,7 +373,7 @@
331 
332 }
333 
-
350 template<typename TSeq = int>
+
350 template<typename TSeq = EPI_DEFAULT_TSEQ>
351 inline Virus<TSeq> * sample_virus_single(Agent<TSeq> * p, Model<TSeq> * m)
352 {
353 
diff --git a/class_l_f_m_c_m_c-members.html b/class_l_f_m_c_m_c-members.html index 5b66a9571..176b60034 100644 --- a/class_l_f_m_c_m_c-members.html +++ b/class_l_f_m_c_m_c-members.html @@ -69,6 +69,8 @@

This is the complete list of members for LFMCMC< TData >, including all inherited members.

+ + @@ -87,7 +89,7 @@ - + diff --git a/class_l_f_m_c_m_c.html b/class_l_f_m_c_m_c.html index ac29a65d8..1569f26f3 100644 --- a/class_l_f_m_c_m_c.html +++ b/class_l_f_m_c_m_c.html @@ -137,6 +137,12 @@ + + + + @@ -149,9 +155,9 @@ - - + +
get_accepted_params() (defined in LFMCMC< TData >)LFMCMC< TData >inline
get_accepted_stats() (defined in LFMCMC< TData >)LFMCMC< TData >inline
get_drawn_prob() (defined in LFMCMC< TData >)LFMCMC< TData >inline
get_epsilon() const (defined in LFMCMC< TData >)LFMCMC< TData >inline
get_n_parameters() const (defined in LFMCMC< TData >)LFMCMC< TData >inline
get_stats_mean() (defined in LFMCMC< TData >)LFMCMC< TData >inline
LFMCMC() (defined in LFMCMC< TData >)LFMCMC< TData >inline
LFMCMC(const TData &observed_data_) (defined in LFMCMC< TData >)LFMCMC< TData >inline
print() (defined in LFMCMC< TData >)LFMCMC< TData >inline
print(size_t burnin=0u) const (defined in LFMCMC< TData >)LFMCMC< TData >inline
rgamma() (defined in LFMCMC< TData >)LFMCMC< TData >inline
rgamma(epiworld_double alpha, epiworld_double beta) (defined in LFMCMC< TData >)LFMCMC< TData >inline
rnorm() (defined in LFMCMC< TData >)LFMCMC< TData >inline
std::vector< TData > * get_sampled_data ()
 
+const std::vector< epiworld_double > & get_accepted_params ()
 
+const std::vector< epiworld_double > & get_accepted_stats ()
 
void set_par_names (std::vector< std::string > names)
 
std::vector< epiworld_double > get_stats_mean ()
 
-void print ()
 
+void print (size_t burnin=0u) const
 
Random number generation
Parameters
diff --git a/class_model_s_e_i_r.html b/class_model_s_e_i_r.html index d8f00c212..8ca9112be 100644 --- a/class_model_s_e_i_r.html +++ b/class_model_s_e_i_r.html @@ -788,8 +788,8 @@

return;
}
ModelSEIR
Template for a Susceptible-Exposed-Infected-Removed (SEIR) model.
Definition: seir.hpp:16
-
epiworld::Agent
Agent (agents)
Definition: epiworld.hpp:13643
-
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6296
+
epiworld::Agent
Agent (agents)
Definition: epiworld.hpp:13673
+
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6326
diff --git a/class_model_s_e_i_r_d.html b/class_model_s_e_i_r_d.html index 8e14c7ad1..21060c737 100644 --- a/class_model_s_e_i_r_d.html +++ b/class_model_s_e_i_r_d.html @@ -892,8 +892,8 @@

return;
}
ModelSEIRD
Template for a Susceptible-Exposed-Infected-Removed-Deceased (SEIRD) model.
Definition: seird.hpp:9
-
epiworld::Agent
Agent (agents)
Definition: epiworld.hpp:13643
-
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6296
+
epiworld::Agent
Agent (agents)
Definition: epiworld.hpp:13673
+
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6326
diff --git a/classepiworld_1_1_l_f_m_c_m_c-members.html b/classepiworld_1_1_l_f_m_c_m_c-members.html index 315d375f7..e22c917a0 100644 --- a/classepiworld_1_1_l_f_m_c_m_c-members.html +++ b/classepiworld_1_1_l_f_m_c_m_c-members.html @@ -73,6 +73,8 @@

This is the complete list of members for epiworld::LFMCMC< TData >, including all inherited members.

+ + @@ -91,7 +93,7 @@ - + diff --git a/classepiworld_1_1_l_f_m_c_m_c.html b/classepiworld_1_1_l_f_m_c_m_c.html index d90fd7a2e..1b957077f 100644 --- a/classepiworld_1_1_l_f_m_c_m_c.html +++ b/classepiworld_1_1_l_f_m_c_m_c.html @@ -141,6 +141,12 @@ + + + + @@ -153,9 +159,9 @@ - - + +
get_accepted_params() (defined in epiworld::LFMCMC< TData >)epiworld::LFMCMC< TData >inline
get_accepted_stats() (defined in epiworld::LFMCMC< TData >)epiworld::LFMCMC< TData >inline
get_drawn_prob() (defined in epiworld::LFMCMC< TData >)epiworld::LFMCMC< TData >inline
get_epsilon() const (defined in epiworld::LFMCMC< TData >)epiworld::LFMCMC< TData >inline
get_n_parameters() const (defined in epiworld::LFMCMC< TData >)epiworld::LFMCMC< TData >inline
get_stats_mean() (defined in epiworld::LFMCMC< TData >)epiworld::LFMCMC< TData >inline
LFMCMC() (defined in epiworld::LFMCMC< TData >)epiworld::LFMCMC< TData >inline
LFMCMC(const TData &observed_data_) (defined in epiworld::LFMCMC< TData >)epiworld::LFMCMC< TData >inline
print() (defined in epiworld::LFMCMC< TData >)epiworld::LFMCMC< TData >inline
print(size_t burnin=0u) const (defined in epiworld::LFMCMC< TData >)epiworld::LFMCMC< TData >inline
rgamma() (defined in epiworld::LFMCMC< TData >)epiworld::LFMCMC< TData >inline
rgamma(epiworld_double alpha, epiworld_double beta) (defined in epiworld::LFMCMC< TData >)epiworld::LFMCMC< TData >inline
rnorm() (defined in epiworld::LFMCMC< TData >)epiworld::LFMCMC< TData >inline
std::vector< TData > * get_sampled_data ()
 
+const std::vector< epiworld_double > & get_accepted_params ()
 
+const std::vector< epiworld_double > & get_accepted_stats ()
 
void set_par_names (std::vector< std::string > names)
 
std::vector< epiworld_double > get_stats_mean ()
 
-void print ()
 
+void print (size_t burnin=0u) const
 
Random number generation
Parameters
diff --git a/classepiworld_1_1_model.html b/classepiworld_1_1_model.html index 06dbad3c5..a00742beb 100644 --- a/classepiworld_1_1_model.html +++ b/classepiworld_1_1_model.html @@ -494,7 +494,7 @@
[name of parameter 1]: [value in double]
[name of parameter 2]: [value in double]
...
-
epiworld::Model::name
std::string name
Name of the model.
Definition: epiworld.hpp:6303
+
epiworld::Model::name
std::string name
Name of the model.
Definition: epiworld.hpp:6333

The only condition for parameter names is that these do not include a colon.

Parameters
diff --git a/classepiworld_1_1epimodels_1_1_model_s_e_i_r.html b/classepiworld_1_1epimodels_1_1_model_s_e_i_r.html index 39967b041..9924e13ba 100644 --- a/classepiworld_1_1epimodels_1_1_model_s_e_i_r.html +++ b/classepiworld_1_1epimodels_1_1_model_s_e_i_r.html @@ -792,8 +792,8 @@

return;
}
ModelSEIR
Template for a Susceptible-Exposed-Infected-Removed (SEIR) model.
Definition: seir.hpp:16
-
epiworld::Agent
Agent (agents)
Definition: epiworld.hpp:13643
-
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6296
+
epiworld::Agent
Agent (agents)
Definition: epiworld.hpp:13673
+
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6326
diff --git a/classepiworld_1_1epimodels_1_1_model_s_e_i_r_d.html b/classepiworld_1_1epimodels_1_1_model_s_e_i_r_d.html index a82c3e8fd..60e9c8fdc 100644 --- a/classepiworld_1_1epimodels_1_1_model_s_e_i_r_d.html +++ b/classepiworld_1_1epimodels_1_1_model_s_e_i_r_d.html @@ -896,8 +896,8 @@

return;
}
ModelSEIRD
Template for a Susceptible-Exposed-Infected-Removed-Deceased (SEIRD) model.
Definition: seird.hpp:9
-
epiworld::Agent
Agent (agents)
Definition: epiworld.hpp:13643
-
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6296
+
epiworld::Agent
Agent (agents)
Definition: epiworld.hpp:13673
+
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6326
diff --git a/diffnet_8hpp_source.html b/diffnet_8hpp_source.html index 5aa168215..b300fdfe4 100644 --- a/diffnet_8hpp_source.html +++ b/diffnet_8hpp_source.html @@ -273,10 +273,10 @@
210 #endif
Agent
Agent (agents)
Definition: agent-bones.hpp:66
ModelDiffNet
Template for a Network Diffusion Model.
Definition: diffnet.hpp:15
-
epiworld::Agent
Agent (agents)
Definition: epiworld.hpp:13643
-
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6296
-
epiworld::Model::get_n_viruses
size_t get_n_viruses() const
Number of viruses in the model.
Definition: epiworld.hpp:8598
-
epiworld::Virus
Virus.
Definition: epiworld.hpp:10105
+
epiworld::Agent
Agent (agents)
Definition: epiworld.hpp:13673
+
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6326
+
epiworld::Model::get_n_viruses
size_t get_n_viruses() const
Number of viruses in the model.
Definition: epiworld.hpp:8628
+
epiworld::Virus
Virus.
Definition: epiworld.hpp:10135
diff --git a/dir_02538684322ef550c75c27a53acd1367.html b/dir_02538684322ef550c75c27a53acd1367.html new file mode 100644 index 000000000..432c79b87 --- /dev/null +++ b/dir_02538684322ef550c75c27a53acd1367.html @@ -0,0 +1,79 @@ + + + + + + + +epiworld: examples/14-community-hosp Directory Reference + + + + + + + + + +
+
+

+ + + + + +
+
epiworld +  0.0-1 +
+
+
+ + + + + + + + +
+
+ + +
+ +
+ + + +
+
+
14-community-hosp Directory Reference
+
+
+
+ +
+Generated by doxygen 1.9.1 +
+ + diff --git a/epiworld_8hpp_source.html b/epiworld_8hpp_source.html index 509e257bb..bc767680d 100644 --- a/epiworld_8hpp_source.html +++ b/epiworld_8hpp_source.html @@ -86,8 +86,8 @@
18 
19 /* Versioning */
20 #define EPIWORLD_VERSION_MAJOR 0
-
21 #define EPIWORLD_VERSION_MINOR 4
-
22 #define EPIWORLD_VERSION_PATCH 3
+
21 #define EPIWORLD_VERSION_MINOR 5
+
22 #define EPIWORLD_VERSION_PATCH 0
23 
24 static const int epiworld_version_major = EPIWORLD_VERSION_MAJOR;
25 static const int epiworld_version_minor = EPIWORLD_VERSION_MINOR;
@@ -556,7 +556,7 @@
582  return false;
583 }
584 
-
598 template<typename TSeq, typename TDbl>
+
598 template<typename TSeq = EPI_DEFAULT_TSEQ, typename TDbl = epiworld_double >
599 inline int roulette(
600  const std::vector< TDbl > & probs,
601  Model<TSeq> * m
@@ -1075,7 +1075,7 @@
1239  epiworld_double * last_elapsed,
1240  std::string * unit_abbr,
1241  bool print
-
1242  );
+
1242  ) const;
1243 
1244  void chrono_start();
1245  void chrono_end();
@@ -1126,9697 +1126,9697 @@
1297  const std::vector< epiworld_double > & get_drawn_prob() {return drawn_prob;};
1298  std::vector< TData > * get_sampled_data() {return sampled_data;};
1299 
-
1300  void set_par_names(std::vector< std::string > names);
-
1301  void set_stats_names(std::vector< std::string > names);
+
1300  const std::vector< epiworld_double > & get_accepted_params() {return accepted_params;};
+
1301  const std::vector< epiworld_double > & get_accepted_stats() {return accepted_stats;};
1302 
-
1303  std::vector< epiworld_double > get_params_mean();
-
1304  std::vector< epiworld_double > get_stats_mean();
-
1305 
-
1306  void print() ;
-
1307 
-
1308 };
+
1303 
+
1304  void set_par_names(std::vector< std::string > names);
+
1305  void set_stats_names(std::vector< std::string > names);
+
1306 
+
1307  std::vector< epiworld_double > get_params_mean();
+
1308  std::vector< epiworld_double > get_stats_mean();
1309 
-
1310 #endif
-
1311 /*//////////////////////////////////////////////////////////////////////////////
+
1310  void print(size_t burnin = 0u) const;
+
1311 
+
1312 };
1313 
-
1314  End of -include/epiworld//math/lfmcmc/lfmcmc-bones.hpp-
-
1315 
-
1318 
+
1314 #endif
+
1315 /*//////////////////////////////////////////////////////////////////////////////
+
1317 
+
1318  End of -include/epiworld//math/lfmcmc/lfmcmc-bones.hpp-
1319 
-
1320 /*//////////////////////////////////////////////////////////////////////////////
1322 
-
1323  Start of -include/epiworld//math/lfmcmc/lfmcmc-meat.hpp-
-
1324 
-
1327 
+
1323 
+
1324 /*//////////////////////////////////////////////////////////////////////////////
+
1326 
+
1327  Start of -include/epiworld//math/lfmcmc/lfmcmc-meat.hpp-
1328 
-
1329 #ifndef EPIWORLD_LFMCMC_MEAT_HPP
-
1330 #define EPIWORLD_LFMCMC_MEAT_HPP
1331 
-
1332 /*//////////////////////////////////////////////////////////////////////////////
-
1334 
-
1335  Start of -include/epiworld//math//lfmcmc/lfmcmc-bones.hpp-
-
1336 
-
1339 
+
1332 
+
1333 #ifndef EPIWORLD_LFMCMC_MEAT_HPP
+
1334 #define EPIWORLD_LFMCMC_MEAT_HPP
+
1335 
+
1336 /*//////////////////////////////////////////////////////////////////////////////
+
1338 
+
1339  Start of -include/epiworld//math//lfmcmc/lfmcmc-bones.hpp-
1340 
-
1341 #ifndef EPIWORLD_LFMCMC_BONES_HPP
-
1342 #define EPIWORLD_LFMCMC_BONES_HPP
1343 
-
1344 #ifndef epiworld_double
-
1345  #define epiworld_double float
-
1346 #endif
+
1344 
+
1345 #ifndef EPIWORLD_LFMCMC_BONES_HPP
+
1346 #define EPIWORLD_LFMCMC_BONES_HPP
1347 
-
1348 
-
1349 template<typename TData>
-
1350 class LFMCMC;
+
1348 #ifndef epiworld_double
+
1349  #define epiworld_double float
+
1350 #endif
1351 
-
1352 template<typename TData>
-
1353 using LFMCMCSimFun = std::function<TData(const std::vector< epiworld_double >&,LFMCMC<TData>*)>;
-
1354 
-
1355 template<typename TData>
-
1356 using LFMCMCSummaryFun = std::function<void(std::vector< epiworld_double >&,const TData&,LFMCMC<TData>*)>;
-
1357 
-
1358 template<typename TData>
-
1359 using LFMCMCProposalFun = std::function<void(std::vector< epiworld_double >&,const std::vector< epiworld_double >&,LFMCMC<TData>*)>;
-
1360 
-
1361 template<typename TData>
-
1362 using LFMCMCKernelFun = std::function<epiworld_double(const std::vector< epiworld_double >&,const std::vector< epiworld_double >&,epiworld_double,LFMCMC<TData>*)>;
-
1363 
-
1371 template<typename TData>
-
1372 inline void proposal_fun_normal(
-
1373  std::vector< epiworld_double >& params_now,
-
1374  const std::vector< epiworld_double >& params_prev,
-
1375  LFMCMC<TData>* m
-
1376 );
-
1377 
-
1390 template<typename TData>
-
1391 inline LFMCMCProposalFun<TData> make_proposal_norm_reflective(
-
1392  epiworld_double scale,
-
1393  epiworld_double lb = std::numeric_limits<epiworld_double>::min(),
-
1394  epiworld_double ub = std::numeric_limits<epiworld_double>::max()
-
1395 );
-
1396 
-
1408 template<typename TData>
-
1409 inline void proposal_fun_unif(
-
1410  std::vector< epiworld_double >& params_now,
-
1411  const std::vector< epiworld_double >& params_prev,
-
1412  LFMCMC<TData>* m
-
1413 );
-
1414 
-
1425 template<typename TData>
-
1426 inline epiworld_double kernel_fun_uniform(
-
1427  const std::vector< epiworld_double >& stats_now,
-
1428  const std::vector< epiworld_double >& stats_obs,
-
1429  epiworld_double epsilon,
-
1430  LFMCMC<TData>* m
-
1431 );
-
1432 
-
1441 template<typename TData>
-
1442 inline epiworld_double kernel_fun_gaussian(
-
1443  const std::vector< epiworld_double >& stats_now,
-
1444  const std::vector< epiworld_double >& stats_obs,
-
1445  epiworld_double epsilon,
-
1446  LFMCMC<TData>* m
-
1447 );
-
1448 
-
1454 template<typename TData>
-
1455 class LFMCMC {
-
1456 private:
-
1457 
-
1458  // Random number sampling
-
1459  std::shared_ptr< std::mt19937 > engine = nullptr;
-
1460 
-
1461  std::shared_ptr< std::uniform_real_distribution<> > runifd =
-
1462  std::make_shared< std::uniform_real_distribution<> >(0.0, 1.0);
-
1463 
-
1464  std::shared_ptr< std::normal_distribution<> > rnormd =
-
1465  std::make_shared< std::normal_distribution<> >(0.0);
-
1466 
-
1467  std::shared_ptr< std::gamma_distribution<> > rgammad =
-
1468  std::make_shared< std::gamma_distribution<> >();
-
1469 
-
1470  // Process data
-
1471  TData observed_data;
-
1472 
-
1473  // Information about the size of the problem
-
1474  size_t n_samples;
-
1475  size_t n_statistics;
-
1476  size_t n_parameters;
-
1477 
-
1478  epiworld_double epsilon;
-
1479 
-
1480  std::vector< epiworld_double > params_now;
-
1481  std::vector< epiworld_double > params_prev;
-
1482  std::vector< epiworld_double > params_init;
+
1352 
+
1353 template<typename TData>
+
1354 class LFMCMC;
+
1355 
+
1356 template<typename TData>
+
1357 using LFMCMCSimFun = std::function<TData(const std::vector< epiworld_double >&,LFMCMC<TData>*)>;
+
1358 
+
1359 template<typename TData>
+
1360 using LFMCMCSummaryFun = std::function<void(std::vector< epiworld_double >&,const TData&,LFMCMC<TData>*)>;
+
1361 
+
1362 template<typename TData>
+
1363 using LFMCMCProposalFun = std::function<void(std::vector< epiworld_double >&,const std::vector< epiworld_double >&,LFMCMC<TData>*)>;
+
1364 
+
1365 template<typename TData>
+
1366 using LFMCMCKernelFun = std::function<epiworld_double(const std::vector< epiworld_double >&,const std::vector< epiworld_double >&,epiworld_double,LFMCMC<TData>*)>;
+
1367 
+
1375 template<typename TData>
+
1376 inline void proposal_fun_normal(
+
1377  std::vector< epiworld_double >& params_now,
+
1378  const std::vector< epiworld_double >& params_prev,
+
1379  LFMCMC<TData>* m
+
1380 );
+
1381 
+
1394 template<typename TData>
+
1395 inline LFMCMCProposalFun<TData> make_proposal_norm_reflective(
+
1396  epiworld_double scale,
+
1397  epiworld_double lb = std::numeric_limits<epiworld_double>::min(),
+
1398  epiworld_double ub = std::numeric_limits<epiworld_double>::max()
+
1399 );
+
1400 
+
1412 template<typename TData>
+
1413 inline void proposal_fun_unif(
+
1414  std::vector< epiworld_double >& params_now,
+
1415  const std::vector< epiworld_double >& params_prev,
+
1416  LFMCMC<TData>* m
+
1417 );
+
1418 
+
1429 template<typename TData>
+
1430 inline epiworld_double kernel_fun_uniform(
+
1431  const std::vector< epiworld_double >& stats_now,
+
1432  const std::vector< epiworld_double >& stats_obs,
+
1433  epiworld_double epsilon,
+
1434  LFMCMC<TData>* m
+
1435 );
+
1436 
+
1445 template<typename TData>
+
1446 inline epiworld_double kernel_fun_gaussian(
+
1447  const std::vector< epiworld_double >& stats_now,
+
1448  const std::vector< epiworld_double >& stats_obs,
+
1449  epiworld_double epsilon,
+
1450  LFMCMC<TData>* m
+
1451 );
+
1452 
+
1458 template<typename TData>
+
1459 class LFMCMC {
+
1460 private:
+
1461 
+
1462  // Random number sampling
+
1463  std::shared_ptr< std::mt19937 > engine = nullptr;
+
1464 
+
1465  std::shared_ptr< std::uniform_real_distribution<> > runifd =
+
1466  std::make_shared< std::uniform_real_distribution<> >(0.0, 1.0);
+
1467 
+
1468  std::shared_ptr< std::normal_distribution<> > rnormd =
+
1469  std::make_shared< std::normal_distribution<> >(0.0);
+
1470 
+
1471  std::shared_ptr< std::gamma_distribution<> > rgammad =
+
1472  std::make_shared< std::gamma_distribution<> >();
+
1473 
+
1474  // Process data
+
1475  TData observed_data;
+
1476 
+
1477  // Information about the size of the problem
+
1478  size_t n_samples;
+
1479  size_t n_statistics;
+
1480  size_t n_parameters;
+
1481 
+
1482  epiworld_double epsilon;
1483 
-
1484  std::vector< epiworld_double > observed_stats; ///< Observed statistics
-
1485 
-
1486  std::vector< epiworld_double > sampled_params; ///< Sampled Parameters
-
1487  std::vector< epiworld_double > sampled_stats; ///< Sampled statistics
-
1488  std::vector< epiworld_double > sampled_stats_prob; ///< Sampled statistics
-
1489  std::vector< bool > sampled_accepted; ///< Indicator of accepted statistics
-
1490 
-
1491  std::vector< epiworld_double > accepted_params; ///< Posterior distribution (accepted samples)
-
1492  std::vector< epiworld_double > accepted_stats; ///< Posterior distribution (accepted samples)
-
1493  std::vector< epiworld_double > accepted_params_prob; ///< Posterior probability
+
1484  std::vector< epiworld_double > params_now;
+
1485  std::vector< epiworld_double > params_prev;
+
1486  std::vector< epiworld_double > params_init;
+
1487 
+
1488  std::vector< epiworld_double > observed_stats; ///< Observed statistics
+
1489 
+
1490  std::vector< epiworld_double > sampled_params; ///< Sampled Parameters
+
1491  std::vector< epiworld_double > sampled_stats; ///< Sampled statistics
+
1492  std::vector< epiworld_double > sampled_stats_prob; ///< Sampled statistics
+
1493  std::vector< bool > sampled_accepted; ///< Indicator of accepted statistics
1494 
-
1495  std::vector< epiworld_double > drawn_prob; ///< Drawn probabilities (runif())
-
1496  std::vector< TData > * sampled_data = nullptr;
-
1497 
-
1498  // Functions
-
1499  LFMCMCSimFun<TData> simulation_fun;
-
1500  LFMCMCSummaryFun<TData> summary_fun;
-
1501  LFMCMCProposalFun<TData> proposal_fun = proposal_fun_normal<TData>;
-
1502  LFMCMCKernelFun<TData> kernel_fun = kernel_fun_uniform<TData>;
-
1503 
-
1504  // Misc
-
1505  std::vector< std::string > names_parameters;
-
1506  std::vector< std::string > names_statistics;
+
1495  std::vector< epiworld_double > accepted_params; ///< Posterior distribution (accepted samples)
+
1496  std::vector< epiworld_double > accepted_stats; ///< Posterior distribution (accepted samples)
+
1497  std::vector< epiworld_double > accepted_params_prob; ///< Posterior probability
+
1498 
+
1499  std::vector< epiworld_double > drawn_prob; ///< Drawn probabilities (runif())
+
1500  std::vector< TData > * sampled_data = nullptr;
+
1501 
+
1502  // Functions
+
1503  LFMCMCSimFun<TData> simulation_fun;
+
1504  LFMCMCSummaryFun<TData> summary_fun;
+
1505  LFMCMCProposalFun<TData> proposal_fun = proposal_fun_normal<TData>;
+
1506  LFMCMCKernelFun<TData> kernel_fun = kernel_fun_uniform<TData>;
1507 
-
1508  std::chrono::time_point<std::chrono::steady_clock> time_start;
-
1509  std::chrono::time_point<std::chrono::steady_clock> time_end;
-
1510 
-
1511  // std::chrono::milliseconds
-
1512  std::chrono::duration<epiworld_double,std::micro> time_elapsed =
-
1513  std::chrono::duration<epiworld_double,std::micro>::zero();
+
1508  // Misc
+
1509  std::vector< std::string > names_parameters;
+
1510  std::vector< std::string > names_statistics;
+
1511 
+
1512  std::chrono::time_point<std::chrono::steady_clock> time_start;
+
1513  std::chrono::time_point<std::chrono::steady_clock> time_end;
1514 
-
1515  inline void get_elapsed(
-
1516  std::string unit,
-
1517  epiworld_double * last_elapsed,
-
1518  std::string * unit_abbr,
-
1519  bool print
-
1520  );
-
1521 
-
1522  void chrono_start();
-
1523  void chrono_end();
-
1524 
-
1525 public:
-
1526 
-
1527  void run(
-
1528  std::vector< epiworld_double > param_init,
-
1529  size_t n_samples_,
-
1530  epiworld_double epsilon_,
-
1531  int seed = -1
-
1532  );
-
1533 
-
1534  LFMCMC() {};
-
1535  LFMCMC(const TData & observed_data_) : observed_data(observed_data_) {};
-
1536  ~LFMCMC() {};
+
1515  // std::chrono::milliseconds
+
1516  std::chrono::duration<epiworld_double,std::micro> time_elapsed =
+
1517  std::chrono::duration<epiworld_double,std::micro>::zero();
+
1518 
+
1519  inline void get_elapsed(
+
1520  std::string unit,
+
1521  epiworld_double * last_elapsed,
+
1522  std::string * unit_abbr,
+
1523  bool print
+
1524  ) const;
+
1525 
+
1526  void chrono_start();
+
1527  void chrono_end();
+
1528 
+
1529 public:
+
1530 
+
1531  void run(
+
1532  std::vector< epiworld_double > param_init,
+
1533  size_t n_samples_,
+
1534  epiworld_double epsilon_,
+
1535  int seed = -1
+
1536  );
1537 
-
1538  void set_observed_data(const TData & observed_data_) {observed_data = observed_data_;};
-
1539  void set_proposal_fun(LFMCMCProposalFun<TData> fun);
-
1540  void set_simulation_fun(LFMCMCSimFun<TData> fun);
-
1541  void set_summary_fun(LFMCMCSummaryFun<TData> fun);
-
1542  void set_kernel_fun(LFMCMCKernelFun<TData> fun);
-
1543 
-
1550  void set_rand_engine(std::shared_ptr< std::mt19937 > & eng);
-
1551  std::shared_ptr< std::mt19937 > & get_rand_endgine();
-
1552  void seed(epiworld_fast_uint s);
-
1553  void set_rand_gamma(epiworld_double alpha, epiworld_double beta);
-
1554  epiworld_double runif();
-
1555  epiworld_double rnorm();
-
1556  epiworld_double rgamma();
-
1557  epiworld_double runif(epiworld_double lb, epiworld_double ub);
-
1558  epiworld_double rnorm(epiworld_double mean, epiworld_double sd);
-
1559  epiworld_double rgamma(epiworld_double alpha, epiworld_double beta);
-
1561 
-
1562  // Accessing parameters of the function
-
1563  size_t get_n_samples() const {return n_samples;};
-
1564  size_t get_n_statistics() const {return n_statistics;};
-
1565  size_t get_n_parameters() const {return n_parameters;};
-
1566  epiworld_double get_epsilon() const {return epsilon;};
-
1567 
-
1568  const std::vector< epiworld_double > & get_params_now() {return params_now;};
-
1569  const std::vector< epiworld_double > & get_params_prev() {return params_prev;};
-
1570  const std::vector< epiworld_double > & get_params_init() {return params_init;};
-
1571  const std::vector< epiworld_double > & get_statistics_obs() {return observed_stats;};
-
1572  const std::vector< epiworld_double > & get_statistics_hist() {return sampled_stats;};
-
1573  const std::vector< bool > & get_statistics_accepted() {return sampled_accepted;};
-
1574  const std::vector< epiworld_double > & get_posterior_lf_prob() {return accepted_params_prob;};
-
1575  const std::vector< epiworld_double > & get_drawn_prob() {return drawn_prob;};
-
1576  std::vector< TData > * get_sampled_data() {return sampled_data;};
-
1577 
-
1578  void set_par_names(std::vector< std::string > names);
-
1579  void set_stats_names(std::vector< std::string > names);
-
1580 
-
1581  std::vector< epiworld_double > get_params_mean();
-
1582  std::vector< epiworld_double > get_stats_mean();
-
1583 
-
1584  void print() ;
+
1538  LFMCMC() {};
+
1539  LFMCMC(const TData & observed_data_) : observed_data(observed_data_) {};
+
1540  ~LFMCMC() {};
+
1541 
+
1542  void set_observed_data(const TData & observed_data_) {observed_data = observed_data_;};
+
1543  void set_proposal_fun(LFMCMCProposalFun<TData> fun);
+
1544  void set_simulation_fun(LFMCMCSimFun<TData> fun);
+
1545  void set_summary_fun(LFMCMCSummaryFun<TData> fun);
+
1546  void set_kernel_fun(LFMCMCKernelFun<TData> fun);
+
1547 
+
1554  void set_rand_engine(std::shared_ptr< std::mt19937 > & eng);
+
1555  std::shared_ptr< std::mt19937 > & get_rand_endgine();
+
1556  void seed(epiworld_fast_uint s);
+
1557  void set_rand_gamma(epiworld_double alpha, epiworld_double beta);
+
1558  epiworld_double runif();
+
1559  epiworld_double rnorm();
+
1560  epiworld_double rgamma();
+
1561  epiworld_double runif(epiworld_double lb, epiworld_double ub);
+
1562  epiworld_double rnorm(epiworld_double mean, epiworld_double sd);
+
1563  epiworld_double rgamma(epiworld_double alpha, epiworld_double beta);
+
1565 
+
1566  // Accessing parameters of the function
+
1567  size_t get_n_samples() const {return n_samples;};
+
1568  size_t get_n_statistics() const {return n_statistics;};
+
1569  size_t get_n_parameters() const {return n_parameters;};
+
1570  epiworld_double get_epsilon() const {return epsilon;};
+
1571 
+
1572  const std::vector< epiworld_double > & get_params_now() {return params_now;};
+
1573  const std::vector< epiworld_double > & get_params_prev() {return params_prev;};
+
1574  const std::vector< epiworld_double > & get_params_init() {return params_init;};
+
1575  const std::vector< epiworld_double > & get_statistics_obs() {return observed_stats;};
+
1576  const std::vector< epiworld_double > & get_statistics_hist() {return sampled_stats;};
+
1577  const std::vector< bool > & get_statistics_accepted() {return sampled_accepted;};
+
1578  const std::vector< epiworld_double > & get_posterior_lf_prob() {return accepted_params_prob;};
+
1579  const std::vector< epiworld_double > & get_drawn_prob() {return drawn_prob;};
+
1580  std::vector< TData > * get_sampled_data() {return sampled_data;};
+
1581 
+
1582  const std::vector< epiworld_double > & get_accepted_params() {return accepted_params;};
+
1583  const std::vector< epiworld_double > & get_accepted_stats() {return accepted_stats;};
+
1584 
1585 
-
1586 };
-
1587 
-
1588 #endif
-
1589 /*//////////////////////////////////////////////////////////////////////////////
+
1586  void set_par_names(std::vector< std::string > names);
+
1587  void set_stats_names(std::vector< std::string > names);
+
1588 
+
1589  std::vector< epiworld_double > get_params_mean();
+
1590  std::vector< epiworld_double > get_stats_mean();
1591 
-
1592  End of -include/epiworld//math//lfmcmc/lfmcmc-bones.hpp-
+
1592  void print(size_t burnin = 0u) const;
1593 
-
1596 
-
1597 
-
1598 
-
1606 template<typename TData>
-
1607 inline void proposal_fun_normal(
-
1608  std::vector< epiworld_double >& params_now,
-
1609  const std::vector< epiworld_double >& params_prev,
-
1610  LFMCMC<TData>* m
-
1611 ) {
-
1612 
-
1613  for (size_t p = 0u; p < m->get_n_parameters(); ++p)
-
1614  params_now[p] = params_prev[p] + m->rnorm();
-
1615 
-
1616  return;
-
1617 }
-
1618 
-
1631 template<typename TData>
-
1632 inline LFMCMCProposalFun<TData> make_proposal_norm_reflective(
-
1633  epiworld_double scale,
-
1634  epiworld_double lb,
-
1635  epiworld_double ub
-
1636 ) {
-
1637 
-
1638  LFMCMCProposalFun<TData> fun =
-
1639  [scale,lb,ub](
-
1640  std::vector< epiworld_double >& params_now,
-
1641  const std::vector< epiworld_double >& params_prev,
-
1642  LFMCMC<TData>* m
-
1643  ) {
-
1644 
-
1645  // Making the proposal
-
1646  for (size_t p = 0u; p < m->get_n_parameters(); ++p)
-
1647  params_now[p] = params_prev[p] + m->rnorm() * scale;
-
1648 
-
1649  // Checking boundaries
-
1650  epiworld_double d = ub - lb;
-
1651  int odd;
-
1652  epiworld_double d_above, d_below;
-
1653  for (auto & p : params_now)
-
1654  {
-
1655 
-
1656  // Correcting if parameter goes above the upper bound
-
1657  if (p > ub)
-
1658  {
-
1659  d_above = p - ub;
-
1660  odd = static_cast<int>(std::floor(d_above / d)) % 2;
-
1661  d_above = d_above - std::floor(d_above / d) * d;
-
1662 
-
1663  p = (lb + d_above) * odd +
-
1664  (ub - d_above) * (1 - odd);
-
1665 
-
1666  // Correcting if parameter goes below upper bound
-
1667  } else if (p < lb)
-
1668  {
-
1669  d_below = lb - p;
-
1670  int odd = static_cast<int>(std::floor(d_below / d)) % 2;
-
1671  d_below = d_below - std::floor(d_below / d) * d;
-
1672 
-
1673  p = (ub - d_below) * odd +
-
1674  (lb + d_below) * (1 - odd);
-
1675  }
-
1676 
-
1677  }
-
1678 
-
1679  #ifdef EPI_DEBUG
-
1680  for (auto & p : params_now)
-
1681  if (p < lb || p > ub)
-
1682  throw std::range_error("The parameter is out of bounds.");
-
1683  #endif
+
1594 };
+
1595 
+
1596 #endif
+
1597 /*//////////////////////////////////////////////////////////////////////////////
+
1599 
+
1600  End of -include/epiworld//math//lfmcmc/lfmcmc-bones.hpp-
+
1601 
+
1604 
+
1605 
+
1606 
+
1614 template<typename TData>
+
1615 inline void proposal_fun_normal(
+
1616  std::vector< epiworld_double >& params_now,
+
1617  const std::vector< epiworld_double >& params_prev,
+
1618  LFMCMC<TData>* m
+
1619 ) {
+
1620 
+
1621  for (size_t p = 0u; p < m->get_n_parameters(); ++p)
+
1622  params_now[p] = params_prev[p] + m->rnorm();
+
1623 
+
1624  return;
+
1625 }
+
1626 
+
1639 template<typename TData>
+
1640 inline LFMCMCProposalFun<TData> make_proposal_norm_reflective(
+
1641  epiworld_double scale,
+
1642  epiworld_double lb,
+
1643  epiworld_double ub
+
1644 ) {
+
1645 
+
1646  LFMCMCProposalFun<TData> fun =
+
1647  [scale,lb,ub](
+
1648  std::vector< epiworld_double >& params_now,
+
1649  const std::vector< epiworld_double >& params_prev,
+
1650  LFMCMC<TData>* m
+
1651  ) {
+
1652 
+
1653  // Making the proposal
+
1654  for (size_t p = 0u; p < m->get_n_parameters(); ++p)
+
1655  params_now[p] = params_prev[p] + m->rnorm() * scale;
+
1656 
+
1657  // Checking boundaries
+
1658  epiworld_double d = ub - lb;
+
1659  int odd;
+
1660  epiworld_double d_above, d_below;
+
1661  for (auto & p : params_now)
+
1662  {
+
1663 
+
1664  // Correcting if parameter goes above the upper bound
+
1665  if (p > ub)
+
1666  {
+
1667  d_above = p - ub;
+
1668  odd = static_cast<int>(std::floor(d_above / d)) % 2;
+
1669  d_above = d_above - std::floor(d_above / d) * d;
+
1670 
+
1671  p = (lb + d_above) * odd +
+
1672  (ub - d_above) * (1 - odd);
+
1673 
+
1674  // Correcting if parameter goes below upper bound
+
1675  } else if (p < lb)
+
1676  {
+
1677  d_below = lb - p;
+
1678  int odd = static_cast<int>(std::floor(d_below / d)) % 2;
+
1679  d_below = d_below - std::floor(d_below / d) * d;
+
1680 
+
1681  p = (ub - d_below) * odd +
+
1682  (lb + d_below) * (1 - odd);
+
1683  }
1684 
-
1685 
-
1686  return;
-
1687 
-
1688  };
-
1689 
-
1690  return fun;
-
1691 }
+
1685  }
+
1686 
+
1687  #ifdef EPI_DEBUG
+
1688  for (auto & p : params_now)
+
1689  if (p < lb || p > ub)
+
1690  throw std::range_error("The parameter is out of bounds.");
+
1691  #endif
1692 
-
1704 template<typename TData>
-
1705 inline void proposal_fun_unif(
-
1706  std::vector< epiworld_double >& params_now,
-
1707  const std::vector< epiworld_double >& params_prev,
-
1708  LFMCMC<TData>* m
-
1709 ) {
-
1710 
-
1711  for (size_t p = 0u; p < m->get_n_parameters(); ++p)
-
1712  params_now[p] = (params_prev[p] + m->runif(-1.0, 1.0));
-
1713 
-
1714  return;
-
1715 }
-
1716 
-
1727 template<typename TData>
-
1728 inline epiworld_double kernel_fun_uniform(
-
1729  const std::vector< epiworld_double >& stats_now,
-
1730  const std::vector< epiworld_double >& stats_obs,
-
1731  epiworld_double epsilon,
-
1732  LFMCMC<TData>* m
-
1733 ) {
-
1734 
-
1735  epiworld_double ans = 0.0;
-
1736  for (size_t p = 0u; p < m->get_n_parameters(); ++p)
-
1737  ans += std::pow(stats_obs[p] - stats_now[p], 2.0);
-
1738 
-
1739  return std::sqrt(ans) < epsilon ? 1.0 : 0.0;
-
1740 
-
1741 }
+
1693 
+
1694  return;
+
1695 
+
1696  };
+
1697 
+
1698  return fun;
+
1699 }
+
1700 
+
1712 template<typename TData>
+
1713 inline void proposal_fun_unif(
+
1714  std::vector< epiworld_double >& params_now,
+
1715  const std::vector< epiworld_double >& params_prev,
+
1716  LFMCMC<TData>* m
+
1717 ) {
+
1718 
+
1719  for (size_t p = 0u; p < m->get_n_parameters(); ++p)
+
1720  params_now[p] = (params_prev[p] + m->runif(-1.0, 1.0));
+
1721 
+
1722  return;
+
1723 }
+
1724 
+
1735 template<typename TData>
+
1736 inline epiworld_double kernel_fun_uniform(
+
1737  const std::vector< epiworld_double >& stats_now,
+
1738  const std::vector< epiworld_double >& stats_obs,
+
1739  epiworld_double epsilon,
+
1740  LFMCMC<TData>* m
+
1741 ) {
1742 
-
1743 #define sqrt2pi() 2.5066282746310002416
-
1744 
-
1753 template<typename TData>
-
1754 inline epiworld_double kernel_fun_gaussian(
-
1755  const std::vector< epiworld_double >& stats_now,
-
1756  const std::vector< epiworld_double >& stats_obs,
-
1757  epiworld_double epsilon,
-
1758  LFMCMC<TData>* m
-
1759 ) {
-
1760 
-
1761  epiworld_double ans = 0.0;
-
1762  for (size_t p = 0u; p < m->get_n_parameters(); ++p)
-
1763  ans += std::pow(stats_obs[p] - stats_now[p], 2.0);
-
1764 
-
1765  return std::exp(
-
1766  -.5 * (ans/std::pow(1 + std::pow(epsilon, 2.0)/3.0, 2.0))
-
1767  ) / sqrt2pi() ;
+
1743  epiworld_double ans = 0.0;
+
1744  for (size_t p = 0u; p < m->get_n_parameters(); ++p)
+
1745  ans += std::pow(stats_obs[p] - stats_now[p], 2.0);
+
1746 
+
1747  return std::sqrt(ans) < epsilon ? 1.0 : 0.0;
+
1748 
+
1749 }
+
1750 
+
1751 #define sqrt2pi() 2.5066282746310002416
+
1752 
+
1761 template<typename TData>
+
1762 inline epiworld_double kernel_fun_gaussian(
+
1763  const std::vector< epiworld_double >& stats_now,
+
1764  const std::vector< epiworld_double >& stats_obs,
+
1765  epiworld_double epsilon,
+
1766  LFMCMC<TData>* m
+
1767 ) {
1768 
-
1769 }
-
1770 
-
1771 
-
1772 template<typename TData>
-
1773 inline void LFMCMC<TData>::set_proposal_fun(LFMCMCProposalFun<TData> fun)
-
1774 {
-
1775  proposal_fun = fun;
-
1776 }
-
1777 
-
1778 template<typename TData>
-
1779 inline void LFMCMC<TData>::set_simulation_fun(LFMCMCSimFun<TData> fun)
-
1780 {
-
1781  simulation_fun = fun;
-
1782 }
-
1783 
-
1784 template<typename TData>
-
1785 inline void LFMCMC<TData>::set_summary_fun(LFMCMCSummaryFun<TData> fun)
-
1786 {
-
1787  summary_fun = fun;
-
1788 }
-
1789 
-
1790 template<typename TData>
-
1791 inline void LFMCMC<TData>::set_kernel_fun(LFMCMCKernelFun<TData> fun)
-
1792 {
-
1793  kernel_fun = fun;
-
1794 }
-
1795 
-
1796 
-
1797 template<typename TData>
-
1798 inline void LFMCMC<TData>::run(
-
1799  std::vector< epiworld_double > params_init_,
-
1800  size_t n_samples_,
-
1801  epiworld_double epsilon_,
-
1802  int seed
-
1803  )
-
1804 {
-
1805 
-
1806  // Starting timing
-
1807  chrono_start();
-
1808 
-
1809  // Setting the baseline parameters of the model
-
1810  n_samples = n_samples_;
-
1811  epsilon = epsilon_;
-
1812  params_init = params_init_;
-
1813  n_parameters = params_init_.size();
-
1814 
-
1815  if (seed >= 0)
-
1816  this->seed(seed);
-
1817 
-
1818  params_now.resize(n_parameters);
-
1819  params_prev.resize(n_parameters);
-
1820 
-
1821  if (sampled_data != nullptr)
-
1822  sampled_data->resize(n_samples);
-
1823 
-
1824  params_prev = params_init;
-
1825  params_now = params_init;
-
1826 
-
1827  // Computing the baseline sufficient statistics
-
1828  summary_fun(observed_stats, observed_data, this);
-
1829  n_statistics = observed_stats.size();
-
1830 
-
1831  // Reserving size
-
1832  drawn_prob.resize(n_samples);
-
1833  sampled_accepted.resize(n_samples, false);
-
1834  sampled_stats.resize(n_samples * n_statistics);
-
1835  sampled_stats_prob.resize(n_samples);
-
1836 
-
1837  accepted_params.resize(n_samples * n_parameters);
-
1838  accepted_stats.resize(n_samples * n_statistics);
-
1839  accepted_params_prob.resize(n_samples);
-
1840 
-
1841  TData data_i = simulation_fun(params_init, this);
-
1842 
-
1843  std::vector< epiworld_double > proposed_stats_i;
-
1844  summary_fun(proposed_stats_i, data_i, this);
-
1845  accepted_params_prob[0u] = kernel_fun(proposed_stats_i, observed_stats, epsilon, this);
-
1846 
-
1847  // Recording statistics
-
1848  for (size_t i = 0u; i < n_statistics; ++i)
-
1849  sampled_stats[i] = proposed_stats_i[i];
+
1769  epiworld_double ans = 0.0;
+
1770  for (size_t p = 0u; p < m->get_n_parameters(); ++p)
+
1771  ans += std::pow(stats_obs[p] - stats_now[p], 2.0);
+
1772 
+
1773  return std::exp(
+
1774  -.5 * (ans/std::pow(1 + std::pow(epsilon, 2.0)/3.0, 2.0))
+
1775  ) / sqrt2pi() ;
+
1776 
+
1777 }
+
1778 
+
1779 
+
1780 template<typename TData>
+
1781 inline void LFMCMC<TData>::set_proposal_fun(LFMCMCProposalFun<TData> fun)
+
1782 {
+
1783  proposal_fun = fun;
+
1784 }
+
1785 
+
1786 template<typename TData>
+
1787 inline void LFMCMC<TData>::set_simulation_fun(LFMCMCSimFun<TData> fun)
+
1788 {
+
1789  simulation_fun = fun;
+
1790 }
+
1791 
+
1792 template<typename TData>
+
1793 inline void LFMCMC<TData>::set_summary_fun(LFMCMCSummaryFun<TData> fun)
+
1794 {
+
1795  summary_fun = fun;
+
1796 }
+
1797 
+
1798 template<typename TData>
+
1799 inline void LFMCMC<TData>::set_kernel_fun(LFMCMCKernelFun<TData> fun)
+
1800 {
+
1801  kernel_fun = fun;
+
1802 }
+
1803 
+
1804 
+
1805 template<typename TData>
+
1806 inline void LFMCMC<TData>::run(
+
1807  std::vector< epiworld_double > params_init_,
+
1808  size_t n_samples_,
+
1809  epiworld_double epsilon_,
+
1810  int seed
+
1811  )
+
1812 {
+
1813 
+
1814  // Starting timing
+
1815  chrono_start();
+
1816 
+
1817  // Setting the baseline parameters of the model
+
1818  n_samples = n_samples_;
+
1819  epsilon = epsilon_;
+
1820  params_init = params_init_;
+
1821  n_parameters = params_init_.size();
+
1822 
+
1823  if (seed >= 0)
+
1824  this->seed(seed);
+
1825 
+
1826  params_now.resize(n_parameters);
+
1827  params_prev.resize(n_parameters);
+
1828 
+
1829  if (sampled_data != nullptr)
+
1830  sampled_data->resize(n_samples);
+
1831 
+
1832  params_prev = params_init;
+
1833  params_now = params_init;
+
1834 
+
1835  // Computing the baseline sufficient statistics
+
1836  summary_fun(observed_stats, observed_data, this);
+
1837  n_statistics = observed_stats.size();
+
1838 
+
1839  // Reserving size
+
1840  drawn_prob.resize(n_samples);
+
1841  sampled_accepted.resize(n_samples, false);
+
1842  sampled_stats.resize(n_samples * n_statistics);
+
1843  sampled_stats_prob.resize(n_samples);
+
1844 
+
1845  accepted_params.resize(n_samples * n_parameters);
+
1846  accepted_stats.resize(n_samples * n_statistics);
+
1847  accepted_params_prob.resize(n_samples);
+
1848 
+
1849  TData data_i = simulation_fun(params_init, this);
1850 
-
1851  for (size_t k = 0u; k < n_statistics; ++k)
-
1852  accepted_params[k] = proposed_stats_i[k];
-
1853 
-
1854  for (size_t i = 1u; i < n_samples; ++i)
-
1855  {
-
1856  // Step 1: Generate a proposal and store it in params_now
-
1857  proposal_fun(params_now, params_prev, this);
-
1858 
-
1859  // Step 2: Using params_now, simulate data
-
1860  TData data_i = simulation_fun(params_now, this);
-
1861 
-
1862  // Are we storing the data?
-
1863  if (sampled_data != nullptr)
-
1864  sampled_data->operator[](i) = data_i;
-
1865 
-
1866  // Step 3: Generate the summary statistics of the data
-
1867  summary_fun(proposed_stats_i, data_i, this);
+
1851  std::vector< epiworld_double > proposed_stats_i;
+
1852  summary_fun(proposed_stats_i, data_i, this);
+
1853  accepted_params_prob[0u] = kernel_fun(
+
1854  proposed_stats_i, observed_stats, epsilon, this
+
1855  );
+
1856 
+
1857  // Recording statistics
+
1858  for (size_t i = 0u; i < n_statistics; ++i)
+
1859  sampled_stats[i] = proposed_stats_i[i];
+
1860 
+
1861  for (size_t k = 0u; k < n_parameters; ++k)
+
1862  accepted_params[k] = params_init[k];
+
1863 
+
1864  for (size_t i = 1u; i < n_samples; ++i)
+
1865  {
+
1866  // Step 1: Generate a proposal and store it in params_now
+
1867  proposal_fun(params_now, params_prev, this);
1868 
-
1869  // Step 4: Compute the hastings ratio using the kernel function
-
1870  epiworld_double hr = kernel_fun(proposed_stats_i, observed_stats, epsilon, this);
-
1871  sampled_stats_prob[i] = hr;
-
1872 
-
1873  // Storing data
-
1874  for (size_t k = 0u; k < n_statistics; ++k)
-
1875  sampled_stats[i * n_statistics + k] = proposed_stats_i[k];
-
1876 
-
1877  // Running Hastings ratio
-
1878  epiworld_double r = runif();
-
1879  drawn_prob[i] = r;
-
1880 
-
1881  // Step 5: Update if likely
-
1882  if (r < std::min(static_cast<epiworld_double>(1.0), hr / accepted_params_prob[i - 1u]))
-
1883  {
-
1884  accepted_params_prob[i] = hr;
-
1885  sampled_accepted[i] = true;
-
1886 
-
1887  for (size_t k = 0u; k < n_statistics; ++k)
-
1888  accepted_stats[i * n_statistics + k] =
-
1889  proposed_stats_i[k];
-
1890 
-
1891  params_prev = params_now;
-
1892 
-
1893  } else
-
1894  {
-
1895 
-
1896  for (size_t k = 0u; k < n_statistics; ++k)
-
1897  accepted_stats[i * n_statistics + k] =
-
1898  accepted_stats[(i - 1) * n_statistics + k];
-
1899 
-
1900  accepted_params_prob[i] = accepted_params_prob[i - 1u];
-
1901  }
-
1902 
+
1869  // Step 2: Using params_now, simulate data
+
1870  TData data_i = simulation_fun(params_now, this);
+
1871 
+
1872  // Are we storing the data?
+
1873  if (sampled_data != nullptr)
+
1874  sampled_data->operator[](i) = data_i;
+
1875 
+
1876  // Step 3: Generate the summary statistics of the data
+
1877  summary_fun(proposed_stats_i, data_i, this);
+
1878 
+
1879  // Step 4: Compute the hastings ratio using the kernel function
+
1880  epiworld_double hr = kernel_fun(
+
1881  proposed_stats_i, observed_stats, epsilon, this
+
1882  );
+
1883 
+
1884  sampled_stats_prob[i] = hr;
+
1885 
+
1886  // Storing data
+
1887  for (size_t k = 0u; k < n_statistics; ++k)
+
1888  sampled_stats[i * n_statistics + k] = proposed_stats_i[k];
+
1889 
+
1890  // Running Hastings ratio
+
1891  epiworld_double r = runif();
+
1892  drawn_prob[i] = r;
+
1893 
+
1894  // Step 5: Update if likely
+
1895  if (r < std::min(static_cast<epiworld_double>(1.0), hr / accepted_params_prob[i - 1u]))
+
1896  {
+
1897  accepted_params_prob[i] = hr;
+
1898  sampled_accepted[i] = true;
+
1899 
+
1900  for (size_t k = 0u; k < n_statistics; ++k)
+
1901  accepted_stats[i * n_statistics + k] =
+
1902  proposed_stats_i[k];
1903 
-
1904  for (size_t k = 0u; k < n_parameters; ++k)
-
1905  accepted_params[i * n_parameters + k] = params_prev[k];
-
1906 
-
1907  }
+
1904  params_prev = params_now;
+
1905 
+
1906  } else
+
1907  {
1908 
-
1909  // End timing
-
1910  chrono_end();
-
1911 
-
1912 }
-
1913 
-
1914 
-
1915 template<typename TData>
-
1916 inline epiworld_double LFMCMC<TData>::runif()
-
1917 {
-
1918  return runifd->operator()(*engine);
-
1919 }
-
1920 
-
1921 template<typename TData>
-
1922 inline epiworld_double LFMCMC<TData>::runif(
-
1923  epiworld_double lb,
-
1924  epiworld_double ub
-
1925 )
-
1926 {
-
1927  return runifd->operator()(*engine) * (ub - lb) + lb;
-
1928 }
-
1929 
-
1930 template<typename TData>
-
1931 inline epiworld_double LFMCMC<TData>::rnorm()
-
1932 {
-
1933  return rnormd->operator()(*engine);
-
1934 }
-
1935 
-
1936 template<typename TData>
-
1937 inline epiworld_double LFMCMC<TData>::rnorm(
-
1938  epiworld_double mean,
-
1939  epiworld_double sd
-
1940  )
-
1941 {
-
1942  return (rnormd->operator()(*engine)) * sd + mean;
-
1943 }
-
1944 
-
1945 template<typename TData>
-
1946 inline epiworld_double LFMCMC<TData>::rgamma()
-
1947 {
-
1948  return rgammad->operator()(*engine);
-
1949 }
-
1950 
-
1951 template<typename TData>
-
1952 inline epiworld_double LFMCMC<TData>::rgamma(
-
1953  epiworld_double alpha,
-
1954  epiworld_double beta
-
1955  )
-
1956 {
+
1909  for (size_t k = 0u; k < n_statistics; ++k)
+
1910  accepted_stats[i * n_statistics + k] =
+
1911  accepted_stats[(i - 1) * n_statistics + k];
+
1912 
+
1913  accepted_params_prob[i] = accepted_params_prob[i - 1u];
+
1914  }
+
1915 
+
1916 
+
1917  for (size_t k = 0u; k < n_parameters; ++k)
+
1918  accepted_params[i * n_parameters + k] = params_prev[k];
+
1919 
+
1920  }
+
1921 
+
1922  // End timing
+
1923  chrono_end();
+
1924 
+
1925 }
+
1926 
+
1927 
+
1928 template<typename TData>
+
1929 inline epiworld_double LFMCMC<TData>::runif()
+
1930 {
+
1931  return runifd->operator()(*engine);
+
1932 }
+
1933 
+
1934 template<typename TData>
+
1935 inline epiworld_double LFMCMC<TData>::runif(
+
1936  epiworld_double lb,
+
1937  epiworld_double ub
+
1938 )
+
1939 {
+
1940  return runifd->operator()(*engine) * (ub - lb) + lb;
+
1941 }
+
1942 
+
1943 template<typename TData>
+
1944 inline epiworld_double LFMCMC<TData>::rnorm()
+
1945 {
+
1946  return rnormd->operator()(*engine);
+
1947 }
+
1948 
+
1949 template<typename TData>
+
1950 inline epiworld_double LFMCMC<TData>::rnorm(
+
1951  epiworld_double mean,
+
1952  epiworld_double sd
+
1953  )
+
1954 {
+
1955  return (rnormd->operator()(*engine)) * sd + mean;
+
1956 }
1957 
-
1958  auto old_param = rgammad->param();
-
1959 
-
1960  rgammad->param(std::gamma_distribution<>::param_type(alpha, beta));
-
1961 
-
1962  epiworld_double ans = rgammad->operator()(*engine);
+
1958 template<typename TData>
+
1959 inline epiworld_double LFMCMC<TData>::rgamma()
+
1960 {
+
1961  return rgammad->operator()(*engine);
+
1962 }
1963 
-
1964  rgammad->param(old_param);
-
1965 
-
1966  return ans;
-
1967 
-
1968 }
-
1969 
-
1970 template<typename TData>
-
1971 inline void LFMCMC<TData>::seed(epiworld_fast_uint s) {
+
1964 template<typename TData>
+
1965 inline epiworld_double LFMCMC<TData>::rgamma(
+
1966  epiworld_double alpha,
+
1967  epiworld_double beta
+
1968  )
+
1969 {
+
1970 
+
1971  auto old_param = rgammad->param();
1972 
-
1973  this->engine->seed(s);
+
1973  rgammad->param(std::gamma_distribution<>::param_type(alpha, beta));
1974 
-
1975 }
+
1975  epiworld_double ans = rgammad->operator()(*engine);
1976 
-
1977 template<typename TData>
-
1978 inline void LFMCMC<TData>::set_rand_engine(std::shared_ptr< std::mt19937 > & eng)
-
1979 {
-
1980  engine = eng;
+
1977  rgammad->param(old_param);
+
1978 
+
1979  return ans;
+
1980 
1981 }
1982 
1983 template<typename TData>
-
1984 inline void LFMCMC<TData>::set_rand_gamma(epiworld_double alpha, epiworld_double beta)
-
1985 {
-
1986  rgammad = std::make_shared<std::gamma_distribution<>>(alpha,beta);
-
1987 }
-
1988 
-
1989 template<typename TData>
-
1990 inline std::shared_ptr< std::mt19937 > & LFMCMC<TData>::get_rand_endgine()
-
1991 {
-
1992  return engine;
-
1993 }
-
1994 
-
1995 // Step 1: Simulate data
-
1996 
-
1997 // Step 2: Compute the sufficient statistics
-
1998 
-
1999 // Step 3: Compute the hastings-ratio
-
2000 
-
2001 // Step 4: Accept/reject, and go back to step 1
-
2002 
-
2003 #define DURCAST(tunit,txtunit) {\
-
2004  elapsed = std::chrono::duration_cast<std::chrono:: tunit>(\
-
2005  time_end - time_start).count(); \
-
2006  abbr_unit = txtunit;}
+
1984 inline void LFMCMC<TData>::seed(epiworld_fast_uint s) {
+
1985 
+
1986  this->engine->seed(s);
+
1987 
+
1988 }
+
1989 
+
1990 template<typename TData>
+
1991 inline void LFMCMC<TData>::set_rand_engine(std::shared_ptr< std::mt19937 > & eng)
+
1992 {
+
1993  engine = eng;
+
1994 }
+
1995 
+
1996 template<typename TData>
+
1997 inline void LFMCMC<TData>::set_rand_gamma(epiworld_double alpha, epiworld_double beta)
+
1998 {
+
1999  rgammad = std::make_shared<std::gamma_distribution<>>(alpha,beta);
+
2000 }
+
2001 
+
2002 template<typename TData>
+
2003 inline std::shared_ptr< std::mt19937 > & LFMCMC<TData>::get_rand_endgine()
+
2004 {
+
2005  return engine;
+
2006 }
2007 
-
2008 template<typename TData>
-
2009 inline void LFMCMC<TData>::get_elapsed(
-
2010  std::string unit,
-
2011  epiworld_double * last_elapsed,
-
2012  std::string * unit_abbr,
-
2013  bool print
-
2014 ) {
+
2008 // Step 1: Simulate data
+
2009 
+
2010 // Step 2: Compute the sufficient statistics
+
2011 
+
2012 // Step 3: Compute the hastings-ratio
+
2013 
+
2014 // Step 4: Accept/reject, and go back to step 1
2015 
-
2016  // Preparing the result
-
2017  epiworld_double elapsed;
-
2018  std::string abbr_unit;
-
2019 
-
2020  // Figuring out the length
-
2021  if (unit == "auto")
-
2022  {
-
2023 
-
2024  size_t tlength = std::to_string(
-
2025  static_cast<int>(floor(time_elapsed.count()))
-
2026  ).length();
-
2027 
-
2028  if (tlength <= 1)
-
2029  unit = "nanoseconds";
-
2030  else if (tlength <= 3)
-
2031  unit = "microseconds";
-
2032  else if (tlength <= 6)
-
2033  unit = "milliseconds";
-
2034  else if (tlength <= 8)
-
2035  unit = "seconds";
-
2036  else if (tlength <= 9)
-
2037  unit = "minutes";
-
2038  else
-
2039  unit = "hours";
-
2040 
-
2041  }
-
2042 
-
2043  if (unit == "nanoseconds") DURCAST(nanoseconds,"ns")
-
2044  else if (unit == "microseconds") DURCAST(microseconds,"\xC2\xB5s")
-
2045  else if (unit == "milliseconds") DURCAST(milliseconds,"ms")
-
2046  else if (unit == "seconds") DURCAST(seconds,"s")
-
2047  else if (unit == "minutes") DURCAST(minutes,"m")
-
2048  else if (unit == "hours") DURCAST(hours,"h")
-
2049  else
-
2050  throw std::range_error("The time unit " + unit + " is not supported.");
-
2051 
-
2052 
-
2053  if (last_elapsed != nullptr)
-
2054  *last_elapsed = elapsed;
-
2055  if (unit_abbr != nullptr)
-
2056  *unit_abbr = abbr_unit;
-
2057 
-
2058  if (!print)
-
2059  return;
-
2060 
-
2061  printf_epiworld("Elapsed time : %.2f%s.\n", elapsed, abbr_unit.c_str());
-
2062 }
-
2063 
-
2064 #undef DURCAST
+
2016 #define DURCAST(tunit,txtunit) {\
+
2017  elapsed = std::chrono::duration_cast<std::chrono:: tunit>(\
+
2018  time_end - time_start).count(); \
+
2019  abbr_unit = txtunit;}
+
2020 
+
2021 template<typename TData>
+
2022 inline void LFMCMC<TData>::get_elapsed(
+
2023  std::string unit,
+
2024  epiworld_double * last_elapsed,
+
2025  std::string * unit_abbr,
+
2026  bool print
+
2027 ) const {
+
2028 
+
2029  // Preparing the result
+
2030  epiworld_double elapsed;
+
2031  std::string abbr_unit;
+
2032 
+
2033  // Figuring out the length
+
2034  if (unit == "auto")
+
2035  {
+
2036 
+
2037  size_t tlength = std::to_string(
+
2038  static_cast<int>(floor(time_elapsed.count()))
+
2039  ).length();
+
2040 
+
2041  if (tlength <= 1)
+
2042  unit = "nanoseconds";
+
2043  else if (tlength <= 3)
+
2044  unit = "microseconds";
+
2045  else if (tlength <= 6)
+
2046  unit = "milliseconds";
+
2047  else if (tlength <= 8)
+
2048  unit = "seconds";
+
2049  else if (tlength <= 9)
+
2050  unit = "minutes";
+
2051  else
+
2052  unit = "hours";
+
2053 
+
2054  }
+
2055 
+
2056  if (unit == "nanoseconds") DURCAST(nanoseconds,"ns")
+
2057  else if (unit == "microseconds") DURCAST(microseconds,"\xC2\xB5s")
+
2058  else if (unit == "milliseconds") DURCAST(milliseconds,"ms")
+
2059  else if (unit == "seconds") DURCAST(seconds,"s")
+
2060  else if (unit == "minutes") DURCAST(minutes,"m")
+
2061  else if (unit == "hours") DURCAST(hours,"h")
+
2062  else
+
2063  throw std::range_error("The time unit " + unit + " is not supported.");
+
2064 
2065 
-
2066 /*//////////////////////////////////////////////////////////////////////////////
-
2068 
-
2069  Start of -include/epiworld//math//lfmcmc/lfmcmc-meat-print.hpp-
+
2066  if (last_elapsed != nullptr)
+
2067  *last_elapsed = elapsed;
+
2068  if (unit_abbr != nullptr)
+
2069  *unit_abbr = abbr_unit;
2070 
+
2071  if (!print)
+
2072  return;
2073 
-
2074 
-
2075 #ifndef LFMCMC_MEAT_PRINT_HPP
-
2076 #define LFMCMC_MEAT_PRINT_HPP
-
2077 
-
2078 template<typename TData>
-
2079 inline void LFMCMC<TData>::print()
-
2080 {
-
2081  std::vector< epiworld_double > summ_params(n_parameters * 3, 0.0);
-
2082  std::vector< epiworld_double > summ_stats(n_statistics * 3, 0.0);
+
2074  printf_epiworld("Elapsed time : %.2f%s.\n", elapsed, abbr_unit.c_str());
+
2075 }
+
2076 
+
2077 #undef DURCAST
+
2078 
+
2079 /*//////////////////////////////////////////////////////////////////////////////
+
2081 
+
2082  Start of -include/epiworld//math//lfmcmc/lfmcmc-meat-print.hpp-
2083 
-
2084  for (size_t k = 0u; k < n_parameters; ++k)
-
2085  {
2086 
-
2087  // Retrieving the relevant parameter
-
2088  std::vector< epiworld_double > par_i(n_samples);
-
2089  for (size_t i = 0u; i < n_samples; ++i)
-
2090  {
-
2091  par_i[i] = accepted_params[i * n_parameters + k];
-
2092  summ_params[k * 3] += par_i[i]/n_samples;
-
2093  }
+
2087 
+
2088 #ifndef LFMCMC_MEAT_PRINT_HPP
+
2089 #define LFMCMC_MEAT_PRINT_HPP
+
2090 
+
2091 template<typename TData>
+
2092 inline void LFMCMC<TData>::print(size_t burnin) const
+
2093 {
2094 
-
2095  // Computing the 95% Credible interval
-
2096  std::sort(par_i.begin(), par_i.end());
+
2095  std::vector< epiworld_double > summ_params(n_parameters * 3, 0.0);
+
2096  std::vector< epiworld_double > summ_stats(n_statistics * 3, 0.0);
2097 
-
2098  summ_params[k * 3 + 1u] =
-
2099  par_i[std::floor(.025 * static_cast<epiworld_double>(n_samples))];
-
2100  summ_params[k * 3 + 2u] =
-
2101  par_i[std::floor(.975 * static_cast<epiworld_double>(n_samples))];
-
2102 
-
2103  }
-
2104 
-
2105  for (size_t k = 0u; k < n_statistics; ++k)
-
2106  {
+
2098  size_t n_samples_print = n_samples;
+
2099  if (burnin > 0)
+
2100  {
+
2101  if (burnin >= n_samples)
+
2102  throw std::length_error(
+
2103  "The burnin is greater than the number of samples."
+
2104  );
+
2105 
+
2106  n_samples_print = n_samples - burnin;
2107 
-
2108  // Retrieving the relevant parameter
-
2109  std::vector< epiworld_double > stat_k(n_samples);
-
2110  for (size_t i = 0u; i < n_samples; ++i)
-
2111  {
-
2112  stat_k[i] = accepted_stats[i * n_statistics + k];
-
2113  summ_stats[k * 3] += stat_k[i]/n_samples;
-
2114  }
-
2115 
-
2116  // Computing the 95% Credible interval
-
2117  std::sort(stat_k.begin(), stat_k.end());
-
2118 
-
2119  summ_stats[k * 3 + 1u] =
-
2120  stat_k[std::floor(.025 * static_cast<epiworld_double>(n_samples))];
-
2121  summ_stats[k * 3 + 2u] =
-
2122  stat_k[std::floor(.975 * static_cast<epiworld_double>(n_samples))];
-
2123 
-
2124  }
-
2125 
-
2126  printf_epiworld("___________________________________________\n\n");
-
2127  printf_epiworld("LIKELIHOOD-FREE MARKOV CHAIN MONTE CARLO\n\n");
-
2128 
-
2129  printf_epiworld("N Samples : %zu\n", n_samples);
-
2130 
-
2131  std::string abbr;
-
2132  epiworld_double elapsed;
-
2133  get_elapsed("auto", &elapsed, &abbr, false);
-
2134  printf_epiworld("Elapsed t : %.2f%s\n\n", elapsed, abbr.c_str());
-
2135 
-
2137  // PARAMETERS
-
2139  printf_epiworld("Parameters:\n");
-
2140 
-
2141  // Figuring out format
-
2142  std::string fmt_params;
-
2143 
-
2144  int nchar_par_num = 0;
-
2145  for (auto & n : summ_params)
-
2146  {
-
2147 
-
2148  int tmp_nchar = std::floor(std::log10(std::abs(n)));
-
2149  if (nchar_par_num < tmp_nchar)
-
2150  nchar_par_num = tmp_nchar;
-
2151  }
-
2152  nchar_par_num += 5; // 1 for neg padd, 2 for decimals, 1 the decimal point, and one b/c log(<10) < 1.
-
2153  std::string charlen = std::to_string(nchar_par_num);
-
2154 
-
2155  if (names_parameters.size() != 0u)
-
2156  {
-
2157  int nchar_par = 0;
-
2158  for (auto & n : names_parameters)
-
2159  {
-
2160  int tmp_nchar = n.length();
-
2161  if (nchar_par < tmp_nchar)
-
2162  nchar_par = tmp_nchar;
-
2163  }
-
2164 
-
2165  fmt_params = std::string(" -%-") +
-
2166  std::to_string(nchar_par) +
-
2167  std::string("s : % ") + charlen +
-
2168  std::string(".2f [% ") + charlen +
-
2169  std::string(".2f, % ") + charlen +
-
2170  std::string(".2f] (initial : % ") +
-
2171  charlen + std::string(".2f)\n");
-
2172 
-
2173  for (size_t k = 0u; k < n_parameters; ++k)
-
2174  {
-
2175  printf_epiworld(
-
2176  fmt_params.c_str(),
-
2177  names_parameters[k].c_str(),
-
2178  summ_params[k * 3],
-
2179  summ_params[k * 3 + 1u],
-
2180  summ_params[k * 3 + 2u],
-
2181  params_init[k]
-
2182  );
-
2183  }
+
2108  }
+
2109 
+
2110  epiworld_double n_samples_dbl = static_cast< epiworld_double >(
+
2111  n_samples_print
+
2112  );
+
2113 
+
2114  for (size_t k = 0u; k < n_parameters; ++k)
+
2115  {
+
2116 
+
2117  // Retrieving the relevant parameter
+
2118  std::vector< epiworld_double > par_i(n_samples_print);
+
2119  for (size_t i = burnin; i < n_samples; ++i)
+
2120  {
+
2121  par_i[i] = accepted_params[i * n_parameters + k];
+
2122  summ_params[k * 3] += par_i[i]/n_samples_dbl;
+
2123  }
+
2124 
+
2125  // Computing the 95% Credible interval
+
2126  std::sort(par_i.begin(), par_i.end());
+
2127 
+
2128  summ_params[k * 3 + 1u] =
+
2129  par_i[std::floor(.025 * n_samples_dbl)];
+
2130  summ_params[k * 3 + 2u] =
+
2131  par_i[std::floor(.975 * n_samples_dbl)];
+
2132 
+
2133  }
+
2134 
+
2135  for (size_t k = 0u; k < n_statistics; ++k)
+
2136  {
+
2137 
+
2138  // Retrieving the relevant parameter
+
2139  std::vector< epiworld_double > stat_k(n_samples_print);
+
2140  for (size_t i = burnin; i < n_samples; ++i)
+
2141  {
+
2142  stat_k[i] = accepted_stats[i * n_statistics + k];
+
2143  summ_stats[k * 3] += stat_k[i]/n_samples_dbl;
+
2144  }
+
2145 
+
2146  // Computing the 95% Credible interval
+
2147  std::sort(stat_k.begin(), stat_k.end());
+
2148 
+
2149  summ_stats[k * 3 + 1u] =
+
2150  stat_k[std::floor(.025 * n_samples_dbl)];
+
2151  summ_stats[k * 3 + 2u] =
+
2152  stat_k[std::floor(.975 * n_samples_dbl)];
+
2153 
+
2154  }
+
2155 
+
2156  printf_epiworld("___________________________________________\n\n");
+
2157  printf_epiworld("LIKELIHOOD-FREE MARKOV CHAIN MONTE CARLO\n\n");
+
2158 
+
2159  printf_epiworld("N Samples : %zu\n", n_samples);
+
2160 
+
2161  std::string abbr;
+
2162  epiworld_double elapsed;
+
2163  get_elapsed("auto", &elapsed, &abbr, false);
+
2164  printf_epiworld("Elapsed t : %.2f%s\n\n", elapsed, abbr.c_str());
+
2165 
+
2167  // PARAMETERS
+
2169  printf_epiworld("Parameters:\n");
+
2170 
+
2171  // Figuring out format
+
2172  std::string fmt_params;
+
2173 
+
2174  int nchar_par_num = 0;
+
2175  for (auto & n : summ_params)
+
2176  {
+
2177 
+
2178  int tmp_nchar = std::floor(std::log10(std::abs(n)));
+
2179  if (nchar_par_num < tmp_nchar)
+
2180  nchar_par_num = tmp_nchar;
+
2181  }
+
2182  nchar_par_num += 5; // 1 for neg padd, 2 for decimals, 1 the decimal point, and one b/c log(<10) < 1.
+
2183  std::string charlen = std::to_string(nchar_par_num);
2184 
-
2185 
-
2186  } else {
-
2187 
-
2188  fmt_params = std::string(" [%-2ld]: % ") + charlen +
-
2189  std::string(".2f [% ") + charlen +
-
2190  std::string(".2f, % ") + charlen +
-
2191  std::string(".2f] (initial : % ") + charlen +
-
2192  std::string(".2f)\n");
-
2193 
-
2194  for (size_t k = 0u; k < n_parameters; ++k)
-
2195  {
-
2196 
-
2197  printf_epiworld(
-
2198  fmt_params.c_str(),
-
2199  k,
-
2200  summ_params[k * 3],
-
2201  summ_params[k * 3 + 1u],
-
2202  summ_params[k * 3 + 2u],
-
2203  params_init[k]
-
2204  );
-
2205  }
-
2206 
-
2207  }
-
2208 
-
2210  // Statistics
-
2212  printf_epiworld("\nStatistics:\n");
-
2213  int nchar = 0;
-
2214  for (auto & s : summ_stats)
-
2215  {
-
2216  int tmp_nchar = std::floor(std::log10(std::abs(s)));
-
2217  if (nchar < tmp_nchar)
-
2218  nchar = tmp_nchar;
-
2219  }
-
2220 
-
2221  nchar += 5; // See above
-
2222 
-
2223  std::string nchar_char = std::to_string(nchar);
-
2224 
-
2225  // Figuring out format
-
2226  std::string fmt_stats;
-
2227  if (names_statistics.size() != 0u)
-
2228  {
-
2229  int nchar_stats = 0;
-
2230  for (auto & n : names_statistics)
-
2231  {
-
2232  int tmp_nchar = n.length();
-
2233  if (nchar_stats < tmp_nchar)
-
2234  nchar_stats = tmp_nchar;
+
2185  if (names_parameters.size() != 0u)
+
2186  {
+
2187  int nchar_par = 0;
+
2188  for (auto & n : names_parameters)
+
2189  {
+
2190  int tmp_nchar = n.length();
+
2191  if (nchar_par < tmp_nchar)
+
2192  nchar_par = tmp_nchar;
+
2193  }
+
2194 
+
2195  fmt_params = std::string(" -%-") +
+
2196  std::to_string(nchar_par) +
+
2197  std::string("s : % ") + charlen +
+
2198  std::string(".2f [% ") + charlen +
+
2199  std::string(".2f, % ") + charlen +
+
2200  std::string(".2f] (initial : % ") +
+
2201  charlen + std::string(".2f)\n");
+
2202 
+
2203  for (size_t k = 0u; k < n_parameters; ++k)
+
2204  {
+
2205  printf_epiworld(
+
2206  fmt_params.c_str(),
+
2207  names_parameters[k].c_str(),
+
2208  summ_params[k * 3],
+
2209  summ_params[k * 3 + 1u],
+
2210  summ_params[k * 3 + 2u],
+
2211  params_init[k]
+
2212  );
+
2213  }
+
2214 
+
2215 
+
2216  } else {
+
2217 
+
2218  fmt_params = std::string(" [%-2ld]: % ") + charlen +
+
2219  std::string(".2f [% ") + charlen +
+
2220  std::string(".2f, % ") + charlen +
+
2221  std::string(".2f] (initial : % ") + charlen +
+
2222  std::string(".2f)\n");
+
2223 
+
2224  for (size_t k = 0u; k < n_parameters; ++k)
+
2225  {
+
2226 
+
2227  printf_epiworld(
+
2228  fmt_params.c_str(),
+
2229  k,
+
2230  summ_params[k * 3],
+
2231  summ_params[k * 3 + 1u],
+
2232  summ_params[k * 3 + 2u],
+
2233  params_init[k]
+
2234  );
2235  }
2236 
-
2237  fmt_stats = std::string(" -%-") +
-
2238  std::to_string(nchar_stats) +
-
2239  std::string("s : % ") + nchar_char +
-
2240  std::string(".2f [% ") + nchar_char +
-
2241  std::string(".2f, % ") + nchar_char +
-
2242  std::string(".2f] (Observed: % ") + nchar_char +
-
2243  std::string(".2f)\n");
-
2244 
-
2245  for (size_t k = 0u; k < n_statistics; ++k)
-
2246  {
-
2247  printf_epiworld(
-
2248  fmt_stats.c_str(),
-
2249  names_statistics[k].c_str(),
-
2250  summ_stats[k * 3],
-
2251  summ_stats[k * 3 + 1u],
-
2252  summ_stats[k * 3 + 2u],
-
2253  observed_stats[k]
-
2254  );
-
2255  }
-
2256 
-
2257 
-
2258  } else {
-
2259 
-
2260  fmt_stats = std::string(" [%-2ld] : % ") +
-
2261  nchar_char +
-
2262  std::string(".2f [% ") + nchar_char +
-
2263  std::string(".2f, % ") + nchar_char +
-
2264  std::string(".2f] (Observed: % ") + nchar_char +
-
2265  std::string(".2f)\n");
+
2237  }
+
2238 
+
2240  // Statistics
+
2242  printf_epiworld("\nStatistics:\n");
+
2243  int nchar = 0;
+
2244  for (auto & s : summ_stats)
+
2245  {
+
2246  int tmp_nchar = std::floor(std::log10(std::abs(s)));
+
2247  if (nchar < tmp_nchar)
+
2248  nchar = tmp_nchar;
+
2249  }
+
2250 
+
2251  nchar += 5; // See above
+
2252 
+
2253  std::string nchar_char = std::to_string(nchar);
+
2254 
+
2255  // Figuring out format
+
2256  std::string fmt_stats;
+
2257  if (names_statistics.size() != 0u)
+
2258  {
+
2259  int nchar_stats = 0;
+
2260  for (auto & n : names_statistics)
+
2261  {
+
2262  int tmp_nchar = n.length();
+
2263  if (nchar_stats < tmp_nchar)
+
2264  nchar_stats = tmp_nchar;
+
2265  }
2266 
-
2267  for (size_t k = 0u; k < n_statistics; ++k)
-
2268  {
-
2269  printf_epiworld(
-
2270  fmt_stats.c_str(),
-
2271  k,
-
2272  summ_stats[k * 3],
-
2273  summ_stats[k * 3 + 1u],
-
2274  summ_stats[k * 3 + 2u],
-
2275  observed_stats[k]
-
2276  );
-
2277  }
-
2278 
-
2279  }
-
2280 
-
2281  printf_epiworld("___________________________________________\n\n");
-
2282 }
-
2283 
-
2284 #endif
-
2285 /*//////////////////////////////////////////////////////////////////////////////
-
2287 
-
2288  End of -include/epiworld//math//lfmcmc/lfmcmc-meat-print.hpp-
+
2267  fmt_stats = std::string(" -%-") +
+
2268  std::to_string(nchar_stats) +
+
2269  std::string("s : % ") + nchar_char +
+
2270  std::string(".2f [% ") + nchar_char +
+
2271  std::string(".2f, % ") + nchar_char +
+
2272  std::string(".2f] (Observed: % ") + nchar_char +
+
2273  std::string(".2f)\n");
+
2274 
+
2275  for (size_t k = 0u; k < n_statistics; ++k)
+
2276  {
+
2277  printf_epiworld(
+
2278  fmt_stats.c_str(),
+
2279  names_statistics[k].c_str(),
+
2280  summ_stats[k * 3],
+
2281  summ_stats[k * 3 + 1u],
+
2282  summ_stats[k * 3 + 2u],
+
2283  observed_stats[k]
+
2284  );
+
2285  }
+
2286 
+
2287 
+
2288  } else {
2289 
-
2292 
-
2293 
-
2294 
-
2295 template<typename TData>
-
2296 inline void LFMCMC<TData>::chrono_start() {
-
2297  time_start = std::chrono::steady_clock::now();
-
2298 }
-
2299 
-
2300 template<typename TData>
-
2301 inline void LFMCMC<TData>::chrono_end() {
-
2302  time_end = std::chrono::steady_clock::now();
-
2303  time_elapsed += (time_end - time_start);
-
2304 }
-
2305 
-
2306 template<typename TData>
-
2307 inline void LFMCMC<TData>::set_par_names(std::vector< std::string > names)
-
2308 {
-
2309 
-
2310  if (names.size() != n_parameters)
-
2311  throw std::length_error("The number of names to add differs from the number of parameters in the model.");
-
2312 
-
2313  names_parameters = names;
-
2314 
-
2315 }
-
2316 template<typename TData>
-
2317 inline void LFMCMC<TData>::set_stats_names(std::vector< std::string > names)
-
2318 {
+
2290  fmt_stats = std::string(" [%-2ld] : % ") +
+
2291  nchar_char +
+
2292  std::string(".2f [% ") + nchar_char +
+
2293  std::string(".2f, % ") + nchar_char +
+
2294  std::string(".2f] (Observed: % ") + nchar_char +
+
2295  std::string(".2f)\n");
+
2296 
+
2297  for (size_t k = 0u; k < n_statistics; ++k)
+
2298  {
+
2299  printf_epiworld(
+
2300  fmt_stats.c_str(),
+
2301  k,
+
2302  summ_stats[k * 3],
+
2303  summ_stats[k * 3 + 1u],
+
2304  summ_stats[k * 3 + 2u],
+
2305  observed_stats[k]
+
2306  );
+
2307  }
+
2308 
+
2309  }
+
2310 
+
2311  printf_epiworld("___________________________________________\n\n");
+
2312 }
+
2313 
+
2314 #endif
+
2315 /*//////////////////////////////////////////////////////////////////////////////
+
2317 
+
2318  End of -include/epiworld//math//lfmcmc/lfmcmc-meat-print.hpp-
2319 
-
2320  if (names.size() != n_statistics)
-
2321  throw std::length_error("The number of names to add differs from the number of statistics in the model.");
2322 
-
2323  names_statistics = names;
+
2323 
2324 
-
2325 }
-
2326 
-
2327 template<typename TData>
-
2328 inline std::vector< epiworld_double > LFMCMC<TData>::get_params_mean()
-
2329 {
-
2330  std::vector< epiworld_double > res(this->n_parameters, 0.0);
-
2331 
-
2332  for (size_t k = 0u; k < n_parameters; ++k)
-
2333  {
-
2334  for (size_t i = 0u; i < n_samples; ++i)
-
2335  res[k] += (this->accepted_params[k + n_parameters * i])/
-
2336  static_cast< epiworld_double >(n_samples);
-
2337  }
-
2338 
-
2339  return res;
-
2340 
-
2341 }
+
2325 template<typename TData>
+
2326 inline void LFMCMC<TData>::chrono_start() {
+
2327  time_start = std::chrono::steady_clock::now();
+
2328 }
+
2329 
+
2330 template<typename TData>
+
2331 inline void LFMCMC<TData>::chrono_end() {
+
2332  time_end = std::chrono::steady_clock::now();
+
2333  time_elapsed += (time_end - time_start);
+
2334 }
+
2335 
+
2336 template<typename TData>
+
2337 inline void LFMCMC<TData>::set_par_names(std::vector< std::string > names)
+
2338 {
+
2339 
+
2340  if (names.size() != n_parameters)
+
2341  throw std::length_error("The number of names to add differs from the number of parameters in the model.");
2342 
-
2343 template<typename TData>
-
2344 inline std::vector< epiworld_double > LFMCMC<TData>::get_stats_mean()
-
2345 {
-
2346  std::vector< epiworld_double > res(this->n_statistics, 0.0);
-
2347 
-
2348  for (size_t k = 0u; k < n_statistics; ++k)
-
2349  {
-
2350  for (size_t i = 0u; i < n_samples; ++i)
-
2351  res[k] += (this->accepted_stats[k + n_statistics * i])/
-
2352  static_cast< epiworld_double >(n_samples);
-
2353  }
+
2343  names_parameters = names;
+
2344 
+
2345 }
+
2346 template<typename TData>
+
2347 inline void LFMCMC<TData>::set_stats_names(std::vector< std::string > names)
+
2348 {
+
2349 
+
2350  if (names.size() != n_statistics)
+
2351  throw std::length_error("The number of names to add differs from the number of statistics in the model.");
+
2352 
+
2353  names_statistics = names;
2354 
-
2355  return res;
+
2355 }
2356 
-
2357 }
-
2358 
-
2359 #endif
-
2360 /*//////////////////////////////////////////////////////////////////////////////
-
2362 
-
2363  End of -include/epiworld//math/lfmcmc/lfmcmc-meat.hpp-
-
2364 
-
2367 
+
2357 template<typename TData>
+
2358 inline std::vector< epiworld_double > LFMCMC<TData>::get_params_mean()
+
2359 {
+
2360  std::vector< epiworld_double > res(this->n_parameters, 0.0);
+
2361 
+
2362  for (size_t k = 0u; k < n_parameters; ++k)
+
2363  {
+
2364  for (size_t i = 0u; i < n_samples; ++i)
+
2365  res[k] += (this->accepted_params[k + n_parameters * i])/
+
2366  static_cast< epiworld_double >(n_samples);
+
2367  }
2368 
-
2369 
-
2370 #endif
-
2371 /*//////////////////////////////////////////////////////////////////////////////
-
2373 
-
2374  End of -include/epiworld/math/lfmcmc.hpp-
-
2375 
-
2378 
-
2379 
-
2380 
-
2381 /*//////////////////////////////////////////////////////////////////////////////
-
2383 
-
2384  Start of -include/epiworld/userdata-bones.hpp-
-
2385 
+
2369  return res;
+
2370 
+
2371 }
+
2372 
+
2373 template<typename TData>
+
2374 inline std::vector< epiworld_double > LFMCMC<TData>::get_stats_mean()
+
2375 {
+
2376  std::vector< epiworld_double > res(this->n_statistics, 0.0);
+
2377 
+
2378  for (size_t k = 0u; k < n_statistics; ++k)
+
2379  {
+
2380  for (size_t i = 0u; i < n_samples; ++i)
+
2381  res[k] += (this->accepted_stats[k + n_statistics * i])/
+
2382  static_cast< epiworld_double >(n_samples);
+
2383  }
+
2384 
+
2385  return res;
+
2386 
+
2387 }
2388 
-
2389 
-
2390 #ifndef EPIWORLD_USERDATA_BONES_HPP
-
2391 #define EPIWORLD_USERDATA_BONES_HPP
+
2389 #endif
+
2390 /*//////////////////////////////////////////////////////////////////////////////
2392 
-
2393 template<typename TSeq>
-
2394 class Model;
-
2395 
-
2396 template<typename TSeq>
-
2397 class DataBase;
+
2393  End of -include/epiworld//math/lfmcmc/lfmcmc-meat.hpp-
+
2394 
+
2397 
2398 
-
2404 template<typename TSeq>
-
2405 class UserData
-
2406 {
-
2407  friend class Model<TSeq>;
-
2408  friend class DataBase<TSeq>;
+
2399 
+
2400 #endif
+
2401 /*//////////////////////////////////////////////////////////////////////////////
+
2403 
+
2404  End of -include/epiworld/math/lfmcmc.hpp-
+
2405 
+
2408 
2409 
-
2410 private:
-
2411  Model<TSeq> * model;
-
2412 
-
2413  std::vector< std::string > data_names;
-
2414  std::vector< int > data_dates;
-
2415  std::vector< epiworld_double > data_data;
-
2416 
-
2417  epiworld_fast_uint k = 0u;
-
2418  epiworld_fast_uint n = 0u;
+
2410 
+
2411 /*//////////////////////////////////////////////////////////////////////////////
+
2413 
+
2414  Start of -include/epiworld/userdata-bones.hpp-
+
2415 
+
2418 
2419 
-
2420  int last_day = -1;
-
2421 
-
2422 public:
-
2423 
-
2424  UserData() = delete;
-
2425  UserData(Model<TSeq> & m) : model(&m) {};
-
2426  UserData(Model<TSeq> * m) : model(m) {};
-
2427 
-
2434  UserData(std::vector< std::string > names);
-
2435 
-
2443  void add(std::vector<epiworld_double> x);
-
2444  void add(
-
2445  epiworld_fast_uint j,
-
2446  epiworld_double x
-
2447  );
+
2420 #ifndef EPIWORLD_USERDATA_BONES_HPP
+
2421 #define EPIWORLD_USERDATA_BONES_HPP
+
2422 
+
2423 template<typename TSeq>
+
2424 class Model;
+
2425 
+
2426 template<typename TSeq>
+
2427 class DataBase;
+
2428 
+
2434 template<typename TSeq>
+
2435 class UserData
+
2436 {
+
2437  friend class Model<TSeq>;
+
2438  friend class DataBase<TSeq>;
+
2439 
+
2440 private:
+
2441  Model<TSeq> * model;
+
2442 
+
2443  std::vector< std::string > data_names;
+
2444  std::vector< int > data_dates;
+
2445  std::vector< epiworld_double > data_data;
+
2446 
+
2447  epiworld_fast_uint k = 0u;
+
2448  epiworld_fast_uint n = 0u;
2449 
-
2458  epiworld_double & operator()(
-
2459  epiworld_fast_uint i,
-
2460  epiworld_fast_uint j
-
2461  );
-
2462 
-
2463  epiworld_double & operator()(
-
2464  epiworld_fast_uint i,
-
2465  std::string name
-
2466  );
-
2468 
-
2469  std::vector< std::string > & get_names();
-
2470 
-
2471  std::vector< int > & get_dates();
-
2472 
-
2473  std::vector< epiworld_double > & get_data();
-
2474 
-
2475  void get_all(
-
2476  std::vector< std::string > * names = nullptr,
-
2477  std::vector< int > * date = nullptr,
-
2478  std::vector< epiworld_double > * data = nullptr
-
2479  );
-
2480 
-
2481  epiworld_fast_uint nrow() const;
-
2482  epiworld_fast_uint ncol() const;
-
2483 
-
2484  void write(std::string fn);
-
2485  void print() const;
-
2486 
-
2487 };
-
2488 
-
2489 #endif
-
2490 /*//////////////////////////////////////////////////////////////////////////////
+
2450  int last_day = -1;
+
2451 
+
2452 public:
+
2453 
+
2454  UserData() = delete;
+
2455  UserData(Model<TSeq> & m) : model(&m) {};
+
2456  UserData(Model<TSeq> * m) : model(m) {};
+
2457 
+
2464  UserData(std::vector< std::string > names);
+
2465 
+
2473  void add(std::vector<epiworld_double> x);
+
2474  void add(
+
2475  epiworld_fast_uint j,
+
2476  epiworld_double x
+
2477  );
+
2479 
+
2488  epiworld_double & operator()(
+
2489  epiworld_fast_uint i,
+
2490  epiworld_fast_uint j
+
2491  );
2492 
-
2493  End of -include/epiworld/userdata-bones.hpp-
-
2494 
-
2497 
+
2493  epiworld_double & operator()(
+
2494  epiworld_fast_uint i,
+
2495  std::string name
+
2496  );
2498 
-
2499 /*//////////////////////////////////////////////////////////////////////////////
-
2501 
-
2502  Start of -include/epiworld/userdata-meat.hpp-
-
2503 
-
2506 
-
2507 
-
2508 #ifndef EPIWORLD_USERDATA_MEAT_HPP
-
2509 #define EPIWORLD_USERDATA_MEAT_HPP
+
2499  std::vector< std::string > & get_names();
+
2500 
+
2501  std::vector< int > & get_dates();
+
2502 
+
2503  std::vector< epiworld_double > & get_data();
+
2504 
+
2505  void get_all(
+
2506  std::vector< std::string > * names = nullptr,
+
2507  std::vector< int > * date = nullptr,
+
2508  std::vector< epiworld_double > * data = nullptr
+
2509  );
2510 
-
2511 template<typename TSeq>
-
2512 class UserData;
+
2511  epiworld_fast_uint nrow() const;
+
2512  epiworld_fast_uint ncol() const;
2513 
-
2514 template<typename TSeq>
-
2515 inline UserData<TSeq>::UserData(std::vector< std::string > names)
-
2516 {
-
2517 
-
2518  k = names.size();
-
2519  data_names = names;
-
2520 
-
2521 }
+
2514  void write(std::string fn);
+
2515  void print() const;
+
2516 
+
2517 };
+
2518 
+
2519 #endif
+
2520 /*//////////////////////////////////////////////////////////////////////////////
2522 
-
2523 template<typename TSeq>
-
2524 inline void UserData<TSeq>::add(std::vector<epiworld_double> x)
-
2525 {
-
2526 
-
2527  if (x.size() != k)
-
2528  throw std::out_of_range(
-
2529  "The size of -x-, " + std::to_string(x.size()) + ", does not match " +
-
2530  "the number of elements registered (" + std::to_string(k));
+
2523  End of -include/epiworld/userdata-bones.hpp-
+
2524 
+
2527 
+
2528 
+
2529 /*//////////////////////////////////////////////////////////////////////////////
2531 
-
2532  for (auto & i : x)
-
2533  data_data.push_back(i);
-
2534 
-
2535  data_dates.push_back(model->today());
+
2532  Start of -include/epiworld/userdata-meat.hpp-
+
2533 
2536 
-
2537  n++;
-
2538  last_day = model->today();
-
2539 
-
2540 }
-
2541 
-
2542 template<typename TSeq>
-
2543 inline void UserData<TSeq>::add(epiworld_fast_uint j, epiworld_double x)
-
2544 {
-
2545 
-
2546  // Starting with a new day?
-
2547  if (static_cast<int>(model->today()) != last_day)
-
2548  {
-
2549 
-
2550  std::vector< epiworld_double > tmp(k, 0.0);
-
2551 
-
2552  tmp[j] = x;
-
2553 
-
2554  add(tmp);
-
2555 
-
2556  }
-
2557  else
-
2558  {
-
2559 
-
2560  this->operator()(n - 1, j) = x;
+
2537 
+
2538 #ifndef EPIWORLD_USERDATA_MEAT_HPP
+
2539 #define EPIWORLD_USERDATA_MEAT_HPP
+
2540 
+
2541 template<typename TSeq>
+
2542 class UserData;
+
2543 
+
2544 template<typename TSeq>
+
2545 inline UserData<TSeq>::UserData(std::vector< std::string > names)
+
2546 {
+
2547 
+
2548  k = names.size();
+
2549  data_names = names;
+
2550 
+
2551 }
+
2552 
+
2553 template<typename TSeq>
+
2554 inline void UserData<TSeq>::add(std::vector<epiworld_double> x)
+
2555 {
+
2556 
+
2557  if (x.size() != k)
+
2558  throw std::out_of_range(
+
2559  "The size of -x-, " + std::to_string(x.size()) + ", does not match " +
+
2560  "the number of elements registered (" + std::to_string(k));
2561 
-
2562  }
-
2563 
-
2564 }
-
2565 
-
2566 template<typename TSeq>
-
2567 inline std::vector< std::string > & UserData<TSeq>::get_names()
-
2568 {
-
2569  return data_names;
+
2562  for (auto & i : x)
+
2563  data_data.push_back(i);
+
2564 
+
2565  data_dates.push_back(model->today());
+
2566 
+
2567  n++;
+
2568  last_day = model->today();
+
2569 
2570 }
2571 
2572 template<typename TSeq>
-
2573 inline std::vector< int > & UserData<TSeq>::get_dates()
+
2573 inline void UserData<TSeq>::add(epiworld_fast_uint j, epiworld_double x)
2574 {
-
2575  return data_dates;
-
2576 }
-
2577 
-
2578 template<typename TSeq>
-
2579 inline std::vector< epiworld_double > & UserData<TSeq>::get_data()
-
2580 {
-
2581  return data_data;
-
2582 }
+
2575 
+
2576  // Starting with a new day?
+
2577  if (static_cast<int>(model->today()) != last_day)
+
2578  {
+
2579 
+
2580  std::vector< epiworld_double > tmp(k, 0.0);
+
2581 
+
2582  tmp[j] = x;
2583 
-
2584 template<typename TSeq>
-
2585 inline void UserData<TSeq>::get_all(
-
2586  std::vector< std::string > * names,
-
2587  std::vector< int > * date,
-
2588  std::vector< epiworld_double > * data
-
2589 )
-
2590 {
-
2591 
-
2592  if (names != nullptr)
-
2593  names = &this->data_names;
-
2594 
-
2595  if (date != nullptr)
-
2596  date = &this->data_dates;
-
2597 
-
2598  if (data != nullptr)
-
2599  data = &this->data_data;
-
2600 
-
2601 }
-
2602 
-
2603 template<typename TSeq>
-
2604 inline epiworld_double & UserData<TSeq>::operator()(
-
2605  epiworld_fast_uint i,
-
2606  epiworld_fast_uint j
-
2607 )
-
2608 {
-
2609 
-
2610  if (j >= k)
-
2611  throw std::out_of_range("j cannot be greater than k - 1.");
-
2612 
-
2613  if (i >= n)
-
2614  throw std::out_of_range("j cannot be greater than n - 1.");
-
2615 
-
2616  return data_data[k * i + j];
-
2617 
-
2618 }
-
2619 
-
2620 template<typename TSeq>
-
2621 inline epiworld_double & UserData<TSeq>::operator()(
-
2622  epiworld_fast_uint i,
-
2623  std::string name
-
2624 )
-
2625 {
-
2626  int loc = -1;
-
2627  for (epiworld_fast_uint l = 0u; l < k; ++l)
-
2628  {
-
2629 
-
2630  if (name == data_names[l])
-
2631  {
+
2584  add(tmp);
+
2585 
+
2586  }
+
2587  else
+
2588  {
+
2589 
+
2590  this->operator()(n - 1, j) = x;
+
2591 
+
2592  }
+
2593 
+
2594 }
+
2595 
+
2596 template<typename TSeq>
+
2597 inline std::vector< std::string > & UserData<TSeq>::get_names()
+
2598 {
+
2599  return data_names;
+
2600 }
+
2601 
+
2602 template<typename TSeq>
+
2603 inline std::vector< int > & UserData<TSeq>::get_dates()
+
2604 {
+
2605  return data_dates;
+
2606 }
+
2607 
+
2608 template<typename TSeq>
+
2609 inline std::vector< epiworld_double > & UserData<TSeq>::get_data()
+
2610 {
+
2611  return data_data;
+
2612 }
+
2613 
+
2614 template<typename TSeq>
+
2615 inline void UserData<TSeq>::get_all(
+
2616  std::vector< std::string > * names,
+
2617  std::vector< int > * date,
+
2618  std::vector< epiworld_double > * data
+
2619 )
+
2620 {
+
2621 
+
2622  if (names != nullptr)
+
2623  names = &this->data_names;
+
2624 
+
2625  if (date != nullptr)
+
2626  date = &this->data_dates;
+
2627 
+
2628  if (data != nullptr)
+
2629  data = &this->data_data;
+
2630 
+
2631 }
2632 
-
2633  loc = l;
-
2634  break;
-
2635 
-
2636  }
-
2637 
-
2638  }
+
2633 template<typename TSeq>
+
2634 inline epiworld_double & UserData<TSeq>::operator()(
+
2635  epiworld_fast_uint i,
+
2636  epiworld_fast_uint j
+
2637 )
+
2638 {
2639 
-
2640  if (loc < 0)
-
2641  throw std::range_error(
-
2642  "The variable \"" + name + "\" is not present " +
-
2643  "in the user UserData database."
-
2644  );
+
2640  if (j >= k)
+
2641  throw std::out_of_range("j cannot be greater than k - 1.");
+
2642 
+
2643  if (i >= n)
+
2644  throw std::out_of_range("j cannot be greater than n - 1.");
2645 
-
2646  return operator()(i, static_cast<epiworld_fast_uint>(loc));
+
2646  return data_data[k * i + j];
2647 
2648 }
2649 
2650 template<typename TSeq>
-
2651 inline epiworld_fast_uint UserData<TSeq>::nrow() const
-
2652 {
-
2653  return n;
-
2654 }
-
2655 
-
2656 template<typename TSeq>
-
2657 inline epiworld_fast_uint UserData<TSeq>::ncol() const
-
2658 {
-
2659  return k;
-
2660 }
-
2661 
-
2662 template<typename TSeq>
-
2663 inline void UserData<TSeq>::write(std::string fn)
-
2664 {
-
2665  std::ofstream file_ud(fn, std::ios_base::out);
-
2666 
-
2667  // File header
-
2668  file_ud << "\"date\"";
-
2669  for (auto & cn : data_names)
-
2670  file_ud << " \"" + cn + "\"";
-
2671  file_ud << "\n";
-
2672 
-
2673  epiworld_fast_uint ndata = 0u;
-
2674  for (epiworld_fast_uint i = 0u; i < n; ++i)
-
2675  {
-
2676  file_ud << data_dates[i];
+
2651 inline epiworld_double & UserData<TSeq>::operator()(
+
2652  epiworld_fast_uint i,
+
2653  std::string name
+
2654 )
+
2655 {
+
2656  int loc = -1;
+
2657  for (epiworld_fast_uint l = 0u; l < k; ++l)
+
2658  {
+
2659 
+
2660  if (name == data_names[l])
+
2661  {
+
2662 
+
2663  loc = l;
+
2664  break;
+
2665 
+
2666  }
+
2667 
+
2668  }
+
2669 
+
2670  if (loc < 0)
+
2671  throw std::range_error(
+
2672  "The variable \"" + name + "\" is not present " +
+
2673  "in the user UserData database."
+
2674  );
+
2675 
+
2676  return operator()(i, static_cast<epiworld_fast_uint>(loc));
2677 
-
2678  for (epiworld_fast_uint j = 0u; j < k; ++j)
-
2679  file_ud << " " << data_data[ndata++];
-
2680 
-
2681  file_ud << "\n";
-
2682  }
-
2683 
-
2684  return;
-
2685 }
-
2686 
-
2687 template<typename TSeq>
-
2688 inline void UserData<TSeq>::print() const
-
2689 {
-
2690  // File header
-
2691  printf_epiworld("Total records: %llu\n", n);
-
2692  printf_epiworld("date");
-
2693 
-
2694  for (auto & cn : data_names)
-
2695  {
+
2678 }
+
2679 
+
2680 template<typename TSeq>
+
2681 inline epiworld_fast_uint UserData<TSeq>::nrow() const
+
2682 {
+
2683  return n;
+
2684 }
+
2685 
+
2686 template<typename TSeq>
+
2687 inline epiworld_fast_uint UserData<TSeq>::ncol() const
+
2688 {
+
2689  return k;
+
2690 }
+
2691 
+
2692 template<typename TSeq>
+
2693 inline void UserData<TSeq>::write(std::string fn)
+
2694 {
+
2695  std::ofstream file_ud(fn, std::ios_base::out);
2696 
-
2697  printf_epiworld(" %s", cn.c_str());
-
2698 
-
2699  }
-
2700 
-
2701  printf_epiworld("\n");
+
2697  // File header
+
2698  file_ud << "\"date\"";
+
2699  for (auto & cn : data_names)
+
2700  file_ud << " \"" + cn + "\"";
+
2701  file_ud << "\n";
2702 
2703  epiworld_fast_uint ndata = 0u;
-
2704 
-
2705  for (epiworld_fast_uint i = 0u; i < n; ++i)
-
2706  {
+
2704  for (epiworld_fast_uint i = 0u; i < n; ++i)
+
2705  {
+
2706  file_ud << data_dates[i];
2707 
-
2708  printf_epiworld("%i", data_dates[i]);
-
2709 
-
2710  for (epiworld_fast_uint j = 0u; j < k; ++j)
-
2711  {
-
2712 
-
2713  printf_epiworld(" %.2f", data_data[ndata++]);
-
2714 
-
2715  }
+
2708  for (epiworld_fast_uint j = 0u; j < k; ++j)
+
2709  file_ud << " " << data_data[ndata++];
+
2710 
+
2711  file_ud << "\n";
+
2712  }
+
2713 
+
2714  return;
+
2715 }
2716 
-
2717  printf_epiworld("\n");
-
2718 
-
2719  }
-
2720 
-
2721  return;
-
2722 }
+
2717 template<typename TSeq>
+
2718 inline void UserData<TSeq>::print() const
+
2719 {
+
2720  // File header
+
2721  printf_epiworld("Total records: %llu\n", n);
+
2722  printf_epiworld("date");
2723 
-
2724 #endif
-
2725 /*//////////////////////////////////////////////////////////////////////////////
-
2727 
-
2728  End of -include/epiworld/userdata-meat.hpp-
-
2729 
-
2732 
-
2733 
-
2734 
-
2735 /*//////////////////////////////////////////////////////////////////////////////
+
2724  for (auto & cn : data_names)
+
2725  {
+
2726 
+
2727  printf_epiworld(" %s", cn.c_str());
+
2728 
+
2729  }
+
2730 
+
2731  printf_epiworld("\n");
+
2732 
+
2733  epiworld_fast_uint ndata = 0u;
+
2734 
+
2735  for (epiworld_fast_uint i = 0u; i < n; ++i)
+
2736  {
2737 
-
2738  Start of -include/epiworld/seq_processing.hpp-
+
2738  printf_epiworld("%i", data_dates[i]);
2739 
+
2740  for (epiworld_fast_uint j = 0u; j < k; ++j)
+
2741  {
2742 
-
2743 
-
2744 #ifndef EPIWORLD_SEQ_PROCESSING_HPP
-
2745 #define EPIWORLD_SEQ_PROCESSING_HPP
+
2743  printf_epiworld(" %.2f", data_data[ndata++]);
+
2744 
+
2745  }
2746 
-
2754 template<typename TSeq>
-
2755 inline std::vector<int> default_seq_hasher(const TSeq & x);
-
2756 
-
2757 template<>
-
2758 inline std::vector<int> default_seq_hasher<std::vector<int>>(const std::vector<int> & x) {
-
2759  return x;
-
2760 }
-
2761 
-
2762 template<>
-
2763 inline std::vector<int> default_seq_hasher<std::vector<bool>>(const std::vector<bool> & x) {
-
2764  std::vector<int> ans(x.size());
-
2765  size_t j = 0;
-
2766  for (const auto & i : x)
-
2767  ans[j++] = i? 1 : 0;
-
2768  return ans;
-
2769 }
-
2770 
-
2771 template<>
-
2772 inline std::vector<int> default_seq_hasher<int>(const int & x) {
-
2773  return {x};
-
2774 }
-
2775 
-
2776 template<>
-
2777 inline std::vector<int> default_seq_hasher<bool>(const bool & x) {
-
2778  return {x ? 1 : 0};
-
2779 }
-
2780 
-
2788 template<typename TSeq = int>
-
2789 inline std::string default_seq_writer(const TSeq & seq);
-
2790 
-
2791 template<>
-
2792 inline std::string default_seq_writer<std::vector<int>>(
-
2793  const std::vector<int> & seq
-
2794 ) {
-
2795 
-
2796  std::string out = "";
-
2797  for (const auto & s : seq)
-
2798  out = out + std::to_string(s);
-
2799 
-
2800  return out;
-
2801 
-
2802 }
-
2803 
-
2804 template<>
-
2805 inline std::string default_seq_writer<std::vector<bool>>(
-
2806  const std::vector<bool> & seq
-
2807 ) {
-
2808 
-
2809  std::string out = "";
-
2810  for (const auto & s : seq)
-
2811  out = out + (s ? "1" : "0");
-
2812 
-
2813  return out;
-
2814 
-
2815 }
-
2816 
-
2817 template<>
-
2818 inline std::string default_seq_writer<bool>(
-
2819  const bool & seq
-
2820 ) {
-
2821 
-
2822  return seq ? "1" : "0";
-
2823 
-
2824 }
+
2747  printf_epiworld("\n");
+
2748 
+
2749  }
+
2750 
+
2751  return;
+
2752 }
+
2753 
+
2754 #endif
+
2755 /*//////////////////////////////////////////////////////////////////////////////
+
2757 
+
2758  End of -include/epiworld/userdata-meat.hpp-
+
2759 
+
2762 
+
2763 
+
2764 
+
2765 /*//////////////////////////////////////////////////////////////////////////////
+
2767 
+
2768  Start of -include/epiworld/seq_processing.hpp-
+
2769 
+
2772 
+
2773 
+
2774 #ifndef EPIWORLD_SEQ_PROCESSING_HPP
+
2775 #define EPIWORLD_SEQ_PROCESSING_HPP
+
2776 
+
2784 template<typename TSeq>
+
2785 inline std::vector<int> default_seq_hasher(const TSeq & x);
+
2786 
+
2787 template<>
+
2788 inline std::vector<int> default_seq_hasher<std::vector<int>>(const std::vector<int> & x) {
+
2789  return x;
+
2790 }
+
2791 
+
2792 template<>
+
2793 inline std::vector<int> default_seq_hasher<std::vector<bool>>(const std::vector<bool> & x) {
+
2794  std::vector<int> ans(x.size());
+
2795  size_t j = 0;
+
2796  for (const auto & i : x)
+
2797  ans[j++] = i? 1 : 0;
+
2798  return ans;
+
2799 }
+
2800 
+
2801 template<>
+
2802 inline std::vector<int> default_seq_hasher<int>(const int & x) {
+
2803  return {x};
+
2804 }
+
2805 
+
2806 template<>
+
2807 inline std::vector<int> default_seq_hasher<bool>(const bool & x) {
+
2808  return {x ? 1 : 0};
+
2809 }
+
2810 
+
2818 template<typename TSeq = int>
+
2819 inline std::string default_seq_writer(const TSeq & seq);
+
2820 
+
2821 template<>
+
2822 inline std::string default_seq_writer<std::vector<int>>(
+
2823  const std::vector<int> & seq
+
2824 ) {
2825 
-
2826 template<>
-
2827 inline std::string default_seq_writer<int>(
-
2828  const int & seq
-
2829 ) {
-
2830 
-
2831  return std::to_string(seq);
-
2832 
-
2833 }
-
2834 
-
2835 
-
2836 
-
2837 #endif
-
2838 /*//////////////////////////////////////////////////////////////////////////////
-
2840 
-
2841  End of -include/epiworld/seq_processing.hpp-
+
2826  std::string out = "";
+
2827  for (const auto & s : seq)
+
2828  out = out + std::to_string(s);
+
2829 
+
2830  return out;
+
2831 
+
2832 }
+
2833 
+
2834 template<>
+
2835 inline std::string default_seq_writer<std::vector<bool>>(
+
2836  const std::vector<bool> & seq
+
2837 ) {
+
2838 
+
2839  std::string out = "";
+
2840  for (const auto & s : seq)
+
2841  out = out + (s ? "1" : "0");
2842 
-
2845 
+
2843  return out;
+
2844 
+
2845 }
2846 
-
2847 
-
2848 /*//////////////////////////////////////////////////////////////////////////////
-
2850 
-
2851  Start of -include/epiworld/database-bones.hpp-
-
2852 
+
2847 template<>
+
2848 inline std::string default_seq_writer<bool>(
+
2849  const bool & seq
+
2850 ) {
+
2851 
+
2852  return seq ? "1" : "0";
+
2853 
+
2854 }
2855 
-
2856 
-
2857 #ifndef EPIWORLD_DATABASE_BONES_HPP
-
2858 #define EPIWORLD_DATABASE_BONES_HPP
-
2859 
-
2860 template<typename TSeq>
-
2861 class Model;
+
2856 template<>
+
2857 inline std::string default_seq_writer<int>(
+
2858  const int & seq
+
2859 ) {
+
2860 
+
2861  return std::to_string(seq);
2862 
-
2863 template<typename TSeq>
-
2864 class Virus;
+
2863 }
+
2864 
2865 
-
2866 template<typename TSeq>
-
2867 class UserData;
-
2868 
-
2869 template<typename TSeq>
-
2870 inline void default_add_virus(Event<TSeq> & a, Model<TSeq> * m);
-
2871 
-
2872 template<typename TSeq>
-
2873 inline void default_add_tool(Event<TSeq> & a, Model<TSeq> * m);
-
2874 
-
2875 template<typename TSeq>
-
2876 inline void default_rm_virus(Event<TSeq> & a, Model<TSeq> * m);
+
2866 
+
2867 #endif
+
2868 /*//////////////////////////////////////////////////////////////////////////////
+
2870 
+
2871  End of -include/epiworld/seq_processing.hpp-
+
2872 
+
2875 
+
2876 
2877 
-
2878 template<typename TSeq>
-
2879 inline void default_rm_tool(Event<TSeq> & a, Model<TSeq> * m);
+
2878 /*//////////////////////////////////////////////////////////////////////////////
2880 
-
2881 template<typename TSeq>
-
2882 inline void default_change_state(Event<TSeq> & a, Model<TSeq> * m);
-
2883 
-
2889 template<typename TSeq>
-
2890 class DataBase {
-
2891  friend class Model<TSeq>;
-
2892  friend void default_add_virus<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
2893  friend void default_add_tool<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
2894  friend void default_rm_virus<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
2895  friend void default_rm_tool<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
2896  friend void default_change_state<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
2897 private:
-
2898  Model<TSeq> * model;
-
2899 
-
2900  // Variants information
-
2901  MapVec_type<int,int> virus_id; ///< The squence is the key
-
2902  std::vector< std::string > virus_name;
-
2903  std::vector< TSeq> virus_sequence;
-
2904  std::vector< int > virus_origin_date;
-
2905  std::vector< int > virus_parent_id;
-
2906 
-
2907  MapVec_type<int,int> tool_id; ///< The squence is the key
-
2908  std::vector< std::string > tool_name;
-
2909  std::vector< TSeq> tool_sequence;
-
2910  std::vector< int > tool_origin_date;
-
2911 
-
2912  std::function<std::vector<int>(const TSeq&)> seq_hasher = default_seq_hasher<TSeq>;
-
2913  std::function<std::string(const TSeq &)> seq_writer = default_seq_writer<TSeq>;
-
2914 
-
2915  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
-
2916  std::vector< std::vector<int> > today_virus;
-
2917 
-
2918  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
-
2919  std::vector< std::vector<int> > today_tool;
-
2920 
-
2921  // {Susceptible, Infected, etc.}
-
2922  std::vector< int > today_total;
-
2923 
-
2924  // Totals
-
2925  int today_total_nviruses_active = 0;
-
2926 
-
2927  int sampling_freq = 1;
-
2928 
-
2929  // Variants history
-
2930  std::vector< int > hist_virus_date;
-
2931  std::vector< int > hist_virus_id;
-
2932  std::vector< epiworld_fast_uint > hist_virus_state;
-
2933  std::vector< int > hist_virus_counts;
-
2934 
-
2935  // Tools history
-
2936  std::vector< int > hist_tool_date;
-
2937  std::vector< int > hist_tool_id;
-
2938  std::vector< epiworld_fast_uint > hist_tool_state;
-
2939  std::vector< int > hist_tool_counts;
-
2940 
-
2941  // Overall hist
-
2942  std::vector< int > hist_total_date;
-
2943  std::vector< int > hist_total_nviruses_active;
-
2944  std::vector< epiworld_fast_uint > hist_total_state;
-
2945  std::vector< int > hist_total_counts;
-
2946  std::vector< int > hist_transition_matrix;
+
2881  Start of -include/epiworld/database-bones.hpp-
+
2882 
+
2885 
+
2886 
+
2887 #ifndef EPIWORLD_DATABASE_BONES_HPP
+
2888 #define EPIWORLD_DATABASE_BONES_HPP
+
2889 
+
2890 template<typename TSeq>
+
2891 class Model;
+
2892 
+
2893 template<typename TSeq>
+
2894 class Virus;
+
2895 
+
2896 template<typename TSeq>
+
2897 class UserData;
+
2898 
+
2899 template<typename TSeq>
+
2900 inline void default_add_virus(Event<TSeq> & a, Model<TSeq> * m);
+
2901 
+
2902 template<typename TSeq>
+
2903 inline void default_add_tool(Event<TSeq> & a, Model<TSeq> * m);
+
2904 
+
2905 template<typename TSeq>
+
2906 inline void default_rm_virus(Event<TSeq> & a, Model<TSeq> * m);
+
2907 
+
2908 template<typename TSeq>
+
2909 inline void default_rm_tool(Event<TSeq> & a, Model<TSeq> * m);
+
2910 
+
2911 template<typename TSeq>
+
2912 inline void default_change_state(Event<TSeq> & a, Model<TSeq> * m);
+
2913 
+
2919 template<typename TSeq>
+
2920 class DataBase {
+
2921  friend class Model<TSeq>;
+
2922  friend void default_add_virus<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
2923  friend void default_add_tool<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
2924  friend void default_rm_virus<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
2925  friend void default_rm_tool<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
2926  friend void default_change_state<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
2927 private:
+
2928  Model<TSeq> * model;
+
2929 
+
2930  // Variants information
+
2931  MapVec_type<int,int> virus_id; ///< The squence is the key
+
2932  std::vector< std::string > virus_name;
+
2933  std::vector< TSeq> virus_sequence;
+
2934  std::vector< int > virus_origin_date;
+
2935  std::vector< int > virus_parent_id;
+
2936 
+
2937  MapVec_type<int,int> tool_id; ///< The squence is the key
+
2938  std::vector< std::string > tool_name;
+
2939  std::vector< TSeq> tool_sequence;
+
2940  std::vector< int > tool_origin_date;
+
2941 
+
2942  std::function<std::vector<int>(const TSeq&)> seq_hasher = default_seq_hasher<TSeq>;
+
2943  std::function<std::string(const TSeq &)> seq_writer = default_seq_writer<TSeq>;
+
2944 
+
2945  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
+
2946  std::vector< std::vector<int> > today_virus;
2947 
-
2948  // Transmission network
-
2949  std::vector< int > transmission_date; ///< Date of the transmission event
-
2950  std::vector< int > transmission_source; ///< Id of the source
-
2951  std::vector< int > transmission_target; ///< Id of the target
-
2952  std::vector< int > transmission_virus; ///< Id of the variant
-
2953  std::vector< int > transmission_source_exposure_date; ///< Date when the source acquired the variant
-
2954 
-
2955  std::vector< int > transition_matrix;
-
2956 
-
2957  UserData<TSeq> user_data;
+
2948  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
+
2949  std::vector< std::vector<int> > today_tool;
+
2950 
+
2951  // {Susceptible, Infected, etc.}
+
2952  std::vector< int > today_total;
+
2953 
+
2954  // Totals
+
2955  int today_total_nviruses_active = 0;
+
2956 
+
2957  int sampling_freq = 1;
2958 
-
2959  void update_state(
-
2960  epiworld_fast_uint prev_state,
-
2961  epiworld_fast_uint new_state,
-
2962  bool undo = false
-
2963  );
+
2959  // Variants history
+
2960  std::vector< int > hist_virus_date;
+
2961  std::vector< int > hist_virus_id;
+
2962  std::vector< epiworld_fast_uint > hist_virus_state;
+
2963  std::vector< int > hist_virus_counts;
2964 
-
2965  void update_virus(
-
2966  epiworld_fast_uint virus_id,
-
2967  epiworld_fast_uint prev_state,
-
2968  epiworld_fast_uint new_state
-
2969  );
+
2965  // Tools history
+
2966  std::vector< int > hist_tool_date;
+
2967  std::vector< int > hist_tool_id;
+
2968  std::vector< epiworld_fast_uint > hist_tool_state;
+
2969  std::vector< int > hist_tool_counts;
2970 
-
2971  void update_tool(
-
2972  epiworld_fast_uint tool_id,
-
2973  epiworld_fast_uint prev_state,
-
2974  epiworld_fast_uint new_state
-
2975  );
-
2976 
-
2977  void record_transition(epiworld_fast_uint from, epiworld_fast_uint to, bool undo);
-
2978 
-
2979 
-
2980 public:
-
2981 
-
2982  #ifdef EPI_DEBUG
-
2983  int n_transmissions_potential = 0;
-
2984  int n_transmissions_today = 0;
-
2985  #endif
+
2971  // Overall hist
+
2972  std::vector< int > hist_total_date;
+
2973  std::vector< int > hist_total_nviruses_active;
+
2974  std::vector< epiworld_fast_uint > hist_total_state;
+
2975  std::vector< int > hist_total_counts;
+
2976  std::vector< int > hist_transition_matrix;
+
2977 
+
2978  // Transmission network
+
2979  std::vector< int > transmission_date; ///< Date of the transmission event
+
2980  std::vector< int > transmission_source; ///< Id of the source
+
2981  std::vector< int > transmission_target; ///< Id of the target
+
2982  std::vector< int > transmission_virus; ///< Id of the variant
+
2983  std::vector< int > transmission_source_exposure_date; ///< Date when the source acquired the variant
+
2984 
+
2985  std::vector< int > transition_matrix;
2986 
-
2987  DataBase() = delete;
-
2988  DataBase(Model<TSeq> & m) : model(&m), user_data(m) {};
-
2989  DataBase(const DataBase<TSeq> & db);
-
2990  // DataBase<TSeq> & operator=(const DataBase<TSeq> & m);
-
2991 
-
3000  void record_virus(Virus<TSeq> & v);
-
3001  void record_tool(Tool<TSeq> & t);
-
3002  void set_seq_hasher(std::function<std::vector<int>(TSeq)> fun);
-
3003  void reset();
-
3004  Model<TSeq> * get_model();
-
3005  void record();
+
2987  UserData<TSeq> user_data;
+
2988 
+
2989  void update_state(
+
2990  epiworld_fast_uint prev_state,
+
2991  epiworld_fast_uint new_state,
+
2992  bool undo = false
+
2993  );
+
2994 
+
2995  void update_virus(
+
2996  epiworld_fast_uint virus_id,
+
2997  epiworld_fast_uint prev_state,
+
2998  epiworld_fast_uint new_state
+
2999  );
+
3000 
+
3001  void update_tool(
+
3002  epiworld_fast_uint tool_id,
+
3003  epiworld_fast_uint prev_state,
+
3004  epiworld_fast_uint new_state
+
3005  );
3006 
-
3007  const std::vector< TSeq > & get_sequence() const;
-
3008  const std::vector< int > & get_nexposed() const;
-
3009  size_t size() const;
-
3010 
-
3024  int get_today_total(std::string what) const;
-
3025  int get_today_total(epiworld_fast_uint what) const;
-
3026  void get_today_total(
-
3027  std::vector< std::string > * state = nullptr,
-
3028  std::vector< int > * counts = nullptr
-
3029  ) const;
-
3030 
-
3031  void get_today_virus(
-
3032  std::vector< std::string > & state,
-
3033  std::vector< int > & id,
-
3034  std::vector< int > & counts
-
3035  ) const;
+
3007  void record_transition(epiworld_fast_uint from, epiworld_fast_uint to, bool undo);
+
3008 
+
3009 
+
3010 public:
+
3011 
+
3012  #ifdef EPI_DEBUG
+
3013  int n_transmissions_potential = 0;
+
3014  int n_transmissions_today = 0;
+
3015  #endif
+
3016 
+
3017  DataBase() = delete;
+
3018  DataBase(Model<TSeq> & m) : model(&m), user_data(m) {};
+
3019  DataBase(const DataBase<TSeq> & db);
+
3020  // DataBase<TSeq> & operator=(const DataBase<TSeq> & m);
+
3021 
+
3030  void record_virus(Virus<TSeq> & v);
+
3031  void record_tool(Tool<TSeq> & t);
+
3032  void set_seq_hasher(std::function<std::vector<int>(TSeq)> fun);
+
3033  void reset();
+
3034  Model<TSeq> * get_model();
+
3035  void record();
3036 
-
3037  void get_today_transition_matrix(
-
3038  std::vector< int > & counts
-
3039  ) const;
+
3037  const std::vector< TSeq > & get_sequence() const;
+
3038  const std::vector< int > & get_nexposed() const;
+
3039  size_t size() const;
3040 
-
3041  void get_hist_total(
-
3042  std::vector< int > * date,
-
3043  std::vector< std::string > * state,
-
3044  std::vector< int > * counts
-
3045  ) const;
-
3046 
-
3047  void get_hist_virus(
-
3048  std::vector< int > & date,
-
3049  std::vector< int > & id,
-
3050  std::vector< std::string > & state,
-
3051  std::vector< int > & counts
-
3052  ) const;
-
3053 
-
3054  void get_hist_tool(
-
3055  std::vector< int > & date,
-
3056  std::vector< int > & id,
-
3057  std::vector< std::string > & state,
-
3058  std::vector< int > & counts
+
3054  int get_today_total(std::string what) const;
+
3055  int get_today_total(epiworld_fast_uint what) const;
+
3056  void get_today_total(
+
3057  std::vector< std::string > * state = nullptr,
+
3058  std::vector< int > * counts = nullptr
3059  ) const;
3060 
-
3061  void get_hist_transition_matrix(
-
3062  std::vector< std::string > & state_from,
-
3063  std::vector< std::string > & state_to,
-
3064  std::vector< int > & date,
-
3065  std::vector< int > & counts,
-
3066  bool skip_zeros
-
3067  ) const;
-
3069 
-
3080  void get_transmissions(
-
3081  std::vector<int> & date,
-
3082  std::vector<int> & source,
-
3083  std::vector<int> & target,
-
3084  std::vector<int> & virus,
-
3085  std::vector<int> & source_exposure_date
-
3086  ) const;
-
3087 
-
3088  void get_transmissions(
-
3089  int * date,
-
3090  int * source,
-
3091  int * target,
-
3092  int * virus,
-
3093  int * source_exposure_date
-
3094  ) const;
-
3096 
-
3097  void write_data(
-
3098  std::string fn_virus_info,
-
3099  std::string fn_virus_hist,
-
3100  std::string fn_tool_info,
-
3101  std::string fn_tool_hist,
-
3102  std::string fn_total_hist,
-
3103  std::string fn_transmission,
-
3104  std::string fn_transition,
-
3105  std::string fn_reproductive_number,
-
3106  std::string fn_generation_time
-
3107  ) const;
-
3108 
-
3109  /***
-
3110  * @brief Record a transmission event
-
3111  */
-
3112  void record_transmission(int i, int j, int virus, int i_expo_date);
-
3113 
-
3114  size_t get_n_viruses() const;
-
3115  size_t get_n_tools() const;
-
3116 
-
3117  void set_user_data(std::vector< std::string > names);
-
3118  void add_user_data(std::vector< epiworld_double > x);
-
3119  void add_user_data(epiworld_fast_uint j, epiworld_double x);
-
3120  UserData<TSeq> & get_user_data();
-
3121 
-
3122 
-
3133  MapVec_type<int,int> reproductive_number() const;
-
3134 
-
3135  void reproductive_number(
-
3136  std::string fn
-
3137  ) const;
-
3139 
-
3145  std::vector< epiworld_double > transition_probability(
-
3146  bool print = true
-
3147  ) const;
-
3148 
-
3149  bool operator==(const DataBase<TSeq> & other) const;
-
3150  bool operator!=(const DataBase<TSeq> & other) const {return !operator==(other);};
+
3061  void get_today_virus(
+
3062  std::vector< std::string > & state,
+
3063  std::vector< int > & id,
+
3064  std::vector< int > & counts
+
3065  ) const;
+
3066 
+
3067  void get_today_transition_matrix(
+
3068  std::vector< int > & counts
+
3069  ) const;
+
3070 
+
3071  void get_hist_total(
+
3072  std::vector< int > * date,
+
3073  std::vector< std::string > * state,
+
3074  std::vector< int > * counts
+
3075  ) const;
+
3076 
+
3077  void get_hist_virus(
+
3078  std::vector< int > & date,
+
3079  std::vector< int > & id,
+
3080  std::vector< std::string > & state,
+
3081  std::vector< int > & counts
+
3082  ) const;
+
3083 
+
3084  void get_hist_tool(
+
3085  std::vector< int > & date,
+
3086  std::vector< int > & id,
+
3087  std::vector< std::string > & state,
+
3088  std::vector< int > & counts
+
3089  ) const;
+
3090 
+
3091  void get_hist_transition_matrix(
+
3092  std::vector< std::string > & state_from,
+
3093  std::vector< std::string > & state_to,
+
3094  std::vector< int > & date,
+
3095  std::vector< int > & counts,
+
3096  bool skip_zeros
+
3097  ) const;
+
3099 
+
3110  void get_transmissions(
+
3111  std::vector<int> & date,
+
3112  std::vector<int> & source,
+
3113  std::vector<int> & target,
+
3114  std::vector<int> & virus,
+
3115  std::vector<int> & source_exposure_date
+
3116  ) const;
+
3117 
+
3118  void get_transmissions(
+
3119  int * date,
+
3120  int * source,
+
3121  int * target,
+
3122  int * virus,
+
3123  int * source_exposure_date
+
3124  ) const;
+
3126 
+
3127  void write_data(
+
3128  std::string fn_virus_info,
+
3129  std::string fn_virus_hist,
+
3130  std::string fn_tool_info,
+
3131  std::string fn_tool_hist,
+
3132  std::string fn_total_hist,
+
3133  std::string fn_transmission,
+
3134  std::string fn_transition,
+
3135  std::string fn_reproductive_number,
+
3136  std::string fn_generation_time
+
3137  ) const;
+
3138 
+
3139  /***
+
3140  * @brief Record a transmission event
+
3141  */
+
3142  void record_transmission(int i, int j, int virus, int i_expo_date);
+
3143 
+
3144  size_t get_n_viruses() const;
+
3145  size_t get_n_tools() const;
+
3146 
+
3147  void set_user_data(std::vector< std::string > names);
+
3148  void add_user_data(std::vector< epiworld_double > x);
+
3149  void add_user_data(epiworld_fast_uint j, epiworld_double x);
+
3150  UserData<TSeq> & get_user_data();
3151 
-
3161  void generation_time(
-
3162  std::vector< int > & agent_id,
-
3163  std::vector< int > & virus_id,
-
3164  std::vector< int > & time,
-
3165  std::vector< int > & gentime
-
3166  ) const;
-
3167 
-
3168  void generation_time(
-
3169  std::string fn
-
3170  ) const;
-
3172 
-
3173 };
-
3174 
-
3175 
-
3176 #endif
-
3177 /*//////////////////////////////////////////////////////////////////////////////
-
3179 
-
3180  End of -include/epiworld/database-bones.hpp-
-
3181 
-
3184 
-
3185 
-
3186 /*//////////////////////////////////////////////////////////////////////////////
-
3188 
-
3189  Start of -include/epiworld/database-meat.hpp-
-
3190 
-
3193 
-
3194 
-
3195 #ifndef EPIWORLD_DATABASE_MEAT_HPP
-
3196 #define EPIWORLD_DATABASE_MEAT_HPP
-
3197 
-
3198 template<typename TSeq>
-
3199 inline void DataBase<TSeq>::reset()
-
3200 {
-
3201 
-
3202  // Initializing the counts
-
3203  today_total.resize(model->nstates);
-
3204  std::fill(today_total.begin(), today_total.end(), 0);
-
3205  for (auto & p : model->get_agents())
-
3206  ++today_total[p.get_state()];
-
3207 
-
3208  #ifdef EPI_DEBUG
-
3209  // Only the first should be different from zero
-
3210  {
-
3211  int n = static_cast<int>(model->size());
-
3212  if (today_total[0] != n)
-
3213  throw std::runtime_error("The number of susceptible agents is not equal to the total number of agents.");
+
3152 
+
3163  MapVec_type<int,int> reproductive_number() const;
+
3164 
+
3165  void reproductive_number(
+
3166  std::string fn
+
3167  ) const;
+
3169 
+
3175  std::vector< epiworld_double > transition_probability(
+
3176  bool print = true
+
3177  ) const;
+
3178 
+
3179  bool operator==(const DataBase<TSeq> & other) const;
+
3180  bool operator!=(const DataBase<TSeq> & other) const {return !operator==(other);};
+
3181 
+
3191  void generation_time(
+
3192  std::vector< int > & agent_id,
+
3193  std::vector< int > & virus_id,
+
3194  std::vector< int > & time,
+
3195  std::vector< int > & gentime
+
3196  ) const;
+
3197 
+
3198  void generation_time(
+
3199  std::string fn
+
3200  ) const;
+
3202 
+
3203 };
+
3204 
+
3205 
+
3206 #endif
+
3207 /*//////////////////////////////////////////////////////////////////////////////
+
3209 
+
3210  End of -include/epiworld/database-bones.hpp-
+
3211 
3214 
-
3215  if (std::accumulate(today_total.begin(), today_total.end(), 0) != n)
-
3216  throw std::runtime_error("The total number of agents is not equal to the sum of the number of agents in each state.");
-
3217 
-
3218  }
-
3219  #endif
+
3215 
+
3216 /*//////////////////////////////////////////////////////////////////////////////
+
3218 
+
3219  Start of -include/epiworld/database-meat.hpp-
3220 
-
3221 
-
3222  transition_matrix.resize(model->nstates * model->nstates);
-
3223  std::fill(transition_matrix.begin(), transition_matrix.end(), 0);
-
3224  for (size_t s = 0u; s < model->nstates; ++s)
-
3225  transition_matrix[s + s * model->nstates] = today_total[s];
-
3226 
-
3227  hist_virus_date.clear();
-
3228  hist_virus_id.clear();
-
3229  hist_virus_state.clear();
-
3230  hist_virus_counts.clear();
+
3223 
+
3224 
+
3225 #ifndef EPIWORLD_DATABASE_MEAT_HPP
+
3226 #define EPIWORLD_DATABASE_MEAT_HPP
+
3227 
+
3228 template<typename TSeq>
+
3229 inline void DataBase<TSeq>::reset()
+
3230 {
3231 
-
3232  hist_tool_date.clear();
-
3233  hist_tool_id.clear();
-
3234  hist_tool_state.clear();
-
3235  hist_tool_counts.clear();
-
3236 
-
3237  today_virus.resize(get_n_viruses());
-
3238  std::fill(today_virus.begin(), today_virus.begin(), std::vector<int>(model->nstates, 0));
-
3239 
-
3240  today_tool.resize(get_n_tools());
-
3241  std::fill(today_tool.begin(), today_tool.begin(), std::vector<int>(model->nstates, 0));
-
3242 
-
3243  hist_total_date.clear();
-
3244  hist_total_state.clear();
-
3245  hist_total_nviruses_active.clear();
-
3246  hist_total_counts.clear();
-
3247  hist_transition_matrix.clear();
-
3248 
-
3249  transmission_date.clear();
-
3250  transmission_virus.clear();
-
3251  transmission_source.clear();
-
3252  transmission_target.clear();
-
3253  transmission_source_exposure_date.clear();
-
3254 
-
3255  return;
+
3232  // Initializing the counts
+
3233  today_total.resize(model->nstates);
+
3234  std::fill(today_total.begin(), today_total.end(), 0);
+
3235  for (auto & p : model->get_agents())
+
3236  ++today_total[p.get_state()];
+
3237 
+
3238  #ifdef EPI_DEBUG
+
3239  // Only the first should be different from zero
+
3240  {
+
3241  int n = static_cast<int>(model->size());
+
3242  if (today_total[0] != n)
+
3243  throw std::runtime_error("The number of susceptible agents is not equal to the total number of agents.");
+
3244 
+
3245  if (std::accumulate(today_total.begin(), today_total.end(), 0) != n)
+
3246  throw std::runtime_error("The total number of agents is not equal to the sum of the number of agents in each state.");
+
3247 
+
3248  }
+
3249  #endif
+
3250 
+
3251 
+
3252  transition_matrix.resize(model->nstates * model->nstates);
+
3253  std::fill(transition_matrix.begin(), transition_matrix.end(), 0);
+
3254  for (size_t s = 0u; s < model->nstates; ++s)
+
3255  transition_matrix[s + s * model->nstates] = today_total[s];
3256 
-
3257 }
-
3258 
-
3259 template<typename TSeq>
-
3260 inline DataBase<TSeq>::DataBase(const DataBase<TSeq> & db) :
-
3261  virus_id(db.virus_id),
-
3262  virus_name(db.virus_name),
-
3263  virus_sequence(db.virus_sequence),
-
3264  virus_origin_date(db.virus_origin_date),
-
3265  virus_parent_id(db.virus_parent_id),
-
3266  tool_id(db.tool_id),
-
3267  tool_name(db.tool_name),
-
3268  tool_sequence(db.tool_sequence),
-
3269  tool_origin_date(db.tool_origin_date),
-
3270  seq_hasher(db.seq_hasher),
-
3271  seq_writer(db.seq_writer),
-
3272  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
-
3273  today_virus(db.today_virus),
-
3274  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
-
3275  today_tool(db.today_tool),
-
3276  // {Susceptible, Infected, etc.}
-
3277  today_total(db.today_total),
-
3278  // Totals
-
3279  today_total_nviruses_active(db.today_total_nviruses_active),
-
3280  sampling_freq(db.sampling_freq),
-
3281  // Variants history
-
3282  hist_virus_date(db.hist_virus_date),
-
3283  hist_virus_id(db.hist_virus_id),
-
3284  hist_virus_state(db.hist_virus_state),
-
3285  hist_virus_counts(db.hist_virus_counts),
-
3286  // Tools history
-
3287  hist_tool_date(db.hist_tool_date),
-
3288  hist_tool_id(db.hist_tool_id),
-
3289  hist_tool_state(db.hist_tool_state),
-
3290  hist_tool_counts(db.hist_tool_counts),
-
3291  // Overall hist
-
3292  hist_total_date(db.hist_total_date),
-
3293  hist_total_nviruses_active(db.hist_total_nviruses_active),
-
3294  hist_total_state(db.hist_total_state),
-
3295  hist_total_counts(db.hist_total_counts),
-
3296  hist_transition_matrix(db.hist_transition_matrix),
-
3297  // Transmission network
-
3298  transmission_date(db.transmission_date),
-
3299  transmission_source(db.transmission_source),
-
3300  transmission_target(db.transmission_target),
-
3301  transmission_virus(db.transmission_virus),
-
3302  transmission_source_exposure_date(db.transmission_source_exposure_date),
-
3303  transition_matrix(db.transition_matrix),
-
3304  user_data(nullptr)
-
3305 {}
-
3306 
-
3307 // DataBase<TSeq> & DataBase<TSeq>::operator=(const DataBase<TSeq> & m)
-
3308 // {
-
3309 
-
3310 // }
-
3311 
-
3312 template<typename TSeq>
-
3313 inline Model<TSeq> * DataBase<TSeq>::get_model() {
-
3314  return model;
-
3315 }
-
3316 
-
3317 template<typename TSeq>
-
3318 inline const std::vector< TSeq > & DataBase<TSeq>::get_sequence() const {
-
3319  return virus_sequence;
-
3320 }
-
3321 
-
3322 template<typename TSeq>
-
3323 inline void DataBase<TSeq>::record()
-
3324 {
-
3325 
-
3327  // DEBUGGING BLOCK
-
3329  EPI_DEBUG_SUM_INT(today_total, model->size())
-
3330  EPI_DEBUG_ALL_NON_NEGATIVE(today_total)
-
3331 
-
3332  #ifdef EPI_DEBUG
-
3333  // Checking whether the sums correspond
-
3334  std::vector< int > _today_total_cp(today_total.size(), 0);
-
3335  for (auto & p : model->population)
-
3336  _today_total_cp[p.get_state()]++;
-
3337 
-
3338  EPI_DEBUG_VECTOR_MATCH_INT(
-
3339  _today_total_cp, today_total,
-
3340  "Sums of __today_total_cp in database-meat.hpp"
-
3341  )
-
3342 
-
3343  if (model->today() == 0)
-
3344  {
-
3345  if (hist_total_date.size() != 0)
-
3346  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_total_date should be of length 0.")
-
3347  if (hist_total_nviruses_active.size() != 0)
-
3348  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_total_nviruses_active should be of length 0.")
-
3349  if (hist_total_state.size() != 0)
-
3350  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_total_state should be of length 0.")
-
3351  if (hist_total_counts.size() != 0)
-
3352  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_total_counts should be of length 0.")
-
3353  if (hist_virus_date.size() != 0)
-
3354  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_virus_date should be of length 0.")
-
3355  if (hist_virus_id.size() != 0)
-
3356  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_virus_id should be of length 0.")
-
3357  if (hist_virus_state.size() != 0)
-
3358  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_virus_state should be of length 0.")
-
3359  if (hist_virus_counts.size() != 0)
-
3360  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_virus_counts should be of length 0.")
-
3361  if (hist_tool_date.size() != 0)
-
3362  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_tool_date should be of length 0.")
-
3363  if (hist_tool_id.size() != 0)
-
3364  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_tool_id should be of length 0.")
-
3365  if (hist_tool_state.size() != 0)
-
3366  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_tool_state should be of length 0.")
-
3367  if (hist_tool_counts.size() != 0)
-
3368  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_tool_counts should be of length 0.")
-
3369  }
-
3370  #endif
+
3257  hist_virus_date.clear();
+
3258  hist_virus_id.clear();
+
3259  hist_virus_state.clear();
+
3260  hist_virus_counts.clear();
+
3261 
+
3262  hist_tool_date.clear();
+
3263  hist_tool_id.clear();
+
3264  hist_tool_state.clear();
+
3265  hist_tool_counts.clear();
+
3266 
+
3267  today_virus.resize(get_n_viruses());
+
3268  std::fill(today_virus.begin(), today_virus.begin(), std::vector<int>(model->nstates, 0));
+
3269 
+
3270  today_tool.resize(get_n_tools());
+
3271  std::fill(today_tool.begin(), today_tool.begin(), std::vector<int>(model->nstates, 0));
+
3272 
+
3273  hist_total_date.clear();
+
3274  hist_total_state.clear();
+
3275  hist_total_nviruses_active.clear();
+
3276  hist_total_counts.clear();
+
3277  hist_transition_matrix.clear();
+
3278 
+
3279  transmission_date.clear();
+
3280  transmission_virus.clear();
+
3281  transmission_source.clear();
+
3282  transmission_target.clear();
+
3283  transmission_source_exposure_date.clear();
+
3284 
+
3285  return;
+
3286 
+
3287 }
+
3288 
+
3289 template<typename TSeq>
+
3290 inline DataBase<TSeq>::DataBase(const DataBase<TSeq> & db) :
+
3291  virus_id(db.virus_id),
+
3292  virus_name(db.virus_name),
+
3293  virus_sequence(db.virus_sequence),
+
3294  virus_origin_date(db.virus_origin_date),
+
3295  virus_parent_id(db.virus_parent_id),
+
3296  tool_id(db.tool_id),
+
3297  tool_name(db.tool_name),
+
3298  tool_sequence(db.tool_sequence),
+
3299  tool_origin_date(db.tool_origin_date),
+
3300  seq_hasher(db.seq_hasher),
+
3301  seq_writer(db.seq_writer),
+
3302  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
+
3303  today_virus(db.today_virus),
+
3304  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
+
3305  today_tool(db.today_tool),
+
3306  // {Susceptible, Infected, etc.}
+
3307  today_total(db.today_total),
+
3308  // Totals
+
3309  today_total_nviruses_active(db.today_total_nviruses_active),
+
3310  sampling_freq(db.sampling_freq),
+
3311  // Variants history
+
3312  hist_virus_date(db.hist_virus_date),
+
3313  hist_virus_id(db.hist_virus_id),
+
3314  hist_virus_state(db.hist_virus_state),
+
3315  hist_virus_counts(db.hist_virus_counts),
+
3316  // Tools history
+
3317  hist_tool_date(db.hist_tool_date),
+
3318  hist_tool_id(db.hist_tool_id),
+
3319  hist_tool_state(db.hist_tool_state),
+
3320  hist_tool_counts(db.hist_tool_counts),
+
3321  // Overall hist
+
3322  hist_total_date(db.hist_total_date),
+
3323  hist_total_nviruses_active(db.hist_total_nviruses_active),
+
3324  hist_total_state(db.hist_total_state),
+
3325  hist_total_counts(db.hist_total_counts),
+
3326  hist_transition_matrix(db.hist_transition_matrix),
+
3327  // Transmission network
+
3328  transmission_date(db.transmission_date),
+
3329  transmission_source(db.transmission_source),
+
3330  transmission_target(db.transmission_target),
+
3331  transmission_virus(db.transmission_virus),
+
3332  transmission_source_exposure_date(db.transmission_source_exposure_date),
+
3333  transition_matrix(db.transition_matrix),
+
3334  user_data(nullptr)
+
3335 {}
+
3336 
+
3337 // DataBase<TSeq> & DataBase<TSeq>::operator=(const DataBase<TSeq> & m)
+
3338 // {
+
3339 
+
3340 // }
+
3341 
+
3342 template<typename TSeq>
+
3343 inline Model<TSeq> * DataBase<TSeq>::get_model() {
+
3344  return model;
+
3345 }
+
3346 
+
3347 template<typename TSeq>
+
3348 inline const std::vector< TSeq > & DataBase<TSeq>::get_sequence() const {
+
3349  return virus_sequence;
+
3350 }
+
3351 
+
3352 template<typename TSeq>
+
3353 inline void DataBase<TSeq>::record()
+
3354 {
+
3355 
+
3357  // DEBUGGING BLOCK
+
3359  EPI_DEBUG_SUM_INT(today_total, model->size())
+
3360  EPI_DEBUG_ALL_NON_NEGATIVE(today_total)
+
3361 
+
3362  #ifdef EPI_DEBUG
+
3363  // Checking whether the sums correspond
+
3364  std::vector< int > _today_total_cp(today_total.size(), 0);
+
3365  for (auto & p : model->population)
+
3366  _today_total_cp[p.get_state()]++;
+
3367 
+
3368  EPI_DEBUG_VECTOR_MATCH_INT(
+
3369  _today_total_cp, today_total,
+
3370  "Sums of __today_total_cp in database-meat.hpp"
+
3371  )
3372 
-
3373  // Only store every now and then
-
3374  if ((model->today() % sampling_freq) == 0)
-
3375  {
-
3376 
-
3377  // Recording virus's history
-
3378  for (auto & p : virus_id)
-
3379  {
-
3380 
-
3381  for (epiworld_fast_uint s = 0u; s < model->nstates; ++s)
-
3382  {
-
3383 
-
3384  hist_virus_date.push_back(model->today());
-
3385  hist_virus_id.push_back(p.second);
-
3386  hist_virus_state.push_back(s);
-
3387  hist_virus_counts.push_back(today_virus[p.second][s]);
-
3388 
-
3389  }
-
3390 
-
3391  }
-
3392 
-
3393  // Recording tool's history
-
3394  for (auto & p : tool_id)
-
3395  {
-
3396 
-
3397  for (epiworld_fast_uint s = 0u; s < model->nstates; ++s)
-
3398  {
-
3399 
-
3400  hist_tool_date.push_back(model->today());
-
3401  hist_tool_id.push_back(p.second);
-
3402  hist_tool_state.push_back(s);
-
3403  hist_tool_counts.push_back(today_tool[p.second][s]);
-
3404 
-
3405  }
+
3373  if (model->today() == 0)
+
3374  {
+
3375  if (hist_total_date.size() != 0)
+
3376  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_total_date should be of length 0.")
+
3377  if (hist_total_nviruses_active.size() != 0)
+
3378  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_total_nviruses_active should be of length 0.")
+
3379  if (hist_total_state.size() != 0)
+
3380  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_total_state should be of length 0.")
+
3381  if (hist_total_counts.size() != 0)
+
3382  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_total_counts should be of length 0.")
+
3383  if (hist_virus_date.size() != 0)
+
3384  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_virus_date should be of length 0.")
+
3385  if (hist_virus_id.size() != 0)
+
3386  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_virus_id should be of length 0.")
+
3387  if (hist_virus_state.size() != 0)
+
3388  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_virus_state should be of length 0.")
+
3389  if (hist_virus_counts.size() != 0)
+
3390  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_virus_counts should be of length 0.")
+
3391  if (hist_tool_date.size() != 0)
+
3392  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_tool_date should be of length 0.")
+
3393  if (hist_tool_id.size() != 0)
+
3394  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_tool_id should be of length 0.")
+
3395  if (hist_tool_state.size() != 0)
+
3396  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_tool_state should be of length 0.")
+
3397  if (hist_tool_counts.size() != 0)
+
3398  EPI_DEBUG_ERROR(std::logic_error, "DataBase::record hist_tool_counts should be of length 0.")
+
3399  }
+
3400  #endif
+
3402 
+
3403  // Only store every now and then
+
3404  if ((model->today() % sampling_freq) == 0)
+
3405  {
3406 
-
3407  }
-
3408 
-
3409  // Recording the overall history
-
3410  for (epiworld_fast_uint s = 0u; s < model->nstates; ++s)
-
3411  {
-
3412  hist_total_date.push_back(model->today());
-
3413  hist_total_nviruses_active.push_back(today_total_nviruses_active);
-
3414  hist_total_state.push_back(s);
-
3415  hist_total_counts.push_back(today_total[s]);
-
3416  }
-
3417 
-
3418  for (auto cell : transition_matrix)
-
3419  hist_transition_matrix.push_back(cell);
+
3407  // Recording virus's history
+
3408  for (auto & p : virus_id)
+
3409  {
+
3410 
+
3411  for (epiworld_fast_uint s = 0u; s < model->nstates; ++s)
+
3412  {
+
3413 
+
3414  hist_virus_date.push_back(model->today());
+
3415  hist_virus_id.push_back(p.second);
+
3416  hist_virus_state.push_back(s);
+
3417  hist_virus_counts.push_back(today_virus[p.second][s]);
+
3418 
+
3419  }
3420 
-
3421  // Now the diagonal must reflect the state
-
3422  for (size_t s_i = 0u; s_i < model->nstates; ++s_i)
-
3423  {
-
3424 
-
3425  for (size_t s_j = 0u; s_j < model->nstates; ++s_j)
-
3426  {
-
3427 
-
3428  if ((s_i != s_j) && (transition_matrix[s_i + s_j * model->nstates] > 0))
-
3429  {
-
3430  transition_matrix[s_j + s_j * model->nstates] +=
-
3431  transition_matrix[s_i + s_j * model->nstates];
-
3432 
-
3433  transition_matrix[s_i + s_j * model->nstates] = 0;
-
3434  }
-
3435 
-
3436  }
-
3437 
-
3438  }
-
3439 
-
3440  #ifdef EPI_DEBUG
-
3441  for (size_t s_i = 0u; s_i < model->nstates; ++s_i)
-
3442  {
-
3443  if (transition_matrix[s_i + s_i * model->nstates] !=
-
3444  today_total[s_i])
-
3445  throw std::logic_error(
-
3446  "The diagonal of the updated transition Matrix should match the daily totals"
-
3447  );
-
3448  }
-
3449  #endif
+
3421  }
+
3422 
+
3423  // Recording tool's history
+
3424  for (auto & p : tool_id)
+
3425  {
+
3426 
+
3427  for (epiworld_fast_uint s = 0u; s < model->nstates; ++s)
+
3428  {
+
3429 
+
3430  hist_tool_date.push_back(model->today());
+
3431  hist_tool_id.push_back(p.second);
+
3432  hist_tool_state.push_back(s);
+
3433  hist_tool_counts.push_back(today_tool[p.second][s]);
+
3434 
+
3435  }
+
3436 
+
3437  }
+
3438 
+
3439  // Recording the overall history
+
3440  for (epiworld_fast_uint s = 0u; s < model->nstates; ++s)
+
3441  {
+
3442  hist_total_date.push_back(model->today());
+
3443  hist_total_nviruses_active.push_back(today_total_nviruses_active);
+
3444  hist_total_state.push_back(s);
+
3445  hist_total_counts.push_back(today_total[s]);
+
3446  }
+
3447 
+
3448  for (auto cell : transition_matrix)
+
3449  hist_transition_matrix.push_back(cell);
3450 
-
3451  }
-
3452 
-
3453 }
+
3451  // Now the diagonal must reflect the state
+
3452  for (size_t s_i = 0u; s_i < model->nstates; ++s_i)
+
3453  {
3454 
-
3455 template<typename TSeq>
-
3456 inline void DataBase<TSeq>::record_virus(Virus<TSeq> & v)
-
3457 {
-
3458 
-
3459  // If no sequence, then need to add one. This is regardless of the case
-
3460  if (v.get_sequence() == nullptr)
-
3461  v.set_sequence(default_sequence<TSeq>(
-
3462  static_cast<int>(virus_name.size())
-
3463  ));
-
3464 
-
3465  // Negative id -> virus hasn't been recorded
-
3466  if (v.get_id() < 0)
-
3467  {
-
3468 
+
3455  for (size_t s_j = 0u; s_j < model->nstates; ++s_j)
+
3456  {
+
3457 
+
3458  if ((s_i != s_j) && (transition_matrix[s_i + s_j * model->nstates] > 0))
+
3459  {
+
3460  transition_matrix[s_j + s_j * model->nstates] +=
+
3461  transition_matrix[s_i + s_j * model->nstates];
+
3462 
+
3463  transition_matrix[s_i + s_j * model->nstates] = 0;
+
3464  }
+
3465 
+
3466  }
+
3467 
+
3468  }
3469 
-
3470  // Generating the hash
-
3471  std::vector< int > hash = seq_hasher(*v.get_sequence());
-
3472 
-
3473  epiworld_fast_uint new_id = virus_id.size();
-
3474  virus_id[hash] = new_id;
-
3475  virus_name.push_back(v.get_name());
-
3476  virus_sequence.push_back(*v.get_sequence());
-
3477  virus_origin_date.push_back(model->today());
-
3478 
-
3479  virus_parent_id.push_back(v.get_id()); // Must be -99
-
3480 
-
3481  today_virus.push_back({});
-
3482  today_virus[new_id].resize(model->nstates, 0);
-
3483 
-
3484  // Updating the variant
-
3485  v.set_id(new_id);
-
3486  v.set_date(model->today());
-
3487 
-
3488  today_total_nviruses_active++;
-
3489 
-
3490  } else { // In this case, the virus is already on record, need to make sure
-
3491  // The new sequence is new.
-
3492 
-
3493  // Updating registry
-
3494  std::vector< int > hash = seq_hasher(*v.get_sequence());
-
3495  epiworld_fast_uint old_id = v.get_id();
-
3496  epiworld_fast_uint new_id;
-
3497 
-
3498  // If the sequence is new, then it means that the
-
3499  if (virus_id.find(hash) == virus_id.end())
-
3500  {
-
3501 
-
3502  new_id = virus_id.size();
-
3503  virus_id[hash] = new_id;
-
3504  virus_name.push_back(v.get_name());
-
3505  virus_sequence.push_back(*v.get_sequence());
-
3506  virus_origin_date.push_back(model->today());
-
3507 
-
3508  virus_parent_id.push_back(old_id);
-
3509 
-
3510  today_virus.push_back({});
-
3511  today_virus[new_id].resize(model->nstates, 0);
-
3512 
-
3513  // Updating the variant
-
3514  v.set_id(new_id);
-
3515  v.set_date(model->today());
-
3516 
-
3517  today_total_nviruses_active++;
-
3518 
-
3519  } else {
-
3520 
-
3521  // Finding the id
-
3522  new_id = virus_id[hash];
-
3523 
-
3524  // Reflecting the change
-
3525  v.set_id(new_id);
-
3526  v.set_date(virus_origin_date[new_id]);
+
3470  #ifdef EPI_DEBUG
+
3471  for (size_t s_i = 0u; s_i < model->nstates; ++s_i)
+
3472  {
+
3473  if (transition_matrix[s_i + s_i * model->nstates] !=
+
3474  today_total[s_i])
+
3475  throw std::logic_error(
+
3476  "The diagonal of the updated transition Matrix should match the daily totals"
+
3477  );
+
3478  }
+
3479  #endif
+
3480 
+
3481  }
+
3482 
+
3483 }
+
3484 
+
3485 template<typename TSeq>
+
3486 inline void DataBase<TSeq>::record_virus(Virus<TSeq> & v)
+
3487 {
+
3488 
+
3489  // If no sequence, then need to add one. This is regardless of the case
+
3490  if (v.get_sequence() == nullptr)
+
3491  v.set_sequence(default_sequence<TSeq>(
+
3492  static_cast<int>(virus_name.size())
+
3493  ));
+
3494 
+
3495  // Negative id -> virus hasn't been recorded
+
3496  if (v.get_id() < 0)
+
3497  {
+
3498 
+
3499 
+
3500  // Generating the hash
+
3501  std::vector< int > hash = seq_hasher(*v.get_sequence());
+
3502 
+
3503  epiworld_fast_uint new_id = virus_id.size();
+
3504  virus_id[hash] = new_id;
+
3505  virus_name.push_back(v.get_name());
+
3506  virus_sequence.push_back(*v.get_sequence());
+
3507  virus_origin_date.push_back(model->today());
+
3508 
+
3509  virus_parent_id.push_back(v.get_id()); // Must be -99
+
3510 
+
3511  today_virus.push_back({});
+
3512  today_virus[new_id].resize(model->nstates, 0);
+
3513 
+
3514  // Updating the variant
+
3515  v.set_id(new_id);
+
3516  v.set_date(model->today());
+
3517 
+
3518  today_total_nviruses_active++;
+
3519 
+
3520  } else { // In this case, the virus is already on record, need to make sure
+
3521  // The new sequence is new.
+
3522 
+
3523  // Updating registry
+
3524  std::vector< int > hash = seq_hasher(*v.get_sequence());
+
3525  epiworld_fast_uint old_id = v.get_id();
+
3526  epiworld_fast_uint new_id;
3527 
-
3528  }
-
3529 
-
3530  // Moving statistics (only if we are affecting an individual)
-
3531  if (v.get_agent() != nullptr)
-
3532  {
-
3533  // Correcting math
-
3534  epiworld_fast_uint tmp_state = v.get_agent()->get_state();
-
3535  today_virus[old_id][tmp_state]--;
-
3536  today_virus[new_id][tmp_state]++;
-
3537 
-
3538  }
-
3539 
-
3540  }
-
3541 
-
3542  return;
-
3543 
-
3544 }
-
3545 
-
3546 template<typename TSeq>
-
3547 inline void DataBase<TSeq>::record_tool(Tool<TSeq> & t)
-
3548 {
-
3549 
-
3550  if (t.get_sequence() == nullptr)
-
3551  t.set_sequence(default_sequence<TSeq>(
-
3552  static_cast<int>(tool_name.size())
-
3553  ));
-
3554 
-
3555  if (t.get_id() < 0)
-
3556  {
+
3528  // If the sequence is new, then it means that the
+
3529  if (virus_id.find(hash) == virus_id.end())
+
3530  {
+
3531 
+
3532  new_id = virus_id.size();
+
3533  virus_id[hash] = new_id;
+
3534  virus_name.push_back(v.get_name());
+
3535  virus_sequence.push_back(*v.get_sequence());
+
3536  virus_origin_date.push_back(model->today());
+
3537 
+
3538  virus_parent_id.push_back(old_id);
+
3539 
+
3540  today_virus.push_back({});
+
3541  today_virus[new_id].resize(model->nstates, 0);
+
3542 
+
3543  // Updating the variant
+
3544  v.set_id(new_id);
+
3545  v.set_date(model->today());
+
3546 
+
3547  today_total_nviruses_active++;
+
3548 
+
3549  } else {
+
3550 
+
3551  // Finding the id
+
3552  new_id = virus_id[hash];
+
3553 
+
3554  // Reflecting the change
+
3555  v.set_id(new_id);
+
3556  v.set_date(virus_origin_date[new_id]);
3557 
-
3558  std::vector< int > hash = seq_hasher(*t.get_sequence());
-
3559  epiworld_fast_uint new_id = tool_id.size();
-
3560  tool_id[hash] = new_id;
-
3561  tool_name.push_back(t.get_name());
-
3562  tool_sequence.push_back(*t.get_sequence());
-
3563  tool_origin_date.push_back(model->today());
-
3564 
-
3565  today_tool.push_back({});
-
3566  today_tool[new_id].resize(model->nstates, 0);
+
3558  }
+
3559 
+
3560  // Moving statistics (only if we are affecting an individual)
+
3561  if (v.get_agent() != nullptr)
+
3562  {
+
3563  // Correcting math
+
3564  epiworld_fast_uint tmp_state = v.get_agent()->get_state();
+
3565  today_virus[old_id][tmp_state]--;
+
3566  today_virus[new_id][tmp_state]++;
3567 
-
3568  // Updating the tool
-
3569  t.set_id(new_id);
-
3570  t.set_date(model->today());
-
3571 
-
3572  } else {
+
3568  }
+
3569 
+
3570  }
+
3571 
+
3572  return;
3573 
-
3574  // Updating registry
-
3575  std::vector< int > hash = seq_hasher(*t.get_sequence());
-
3576  epiworld_fast_uint old_id = t.get_id();
-
3577  epiworld_fast_uint new_id;
-
3578 
-
3579  if (tool_id.find(hash) == tool_id.end())
-
3580  {
-
3581 
-
3582  new_id = tool_id.size();
-
3583  tool_id[hash] = new_id;
-
3584  tool_name.push_back(t.get_name());
-
3585  tool_sequence.push_back(*t.get_sequence());
-
3586  tool_origin_date.push_back(model->today());
-
3587 
-
3588  today_tool.push_back({});
-
3589  today_tool[new_id].resize(model->nstates, 0);
-
3590 
-
3591  // Updating the tool
-
3592  t.set_id(new_id);
-
3593  t.set_date(model->today());
-
3594 
-
3595  } else {
-
3596 
-
3597  // Finding the id
-
3598  new_id = tool_id[hash];
-
3599 
-
3600  // Reflecting the change
-
3601  t.set_id(new_id);
-
3602  t.set_date(tool_origin_date[new_id]);
+
3574 }
+
3575 
+
3576 template<typename TSeq>
+
3577 inline void DataBase<TSeq>::record_tool(Tool<TSeq> & t)
+
3578 {
+
3579 
+
3580  if (t.get_sequence() == nullptr)
+
3581  t.set_sequence(default_sequence<TSeq>(
+
3582  static_cast<int>(tool_name.size())
+
3583  ));
+
3584 
+
3585  if (t.get_id() < 0)
+
3586  {
+
3587 
+
3588  std::vector< int > hash = seq_hasher(*t.get_sequence());
+
3589  epiworld_fast_uint new_id = tool_id.size();
+
3590  tool_id[hash] = new_id;
+
3591  tool_name.push_back(t.get_name());
+
3592  tool_sequence.push_back(*t.get_sequence());
+
3593  tool_origin_date.push_back(model->today());
+
3594 
+
3595  today_tool.push_back({});
+
3596  today_tool[new_id].resize(model->nstates, 0);
+
3597 
+
3598  // Updating the tool
+
3599  t.set_id(new_id);
+
3600  t.set_date(model->today());
+
3601 
+
3602  } else {
3603 
-
3604  }
-
3605 
-
3606  // Moving statistics (only if we are affecting an individual)
-
3607  if (t.get_agent() != nullptr)
-
3608  {
-
3609  // Correcting math
-
3610  epiworld_fast_uint tmp_state = t.get_agent()->get_state();
-
3611  today_tool[old_id][tmp_state]--;
-
3612  today_tool[new_id][tmp_state]++;
-
3613 
-
3614  }
-
3615 
-
3616  }
-
3617 
-
3618 
-
3619 
-
3620  return;
-
3621 }
-
3622 
-
3623 template<typename TSeq>
-
3624 inline size_t DataBase<TSeq>::size() const
-
3625 {
-
3626  return virus_id.size();
-
3627 }
-
3628 
-
3629 template<typename TSeq>
-
3630 inline void DataBase<TSeq>::update_state(
-
3631  epiworld_fast_uint prev_state,
-
3632  epiworld_fast_uint new_state,
-
3633  bool undo
-
3634 ) {
+
3604  // Updating registry
+
3605  std::vector< int > hash = seq_hasher(*t.get_sequence());
+
3606  epiworld_fast_uint old_id = t.get_id();
+
3607  epiworld_fast_uint new_id;
+
3608 
+
3609  if (tool_id.find(hash) == tool_id.end())
+
3610  {
+
3611 
+
3612  new_id = tool_id.size();
+
3613  tool_id[hash] = new_id;
+
3614  tool_name.push_back(t.get_name());
+
3615  tool_sequence.push_back(*t.get_sequence());
+
3616  tool_origin_date.push_back(model->today());
+
3617 
+
3618  today_tool.push_back({});
+
3619  today_tool[new_id].resize(model->nstates, 0);
+
3620 
+
3621  // Updating the tool
+
3622  t.set_id(new_id);
+
3623  t.set_date(model->today());
+
3624 
+
3625  } else {
+
3626 
+
3627  // Finding the id
+
3628  new_id = tool_id[hash];
+
3629 
+
3630  // Reflecting the change
+
3631  t.set_id(new_id);
+
3632  t.set_date(tool_origin_date[new_id]);
+
3633 
+
3634  }
3635 
-
3636  if (undo)
-
3637  {
-
3638 
-
3639  today_total[prev_state]++;
-
3640  today_total[new_state]--;
-
3641 
-
3642  } else {
+
3636  // Moving statistics (only if we are affecting an individual)
+
3637  if (t.get_agent() != nullptr)
+
3638  {
+
3639  // Correcting math
+
3640  epiworld_fast_uint tmp_state = t.get_agent()->get_state();
+
3641  today_tool[old_id][tmp_state]--;
+
3642  today_tool[new_id][tmp_state]++;
3643 
-
3644  today_total[prev_state]--;
-
3645  today_total[new_state]++;
-
3646 
-
3647  }
-
3648 
-
3649  record_transition(prev_state, new_state, undo);
-
3650 
-
3651  return;
-
3652 }
-
3653 
-
3654 template<typename TSeq>
-
3655 inline void DataBase<TSeq>::update_virus(
-
3656  epiworld_fast_uint virus_id,
-
3657  epiworld_fast_uint prev_state,
-
3658  epiworld_fast_uint new_state
-
3659 ) {
-
3660 
-
3661  today_virus[virus_id][prev_state]--;
-
3662  today_virus[virus_id][new_state]++;
-
3663 
-
3664  return;
-
3665 
-
3666 }
-
3667 
-
3668 template<typename TSeq>
-
3669 inline void DataBase<TSeq>::update_tool(
-
3670  epiworld_fast_uint tool_id,
-
3671  epiworld_fast_uint prev_state,
-
3672  epiworld_fast_uint new_state
-
3673 ) {
-
3674 
-
3675 
-
3676  today_tool[tool_id][prev_state]--;
-
3677  today_tool[tool_id][new_state]++;
+
3644  }
+
3645 
+
3646  }
+
3647 
+
3648 
+
3649 
+
3650  return;
+
3651 }
+
3652 
+
3653 template<typename TSeq>
+
3654 inline size_t DataBase<TSeq>::size() const
+
3655 {
+
3656  return virus_id.size();
+
3657 }
+
3658 
+
3659 template<typename TSeq>
+
3660 inline void DataBase<TSeq>::update_state(
+
3661  epiworld_fast_uint prev_state,
+
3662  epiworld_fast_uint new_state,
+
3663  bool undo
+
3664 ) {
+
3665 
+
3666  if (undo)
+
3667  {
+
3668 
+
3669  today_total[prev_state]++;
+
3670  today_total[new_state]--;
+
3671 
+
3672  } else {
+
3673 
+
3674  today_total[prev_state]--;
+
3675  today_total[new_state]++;
+
3676 
+
3677  }
3678 
-
3679  return;
-
3680 
-
3681 }
-
3682 
-
3683 template<typename TSeq>
-
3684 inline void DataBase<TSeq>::record_transition(
-
3685  epiworld_fast_uint from,
-
3686  epiworld_fast_uint to,
-
3687  bool undo
-
3688 ) {
-
3689 
-
3690  if (undo)
-
3691  {
-
3692 
-
3693  transition_matrix[to * model->nstates + from]--;
-
3694  transition_matrix[from * model->nstates + from]++;
-
3695 
-
3696  } else {
+
3679  record_transition(prev_state, new_state, undo);
+
3680 
+
3681  return;
+
3682 }
+
3683 
+
3684 template<typename TSeq>
+
3685 inline void DataBase<TSeq>::update_virus(
+
3686  epiworld_fast_uint virus_id,
+
3687  epiworld_fast_uint prev_state,
+
3688  epiworld_fast_uint new_state
+
3689 ) {
+
3690 
+
3691  today_virus[virus_id][prev_state]--;
+
3692  today_virus[virus_id][new_state]++;
+
3693 
+
3694  return;
+
3695 
+
3696 }
3697 
-
3698  transition_matrix[to * model->nstates + from]++;
-
3699  transition_matrix[from * model->nstates + from]--;
-
3700 
-
3701  }
-
3702 
-
3703  #ifdef EPI_DEBUG
-
3704  if (transition_matrix[from * model->nstates + from] < 0)
-
3705  throw std::logic_error("An entry in transition matrix is negative.");
-
3706  #endif
-
3707 
-
3708 }
-
3709 
-
3710 template<typename TSeq>
-
3711 inline int DataBase<TSeq>::get_today_total(
-
3712  std::string what
-
3713 ) const
-
3714 {
-
3715 
-
3716  for (auto i = 0u; i < model->states_labels.size(); ++i)
-
3717  {
-
3718  if (model->states_labels[i] == what)
-
3719  return today_total[i];
-
3720  }
-
3721 
-
3722  throw std::range_error("The value '" + what + "' is not in the model.");
-
3723 
-
3724 }
+
3698 template<typename TSeq>
+
3699 inline void DataBase<TSeq>::update_tool(
+
3700  epiworld_fast_uint tool_id,
+
3701  epiworld_fast_uint prev_state,
+
3702  epiworld_fast_uint new_state
+
3703 ) {
+
3704 
+
3705 
+
3706  today_tool[tool_id][prev_state]--;
+
3707  today_tool[tool_id][new_state]++;
+
3708 
+
3709  return;
+
3710 
+
3711 }
+
3712 
+
3713 template<typename TSeq>
+
3714 inline void DataBase<TSeq>::record_transition(
+
3715  epiworld_fast_uint from,
+
3716  epiworld_fast_uint to,
+
3717  bool undo
+
3718 ) {
+
3719 
+
3720  if (undo)
+
3721  {
+
3722 
+
3723  transition_matrix[to * model->nstates + from]--;
+
3724  transition_matrix[from * model->nstates + from]++;
3725 
-
3726 template<typename TSeq>
-
3727 inline void DataBase<TSeq>::get_today_total(
-
3728  std::vector< std::string > * state,
-
3729  std::vector< int > * counts
-
3730 ) const
-
3731 {
-
3732  if (state != nullptr)
-
3733  (*state) = model->states_labels;
-
3734 
-
3735  if (counts != nullptr)
-
3736  *counts = today_total;
+
3726  } else {
+
3727 
+
3728  transition_matrix[to * model->nstates + from]++;
+
3729  transition_matrix[from * model->nstates + from]--;
+
3730 
+
3731  }
+
3732 
+
3733  #ifdef EPI_DEBUG
+
3734  if (transition_matrix[from * model->nstates + from] < 0)
+
3735  throw std::logic_error("An entry in transition matrix is negative.");
+
3736  #endif
3737 
3738 }
3739 
3740 template<typename TSeq>
-
3741 inline void DataBase<TSeq>::get_today_virus(
-
3742  std::vector< std::string > & state,
-
3743  std::vector< int > & id,
-
3744  std::vector< int > & counts
-
3745  ) const
-
3746 {
-
3747 
-
3748  state.resize(today_virus.size(), "");
-
3749  id.resize(today_virus.size(), 0);
-
3750  counts.resize(today_virus.size(),0);
+
3741 inline int DataBase<TSeq>::get_today_total(
+
3742  std::string what
+
3743 ) const
+
3744 {
+
3745 
+
3746  for (auto i = 0u; i < model->states_labels.size(); ++i)
+
3747  {
+
3748  if (model->states_labels[i] == what)
+
3749  return today_total[i];
+
3750  }
3751 
-
3752  int n = 0u;
-
3753  for (epiworld_fast_uint v = 0u; v < today_virus.size(); ++v)
-
3754  for (epiworld_fast_uint s = 0u; s < model->states_labels.size(); ++s)
-
3755  {
-
3756  state[n] = model->states_labels[s];
-
3757  id[n] = static_cast<int>(v);
-
3758  counts[n++] = today_virus[v][s];
-
3759 
-
3760  }
-
3761 
-
3762 }
-
3763 
-
3764 template<typename TSeq>
-
3765 inline void DataBase<TSeq>::get_hist_total(
-
3766  std::vector< int > * date,
-
3767  std::vector< std::string > * state,
-
3768  std::vector< int > * counts
-
3769 ) const
-
3770 {
-
3771 
-
3772  if (date != nullptr)
-
3773  *date = hist_total_date;
-
3774 
-
3775  if (state != nullptr)
-
3776  {
-
3777  state->resize(hist_total_state.size(), "");
-
3778  for (epiworld_fast_uint i = 0u; i < hist_total_state.size(); ++i)
-
3779  state->operator[](i) = model->states_labels[hist_total_state[i]];
-
3780  }
+
3752  throw std::range_error("The value '" + what + "' is not in the model.");
+
3753 
+
3754 }
+
3755 
+
3756 template<typename TSeq>
+
3757 inline void DataBase<TSeq>::get_today_total(
+
3758  std::vector< std::string > * state,
+
3759  std::vector< int > * counts
+
3760 ) const
+
3761 {
+
3762  if (state != nullptr)
+
3763  (*state) = model->states_labels;
+
3764 
+
3765  if (counts != nullptr)
+
3766  *counts = today_total;
+
3767 
+
3768 }
+
3769 
+
3770 template<typename TSeq>
+
3771 inline void DataBase<TSeq>::get_today_virus(
+
3772  std::vector< std::string > & state,
+
3773  std::vector< int > & id,
+
3774  std::vector< int > & counts
+
3775  ) const
+
3776 {
+
3777 
+
3778  state.resize(today_virus.size(), "");
+
3779  id.resize(today_virus.size(), 0);
+
3780  counts.resize(today_virus.size(),0);
3781 
-
3782  if (counts != nullptr)
-
3783  *counts = hist_total_counts;
-
3784 
-
3785  return;
-
3786 
-
3787 }
-
3788 
-
3789 template<typename TSeq>
-
3790 inline void DataBase<TSeq>::get_hist_virus(
-
3791  std::vector< int > & date,
-
3792  std::vector< int > & id,
-
3793  std::vector< std::string > & state,
-
3794  std::vector< int > & counts
-
3795 ) const {
-
3796 
-
3797  date = hist_virus_date;
-
3798  std::vector< std::string > labels;
-
3799  labels = model->states_labels;
-
3800 
-
3801  id = hist_virus_id;
-
3802  state.resize(hist_virus_state.size(), "");
-
3803  for (epiworld_fast_uint i = 0u; i < hist_virus_state.size(); ++i)
-
3804  state[i] = labels[hist_virus_state[i]];
-
3805 
-
3806  counts = hist_virus_counts;
-
3807 
-
3808  return;
-
3809 
-
3810 }
+
3782  int n = 0u;
+
3783  for (epiworld_fast_uint v = 0u; v < today_virus.size(); ++v)
+
3784  for (epiworld_fast_uint s = 0u; s < model->states_labels.size(); ++s)
+
3785  {
+
3786  state[n] = model->states_labels[s];
+
3787  id[n] = static_cast<int>(v);
+
3788  counts[n++] = today_virus[v][s];
+
3789 
+
3790  }
+
3791 
+
3792 }
+
3793 
+
3794 template<typename TSeq>
+
3795 inline void DataBase<TSeq>::get_hist_total(
+
3796  std::vector< int > * date,
+
3797  std::vector< std::string > * state,
+
3798  std::vector< int > * counts
+
3799 ) const
+
3800 {
+
3801 
+
3802  if (date != nullptr)
+
3803  *date = hist_total_date;
+
3804 
+
3805  if (state != nullptr)
+
3806  {
+
3807  state->resize(hist_total_state.size(), "");
+
3808  for (epiworld_fast_uint i = 0u; i < hist_total_state.size(); ++i)
+
3809  state->operator[](i) = model->states_labels[hist_total_state[i]];
+
3810  }
3811 
-
3812 
-
3813 template<typename TSeq>
-
3814 inline void DataBase<TSeq>::get_hist_tool(
-
3815  std::vector< int > & date,
-
3816  std::vector< int > & id,
-
3817  std::vector< std::string > & state,
-
3818  std::vector< int > & counts
-
3819 ) const {
-
3820 
-
3821  date = hist_tool_date;
-
3822  std::vector< std::string > labels;
-
3823  labels = model->states_labels;
-
3824 
-
3825  id = hist_tool_id;
-
3826  state.resize(hist_tool_state.size(), "");
-
3827  for (size_t i = 0u; i < hist_tool_state.size(); ++i)
-
3828  state[i] = labels[hist_tool_state[i]];
-
3829 
-
3830  counts = hist_tool_counts;
-
3831 
-
3832  return;
-
3833 
-
3834 }
+
3812  if (counts != nullptr)
+
3813  *counts = hist_total_counts;
+
3814 
+
3815  return;
+
3816 
+
3817 }
+
3818 
+
3819 template<typename TSeq>
+
3820 inline void DataBase<TSeq>::get_hist_virus(
+
3821  std::vector< int > & date,
+
3822  std::vector< int > & id,
+
3823  std::vector< std::string > & state,
+
3824  std::vector< int > & counts
+
3825 ) const {
+
3826 
+
3827  date = hist_virus_date;
+
3828  std::vector< std::string > labels;
+
3829  labels = model->states_labels;
+
3830 
+
3831  id = hist_virus_id;
+
3832  state.resize(hist_virus_state.size(), "");
+
3833  for (epiworld_fast_uint i = 0u; i < hist_virus_state.size(); ++i)
+
3834  state[i] = labels[hist_virus_state[i]];
3835 
-
3836 template<typename TSeq>
-
3837 inline void DataBase<TSeq>::get_today_transition_matrix(
-
3838  std::vector< int > & counts
-
3839 ) const
-
3840 {
+
3836  counts = hist_virus_counts;
+
3837 
+
3838  return;
+
3839 
+
3840 }
3841 
-
3842  counts = transition_matrix;
-
3843 
-
3844  return;
-
3845 
-
3846 }
-
3847 
-
3848 template<typename TSeq>
-
3849 inline void DataBase<TSeq>::get_hist_transition_matrix(
-
3850  std::vector< std::string > & state_from,
-
3851  std::vector< std::string > & state_to,
-
3852  std::vector< int > & date,
-
3853  std::vector< int > & counts,
-
3854  bool skip_zeros
-
3855 ) const
-
3856 {
-
3857 
-
3858  size_t n = this->hist_transition_matrix.size();
-
3859 
-
3860  // Clearing the previous vectors
-
3861  state_from.clear();
-
3862  state_to.clear();
-
3863  date.clear();
-
3864  counts.clear();
+
3842 
+
3843 template<typename TSeq>
+
3844 inline void DataBase<TSeq>::get_hist_tool(
+
3845  std::vector< int > & date,
+
3846  std::vector< int > & id,
+
3847  std::vector< std::string > & state,
+
3848  std::vector< int > & counts
+
3849 ) const {
+
3850 
+
3851  date = hist_tool_date;
+
3852  std::vector< std::string > labels;
+
3853  labels = model->states_labels;
+
3854 
+
3855  id = hist_tool_id;
+
3856  state.resize(hist_tool_state.size(), "");
+
3857  for (size_t i = 0u; i < hist_tool_state.size(); ++i)
+
3858  state[i] = labels[hist_tool_state[i]];
+
3859 
+
3860  counts = hist_tool_counts;
+
3861 
+
3862  return;
+
3863 
+
3864 }
3865 
-
3866  // Reserving space
-
3867  state_from.reserve(n);
-
3868  state_to.reserve(n);
-
3869  date.reserve(n);
-
3870  counts.reserve(n);
+
3866 template<typename TSeq>
+
3867 inline void DataBase<TSeq>::get_today_transition_matrix(
+
3868  std::vector< int > & counts
+
3869 ) const
+
3870 {
3871 
-
3872  size_t n_states = model->nstates;
-
3873  size_t n_steps = model->get_ndays();
-
3874 
-
3875  // If n is zero, then we are done
-
3876  if (n == 0u)
-
3877  return;
-
3878 
-
3879  for (size_t step = 0u; step <= n_steps; ++step) // The final step counts
-
3880  {
-
3881  for (size_t j = 0u; j < n_states; ++j) // Column major storage
-
3882  {
-
3883  for (size_t i = 0u; i < n_states; ++i)
-
3884  {
-
3885  // Retrieving the value of the day
-
3886  int v = hist_transition_matrix[
-
3887  step * n_states * n_states + // Day of the data
-
3888  j * n_states + // Column (to)
-
3889  i // Row (from)
-
3890  ];
-
3891 
-
3892  // If we are skipping the zeros and it is zero, then don't save
-
3893  if (skip_zeros && v == 0)
-
3894  continue;
-
3895 
-
3896  state_from.push_back(model->states_labels[i]);
-
3897  state_to.push_back(model->states_labels[j]);
-
3898  date.push_back(hist_total_date[step * n_states]);
-
3899  counts.push_back(v);
-
3900 
-
3901  }
-
3902 
-
3903  }
-
3904  }
-
3905 
-
3906  return;
-
3907 
+
3872  counts = transition_matrix;
+
3873 
+
3874  return;
+
3875 
+
3876 }
+
3877 
+
3878 template<typename TSeq>
+
3879 inline void DataBase<TSeq>::get_hist_transition_matrix(
+
3880  std::vector< std::string > & state_from,
+
3881  std::vector< std::string > & state_to,
+
3882  std::vector< int > & date,
+
3883  std::vector< int > & counts,
+
3884  bool skip_zeros
+
3885 ) const
+
3886 {
+
3887 
+
3888  size_t n = this->hist_transition_matrix.size();
+
3889 
+
3890  // Clearing the previous vectors
+
3891  state_from.clear();
+
3892  state_to.clear();
+
3893  date.clear();
+
3894  counts.clear();
+
3895 
+
3896  // Reserving space
+
3897  state_from.reserve(n);
+
3898  state_to.reserve(n);
+
3899  date.reserve(n);
+
3900  counts.reserve(n);
+
3901 
+
3902  size_t n_states = model->nstates;
+
3903  size_t n_steps = model->get_ndays();
+
3904 
+
3905  // If n is zero, then we are done
+
3906  if (n == 0u)
+
3907  return;
3908 
-
3909 }
-
3910 
-
3911 template<typename TSeq>
-
3912 inline void DataBase<TSeq>::get_transmissions(
-
3913  std::vector<int> & date,
-
3914  std::vector<int> & source,
-
3915  std::vector<int> & target,
-
3916  std::vector<int> & virus,
-
3917  std::vector<int> & source_exposure_date
-
3918 ) const
-
3919 {
-
3920 
-
3921  size_t nevents = transmission_date.size();
-
3922 
-
3923  date.resize(nevents);
-
3924  source.resize(nevents);
-
3925  target.resize(nevents);
-
3926  virus.resize(nevents);
-
3927  source_exposure_date.resize(nevents);
-
3928 
-
3929  get_transmissions(
-
3930  &date[0u],
-
3931  &source[0u],
-
3932  &target[0u],
-
3933  &virus[0u],
-
3934  &source_exposure_date[0u]
-
3935  );
-
3936 
-
3937 }
+
3909  for (size_t step = 0u; step <= n_steps; ++step) // The final step counts
+
3910  {
+
3911  for (size_t j = 0u; j < n_states; ++j) // Column major storage
+
3912  {
+
3913  for (size_t i = 0u; i < n_states; ++i)
+
3914  {
+
3915  // Retrieving the value of the day
+
3916  int v = hist_transition_matrix[
+
3917  step * n_states * n_states + // Day of the data
+
3918  j * n_states + // Column (to)
+
3919  i // Row (from)
+
3920  ];
+
3921 
+
3922  // If we are skipping the zeros and it is zero, then don't save
+
3923  if (skip_zeros && v == 0)
+
3924  continue;
+
3925 
+
3926  state_from.push_back(model->states_labels[i]);
+
3927  state_to.push_back(model->states_labels[j]);
+
3928  date.push_back(hist_total_date[step * n_states]);
+
3929  counts.push_back(v);
+
3930 
+
3931  }
+
3932 
+
3933  }
+
3934  }
+
3935 
+
3936  return;
+
3937 
3938 
-
3939 template<typename TSeq>
-
3940 inline void DataBase<TSeq>::get_transmissions(
-
3941  int * date,
-
3942  int * source,
-
3943  int * target,
-
3944  int * virus,
-
3945  int * source_exposure_date
-
3946 ) const
-
3947 {
-
3948 
-
3949  size_t nevents = transmission_date.size();
+
3939 }
+
3940 
+
3941 template<typename TSeq>
+
3942 inline void DataBase<TSeq>::get_transmissions(
+
3943  std::vector<int> & date,
+
3944  std::vector<int> & source,
+
3945  std::vector<int> & target,
+
3946  std::vector<int> & virus,
+
3947  std::vector<int> & source_exposure_date
+
3948 ) const
+
3949 {
3950 
-
3951  for (size_t i = 0u; i < nevents; ++i)
-
3952  {
-
3953 
-
3954  *(date + i) = transmission_date.at(i);
-
3955  *(source + i) = transmission_source.at(i);
-
3956  *(target + i) = transmission_target.at(i);
-
3957  *(virus + i) = transmission_virus.at(i);
-
3958  *(source_exposure_date + i) = transmission_source_exposure_date.at(i);
-
3959 
-
3960  }
-
3961 
-
3962 }
-
3963 
-
3964 template<typename TSeq>
-
3965 inline void DataBase<TSeq>::write_data(
-
3966  std::string fn_virus_info,
-
3967  std::string fn_virus_hist,
-
3968  std::string fn_tool_info,
-
3969  std::string fn_tool_hist,
-
3970  std::string fn_total_hist,
-
3971  std::string fn_transmission,
-
3972  std::string fn_transition,
-
3973  std::string fn_reproductive_number,
-
3974  std::string fn_generation_time
-
3975 ) const
-
3976 {
-
3977 
-
3978  if (fn_virus_info != "")
-
3979  {
-
3980  std::ofstream file_virus_info(fn_virus_info, std::ios_base::out);
-
3981 
-
3982  // Check if the file exists and throw an error if it doesn't
-
3983  if (!file_virus_info)
-
3984  {
-
3985  throw std::runtime_error(
-
3986  "Could not open file \"" + fn_virus_info +
-
3987  "\" for writing.")
-
3988  ;
-
3989  }
-
3990 
+
3951  size_t nevents = transmission_date.size();
+
3952 
+
3953  date.resize(nevents);
+
3954  source.resize(nevents);
+
3955  target.resize(nevents);
+
3956  virus.resize(nevents);
+
3957  source_exposure_date.resize(nevents);
+
3958 
+
3959  get_transmissions(
+
3960  &date[0u],
+
3961  &source[0u],
+
3962  &target[0u],
+
3963  &virus[0u],
+
3964  &source_exposure_date[0u]
+
3965  );
+
3966 
+
3967 }
+
3968 
+
3969 template<typename TSeq>
+
3970 inline void DataBase<TSeq>::get_transmissions(
+
3971  int * date,
+
3972  int * source,
+
3973  int * target,
+
3974  int * virus,
+
3975  int * source_exposure_date
+
3976 ) const
+
3977 {
+
3978 
+
3979  size_t nevents = transmission_date.size();
+
3980 
+
3981  for (size_t i = 0u; i < nevents; ++i)
+
3982  {
+
3983 
+
3984  *(date + i) = transmission_date.at(i);
+
3985  *(source + i) = transmission_source.at(i);
+
3986  *(target + i) = transmission_target.at(i);
+
3987  *(virus + i) = transmission_virus.at(i);
+
3988  *(source_exposure_date + i) = transmission_source_exposure_date.at(i);
+
3989 
+
3990  }
3991 
-
3992  file_virus_info <<
-
3993  #ifdef EPI_DEBUG
-
3994  "thread" << "virus_id " << "virus " << "virus_sequence " << "date_recorded " << "parent\n";
-
3995  #else
-
3996  "virus_id " << "virus " << "virus_sequence " << "date_recorded " << "parent\n";
-
3997  #endif
-
3998 
-
3999  for (const auto & v : virus_id)
-
4000  {
-
4001  int id = v.second;
-
4002  file_virus_info <<
-
4003  #ifdef EPI_DEBUG
-
4004  EPI_GET_THREAD_ID() << " " <<
-
4005  #endif
-
4006  id << " \"" <<
-
4007  virus_name[id] << "\" " <<
-
4008  seq_writer(virus_sequence[id]) << " " <<
-
4009  virus_origin_date[id] << " " <<
-
4010  virus_parent_id[id] << "\n";
-
4011  }
-
4012 
-
4013  }
-
4014 
-
4015  if (fn_virus_hist != "")
-
4016  {
-
4017  std::ofstream file_virus(fn_virus_hist, std::ios_base::out);
-
4018 
-
4019  // Repeat the same error if the file doesn't exists
-
4020  if (!file_virus)
-
4021  {
-
4022  throw std::runtime_error(
-
4023  "Could not open file \"" + fn_virus_hist +
-
4024  "\" for writing.")
-
4025  ;
-
4026  }
-
4027 
-
4028  file_virus <<
-
4029  #ifdef EPI_DEBUG
-
4030  "thread "<< "date " << "virus_id " << "virus " << "state " << "n\n";
-
4031  #else
-
4032  "date " << "virus_id " << "virus " << "state " << "n\n";
-
4033  #endif
-
4034 
-
4035  for (epiworld_fast_uint i = 0; i < hist_virus_id.size(); ++i)
-
4036  file_virus <<
-
4037  #ifdef EPI_DEBUG
-
4038  EPI_GET_THREAD_ID() << " " <<
-
4039  #endif
-
4040  hist_virus_date[i] << " " <<
-
4041  hist_virus_id[i] << " \"" <<
-
4042  virus_name[hist_virus_id[i]] << "\" " <<
-
4043  model->states_labels[hist_virus_state[i]] << " " <<
-
4044  hist_virus_counts[i] << "\n";
-
4045  }
-
4046 
-
4047  if (fn_tool_info != "")
-
4048  {
-
4049  std::ofstream file_tool_info(fn_tool_info, std::ios_base::out);
-
4050 
-
4051  // Repeat the same error if the file doesn't exists
-
4052  if (!file_tool_info)
-
4053  {
-
4054  throw std::runtime_error(
-
4055  "Could not open file \"" + fn_tool_info +
-
4056  "\" for writing.")
-
4057  ;
-
4058  }
-
4059 
-
4060  file_tool_info <<
-
4061  #ifdef EPI_DEBUG
-
4062  "thread " <<
+
3992 }
+
3993 
+
3994 template<typename TSeq>
+
3995 inline void DataBase<TSeq>::write_data(
+
3996  std::string fn_virus_info,
+
3997  std::string fn_virus_hist,
+
3998  std::string fn_tool_info,
+
3999  std::string fn_tool_hist,
+
4000  std::string fn_total_hist,
+
4001  std::string fn_transmission,
+
4002  std::string fn_transition,
+
4003  std::string fn_reproductive_number,
+
4004  std::string fn_generation_time
+
4005 ) const
+
4006 {
+
4007 
+
4008  if (fn_virus_info != "")
+
4009  {
+
4010  std::ofstream file_virus_info(fn_virus_info, std::ios_base::out);
+
4011 
+
4012  // Check if the file exists and throw an error if it doesn't
+
4013  if (!file_virus_info)
+
4014  {
+
4015  throw std::runtime_error(
+
4016  "Could not open file \"" + fn_virus_info +
+
4017  "\" for writing.")
+
4018  ;
+
4019  }
+
4020 
+
4021 
+
4022  file_virus_info <<
+
4023  #ifdef EPI_DEBUG
+
4024  "thread" << "virus_id " << "virus " << "virus_sequence " << "date_recorded " << "parent\n";
+
4025  #else
+
4026  "virus_id " << "virus " << "virus_sequence " << "date_recorded " << "parent\n";
+
4027  #endif
+
4028 
+
4029  for (const auto & v : virus_id)
+
4030  {
+
4031  int id = v.second;
+
4032  file_virus_info <<
+
4033  #ifdef EPI_DEBUG
+
4034  EPI_GET_THREAD_ID() << " " <<
+
4035  #endif
+
4036  id << " \"" <<
+
4037  virus_name[id] << "\" " <<
+
4038  seq_writer(virus_sequence[id]) << " " <<
+
4039  virus_origin_date[id] << " " <<
+
4040  virus_parent_id[id] << "\n";
+
4041  }
+
4042 
+
4043  }
+
4044 
+
4045  if (fn_virus_hist != "")
+
4046  {
+
4047  std::ofstream file_virus(fn_virus_hist, std::ios_base::out);
+
4048 
+
4049  // Repeat the same error if the file doesn't exists
+
4050  if (!file_virus)
+
4051  {
+
4052  throw std::runtime_error(
+
4053  "Could not open file \"" + fn_virus_hist +
+
4054  "\" for writing.")
+
4055  ;
+
4056  }
+
4057 
+
4058  file_virus <<
+
4059  #ifdef EPI_DEBUG
+
4060  "thread "<< "date " << "virus_id " << "virus " << "state " << "n\n";
+
4061  #else
+
4062  "date " << "virus_id " << "virus " << "state " << "n\n";
4063  #endif
-
4064  "id " << "tool_name " << "tool_sequence " << "date_recorded\n";
-
4065 
-
4066  for (const auto & t : tool_id)
-
4067  {
-
4068  int id = t.second;
-
4069  file_tool_info <<
-
4070  #ifdef EPI_DEBUG
-
4071  EPI_GET_THREAD_ID() << " " <<
-
4072  #endif
-
4073  id << " \"" <<
-
4074  tool_name[id] << "\" " <<
-
4075  seq_writer(tool_sequence[id]) << " " <<
-
4076  tool_origin_date[id] << "\n";
-
4077  }
-
4078 
-
4079  }
+
4064 
+
4065  for (epiworld_fast_uint i = 0; i < hist_virus_id.size(); ++i)
+
4066  file_virus <<
+
4067  #ifdef EPI_DEBUG
+
4068  EPI_GET_THREAD_ID() << " " <<
+
4069  #endif
+
4070  hist_virus_date[i] << " " <<
+
4071  hist_virus_id[i] << " \"" <<
+
4072  virus_name[hist_virus_id[i]] << "\" " <<
+
4073  model->states_labels[hist_virus_state[i]] << " " <<
+
4074  hist_virus_counts[i] << "\n";
+
4075  }
+
4076 
+
4077  if (fn_tool_info != "")
+
4078  {
+
4079  std::ofstream file_tool_info(fn_tool_info, std::ios_base::out);
4080 
-
4081  if (fn_tool_hist != "")
-
4082  {
-
4083  std::ofstream file_tool_hist(fn_tool_hist, std::ios_base::out);
-
4084 
-
4085  // Repeat the same error if the file doesn't exists
-
4086  if (!file_tool_hist)
-
4087  {
-
4088  throw std::runtime_error(
-
4089  "Could not open file \"" + fn_tool_hist +
-
4090  "\" for writing.")
-
4091  ;
-
4092  }
-
4093 
-
4094  file_tool_hist <<
-
4095  #ifdef EPI_DEBUG
-
4096  "thread " <<
-
4097  #endif
-
4098  "date " << "id " << "state " << "n\n";
-
4099 
-
4100  for (epiworld_fast_uint i = 0; i < hist_tool_id.size(); ++i)
-
4101  file_tool_hist <<
-
4102  #ifdef EPI_DEBUG
-
4103  EPI_GET_THREAD_ID() << " " <<
-
4104  #endif
-
4105  hist_tool_date[i] << " " <<
-
4106  hist_tool_id[i] << " " <<
-
4107  model->states_labels[hist_tool_state[i]] << " " <<
-
4108  hist_tool_counts[i] << "\n";
+
4081  // Repeat the same error if the file doesn't exists
+
4082  if (!file_tool_info)
+
4083  {
+
4084  throw std::runtime_error(
+
4085  "Could not open file \"" + fn_tool_info +
+
4086  "\" for writing.")
+
4087  ;
+
4088  }
+
4089 
+
4090  file_tool_info <<
+
4091  #ifdef EPI_DEBUG
+
4092  "thread " <<
+
4093  #endif
+
4094  "id " << "tool_name " << "tool_sequence " << "date_recorded\n";
+
4095 
+
4096  for (const auto & t : tool_id)
+
4097  {
+
4098  int id = t.second;
+
4099  file_tool_info <<
+
4100  #ifdef EPI_DEBUG
+
4101  EPI_GET_THREAD_ID() << " " <<
+
4102  #endif
+
4103  id << " \"" <<
+
4104  tool_name[id] << "\" " <<
+
4105  seq_writer(tool_sequence[id]) << " " <<
+
4106  tool_origin_date[id] << "\n";
+
4107  }
+
4108 
4109  }
4110 
-
4111  if (fn_total_hist != "")
+
4111  if (fn_tool_hist != "")
4112  {
-
4113  std::ofstream file_total(fn_total_hist, std::ios_base::out);
+
4113  std::ofstream file_tool_hist(fn_tool_hist, std::ios_base::out);
4114 
4115  // Repeat the same error if the file doesn't exists
-
4116  if (!file_total)
+
4116  if (!file_tool_hist)
4117  {
4118  throw std::runtime_error(
-
4119  "Could not open file \"" + fn_total_hist +
+
4119  "Could not open file \"" + fn_tool_hist +
4120  "\" for writing.")
4121  ;
4122  }
-
4123 
-
4124  file_total <<
+
4123 
+
4124  file_tool_hist <<
4125  #ifdef EPI_DEBUG
4126  "thread " <<
4127  #endif
-
4128  "date " << "nviruses " << "state " << "counts\n";
+
4128  "date " << "id " << "state " << "n\n";
4129 
-
4130  for (epiworld_fast_uint i = 0; i < hist_total_date.size(); ++i)
-
4131  file_total <<
+
4130  for (epiworld_fast_uint i = 0; i < hist_tool_id.size(); ++i)
+
4131  file_tool_hist <<
4132  #ifdef EPI_DEBUG
4133  EPI_GET_THREAD_ID() << " " <<
4134  #endif
-
4135  hist_total_date[i] << " " <<
-
4136  hist_total_nviruses_active[i] << " \"" <<
-
4137  model->states_labels[hist_total_state[i]] << "\" " <<
-
4138  hist_total_counts[i] << "\n";
+
4135  hist_tool_date[i] << " " <<
+
4136  hist_tool_id[i] << " " <<
+
4137  model->states_labels[hist_tool_state[i]] << " " <<
+
4138  hist_tool_counts[i] << "\n";
4139  }
4140 
-
4141  if (fn_transmission != "")
+
4141  if (fn_total_hist != "")
4142  {
-
4143  std::ofstream file_transmission(fn_transmission, std::ios_base::out);
+
4143  std::ofstream file_total(fn_total_hist, std::ios_base::out);
4144 
4145  // Repeat the same error if the file doesn't exists
-
4146  if (!file_transmission)
+
4146  if (!file_total)
4147  {
4148  throw std::runtime_error(
-
4149  "Could not open file \"" + fn_transmission +
+
4149  "Could not open file \"" + fn_total_hist +
4150  "\" for writing.")
4151  ;
4152  }
4153 
-
4154  file_transmission <<
+
4154  file_total <<
4155  #ifdef EPI_DEBUG
4156  "thread " <<
4157  #endif
-
4158  "date " << "virus_id virus " << "source_exposure_date " << "source " << "target\n";
+
4158  "date " << "nviruses " << "state " << "counts\n";
4159 
-
4160  for (epiworld_fast_uint i = 0; i < transmission_target.size(); ++i)
-
4161  file_transmission <<
+
4160  for (epiworld_fast_uint i = 0; i < hist_total_date.size(); ++i)
+
4161  file_total <<
4162  #ifdef EPI_DEBUG
4163  EPI_GET_THREAD_ID() << " " <<
4164  #endif
-
4165  transmission_date[i] << " " <<
-
4166  transmission_virus[i] << " \"" <<
-
4167  virus_name[transmission_virus[i]] << "\" " <<
-
4168  transmission_source_exposure_date[i] << " " <<
-
4169  transmission_source[i] << " " <<
-
4170  transmission_target[i] << "\n";
-
4171 
-
4172  }
-
4173 
-
4174  if (fn_transition != "")
-
4175  {
-
4176  std::ofstream file_transition(fn_transition, std::ios_base::out);
-
4177 
-
4178  // Repeat the same error if the file doesn't exists
-
4179  if (!file_transition)
-
4180  {
-
4181  throw std::runtime_error(
-
4182  "Could not open file \"" + fn_transition +
-
4183  "\" for writing.")
-
4184  ;
-
4185  }
-
4186 
-
4187  file_transition <<
-
4188  #ifdef EPI_DEBUG
-
4189  "thread " <<
-
4190  #endif
-
4191  "date " << "from " << "to " << "counts\n";
-
4192 
-
4193  int ns = model->nstates;
-
4194 
-
4195  for (int i = 0; i <= model->today(); ++i)
-
4196  {
-
4197 
-
4198  for (int from = 0u; from < ns; ++from)
-
4199  for (int to = 0u; to < ns; ++to)
-
4200  file_transition <<
-
4201  #ifdef EPI_DEBUG
-
4202  EPI_GET_THREAD_ID() << " " <<
-
4203  #endif
-
4204  i << " \"" <<
-
4205  model->states_labels[from] << "\" \"" <<
-
4206  model->states_labels[to] << "\" " <<
-
4207  hist_transition_matrix[i * (ns * ns) + to * ns + from] << "\n";
-
4208 
-
4209  }
-
4210 
-
4211  }
-
4212 
-
4213  if (fn_reproductive_number != "")
-
4214  reproductive_number(fn_reproductive_number);
-
4215 
-
4216  if (fn_generation_time != "")
-
4217  generation_time(fn_generation_time);
-
4218 
-
4219 }
-
4220 
-
4221 template<typename TSeq>
-
4222 inline void DataBase<TSeq>::record_transmission(
-
4223  int i,
-
4224  int j,
-
4225  int virus,
-
4226  int i_expo_date
-
4227 ) {
-
4228 
-
4229  transmission_date.push_back(model->today());
-
4230  transmission_source.push_back(i);
-
4231  transmission_target.push_back(j);
-
4232  transmission_virus.push_back(virus);
-
4233  transmission_source_exposure_date.push_back(i_expo_date);
-
4234 
-
4235 }
-
4236 
-
4237 template<typename TSeq>
-
4238 inline size_t DataBase<TSeq>::get_n_viruses() const
-
4239 {
-
4240  return virus_id.size();
-
4241 }
+
4165  hist_total_date[i] << " " <<
+
4166  hist_total_nviruses_active[i] << " \"" <<
+
4167  model->states_labels[hist_total_state[i]] << "\" " <<
+
4168  hist_total_counts[i] << "\n";
+
4169  }
+
4170 
+
4171  if (fn_transmission != "")
+
4172  {
+
4173  std::ofstream file_transmission(fn_transmission, std::ios_base::out);
+
4174 
+
4175  // Repeat the same error if the file doesn't exists
+
4176  if (!file_transmission)
+
4177  {
+
4178  throw std::runtime_error(
+
4179  "Could not open file \"" + fn_transmission +
+
4180  "\" for writing.")
+
4181  ;
+
4182  }
+
4183 
+
4184  file_transmission <<
+
4185  #ifdef EPI_DEBUG
+
4186  "thread " <<
+
4187  #endif
+
4188  "date " << "virus_id virus " << "source_exposure_date " << "source " << "target\n";
+
4189 
+
4190  for (epiworld_fast_uint i = 0; i < transmission_target.size(); ++i)
+
4191  file_transmission <<
+
4192  #ifdef EPI_DEBUG
+
4193  EPI_GET_THREAD_ID() << " " <<
+
4194  #endif
+
4195  transmission_date[i] << " " <<
+
4196  transmission_virus[i] << " \"" <<
+
4197  virus_name[transmission_virus[i]] << "\" " <<
+
4198  transmission_source_exposure_date[i] << " " <<
+
4199  transmission_source[i] << " " <<
+
4200  transmission_target[i] << "\n";
+
4201 
+
4202  }
+
4203 
+
4204  if (fn_transition != "")
+
4205  {
+
4206  std::ofstream file_transition(fn_transition, std::ios_base::out);
+
4207 
+
4208  // Repeat the same error if the file doesn't exists
+
4209  if (!file_transition)
+
4210  {
+
4211  throw std::runtime_error(
+
4212  "Could not open file \"" + fn_transition +
+
4213  "\" for writing.")
+
4214  ;
+
4215  }
+
4216 
+
4217  file_transition <<
+
4218  #ifdef EPI_DEBUG
+
4219  "thread " <<
+
4220  #endif
+
4221  "date " << "from " << "to " << "counts\n";
+
4222 
+
4223  int ns = model->nstates;
+
4224 
+
4225  for (int i = 0; i <= model->today(); ++i)
+
4226  {
+
4227 
+
4228  for (int from = 0u; from < ns; ++from)
+
4229  for (int to = 0u; to < ns; ++to)
+
4230  file_transition <<
+
4231  #ifdef EPI_DEBUG
+
4232  EPI_GET_THREAD_ID() << " " <<
+
4233  #endif
+
4234  i << " \"" <<
+
4235  model->states_labels[from] << "\" \"" <<
+
4236  model->states_labels[to] << "\" " <<
+
4237  hist_transition_matrix[i * (ns * ns) + to * ns + from] << "\n";
+
4238 
+
4239  }
+
4240 
+
4241  }
4242 
-
4243 template<typename TSeq>
-
4244 inline size_t DataBase<TSeq>::get_n_tools() const
-
4245 {
-
4246  return tool_id.size();
-
4247 }
+
4243  if (fn_reproductive_number != "")
+
4244  reproductive_number(fn_reproductive_number);
+
4245 
+
4246  if (fn_generation_time != "")
+
4247  generation_time(fn_generation_time);
4248 
-
4249 
-
4250 template<typename TSeq>
-
4251 inline void DataBase<TSeq>::set_user_data(
-
4252  std::vector< std::string > names
-
4253 )
-
4254 {
-
4255  user_data = UserData<TSeq>(names);
-
4256  user_data.model = model;
-
4257 }
+
4249 }
+
4250 
+
4251 template<typename TSeq>
+
4252 inline void DataBase<TSeq>::record_transmission(
+
4253  int i,
+
4254  int j,
+
4255  int virus,
+
4256  int i_expo_date
+
4257 ) {
4258 
-
4259 template<typename TSeq>
-
4260 inline void DataBase<TSeq>::add_user_data(
-
4261  std::vector< epiworld_double > x
-
4262 )
-
4263 {
+
4259  transmission_date.push_back(model->today());
+
4260  transmission_source.push_back(i);
+
4261  transmission_target.push_back(j);
+
4262  transmission_virus.push_back(virus);
+
4263  transmission_source_exposure_date.push_back(i_expo_date);
4264 
-
4265  user_data.add(x);
+
4265 }
4266 
-
4267 }
-
4268 
-
4269 template<typename TSeq>
-
4270 inline void DataBase<TSeq>::add_user_data(
-
4271  epiworld_fast_uint k,
-
4272  epiworld_double x
-
4273 )
-
4274 {
-
4275 
-
4276  user_data.add(k, x);
-
4277 
-
4278 }
+
4267 template<typename TSeq>
+
4268 inline size_t DataBase<TSeq>::get_n_viruses() const
+
4269 {
+
4270  return virus_id.size();
+
4271 }
+
4272 
+
4273 template<typename TSeq>
+
4274 inline size_t DataBase<TSeq>::get_n_tools() const
+
4275 {
+
4276  return tool_id.size();
+
4277 }
+
4278 
4279 
4280 template<typename TSeq>
-
4281 inline UserData<TSeq> & DataBase<TSeq>::get_user_data()
-
4282 {
-
4283  return user_data;
-
4284 }
-
4285 
-
4286 template<typename TSeq>
-
4287 inline MapVec_type<int,int> DataBase<TSeq>::reproductive_number()
-
4288 const {
-
4289 
-
4290  // Checking size
-
4291  MapVec_type<int,int> map;
-
4292 
-
4293  // Number of digits of maxid
-
4294  for (size_t i = 0u; i < transmission_date.size(); ++i)
-
4295  {
-
4296  // Fabricating id
-
4297  std::vector< int > h = {
-
4298  transmission_virus[i],
-
4299  transmission_source[i],
-
4300  transmission_source_exposure_date[i]
-
4301  };
-
4302 
-
4303  // Adding to counter
-
4304  if (map.find(h) == map.end())
-
4305  map[h] = 1;
-
4306  else
-
4307  map[h]++;
-
4308 
-
4309  // The target is added
-
4310  std::vector< int > h_target = {
-
4311  transmission_virus[i],
-
4312  transmission_target[i],
-
4313  transmission_date[i]
-
4314  };
+
4281 inline void DataBase<TSeq>::set_user_data(
+
4282  std::vector< std::string > names
+
4283 )
+
4284 {
+
4285  user_data = UserData<TSeq>(names);
+
4286  user_data.model = model;
+
4287 }
+
4288 
+
4289 template<typename TSeq>
+
4290 inline void DataBase<TSeq>::add_user_data(
+
4291  std::vector< epiworld_double > x
+
4292 )
+
4293 {
+
4294 
+
4295  user_data.add(x);
+
4296 
+
4297 }
+
4298 
+
4299 template<typename TSeq>
+
4300 inline void DataBase<TSeq>::add_user_data(
+
4301  epiworld_fast_uint k,
+
4302  epiworld_double x
+
4303 )
+
4304 {
+
4305 
+
4306  user_data.add(k, x);
+
4307 
+
4308 }
+
4309 
+
4310 template<typename TSeq>
+
4311 inline UserData<TSeq> & DataBase<TSeq>::get_user_data()
+
4312 {
+
4313  return user_data;
+
4314 }
4315 
-
4316  map[h_target] = 0;
-
4317 
-
4318  }
+
4316 template<typename TSeq>
+
4317 inline MapVec_type<int,int> DataBase<TSeq>::reproductive_number()
+
4318 const {
4319 
-
4320  return map;
-
4321 
-
4322 }
-
4323 
-
4324 template<typename TSeq>
-
4325 inline void DataBase<TSeq>::reproductive_number(
-
4326  std::string fn
-
4327 ) const {
-
4328 
-
4329 
-
4330  auto map = reproductive_number();
-
4331 
-
4332  std::ofstream fn_file(fn, std::ios_base::out);
-
4333 
-
4334  // Repeat the same error if the file doesn't exists
-
4335  if (!fn_file)
-
4336  {
-
4337  throw std::runtime_error(
-
4338  "Could not open file \"" + fn +
-
4339  "\" for writing.")
-
4340  ;
-
4341  }
-
4342 
-
4343  fn_file <<
-
4344  #ifdef EPI_DEBUG
-
4345  "thread " <<
-
4346  #endif
-
4347  "virus_id virus source source_exposure_date rt\n";
-
4348 
+
4320  // Checking size
+
4321  MapVec_type<int,int> map;
+
4322 
+
4323  // Number of digits of maxid
+
4324  for (size_t i = 0u; i < transmission_date.size(); ++i)
+
4325  {
+
4326  // Fabricating id
+
4327  std::vector< int > h = {
+
4328  transmission_virus[i],
+
4329  transmission_source[i],
+
4330  transmission_source_exposure_date[i]
+
4331  };
+
4332 
+
4333  // Adding to counter
+
4334  if (map.find(h) == map.end())
+
4335  map[h] = 1;
+
4336  else
+
4337  map[h]++;
+
4338 
+
4339  // The target is added
+
4340  std::vector< int > h_target = {
+
4341  transmission_virus[i],
+
4342  transmission_target[i],
+
4343  transmission_date[i]
+
4344  };
+
4345 
+
4346  map[h_target] = 0;
+
4347 
+
4348  }
4349 
-
4350  for (auto & m : map)
-
4351  fn_file <<
-
4352  #ifdef EPI_DEBUG
-
4353  EPI_GET_THREAD_ID() << " " <<
-
4354  #endif
-
4355  m.first[0u] << " \"" <<
-
4356  virus_name[m.first[0u]] << "\" " <<
-
4357  m.first[1u] << " " <<
-
4358  m.first[2u] << " " <<
-
4359  m.second << "\n";
-
4360 
-
4361  return;
-
4362 
-
4363 }
-
4364 
-
4365 template<typename TSeq>
-
4366 inline std::vector< epiworld_double > DataBase<TSeq>::transition_probability(
-
4367  bool print
-
4368 ) const {
-
4369 
-
4370  auto states_labels = model->get_states();
-
4371  size_t n_state = states_labels.size();
-
4372  size_t n_days = model->get_ndays();
-
4373  std::vector< epiworld_double > res(n_state * n_state, 0.0);
-
4374  std::vector< epiworld_double > days_to_include(n_state, 0.0);
-
4375 
-
4376  for (size_t t = 1; t < n_days; ++t)
-
4377  {
+
4350  return map;
+
4351 
+
4352 }
+
4353 
+
4354 template<typename TSeq>
+
4355 inline void DataBase<TSeq>::reproductive_number(
+
4356  std::string fn
+
4357 ) const {
+
4358 
+
4359 
+
4360  auto map = reproductive_number();
+
4361 
+
4362  std::ofstream fn_file(fn, std::ios_base::out);
+
4363 
+
4364  // Repeat the same error if the file doesn't exists
+
4365  if (!fn_file)
+
4366  {
+
4367  throw std::runtime_error(
+
4368  "Could not open file \"" + fn +
+
4369  "\" for writing.")
+
4370  ;
+
4371  }
+
4372 
+
4373  fn_file <<
+
4374  #ifdef EPI_DEBUG
+
4375  "thread " <<
+
4376  #endif
+
4377  "virus_id virus source source_exposure_date rt\n";
4378 
-
4379  for (size_t s_i = 0; s_i < n_state; ++s_i)
-
4380  {
-
4381  epiworld_double daily_total = hist_total_counts[(t - 1) * n_state + s_i];
-
4382 
-
4383  if (daily_total == 0)
-
4384  continue;
-
4385 
-
4386  days_to_include[s_i] += 1.0;
-
4387 
-
4388  for (size_t s_j = 0u; s_j < n_state; ++s_j)
-
4389  {
-
4390  #ifdef EPI_DEBUG
-
4391  epiworld_double entry = hist_transition_matrix[
-
4392  s_i + s_j * n_state +
-
4393  t * (n_state * n_state)
-
4394  ];
-
4395 
-
4396  if (entry > daily_total)
-
4397  throw std::logic_error(
-
4398  "The entry in hist_transition_matrix cannot have more elememnts than the total"
-
4399  );
-
4400 
-
4401  res[s_i + s_j * n_state] += (entry / daily_total);
-
4402  #else
-
4403  res[s_i + s_j * n_state] += (
-
4404  hist_transition_matrix[
-
4405  s_i + s_j * n_state +
-
4406  t * (n_state * n_state)
-
4407  ] / daily_total
-
4408  );
-
4409  #endif
-
4410  }
-
4411 
-
4412  }
-
4413 
-
4414  }
+
4379 
+
4380  for (auto & m : map)
+
4381  fn_file <<
+
4382  #ifdef EPI_DEBUG
+
4383  EPI_GET_THREAD_ID() << " " <<
+
4384  #endif
+
4385  m.first[0u] << " \"" <<
+
4386  virus_name[m.first[0u]] << "\" " <<
+
4387  m.first[1u] << " " <<
+
4388  m.first[2u] << " " <<
+
4389  m.second << "\n";
+
4390 
+
4391  return;
+
4392 
+
4393 }
+
4394 
+
4395 template<typename TSeq>
+
4396 inline std::vector< epiworld_double > DataBase<TSeq>::transition_probability(
+
4397  bool print
+
4398 ) const {
+
4399 
+
4400  auto states_labels = model->get_states();
+
4401  size_t n_state = states_labels.size();
+
4402  size_t n_days = model->get_ndays();
+
4403  std::vector< epiworld_double > res(n_state * n_state, 0.0);
+
4404  std::vector< epiworld_double > days_to_include(n_state, 0.0);
+
4405 
+
4406  for (size_t t = 1; t < n_days; ++t)
+
4407  {
+
4408 
+
4409  for (size_t s_i = 0; s_i < n_state; ++s_i)
+
4410  {
+
4411  epiworld_double daily_total = hist_total_counts[(t - 1) * n_state + s_i];
+
4412 
+
4413  if (daily_total == 0)
+
4414  continue;
4415 
-
4416  for (size_t s_i = 0; s_i < n_state; ++s_i)
-
4417  {
-
4418  for (size_t s_j = 0; s_j < n_state; ++s_j)
-
4419  res[s_i + s_j * n_state] /= days_to_include[s_i];
-
4420  }
-
4421 
-
4422  if (print)
-
4423  {
-
4424 
-
4425  size_t nchar = 0u;
-
4426  for (auto & l : states_labels)
-
4427  if (l.length() > nchar)
-
4428  nchar = l.length();
-
4429 
-
4430  std::string fmt = " - %-" + std::to_string(nchar) + "s";
-
4431 
-
4432  printf_epiworld("\nTransition Probabilities:\n");
-
4433  for (size_t s_i = 0u; s_i < n_state; ++s_i)
-
4434  {
-
4435  printf_epiworld(fmt.c_str(), states_labels[s_i].c_str());
-
4436  for (size_t s_j = 0u; s_j < n_state; ++s_j)
-
4437  {
-
4438  if (std::isnan(res[s_i + s_j * n_state]))
-
4439  {
-
4440  printf_epiworld(" -");
-
4441  } else {
-
4442  printf_epiworld(" % 4.2f", res[s_i + s_j * n_state]);
-
4443  }
-
4444  }
-
4445  printf_epiworld("\n");
-
4446  }
-
4447 
-
4448  printf_epiworld("\n");
-
4449 
+
4416  days_to_include[s_i] += 1.0;
+
4417 
+
4418  for (size_t s_j = 0u; s_j < n_state; ++s_j)
+
4419  {
+
4420  #ifdef EPI_DEBUG
+
4421  epiworld_double entry = hist_transition_matrix[
+
4422  s_i + s_j * n_state +
+
4423  t * (n_state * n_state)
+
4424  ];
+
4425 
+
4426  if (entry > daily_total)
+
4427  throw std::logic_error(
+
4428  "The entry in hist_transition_matrix cannot have more elememnts than the total"
+
4429  );
+
4430 
+
4431  res[s_i + s_j * n_state] += (entry / daily_total);
+
4432  #else
+
4433  res[s_i + s_j * n_state] += (
+
4434  hist_transition_matrix[
+
4435  s_i + s_j * n_state +
+
4436  t * (n_state * n_state)
+
4437  ] / daily_total
+
4438  );
+
4439  #endif
+
4440  }
+
4441 
+
4442  }
+
4443 
+
4444  }
+
4445 
+
4446  for (size_t s_i = 0; s_i < n_state; ++s_i)
+
4447  {
+
4448  for (size_t s_j = 0; s_j < n_state; ++s_j)
+
4449  res[s_i + s_j * n_state] /= days_to_include[s_i];
4450  }
4451 
-
4452  return res;
-
4453 
+
4452  if (print)
+
4453  {
4454 
-
4455 }
-
4456 
-
4457 #define VECT_MATCH(a, b, c) \
-
4458  EPI_DEBUG_FAIL_AT_TRUE(a.size() != b.size(), c) \
-
4459  for (size_t __i = 0u; __i < a.size(); ++__i) \
-
4460  {\
-
4461  EPI_DEBUG_FAIL_AT_TRUE(a[__i] != b[__i], c) \
-
4462  }
-
4463 
-
4464 template<>
-
4465 inline bool DataBase<std::vector<int>>::operator==(const DataBase<std::vector<int>> & other) const
-
4466 {
-
4467  VECT_MATCH(
-
4468  virus_name, other.virus_name,
-
4469  "DataBase:: virus_name don't match"
-
4470  )
-
4471 
-
4472  EPI_DEBUG_FAIL_AT_TRUE(
-
4473  virus_sequence.size() != other.virus_sequence.size(),
-
4474  "DataBase:: virus_sequence don't match."
-
4475  )
-
4476 
-
4477  for (size_t i = 0u; i < virus_sequence.size(); ++i)
-
4478  {
-
4479  VECT_MATCH(
-
4480  virus_sequence[i], other.virus_sequence[i],
-
4481  "DataBase:: virus_sequence[i] don't match"
-
4482  )
-
4483  }
+
4455  size_t nchar = 0u;
+
4456  for (auto & l : states_labels)
+
4457  if (l.length() > nchar)
+
4458  nchar = l.length();
+
4459 
+
4460  std::string fmt = " - %-" + std::to_string(nchar) + "s";
+
4461 
+
4462  printf_epiworld("\nTransition Probabilities:\n");
+
4463  for (size_t s_i = 0u; s_i < n_state; ++s_i)
+
4464  {
+
4465  printf_epiworld(fmt.c_str(), states_labels[s_i].c_str());
+
4466  for (size_t s_j = 0u; s_j < n_state; ++s_j)
+
4467  {
+
4468  if (std::isnan(res[s_i + s_j * n_state]))
+
4469  {
+
4470  printf_epiworld(" -");
+
4471  } else {
+
4472  printf_epiworld(" % 4.2f", res[s_i + s_j * n_state]);
+
4473  }
+
4474  }
+
4475  printf_epiworld("\n");
+
4476  }
+
4477 
+
4478  printf_epiworld("\n");
+
4479 
+
4480  }
+
4481 
+
4482  return res;
+
4483 
4484 
-
4485  VECT_MATCH(
-
4486  virus_origin_date,
-
4487  other.virus_origin_date,
-
4488  "DataBase:: virus_origin_date[i] don't match"
-
4489  )
-
4490 
-
4491  VECT_MATCH(
-
4492  virus_parent_id,
-
4493  other.virus_parent_id,
-
4494  "DataBase:: virus_parent_id[i] don't match"
-
4495  )
-
4496 
+
4485 }
+
4486 
+
4487 #define VECT_MATCH(a, b, c) \
+
4488  EPI_DEBUG_FAIL_AT_TRUE(a.size() != b.size(), c) \
+
4489  for (size_t __i = 0u; __i < a.size(); ++__i) \
+
4490  {\
+
4491  EPI_DEBUG_FAIL_AT_TRUE(a[__i] != b[__i], c) \
+
4492  }
+
4493 
+
4494 template<>
+
4495 inline bool DataBase<std::vector<int>>::operator==(const DataBase<std::vector<int>> & other) const
+
4496 {
4497  VECT_MATCH(
-
4498  tool_name,
-
4499  other.tool_name,
-
4500  "DataBase:: tool_name[i] don't match"
-
4501  )
-
4502 
-
4503  VECT_MATCH(
-
4504  tool_sequence,
-
4505  other.tool_sequence,
-
4506  "DataBase:: tool_sequence[i] don't match"
-
4507  )
-
4508 
-
4509  VECT_MATCH(
-
4510  tool_origin_date,
-
4511  other.tool_origin_date,
-
4512  "DataBase:: tool_origin_date[i] don't match"
-
4513  )
+
4498  virus_name, other.virus_name,
+
4499  "DataBase:: virus_name don't match"
+
4500  )
+
4501 
+
4502  EPI_DEBUG_FAIL_AT_TRUE(
+
4503  virus_sequence.size() != other.virus_sequence.size(),
+
4504  "DataBase:: virus_sequence don't match."
+
4505  )
+
4506 
+
4507  for (size_t i = 0u; i < virus_sequence.size(); ++i)
+
4508  {
+
4509  VECT_MATCH(
+
4510  virus_sequence[i], other.virus_sequence[i],
+
4511  "DataBase:: virus_sequence[i] don't match"
+
4512  )
+
4513  }
4514 
-
4515 
-
4516  EPI_DEBUG_FAIL_AT_TRUE(
-
4517  sampling_freq != other.sampling_freq,
-
4518  "DataBase:: sampling_freq don't match."
-
4519  )
+
4515  VECT_MATCH(
+
4516  virus_origin_date,
+
4517  other.virus_origin_date,
+
4518  "DataBase:: virus_origin_date[i] don't match"
+
4519  )
4520 
-
4521  // Variants history
-
4522  VECT_MATCH(
-
4523  hist_virus_date,
-
4524  other.hist_virus_date,
-
4525  "DataBase:: hist_virus_date[i] don't match"
-
4526  )
-
4527 
-
4528  VECT_MATCH(
-
4529  hist_virus_id,
-
4530  other.hist_virus_id,
-
4531  "DataBase:: hist_virus_id[i] don't match"
-
4532  )
-
4533 
-
4534  VECT_MATCH(
-
4535  hist_virus_state,
-
4536  other.hist_virus_state,
-
4537  "DataBase:: hist_virus_state[i] don't match"
-
4538  )
-
4539 
-
4540  VECT_MATCH(
-
4541  hist_virus_counts,
-
4542  other.hist_virus_counts,
-
4543  "DataBase:: hist_virus_counts[i] don't match"
-
4544  )
+
4521  VECT_MATCH(
+
4522  virus_parent_id,
+
4523  other.virus_parent_id,
+
4524  "DataBase:: virus_parent_id[i] don't match"
+
4525  )
+
4526 
+
4527  VECT_MATCH(
+
4528  tool_name,
+
4529  other.tool_name,
+
4530  "DataBase:: tool_name[i] don't match"
+
4531  )
+
4532 
+
4533  VECT_MATCH(
+
4534  tool_sequence,
+
4535  other.tool_sequence,
+
4536  "DataBase:: tool_sequence[i] don't match"
+
4537  )
+
4538 
+
4539  VECT_MATCH(
+
4540  tool_origin_date,
+
4541  other.tool_origin_date,
+
4542  "DataBase:: tool_origin_date[i] don't match"
+
4543  )
+
4544 
4545 
-
4546  // Tools history
-
4547  VECT_MATCH(
-
4548  hist_tool_date,
-
4549  other.hist_tool_date,
-
4550  "DataBase:: hist_tool_date[i] don't match"
-
4551  )
-
4552 
-
4553  VECT_MATCH(
-
4554  hist_tool_id,
-
4555  other.hist_tool_id,
-
4556  "DataBase:: hist_tool_id[i] don't match"
-
4557  )
-
4558 
-
4559  VECT_MATCH(
-
4560  hist_tool_state,
-
4561  other.hist_tool_state,
-
4562  "DataBase:: hist_tool_state[i] don't match"
-
4563  )
-
4564 
-
4565  VECT_MATCH(
-
4566  hist_tool_counts,
-
4567  other.hist_tool_counts,
-
4568  "DataBase:: hist_tool_counts[i] don't match"
-
4569  )
-
4570 
-
4571  // Overall hist
-
4572  VECT_MATCH(
-
4573  hist_total_date,
-
4574  other.hist_total_date,
-
4575  "DataBase:: hist_total_date[i] don't match"
-
4576  )
-
4577 
-
4578  VECT_MATCH(
-
4579  hist_total_nviruses_active,
-
4580  other.hist_total_nviruses_active,
-
4581  "DataBase:: hist_total_nviruses_active[i] don't match"
-
4582  )
-
4583 
-
4584  VECT_MATCH(
-
4585  hist_total_state,
-
4586  other.hist_total_state,
-
4587  "DataBase:: hist_total_state[i] don't match"
-
4588  )
-
4589 
-
4590  VECT_MATCH(
-
4591  hist_total_counts,
-
4592  other.hist_total_counts,
-
4593  "DataBase:: hist_total_counts[i] don't match"
-
4594  )
-
4595 
-
4596  VECT_MATCH(
-
4597  hist_transition_matrix,
-
4598  other.hist_transition_matrix,
-
4599  "DataBase:: hist_transition_matrix[i] don't match"
-
4600  )
-
4601 
-
4602  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
-
4603  EPI_DEBUG_FAIL_AT_TRUE(
-
4604  today_virus.size() != other.today_virus.size(),
-
4605  "DataBase:: today_virus don't match."
+
4546  EPI_DEBUG_FAIL_AT_TRUE(
+
4547  sampling_freq != other.sampling_freq,
+
4548  "DataBase:: sampling_freq don't match."
+
4549  )
+
4550 
+
4551  // Variants history
+
4552  VECT_MATCH(
+
4553  hist_virus_date,
+
4554  other.hist_virus_date,
+
4555  "DataBase:: hist_virus_date[i] don't match"
+
4556  )
+
4557 
+
4558  VECT_MATCH(
+
4559  hist_virus_id,
+
4560  other.hist_virus_id,
+
4561  "DataBase:: hist_virus_id[i] don't match"
+
4562  )
+
4563 
+
4564  VECT_MATCH(
+
4565  hist_virus_state,
+
4566  other.hist_virus_state,
+
4567  "DataBase:: hist_virus_state[i] don't match"
+
4568  )
+
4569 
+
4570  VECT_MATCH(
+
4571  hist_virus_counts,
+
4572  other.hist_virus_counts,
+
4573  "DataBase:: hist_virus_counts[i] don't match"
+
4574  )
+
4575 
+
4576  // Tools history
+
4577  VECT_MATCH(
+
4578  hist_tool_date,
+
4579  other.hist_tool_date,
+
4580  "DataBase:: hist_tool_date[i] don't match"
+
4581  )
+
4582 
+
4583  VECT_MATCH(
+
4584  hist_tool_id,
+
4585  other.hist_tool_id,
+
4586  "DataBase:: hist_tool_id[i] don't match"
+
4587  )
+
4588 
+
4589  VECT_MATCH(
+
4590  hist_tool_state,
+
4591  other.hist_tool_state,
+
4592  "DataBase:: hist_tool_state[i] don't match"
+
4593  )
+
4594 
+
4595  VECT_MATCH(
+
4596  hist_tool_counts,
+
4597  other.hist_tool_counts,
+
4598  "DataBase:: hist_tool_counts[i] don't match"
+
4599  )
+
4600 
+
4601  // Overall hist
+
4602  VECT_MATCH(
+
4603  hist_total_date,
+
4604  other.hist_total_date,
+
4605  "DataBase:: hist_total_date[i] don't match"
4606  )
-
4607 
-
4608  for (size_t i = 0u; i < today_virus.size(); ++i)
-
4609  {
-
4610  VECT_MATCH(
-
4611  today_virus[i], other.today_virus[i],
-
4612  "DataBase:: today_virus[i] don't match"
-
4613  )
-
4614  }
-
4615 
-
4616  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
-
4617  if (today_tool.size() != other.today_tool.size())
-
4618  return false;
-
4619 
-
4620  for (size_t i = 0u; i < today_tool.size(); ++i)
-
4621  {
-
4622  VECT_MATCH(
-
4623  today_tool[i], other.today_tool[i],
-
4624  "DataBase:: today_tool[i] don't match"
-
4625  )
-
4626  }
-
4627 
-
4628  // {Susceptible, Infected, etc.}
-
4629  VECT_MATCH(
-
4630  today_total, other.today_total,
-
4631  "DataBase:: today_total don't match"
-
4632  )
-
4633 
-
4634  // Totals
-
4635  EPI_DEBUG_FAIL_AT_TRUE(
-
4636  today_total_nviruses_active != other.today_total_nviruses_active,
-
4637  "DataBase:: today_total_nviruses_active don't match."
-
4638  )
-
4639 
-
4640  // Transmission network
-
4641  VECT_MATCH(
-
4642  transmission_date,
-
4643  other.transmission_date, ///< Date of the transmission eve,
-
4644  "DataBase:: transmission_date[i] don't match"
-
4645  )
-
4646 
-
4647  VECT_MATCH(
-
4648  transmission_source,
-
4649  other.transmission_source, ///< Id of the sour,
-
4650  "DataBase:: transmission_source[i] don't match"
-
4651  )
-
4652 
-
4653  VECT_MATCH(
-
4654  transmission_target,
-
4655  other.transmission_target, ///< Id of the targ,
-
4656  "DataBase:: transmission_target[i] don't match"
-
4657  )
-
4658 
+
4607 
+
4608  VECT_MATCH(
+
4609  hist_total_nviruses_active,
+
4610  other.hist_total_nviruses_active,
+
4611  "DataBase:: hist_total_nviruses_active[i] don't match"
+
4612  )
+
4613 
+
4614  VECT_MATCH(
+
4615  hist_total_state,
+
4616  other.hist_total_state,
+
4617  "DataBase:: hist_total_state[i] don't match"
+
4618  )
+
4619 
+
4620  VECT_MATCH(
+
4621  hist_total_counts,
+
4622  other.hist_total_counts,
+
4623  "DataBase:: hist_total_counts[i] don't match"
+
4624  )
+
4625 
+
4626  VECT_MATCH(
+
4627  hist_transition_matrix,
+
4628  other.hist_transition_matrix,
+
4629  "DataBase:: hist_transition_matrix[i] don't match"
+
4630  )
+
4631 
+
4632  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
+
4633  EPI_DEBUG_FAIL_AT_TRUE(
+
4634  today_virus.size() != other.today_virus.size(),
+
4635  "DataBase:: today_virus don't match."
+
4636  )
+
4637 
+
4638  for (size_t i = 0u; i < today_virus.size(); ++i)
+
4639  {
+
4640  VECT_MATCH(
+
4641  today_virus[i], other.today_virus[i],
+
4642  "DataBase:: today_virus[i] don't match"
+
4643  )
+
4644  }
+
4645 
+
4646  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
+
4647  if (today_tool.size() != other.today_tool.size())
+
4648  return false;
+
4649 
+
4650  for (size_t i = 0u; i < today_tool.size(); ++i)
+
4651  {
+
4652  VECT_MATCH(
+
4653  today_tool[i], other.today_tool[i],
+
4654  "DataBase:: today_tool[i] don't match"
+
4655  )
+
4656  }
+
4657 
+
4658  // {Susceptible, Infected, etc.}
4659  VECT_MATCH(
-
4660  transmission_virus,
-
4661  other.transmission_virus, ///< Id of the varia,
-
4662  "DataBase:: transmission_virus[i] don't match"
-
4663  )
-
4664 
-
4665  VECT_MATCH(
-
4666  transmission_source_exposure_date,
-
4667  other.transmission_source_exposure_date, ///< Date when the source acquired the varia,
-
4668  "DataBase:: transmission_source_exposure_date[i] don't match"
-
4669  )
-
4670 
-
4671 
-
4672  VECT_MATCH(
-
4673  transition_matrix,
-
4674  other.transition_matrix,
-
4675  "DataBase:: transition_matrix[i] don't match"
-
4676  )
-
4677 
-
4678 
-
4679  return true;
-
4680 
-
4681 }
+
4660  today_total, other.today_total,
+
4661  "DataBase:: today_total don't match"
+
4662  )
+
4663 
+
4664  // Totals
+
4665  EPI_DEBUG_FAIL_AT_TRUE(
+
4666  today_total_nviruses_active != other.today_total_nviruses_active,
+
4667  "DataBase:: today_total_nviruses_active don't match."
+
4668  )
+
4669 
+
4670  // Transmission network
+
4671  VECT_MATCH(
+
4672  transmission_date,
+
4673  other.transmission_date, ///< Date of the transmission eve,
+
4674  "DataBase:: transmission_date[i] don't match"
+
4675  )
+
4676 
+
4677  VECT_MATCH(
+
4678  transmission_source,
+
4679  other.transmission_source, ///< Id of the sour,
+
4680  "DataBase:: transmission_source[i] don't match"
+
4681  )
4682 
-
4683 template<typename TSeq>
-
4684 inline bool DataBase<TSeq>::operator==(const DataBase<TSeq> & other) const
-
4685 {
-
4686  VECT_MATCH(
-
4687  virus_name,
-
4688  other.virus_name,
-
4689  "DataBase:: virus_name[i] don't match"
-
4690  )
-
4691 
-
4692  VECT_MATCH(
-
4693  virus_sequence,
-
4694  other.virus_sequence,
-
4695  "DataBase:: virus_sequence[i] don't match"
-
4696  )
-
4697 
-
4698  VECT_MATCH(
-
4699  virus_origin_date,
-
4700  other.virus_origin_date,
-
4701  "DataBase:: virus_origin_date[i] don't match"
-
4702  )
-
4703 
-
4704  VECT_MATCH(
-
4705  virus_parent_id,
-
4706  other.virus_parent_id,
-
4707  "DataBase:: virus_parent_id[i] don't match"
-
4708  )
-
4709 
-
4710  VECT_MATCH(
-
4711  tool_name,
-
4712  other.tool_name,
-
4713  "DataBase:: tool_name[i] don't match"
-
4714  )
-
4715 
+
4683  VECT_MATCH(
+
4684  transmission_target,
+
4685  other.transmission_target, ///< Id of the targ,
+
4686  "DataBase:: transmission_target[i] don't match"
+
4687  )
+
4688 
+
4689  VECT_MATCH(
+
4690  transmission_virus,
+
4691  other.transmission_virus, ///< Id of the varia,
+
4692  "DataBase:: transmission_virus[i] don't match"
+
4693  )
+
4694 
+
4695  VECT_MATCH(
+
4696  transmission_source_exposure_date,
+
4697  other.transmission_source_exposure_date, ///< Date when the source acquired the varia,
+
4698  "DataBase:: transmission_source_exposure_date[i] don't match"
+
4699  )
+
4700 
+
4701 
+
4702  VECT_MATCH(
+
4703  transition_matrix,
+
4704  other.transition_matrix,
+
4705  "DataBase:: transition_matrix[i] don't match"
+
4706  )
+
4707 
+
4708 
+
4709  return true;
+
4710 
+
4711 }
+
4712 
+
4713 template<typename TSeq>
+
4714 inline bool DataBase<TSeq>::operator==(const DataBase<TSeq> & other) const
+
4715 {
4716  VECT_MATCH(
-
4717  tool_sequence,
-
4718  other.tool_sequence,
-
4719  "DataBase:: tool_sequence[i] don't match"
+
4717  virus_name,
+
4718  other.virus_name,
+
4719  "DataBase:: virus_name[i] don't match"
4720  )
4721 
4722  VECT_MATCH(
-
4723  tool_origin_date,
-
4724  other.tool_origin_date,
-
4725  "DataBase:: tool_origin_date[i] don't match"
+
4723  virus_sequence,
+
4724  other.virus_sequence,
+
4725  "DataBase:: virus_sequence[i] don't match"
4726  )
4727 
-
4728 
-
4729  EPI_DEBUG_FAIL_AT_TRUE(
-
4730  sampling_freq != other.sampling_freq,
-
4731  "DataBase:: sampling_freq don't match."
+
4728  VECT_MATCH(
+
4729  virus_origin_date,
+
4730  other.virus_origin_date,
+
4731  "DataBase:: virus_origin_date[i] don't match"
4732  )
4733 
-
4734  // Variants history
-
4735  VECT_MATCH(
-
4736  hist_virus_date,
-
4737  other.hist_virus_date,
-
4738  "DataBase:: hist_virus_date[i] don't match"
-
4739  )
-
4740 
-
4741  VECT_MATCH(
-
4742  hist_virus_id,
-
4743  other.hist_virus_id,
-
4744  "DataBase:: hist_virus_id[i] don't match"
-
4745  )
-
4746 
-
4747  VECT_MATCH(
-
4748  hist_virus_state,
-
4749  other.hist_virus_state,
-
4750  "DataBase:: hist_virus_state[i] don't match"
-
4751  )
-
4752 
-
4753  VECT_MATCH(
-
4754  hist_virus_counts,
-
4755  other.hist_virus_counts,
-
4756  "DataBase:: hist_virus_counts[i] don't match"
-
4757  )
-
4758 
-
4759  // Tools history
-
4760  VECT_MATCH(
-
4761  hist_tool_date,
-
4762  other.hist_tool_date,
-
4763  "DataBase:: hist_tool_date[i] don't match"
-
4764  )
-
4765 
-
4766  VECT_MATCH(
-
4767  hist_tool_id,
-
4768  other.hist_tool_id,
-
4769  "DataBase:: hist_tool_id[i] don't match"
-
4770  )
-
4771 
-
4772  VECT_MATCH(
-
4773  hist_tool_state,
-
4774  other.hist_tool_state,
-
4775  "DataBase:: hist_tool_state[i] don't match"
-
4776  )
-
4777 
-
4778  VECT_MATCH(
-
4779  hist_tool_counts,
-
4780  other.hist_tool_counts,
-
4781  "DataBase:: hist_tool_counts[i] don't match"
-
4782  )
-
4783 
-
4784  // Overall hist
-
4785  VECT_MATCH(
-
4786  hist_total_date,
-
4787  other.hist_total_date,
-
4788  "DataBase:: hist_total_date[i] don't match"
-
4789  )
-
4790 
-
4791  VECT_MATCH(
-
4792  hist_total_nviruses_active,
-
4793  other.hist_total_nviruses_active,
-
4794  "DataBase:: hist_total_nviruses_active[i] don't match"
-
4795  )
-
4796 
-
4797  VECT_MATCH(
-
4798  hist_total_state,
-
4799  other.hist_total_state,
-
4800  "DataBase:: hist_total_state[i] don't match"
-
4801  )
-
4802 
-
4803  VECT_MATCH(
-
4804  hist_total_counts,
-
4805  other.hist_total_counts,
-
4806  "DataBase:: hist_total_counts[i] don't match"
-
4807  )
-
4808 
-
4809  VECT_MATCH(
-
4810  hist_transition_matrix,
-
4811  other.hist_transition_matrix,
-
4812  "DataBase:: hist_transition_matrix[i] don't match"
-
4813  )
-
4814 
-
4815  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
-
4816  EPI_DEBUG_FAIL_AT_TRUE(
-
4817  today_virus.size() != other.today_virus.size(),
-
4818  "DataBase:: today_virus.size() don't match."
+
4734  VECT_MATCH(
+
4735  virus_parent_id,
+
4736  other.virus_parent_id,
+
4737  "DataBase:: virus_parent_id[i] don't match"
+
4738  )
+
4739 
+
4740  VECT_MATCH(
+
4741  tool_name,
+
4742  other.tool_name,
+
4743  "DataBase:: tool_name[i] don't match"
+
4744  )
+
4745 
+
4746  VECT_MATCH(
+
4747  tool_sequence,
+
4748  other.tool_sequence,
+
4749  "DataBase:: tool_sequence[i] don't match"
+
4750  )
+
4751 
+
4752  VECT_MATCH(
+
4753  tool_origin_date,
+
4754  other.tool_origin_date,
+
4755  "DataBase:: tool_origin_date[i] don't match"
+
4756  )
+
4757 
+
4758 
+
4759  EPI_DEBUG_FAIL_AT_TRUE(
+
4760  sampling_freq != other.sampling_freq,
+
4761  "DataBase:: sampling_freq don't match."
+
4762  )
+
4763 
+
4764  // Variants history
+
4765  VECT_MATCH(
+
4766  hist_virus_date,
+
4767  other.hist_virus_date,
+
4768  "DataBase:: hist_virus_date[i] don't match"
+
4769  )
+
4770 
+
4771  VECT_MATCH(
+
4772  hist_virus_id,
+
4773  other.hist_virus_id,
+
4774  "DataBase:: hist_virus_id[i] don't match"
+
4775  )
+
4776 
+
4777  VECT_MATCH(
+
4778  hist_virus_state,
+
4779  other.hist_virus_state,
+
4780  "DataBase:: hist_virus_state[i] don't match"
+
4781  )
+
4782 
+
4783  VECT_MATCH(
+
4784  hist_virus_counts,
+
4785  other.hist_virus_counts,
+
4786  "DataBase:: hist_virus_counts[i] don't match"
+
4787  )
+
4788 
+
4789  // Tools history
+
4790  VECT_MATCH(
+
4791  hist_tool_date,
+
4792  other.hist_tool_date,
+
4793  "DataBase:: hist_tool_date[i] don't match"
+
4794  )
+
4795 
+
4796  VECT_MATCH(
+
4797  hist_tool_id,
+
4798  other.hist_tool_id,
+
4799  "DataBase:: hist_tool_id[i] don't match"
+
4800  )
+
4801 
+
4802  VECT_MATCH(
+
4803  hist_tool_state,
+
4804  other.hist_tool_state,
+
4805  "DataBase:: hist_tool_state[i] don't match"
+
4806  )
+
4807 
+
4808  VECT_MATCH(
+
4809  hist_tool_counts,
+
4810  other.hist_tool_counts,
+
4811  "DataBase:: hist_tool_counts[i] don't match"
+
4812  )
+
4813 
+
4814  // Overall hist
+
4815  VECT_MATCH(
+
4816  hist_total_date,
+
4817  other.hist_total_date,
+
4818  "DataBase:: hist_total_date[i] don't match"
4819  )
-
4820 
-
4821  for (size_t i = 0u; i < today_virus.size(); ++i)
-
4822  {
-
4823  VECT_MATCH(
-
4824  today_virus[i], other.today_virus[i],
-
4825  "DataBase:: today_virus[i] don't match"
-
4826  )
-
4827  }
-
4828 
-
4829  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
-
4830  EPI_DEBUG_FAIL_AT_TRUE(
-
4831  today_tool.size() != other.today_tool.size(),
-
4832  "DataBase:: today_tool.size() don't match."
-
4833  )
-
4834 
-
4835  for (size_t i = 0u; i < today_tool.size(); ++i)
-
4836  {
-
4837  VECT_MATCH(
-
4838  today_tool[i], other.today_tool[i],
-
4839  "DataBase:: today_tool[i] don't match"
-
4840  )
-
4841  }
-
4842 
-
4843  // {Susceptible, Infected, etc.}
-
4844  VECT_MATCH(
-
4845  today_total, other.today_total,
-
4846  "DataBase:: today_total[i] don't match"
-
4847  )
-
4848 
-
4849  // Totals
-
4850  EPI_DEBUG_FAIL_AT_TRUE(
-
4851  today_total_nviruses_active != other.today_total_nviruses_active,
-
4852  "DataBase:: today_total_nviruses_active don't match."
-
4853  )
-
4854 
-
4855  // Transmission network
-
4856  VECT_MATCH( ///< Date of the transmission eve
-
4857  transmission_date,
-
4858  other.transmission_date,
-
4859  "DataBase:: transmission_date[i] don't match"
-
4860  )
-
4861 
-
4862  VECT_MATCH( ///< Id of the sour
-
4863  transmission_source,
-
4864  other.transmission_source,
-
4865  "DataBase:: transmission_source[i] don't match"
-
4866  )
-
4867 
-
4868  VECT_MATCH( ///< Id of the targ
-
4869  transmission_target,
-
4870  other.transmission_target,
-
4871  "DataBase:: transmission_target[i] don't match"
-
4872  )
-
4873 
-
4874  VECT_MATCH( ///< Id of the varia
-
4875  transmission_virus,
-
4876  other.transmission_virus,
-
4877  "DataBase:: transmission_virus[i] don't match"
-
4878  )
-
4879 
-
4880  VECT_MATCH( ///< Date when the source acquired the varia
-
4881  transmission_source_exposure_date,
-
4882  other.transmission_source_exposure_date,
-
4883  "DataBase:: transmission_source_exposure_date[i] don't match"
-
4884  )
-
4885 
-
4886  VECT_MATCH(
-
4887  transition_matrix,
-
4888  other.transition_matrix,
-
4889  "DataBase:: transition_matrix[i] don't match"
+
4820 
+
4821  VECT_MATCH(
+
4822  hist_total_nviruses_active,
+
4823  other.hist_total_nviruses_active,
+
4824  "DataBase:: hist_total_nviruses_active[i] don't match"
+
4825  )
+
4826 
+
4827  VECT_MATCH(
+
4828  hist_total_state,
+
4829  other.hist_total_state,
+
4830  "DataBase:: hist_total_state[i] don't match"
+
4831  )
+
4832 
+
4833  VECT_MATCH(
+
4834  hist_total_counts,
+
4835  other.hist_total_counts,
+
4836  "DataBase:: hist_total_counts[i] don't match"
+
4837  )
+
4838 
+
4839  VECT_MATCH(
+
4840  hist_transition_matrix,
+
4841  other.hist_transition_matrix,
+
4842  "DataBase:: hist_transition_matrix[i] don't match"
+
4843  )
+
4844 
+
4845  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
+
4846  EPI_DEBUG_FAIL_AT_TRUE(
+
4847  today_virus.size() != other.today_virus.size(),
+
4848  "DataBase:: today_virus.size() don't match."
+
4849  )
+
4850 
+
4851  for (size_t i = 0u; i < today_virus.size(); ++i)
+
4852  {
+
4853  VECT_MATCH(
+
4854  today_virus[i], other.today_virus[i],
+
4855  "DataBase:: today_virus[i] don't match"
+
4856  )
+
4857  }
+
4858 
+
4859  // {Variant 1: {state 1, state 2, etc.}, Variant 2: {...}, ...}
+
4860  EPI_DEBUG_FAIL_AT_TRUE(
+
4861  today_tool.size() != other.today_tool.size(),
+
4862  "DataBase:: today_tool.size() don't match."
+
4863  )
+
4864 
+
4865  for (size_t i = 0u; i < today_tool.size(); ++i)
+
4866  {
+
4867  VECT_MATCH(
+
4868  today_tool[i], other.today_tool[i],
+
4869  "DataBase:: today_tool[i] don't match"
+
4870  )
+
4871  }
+
4872 
+
4873  // {Susceptible, Infected, etc.}
+
4874  VECT_MATCH(
+
4875  today_total, other.today_total,
+
4876  "DataBase:: today_total[i] don't match"
+
4877  )
+
4878 
+
4879  // Totals
+
4880  EPI_DEBUG_FAIL_AT_TRUE(
+
4881  today_total_nviruses_active != other.today_total_nviruses_active,
+
4882  "DataBase:: today_total_nviruses_active don't match."
+
4883  )
+
4884 
+
4885  // Transmission network
+
4886  VECT_MATCH( ///< Date of the transmission eve
+
4887  transmission_date,
+
4888  other.transmission_date,
+
4889  "DataBase:: transmission_date[i] don't match"
4890  )
4891 
-
4892  return true;
-
4893 
-
4894 }
-
4895 
-
4896 template<typename TSeq>
-
4897 inline void DataBase<TSeq>::generation_time(
-
4898  std::vector< int > & agent_id,
-
4899  std::vector< int > & virus_id,
-
4900  std::vector< int > & time,
-
4901  std::vector< int > & gentime
-
4902 ) const {
-
4903 
-
4904  size_t nevents = transmission_date.size();
-
4905 
-
4906  agent_id.reserve(nevents);
-
4907  virus_id.reserve(nevents);
-
4908  time.reserve(nevents);
-
4909  gentime.reserve(nevents);
-
4910 
-
4911  // Iterating through the individuals
-
4912  for (size_t i = 0u; i < nevents; ++i)
-
4913  {
-
4914  int agent_id_i = transmission_target[i];
-
4915  agent_id.push_back(agent_id_i);
-
4916  virus_id.push_back(transmission_virus[i]);
-
4917  time.push_back(transmission_date[i]);
-
4918 
-
4919  bool found = false;
-
4920  for (size_t j = i; j < nevents; ++j)
-
4921  {
-
4922 
-
4923  if (transmission_source[j] == agent_id_i)
-
4924  {
-
4925  gentime.push_back(transmission_date[j] - time[i]);
-
4926  found = true;
-
4927  break;
-
4928  }
-
4929 
-
4930  }
-
4931 
-
4932  // If there's no transmission, we set the generation time to
-
4933  // minus 1;
-
4934  if (!found)
-
4935  gentime.push_back(-1);
-
4936 
-
4937  }
-
4938 
-
4939  agent_id.shrink_to_fit();
-
4940  virus_id.shrink_to_fit();
-
4941  time.shrink_to_fit();
-
4942  gentime.shrink_to_fit();
-
4943 
-
4944  return;
-
4945 
-
4946 }
-
4947 
-
4948 template<typename TSeq>
-
4949 inline void DataBase<TSeq>::generation_time(
-
4950  std::string fn
-
4951 ) const
-
4952 {
-
4953 
-
4954  std::vector< int > agent_id;
-
4955  std::vector< int > virus_id;
-
4956  std::vector< int > time;
-
4957  std::vector< int > gentime;
-
4958 
-
4959  generation_time(agent_id, virus_id, time, gentime);
-
4960 
-
4961  std::ofstream fn_file(fn, std::ios_base::out);
-
4962 
-
4963  // Throw an error if the file doesn't exists using throw
-
4964  if (!fn_file)
-
4965  {
-
4966  throw std::runtime_error(
-
4967  "DataBase::generation_time: "
-
4968  "Cannot open file " + fn + "."
-
4969  );
-
4970  }
-
4971 
-
4972 
+
4892  VECT_MATCH( ///< Id of the sour
+
4893  transmission_source,
+
4894  other.transmission_source,
+
4895  "DataBase:: transmission_source[i] don't match"
+
4896  )
+
4897 
+
4898  VECT_MATCH( ///< Id of the targ
+
4899  transmission_target,
+
4900  other.transmission_target,
+
4901  "DataBase:: transmission_target[i] don't match"
+
4902  )
+
4903 
+
4904  VECT_MATCH( ///< Id of the varia
+
4905  transmission_virus,
+
4906  other.transmission_virus,
+
4907  "DataBase:: transmission_virus[i] don't match"
+
4908  )
+
4909 
+
4910  VECT_MATCH( ///< Date when the source acquired the varia
+
4911  transmission_source_exposure_date,
+
4912  other.transmission_source_exposure_date,
+
4913  "DataBase:: transmission_source_exposure_date[i] don't match"
+
4914  )
+
4915 
+
4916  VECT_MATCH(
+
4917  transition_matrix,
+
4918  other.transition_matrix,
+
4919  "DataBase:: transition_matrix[i] don't match"
+
4920  )
+
4921 
+
4922  return true;
+
4923 
+
4924 }
+
4925 
+
4926 template<typename TSeq>
+
4927 inline void DataBase<TSeq>::generation_time(
+
4928  std::vector< int > & agent_id,
+
4929  std::vector< int > & virus_id,
+
4930  std::vector< int > & time,
+
4931  std::vector< int > & gentime
+
4932 ) const {
+
4933 
+
4934  size_t nevents = transmission_date.size();
+
4935 
+
4936  agent_id.reserve(nevents);
+
4937  virus_id.reserve(nevents);
+
4938  time.reserve(nevents);
+
4939  gentime.reserve(nevents);
+
4940 
+
4941  // Iterating through the individuals
+
4942  for (size_t i = 0u; i < nevents; ++i)
+
4943  {
+
4944  int agent_id_i = transmission_target[i];
+
4945  agent_id.push_back(agent_id_i);
+
4946  virus_id.push_back(transmission_virus[i]);
+
4947  time.push_back(transmission_date[i]);
+
4948 
+
4949  bool found = false;
+
4950  for (size_t j = i; j < nevents; ++j)
+
4951  {
+
4952 
+
4953  if (transmission_source[j] == agent_id_i)
+
4954  {
+
4955  gentime.push_back(transmission_date[j] - time[i]);
+
4956  found = true;
+
4957  break;
+
4958  }
+
4959 
+
4960  }
+
4961 
+
4962  // If there's no transmission, we set the generation time to
+
4963  // minus 1;
+
4964  if (!found)
+
4965  gentime.push_back(-1);
+
4966 
+
4967  }
+
4968 
+
4969  agent_id.shrink_to_fit();
+
4970  virus_id.shrink_to_fit();
+
4971  time.shrink_to_fit();
+
4972  gentime.shrink_to_fit();
4973 
-
4974  fn_file <<
-
4975  #ifdef EPI_DEBUG
-
4976  "thread " <<
-
4977  #endif
-
4978  "virus source source_exposure_date gentime\n";
-
4979 
-
4980  size_t n = agent_id.size();
-
4981  for (size_t i = 0u; i < n; ++i)
-
4982  fn_file <<
-
4983  #ifdef EPI_DEBUG
-
4984  EPI_GET_THREAD_ID() << " " <<
-
4985  #endif
-
4986  virus_id[i] << " " <<
-
4987  agent_id[i] << " " <<
-
4988  time[i] << " " <<
-
4989  gentime[i] << "\n";
+
4974  return;
+
4975 
+
4976 }
+
4977 
+
4978 template<typename TSeq>
+
4979 inline void DataBase<TSeq>::generation_time(
+
4980  std::string fn
+
4981 ) const
+
4982 {
+
4983 
+
4984  std::vector< int > agent_id;
+
4985  std::vector< int > virus_id;
+
4986  std::vector< int > time;
+
4987  std::vector< int > gentime;
+
4988 
+
4989  generation_time(agent_id, virus_id, time, gentime);
4990 
-
4991  return;
+
4991  std::ofstream fn_file(fn, std::ios_base::out);
4992 
-
4993 }
-
4994 
-
4995 #undef VECT_MATCH
-
4996 
-
4997 #endif
-
4998 /*//////////////////////////////////////////////////////////////////////////////
-
5000 
-
5001  End of -include/epiworld/database-meat.hpp-
+
4993  // Throw an error if the file doesn't exists using throw
+
4994  if (!fn_file)
+
4995  {
+
4996  throw std::runtime_error(
+
4997  "DataBase::generation_time: "
+
4998  "Cannot open file " + fn + "."
+
4999  );
+
5000  }
+
5001 
5002 
-
5005 
-
5006 
-
5007 /*//////////////////////////////////////////////////////////////////////////////
+
5003 
+
5004  fn_file <<
+
5005  #ifdef EPI_DEBUG
+
5006  "thread " <<
+
5007  #endif
+
5008  "virus source source_exposure_date gentime\n";
5009 
-
5010  Start of -include/epiworld/adjlist-bones.hpp-
-
5011 
-
5014 
-
5015 
-
5016 #ifndef EPIWORLD_ADJLIST_BONES_HPP
-
5017 #define EPIWORLD_ADJLIST_BONES_HPP
-
5018 
-
5019 class AdjList {
-
5020 private:
-
5021 
-
5022  std::vector<std::map<int, int>> dat;
-
5023  bool directed;
-
5024  epiworld_fast_uint N = 0;
-
5025  epiworld_fast_uint E = 0;
+
5010  size_t n = agent_id.size();
+
5011  for (size_t i = 0u; i < n; ++i)
+
5012  fn_file <<
+
5013  #ifdef EPI_DEBUG
+
5014  EPI_GET_THREAD_ID() << " " <<
+
5015  #endif
+
5016  virus_id[i] << " " <<
+
5017  agent_id[i] << " " <<
+
5018  time[i] << " " <<
+
5019  gentime[i] << "\n";
+
5020 
+
5021  return;
+
5022 
+
5023 }
+
5024 
+
5025 #undef VECT_MATCH
5026 
-
5027 public:
-
5028 
-
5029  AdjList() {};
+
5027 #endif
+
5028 /*//////////////////////////////////////////////////////////////////////////////
5030 
-
5042  AdjList(
-
5043  const std::vector< int > & source,
-
5044  const std::vector< int > & target,
-
5045  int size,
-
5046  bool directed
-
5047  );
+
5031  End of -include/epiworld/database-meat.hpp-
+
5032 
+
5035 
+
5036 
+
5037 /*//////////////////////////////////////////////////////////////////////////////
+
5039 
+
5040  Start of -include/epiworld/adjlist-bones.hpp-
+
5041 
+
5044 
+
5045 
+
5046 #ifndef EPIWORLD_ADJLIST_BONES_HPP
+
5047 #define EPIWORLD_ADJLIST_BONES_HPP
5048 
-
5049  AdjList(AdjList && a); // Move constructor
-
5050  AdjList(const AdjList & a); // Copy constructor
-
5051  AdjList& operator=(const AdjList& a);
-
5052 
-
5053 
-
5064  void read_edgelist(
-
5065  std::string fn,
-
5066  int size,
-
5067  int skip = 0,
-
5068  bool directed = true
-
5069  );
-
5070 
-
5071  std::map<int, int> operator()(
-
5072  epiworld_fast_uint i
-
5073  ) const;
-
5074 
-
5075  void print(epiworld_fast_uint limit = 20u) const;
-
5076  size_t vcount() const; ///< Number of vertices/nodes in the network.
-
5077  size_t ecount() const; ///< Number of edges/arcs/ties in the network.
-
5078 
-
5079  std::vector<std::map<int,int>> & get_dat() {
-
5080  return dat;
-
5081  };
+
5049 class AdjList {
+
5050 private:
+
5051 
+
5052  std::vector<std::map<int, int>> dat;
+
5053  bool directed;
+
5054  epiworld_fast_uint N = 0;
+
5055  epiworld_fast_uint E = 0;
+
5056 
+
5057 public:
+
5058 
+
5059  AdjList() {};
+
5060 
+
5072  AdjList(
+
5073  const std::vector< int > & source,
+
5074  const std::vector< int > & target,
+
5075  int size,
+
5076  bool directed
+
5077  );
+
5078 
+
5079  AdjList(AdjList && a); // Move constructor
+
5080  AdjList(const AdjList & a); // Copy constructor
+
5081  AdjList& operator=(const AdjList& a);
5082 
-
5083  bool is_directed() const; ///< `true` if the network is directed.
-
5084 
-
5085 };
-
5086 
-
5087 
-
5088 #endif
-
5089 
-
5090 /*//////////////////////////////////////////////////////////////////////////////
-
5092 
-
5093  End of -include/epiworld/adjlist-bones.hpp-
-
5094 
-
5097 
-
5098 
-
5099 /*//////////////////////////////////////////////////////////////////////////////
-
5101 
-
5102  Start of -include/epiworld/adjlist-meat.hpp-
-
5103 
-
5106 
-
5107 
-
5108 #ifndef EPIWORLD_ADJLIST_MEAT_HPP
-
5109 #define EPIWORLD_ADJLIST_MEAT_HPP
-
5110 
-
5111 inline AdjList::AdjList(
-
5112  const std::vector< int > & source,
-
5113  const std::vector< int > & target,
-
5114  int size,
-
5115  bool directed
-
5116 ) : directed(directed) {
+
5083 
+
5094  void read_edgelist(
+
5095  std::string fn,
+
5096  int size,
+
5097  int skip = 0,
+
5098  bool directed = true
+
5099  );
+
5100 
+
5101  std::map<int, int> operator()(
+
5102  epiworld_fast_uint i
+
5103  ) const;
+
5104 
+
5105  void print(epiworld_fast_uint limit = 20u) const;
+
5106  size_t vcount() const; ///< Number of vertices/nodes in the network.
+
5107  size_t ecount() const; ///< Number of edges/arcs/ties in the network.
+
5108 
+
5109  std::vector<std::map<int,int>> & get_dat() {
+
5110  return dat;
+
5111  };
+
5112 
+
5113  bool is_directed() const; ///< `true` if the network is directed.
+
5114 
+
5115 };
+
5116 
5117 
-
5118 
-
5119  dat.resize(size, std::map<int,int>({}));
-
5120  int max_id = size - 1;
-
5121 
-
5122  int i,j;
-
5123  for (int m = 0; m < static_cast<int>(source.size()); ++m)
-
5124  {
-
5125 
-
5126  i = source[m];
-
5127  j = target[m];
+
5118 #endif
+
5119 
+
5120 /*//////////////////////////////////////////////////////////////////////////////
+
5122 
+
5123  End of -include/epiworld/adjlist-bones.hpp-
+
5124 
+
5127 
5128 
-
5129  if (i > max_id)
-
5130  throw std::range_error(
-
5131  "The source["+std::to_string(m)+"] = " + std::to_string(i) +
-
5132  " is above the max_id " + std::to_string(max_id)
-
5133  );
-
5134 
-
5135  if (j > max_id)
-
5136  throw std::range_error(
-
5137  "The target["+std::to_string(m)+"] = " + std::to_string(j) +
-
5138  " is above the max_id " + std::to_string(max_id)
-
5139  );
+
5129 /*//////////////////////////////////////////////////////////////////////////////
+
5131 
+
5132  Start of -include/epiworld/adjlist-meat.hpp-
+
5133 
+
5136 
+
5137 
+
5138 #ifndef EPIWORLD_ADJLIST_MEAT_HPP
+
5139 #define EPIWORLD_ADJLIST_MEAT_HPP
5140 
-
5141  // Adding nodes
-
5142  if (dat[i].find(j) == dat[i].end())
-
5143  dat[i].insert(std::pair<int, int>(j, 1u));
-
5144  else
-
5145  dat[i][j]++;
-
5146 
-
5147  if (!directed)
-
5148  {
-
5149 
-
5150  if (dat[j].find(i) == dat[j].end())
-
5151  dat[j].insert(std::pair<int, int>(i, 1u));
-
5152  else
-
5153  dat[j][i]++;
-
5154 
-
5155  }
-
5156 
-
5157  E++;
+
5141 inline AdjList::AdjList(
+
5142  const std::vector< int > & source,
+
5143  const std::vector< int > & target,
+
5144  int size,
+
5145  bool directed
+
5146 ) : directed(directed) {
+
5147 
+
5148 
+
5149  dat.resize(size, std::map<int,int>({}));
+
5150  int max_id = size - 1;
+
5151 
+
5152  int i,j;
+
5153  for (int m = 0; m < static_cast<int>(source.size()); ++m)
+
5154  {
+
5155 
+
5156  i = source[m];
+
5157  j = target[m];
5158 
-
5159  }
-
5160 
-
5161  N = size;
-
5162 
-
5163  return;
+
5159  if (i > max_id)
+
5160  throw std::range_error(
+
5161  "The source["+std::to_string(m)+"] = " + std::to_string(i) +
+
5162  " is above the max_id " + std::to_string(max_id)
+
5163  );
5164 
-
5165 }
-
5166 
-
5167 
-
5168 inline AdjList::AdjList(AdjList && a) :
-
5169  dat(std::move(a.dat)),
-
5170  directed(a.directed),
-
5171  N(a.N),
-
5172  E(a.E)
-
5173 {
-
5174 
-
5175 }
-
5176 
-
5177 inline AdjList::AdjList(const AdjList & a) :
-
5178  dat(a.dat),
-
5179  directed(a.directed),
-
5180  N(a.N),
-
5181  E(a.E)
-
5182 {
-
5183 
-
5184 }
-
5185 
-
5186 inline AdjList& AdjList::operator=(const AdjList& a)
-
5187 {
-
5188  if (this == &a)
-
5189  return *this;
+
5165  if (j > max_id)
+
5166  throw std::range_error(
+
5167  "The target["+std::to_string(m)+"] = " + std::to_string(j) +
+
5168  " is above the max_id " + std::to_string(max_id)
+
5169  );
+
5170 
+
5171  // Adding nodes
+
5172  if (dat[i].find(j) == dat[i].end())
+
5173  dat[i].insert(std::pair<int, int>(j, 1u));
+
5174  else
+
5175  dat[i][j]++;
+
5176 
+
5177  if (!directed)
+
5178  {
+
5179 
+
5180  if (dat[j].find(i) == dat[j].end())
+
5181  dat[j].insert(std::pair<int, int>(i, 1u));
+
5182  else
+
5183  dat[j][i]++;
+
5184 
+
5185  }
+
5186 
+
5187  E++;
+
5188 
+
5189  }
5190 
-
5191  this->dat = a.dat;
-
5192  this->directed = a.directed;
-
5193  this->N = a.N;
-
5194  this->E = a.E;
-
5195 
-
5196  return *this;
-
5197 }
-
5198 
-
5199 inline void AdjList::read_edgelist(
-
5200  std::string fn,
-
5201  int size,
-
5202  int skip,
-
5203  bool directed
-
5204 ) {
-
5205 
-
5206  int i,j;
-
5207  std::ifstream filei(fn);
-
5208 
-
5209  if (!filei)
-
5210  throw std::logic_error("The file " + fn + " was not found.");
-
5211 
-
5212  int linenum = 0;
-
5213  std::vector< int > source_;
-
5214  std::vector< int > target_;
+
5191  N = size;
+
5192 
+
5193  return;
+
5194 
+
5195 }
+
5196 
+
5197 
+
5198 inline AdjList::AdjList(AdjList && a) :
+
5199  dat(std::move(a.dat)),
+
5200  directed(a.directed),
+
5201  N(a.N),
+
5202  E(a.E)
+
5203 {
+
5204 
+
5205 }
+
5206 
+
5207 inline AdjList::AdjList(const AdjList & a) :
+
5208  dat(a.dat),
+
5209  directed(a.directed),
+
5210  N(a.N),
+
5211  E(a.E)
+
5212 {
+
5213 
+
5214 }
5215 
-
5216  source_.reserve(1e5);
-
5217  target_.reserve(1e5);
-
5218 
-
5219  int max_id = size - 1;
+
5216 inline AdjList& AdjList::operator=(const AdjList& a)
+
5217 {
+
5218  if (this == &a)
+
5219  return *this;
5220 
-
5221  while (!filei.eof())
-
5222  {
-
5223 
-
5224  if (linenum++ < skip)
-
5225  continue;
-
5226 
-
5227  filei >> i >> j;
+
5221  this->dat = a.dat;
+
5222  this->directed = a.directed;
+
5223  this->N = a.N;
+
5224  this->E = a.E;
+
5225 
+
5226  return *this;
+
5227 }
5228 
-
5229  // Looking for exceptions
-
5230  if (filei.bad())
-
5231  throw std::logic_error(
-
5232  "I/O error while reading the file " +
-
5233  fn
-
5234  );
+
5229 inline void AdjList::read_edgelist(
+
5230  std::string fn,
+
5231  int size,
+
5232  int skip,
+
5233  bool directed
+
5234 ) {
5235 
-
5236  if (filei.fail())
-
5237  break;
+
5236  int i,j;
+
5237  std::ifstream filei(fn);
5238 
-
5239  if (i > max_id)
-
5240  throw std::range_error(
-
5241  "The source["+std::to_string(linenum)+"] = " + std::to_string(i) +
-
5242  " is above the max_id " + std::to_string(max_id)
-
5243  );
-
5244 
-
5245  if (j > max_id)
-
5246  throw std::range_error(
-
5247  "The target["+std::to_string(linenum)+"] = " + std::to_string(j) +
-
5248  " is above the max_id " + std::to_string(max_id)
-
5249  );
+
5239  if (!filei)
+
5240  throw std::logic_error("The file " + fn + " was not found.");
+
5241 
+
5242  int linenum = 0;
+
5243  std::vector< int > source_;
+
5244  std::vector< int > target_;
+
5245 
+
5246  source_.reserve(1e5);
+
5247  target_.reserve(1e5);
+
5248 
+
5249  int max_id = size - 1;
5250 
-
5251  source_.push_back(i);
-
5252  target_.push_back(j);
+
5251  while (!filei.eof())
+
5252  {
5253 
-
5254  }
-
5255 
-
5256  // Now using the right constructor
-
5257  *this = AdjList(source_, target_, size, directed);
+
5254  if (linenum++ < skip)
+
5255  continue;
+
5256 
+
5257  filei >> i >> j;
5258 
-
5259  return;
-
5260 
-
5261 }
-
5262 
-
5263 inline std::map<int,int> AdjList::operator()(
-
5264  epiworld_fast_uint i
-
5265  ) const {
-
5266 
-
5267  if (i >= N)
-
5268  throw std::range_error(
-
5269  "The vertex id " + std::to_string(i) + " is not in the network."
-
5270  );
-
5271 
-
5272  return dat[i];
-
5273 
-
5274 }
-
5275 
-
5276 inline void AdjList::print(epiworld_fast_uint limit) const {
-
5277 
-
5278 
-
5279  epiworld_fast_uint counter = 0;
-
5280  printf_epiworld("Nodeset:\n");
-
5281  int i = -1;
-
5282  for (auto & n : dat)
-
5283  {
-
5284 
-
5285  if (counter++ > limit)
-
5286  break;
-
5287 
-
5288  printf_epiworld(" % 3i: {", ++i);
-
5289  int niter = 0;
-
5290  for (auto n_n : n)
-
5291  if (++niter < static_cast<int>(n.size()))
-
5292  {
-
5293  printf_epiworld("%i, ", static_cast<int>(n_n.first));
-
5294  }
-
5295  else {
-
5296  printf_epiworld("%i}\n", static_cast<int>(n_n.first));
-
5297  }
-
5298  }
-
5299 
-
5300  if (limit < dat.size())
-
5301  {
-
5302  printf_epiworld(
-
5303  " (... skipping %i records ...)\n",
-
5304  static_cast<int>(dat.size() - limit)
-
5305  );
-
5306  }
+
5259  // Looking for exceptions
+
5260  if (filei.bad())
+
5261  throw std::logic_error(
+
5262  "I/O error while reading the file " +
+
5263  fn
+
5264  );
+
5265 
+
5266  if (filei.fail())
+
5267  break;
+
5268 
+
5269  if (i > max_id)
+
5270  throw std::range_error(
+
5271  "The source["+std::to_string(linenum)+"] = " + std::to_string(i) +
+
5272  " is above the max_id " + std::to_string(max_id)
+
5273  );
+
5274 
+
5275  if (j > max_id)
+
5276  throw std::range_error(
+
5277  "The target["+std::to_string(linenum)+"] = " + std::to_string(j) +
+
5278  " is above the max_id " + std::to_string(max_id)
+
5279  );
+
5280 
+
5281  source_.push_back(i);
+
5282  target_.push_back(j);
+
5283 
+
5284  }
+
5285 
+
5286  // Now using the right constructor
+
5287  *this = AdjList(source_, target_, size, directed);
+
5288 
+
5289  return;
+
5290 
+
5291 }
+
5292 
+
5293 inline std::map<int,int> AdjList::operator()(
+
5294  epiworld_fast_uint i
+
5295  ) const {
+
5296 
+
5297  if (i >= N)
+
5298  throw std::range_error(
+
5299  "The vertex id " + std::to_string(i) + " is not in the network."
+
5300  );
+
5301 
+
5302  return dat[i];
+
5303 
+
5304 }
+
5305 
+
5306 inline void AdjList::print(epiworld_fast_uint limit) const {
5307 
-
5308 }
-
5309 
-
5310 inline size_t AdjList::vcount() const
-
5311 {
-
5312  return N;
-
5313 }
+
5308 
+
5309  epiworld_fast_uint counter = 0;
+
5310  printf_epiworld("Nodeset:\n");
+
5311  int i = -1;
+
5312  for (auto & n : dat)
+
5313  {
5314 
-
5315 inline size_t AdjList::ecount() const
-
5316 {
-
5317  return E;
-
5318 }
-
5319 
-
5320 inline bool AdjList::is_directed() const {
-
5321 
-
5322  if (dat.size() == 0u)
-
5323  throw std::logic_error("The edgelist is empty.");
-
5324 
-
5325  return directed;
-
5326 
-
5327 }
-
5328 
-
5329 #endif
-
5330 /*//////////////////////////////////////////////////////////////////////////////
-
5332 
-
5333  End of -include/epiworld/adjlist-meat.hpp-
-
5334 
+
5315  if (counter++ > limit)
+
5316  break;
+
5317 
+
5318  printf_epiworld(" % 3i: {", ++i);
+
5319  int niter = 0;
+
5320  for (auto n_n : n)
+
5321  if (++niter < static_cast<int>(n.size()))
+
5322  {
+
5323  printf_epiworld("%i, ", static_cast<int>(n_n.first));
+
5324  }
+
5325  else {
+
5326  printf_epiworld("%i}\n", static_cast<int>(n_n.first));
+
5327  }
+
5328  }
+
5329 
+
5330  if (limit < dat.size())
+
5331  {
+
5332  printf_epiworld(
+
5333  " (... skipping %i records ...)\n",
+
5334  static_cast<int>(dat.size() - limit)
+
5335  );
+
5336  }
5337 
-
5338 
+
5338 }
5339 
-
5340 /*//////////////////////////////////////////////////////////////////////////////
-
5342 
-
5343  Start of -include/epiworld/randgraph.hpp-
+
5340 inline size_t AdjList::vcount() const
+
5341 {
+
5342  return N;
+
5343 }
5344 
-
5347 
-
5348 
-
5349 #ifndef EPIWORLD_RANDGRA
-
5350 #define EPIWORLD_RANDGRA
+
5345 inline size_t AdjList::ecount() const
+
5346 {
+
5347  return E;
+
5348 }
+
5349 
+
5350 inline bool AdjList::is_directed() const {
5351 
-
5352 template<typename TSeq>
-
5353 class Model;
-
5354 
-
5355 template<typename TSeq>
-
5356 class Agent;
-
5357 
-
5358 class AdjList;
-
5359 
-
5360 
-
5361 template<typename TSeq, typename TDat>
-
5362 inline void rewire_degseq(
-
5363  TDat * agents,
-
5364  Model<TSeq> * model,
-
5365  epiworld_double proportion
-
5366  );
+
5352  if (dat.size() == 0u)
+
5353  throw std::logic_error("The edgelist is empty.");
+
5354 
+
5355  return directed;
+
5356 
+
5357 }
+
5358 
+
5359 #endif
+
5360 /*//////////////////////////////////////////////////////////////////////////////
+
5362 
+
5363  End of -include/epiworld/adjlist-meat.hpp-
+
5364 
5367 
-
5368 template<typename TSeq = int>
-
5369 inline void rewire_degseq(
-
5370  std::vector< Agent<TSeq> > * agents,
-
5371  Model<TSeq> * model,
-
5372  epiworld_double proportion
-
5373  )
-
5374 {
-
5375 
-
5376  #ifdef EPI_DEBUG
-
5377  std::vector< int > _degree0(agents->size(), 0);
-
5378  for (size_t i = 0u; i < _degree0.size(); ++i)
-
5379  _degree0[i] = model->get_agents()[i].get_neighbors().size();
-
5380  #endif
+
5368 
+
5369 
+
5370 /*//////////////////////////////////////////////////////////////////////////////
+
5372 
+
5373  Start of -include/epiworld/randgraph.hpp-
+
5374 
+
5377 
+
5378 
+
5379 #ifndef EPIWORLD_RANDGRA
+
5380 #define EPIWORLD_RANDGRA
5381 
-
5382  // Identifying individuals with degree > 0
-
5383  std::vector< epiworld_fast_uint > non_isolates;
-
5384  std::vector< epiworld_double > weights;
-
5385  epiworld_double nedges = 0.0;
-
5386 
-
5387  for (epiworld_fast_uint i = 0u; i < agents->size(); ++i)
-
5388  {
-
5389  if (agents->operator[](i).get_neighbors().size() > 0u)
-
5390  {
-
5391  non_isolates.push_back(i);
-
5392  epiworld_double wtemp = static_cast<epiworld_double>(
-
5393  agents->operator[](i).get_neighbors().size()
-
5394  );
-
5395  weights.push_back(wtemp);
-
5396  nedges += wtemp;
-
5397  }
-
5398  }
-
5399 
-
5400  if (non_isolates.size() == 0u)
-
5401  throw std::logic_error("The graph is completely disconnected.");
-
5402 
-
5403  // Cumulative probs
-
5404  weights[0u] /= nedges;
-
5405  for (epiworld_fast_uint i = 1u; i < non_isolates.size(); ++i)
-
5406  {
-
5407  weights[i] /= nedges;
-
5408  weights[i] += weights[i - 1u];
-
5409  }
-
5410 
-
5411  // Only swap if needed
-
5412  epiworld_fast_uint N = non_isolates.size();
-
5413  epiworld_double prob;
-
5414  int nrewires = floor(proportion * nedges);
-
5415  while (nrewires-- > 0)
-
5416  {
-
5417 
-
5418  // Picking egos
-
5419  prob = model->runif();
-
5420  int id0 = N - 1;
-
5421  for (epiworld_fast_uint i = 0u; i < N; ++i)
-
5422  if (prob <= weights[i])
-
5423  {
-
5424  id0 = i;
-
5425  break;
-
5426  }
-
5427 
-
5428  prob = model->runif();
-
5429  int id1 = N - 1;
-
5430  for (epiworld_fast_uint i = 0u; i < N; ++i)
-
5431  if (prob <= weights[i])
-
5432  {
-
5433  id1 = i;
-
5434  break;
-
5435  }
-
5436 
-
5437  // Correcting for under or overflow.
-
5438  if (id1 == id0)
-
5439  id1++;
+
5382 template<typename TSeq>
+
5383 class Model;
+
5384 
+
5385 template<typename TSeq>
+
5386 class Agent;
+
5387 
+
5388 class AdjList;
+
5389 
+
5390 
+
5391 template<typename TSeq, typename TDat>
+
5392 inline void rewire_degseq(
+
5393  TDat * agents,
+
5394  Model<TSeq> * model,
+
5395  epiworld_double proportion
+
5396  );
+
5397 
+
5398 template<typename TSeq = int>
+
5399 inline void rewire_degseq(
+
5400  std::vector< Agent<TSeq> > * agents,
+
5401  Model<TSeq> * model,
+
5402  epiworld_double proportion
+
5403  )
+
5404 {
+
5405 
+
5406  #ifdef EPI_DEBUG
+
5407  std::vector< int > _degree0(agents->size(), 0);
+
5408  for (size_t i = 0u; i < _degree0.size(); ++i)
+
5409  _degree0[i] = model->get_agents()[i].get_neighbors().size();
+
5410  #endif
+
5411 
+
5412  // Identifying individuals with degree > 0
+
5413  std::vector< epiworld_fast_uint > non_isolates;
+
5414  std::vector< epiworld_double > weights;
+
5415  epiworld_double nedges = 0.0;
+
5416 
+
5417  for (epiworld_fast_uint i = 0u; i < agents->size(); ++i)
+
5418  {
+
5419  if (agents->operator[](i).get_neighbors().size() > 0u)
+
5420  {
+
5421  non_isolates.push_back(i);
+
5422  epiworld_double wtemp = static_cast<epiworld_double>(
+
5423  agents->operator[](i).get_neighbors().size()
+
5424  );
+
5425  weights.push_back(wtemp);
+
5426  nedges += wtemp;
+
5427  }
+
5428  }
+
5429 
+
5430  if (non_isolates.size() == 0u)
+
5431  throw std::logic_error("The graph is completely disconnected.");
+
5432 
+
5433  // Cumulative probs
+
5434  weights[0u] /= nedges;
+
5435  for (epiworld_fast_uint i = 1u; i < non_isolates.size(); ++i)
+
5436  {
+
5437  weights[i] /= nedges;
+
5438  weights[i] += weights[i - 1u];
+
5439  }
5440 
-
5441  if (id1 >= static_cast<int>(N))
-
5442  id1 = 0;
-
5443 
-
5444  Agent<TSeq> & p0 = agents->operator[](non_isolates[id0]);
-
5445  Agent<TSeq> & p1 = agents->operator[](non_isolates[id1]);
-
5446 
-
5447  // Picking alters (relative location in their lists)
-
5448  // In this case, these are uniformly distributed within the list
-
5449  int id01 = std::floor(p0.get_n_neighbors() * model->runif());
-
5450  int id11 = std::floor(p1.get_n_neighbors() * model->runif());
-
5451 
-
5452  // When rewiring, we need to flip the individuals from the other
-
5453  // end as well, since we are dealing withi an undirected graph
-
5454 
-
5455  // Finding what neighbour is id0
-
5456  model->get_agents()[id0].swap_neighbors(
-
5457  model->get_agents()[id1],
-
5458  id01,
-
5459  id11
-
5460  );
-
5461 
-
5462 
-
5463  }
-
5464 
-
5465  #ifdef EPI_DEBUG
-
5466  for (size_t _i = 0u; _i < _degree0.size(); ++_i)
-
5467  {
-
5468  if (_degree0[_i] != static_cast<int>(model->get_agents()[_i].get_n_neighbors()))
-
5469  throw std::logic_error("[epi-debug] Degree does not match afted rewire_degseq.");
-
5470  }
-
5471  #endif
-
5472 
-
5473  return;
-
5474 
-
5475 }
+
5441  // Only swap if needed
+
5442  epiworld_fast_uint N = non_isolates.size();
+
5443  epiworld_double prob;
+
5444  int nrewires = floor(proportion * nedges);
+
5445  while (nrewires-- > 0)
+
5446  {
+
5447 
+
5448  // Picking egos
+
5449  prob = model->runif();
+
5450  int id0 = N - 1;
+
5451  for (epiworld_fast_uint i = 0u; i < N; ++i)
+
5452  if (prob <= weights[i])
+
5453  {
+
5454  id0 = i;
+
5455  break;
+
5456  }
+
5457 
+
5458  prob = model->runif();
+
5459  int id1 = N - 1;
+
5460  for (epiworld_fast_uint i = 0u; i < N; ++i)
+
5461  if (prob <= weights[i])
+
5462  {
+
5463  id1 = i;
+
5464  break;
+
5465  }
+
5466 
+
5467  // Correcting for under or overflow.
+
5468  if (id1 == id0)
+
5469  id1++;
+
5470 
+
5471  if (id1 >= static_cast<int>(N))
+
5472  id1 = 0;
+
5473 
+
5474  Agent<TSeq> & p0 = agents->operator[](non_isolates[id0]);
+
5475  Agent<TSeq> & p1 = agents->operator[](non_isolates[id1]);
5476 
-
5477 template<typename TSeq>
-
5478 inline void rewire_degseq(
-
5479  AdjList * agents,
-
5480  Model<TSeq> * model,
-
5481  epiworld_double proportion
-
5482  )
-
5483 {
-
5484 
-
5485  // Identifying individuals with degree > 0
-
5486  std::vector< epiworld_fast_int > nties(agents->vcount(), 0);
-
5487 
-
5488  #ifdef EPI_DEBUG
-
5489  std::vector< int > _degree0(agents->vcount(), 0);
-
5490  for (size_t i = 0u; i < _degree0.size(); ++i)
-
5491  _degree0[i] = agents->get_dat()[i].size();
-
5492  #endif
-
5493 
-
5494  std::vector< epiworld_fast_uint > non_isolates;
-
5495  non_isolates.reserve(nties.size());
-
5496 
-
5497  std::vector< epiworld_double > weights;
-
5498  weights.reserve(nties.size());
-
5499 
-
5500  epiworld_double nedges = 0.0;
-
5501  auto & dat = agents->get_dat();
+
5477  // Picking alters (relative location in their lists)
+
5478  // In this case, these are uniformly distributed within the list
+
5479  int id01 = std::floor(p0.get_n_neighbors() * model->runif());
+
5480  int id11 = std::floor(p1.get_n_neighbors() * model->runif());
+
5481 
+
5482  // When rewiring, we need to flip the individuals from the other
+
5483  // end as well, since we are dealing withi an undirected graph
+
5484 
+
5485  // Finding what neighbour is id0
+
5486  model->get_agents()[id0].swap_neighbors(
+
5487  model->get_agents()[id1],
+
5488  id01,
+
5489  id11
+
5490  );
+
5491 
+
5492 
+
5493  }
+
5494 
+
5495  #ifdef EPI_DEBUG
+
5496  for (size_t _i = 0u; _i < _degree0.size(); ++_i)
+
5497  {
+
5498  if (_degree0[_i] != static_cast<int>(model->get_agents()[_i].get_n_neighbors()))
+
5499  throw std::logic_error("[epi-debug] Degree does not match afted rewire_degseq.");
+
5500  }
+
5501  #endif
5502 
-
5503  for (size_t i = 0u; i < dat.size(); ++i)
-
5504  nties[i] += dat[i].size();
-
5505 
-
5506  bool directed = agents->is_directed();
-
5507  for (size_t i = 0u; i < dat.size(); ++i)
-
5508  {
-
5509  if (nties[i] > 0)
-
5510  {
-
5511  non_isolates.push_back(i);
-
5512  if (directed)
-
5513  {
-
5514  weights.push_back(
-
5515  static_cast<epiworld_double>(nties[i])
-
5516  );
-
5517  nedges += static_cast<epiworld_double>(nties[i]);
-
5518  }
-
5519  else {
-
5520  weights.push_back(
-
5521  static_cast<epiworld_double>(nties[i])/2.0
-
5522  );
-
5523  nedges += static_cast<epiworld_double>(nties[i]) / 2.0;
-
5524  }
-
5525  }
-
5526  }
-
5527 
-
5528  if (non_isolates.size() == 0u)
-
5529  throw std::logic_error("The graph is completely disconnected.");
-
5530 
-
5531  // Cumulative probs
-
5532  weights[0u] /= nedges;
-
5533  for (epiworld_fast_uint i = 1u; i < non_isolates.size(); ++i)
-
5534  {
-
5535  weights[i] /= nedges;
-
5536  weights[i] += weights[i - 1u];
-
5537  }
-
5538 
-
5539  // Only swap if needed
-
5540  epiworld_fast_uint N = non_isolates.size();
-
5541  epiworld_double prob;
-
5542  int nrewires = floor(proportion * nedges / (
-
5543  agents->is_directed() ? 1.0 : 2.0
-
5544  ));
-
5545 
-
5546  while (nrewires-- > 0)
-
5547  {
-
5548 
-
5549  // Picking egos
-
5550  prob = model->runif();
-
5551  int id0 = N - 1;
-
5552  for (epiworld_fast_uint i = 0u; i < N; ++i)
-
5553  if (prob <= weights[i])
-
5554  {
-
5555  id0 = i;
-
5556  break;
-
5557  }
-
5558 
-
5559  prob = model->runif();
-
5560  int id1 = N - 1;
-
5561  for (epiworld_fast_uint i = 0u; i < N; ++i)
-
5562  if (prob <= weights[i])
-
5563  {
-
5564  id1 = i;
-
5565  break;
-
5566  }
-
5567 
-
5568  // Correcting for under or overflow.
-
5569  if (id1 == id0)
-
5570  id1++;
-
5571 
-
5572  if (id1 >= static_cast<int>(N))
-
5573  id1 = 0;
-
5574 
-
5575  std::map<int,int> & p0 = agents->get_dat()[non_isolates[id0]];
-
5576  std::map<int,int> & p1 = agents->get_dat()[non_isolates[id1]];
-
5577 
-
5578  // Picking alters (relative location in their lists)
-
5579  // In this case, these are uniformly distributed within the list
-
5580  int id01 = std::floor(p0.size() * model->runif());
-
5581  int id11 = std::floor(p1.size() * model->runif());
-
5582 
-
5583  // Since it is a map, we need to find the actual ids (positions)
-
5584  // are not good enough.
-
5585  int count = 0;
-
5586  for (auto & n : p0)
-
5587  if (count++ == id01)
-
5588  id01 = n.first;
-
5589 
-
5590  count = 0;
-
5591  for (auto & n : p1)
-
5592  if (count++ == id11)
-
5593  id11 = n.first;
-
5594 
-
5595  // When rewiring, we need to flip the individuals from the other
-
5596  // end as well, since we are dealing withi an undirected graph
-
5597 
-
5598  // Finding what neighbour is id0
-
5599  if (!agents->is_directed())
-
5600  {
+
5503  return;
+
5504 
+
5505 }
+
5506 
+
5507 template<typename TSeq>
+
5508 inline void rewire_degseq(
+
5509  AdjList * agents,
+
5510  Model<TSeq> * model,
+
5511  epiworld_double proportion
+
5512  )
+
5513 {
+
5514 
+
5515  // Identifying individuals with degree > 0
+
5516  std::vector< epiworld_fast_int > nties(agents->vcount(), 0);
+
5517 
+
5518  #ifdef EPI_DEBUG
+
5519  std::vector< int > _degree0(agents->vcount(), 0);
+
5520  for (size_t i = 0u; i < _degree0.size(); ++i)
+
5521  _degree0[i] = agents->get_dat()[i].size();
+
5522  #endif
+
5523 
+
5524  std::vector< epiworld_fast_uint > non_isolates;
+
5525  non_isolates.reserve(nties.size());
+
5526 
+
5527  std::vector< epiworld_double > weights;
+
5528  weights.reserve(nties.size());
+
5529 
+
5530  epiworld_double nedges = 0.0;
+
5531  auto & dat = agents->get_dat();
+
5532 
+
5533  for (size_t i = 0u; i < dat.size(); ++i)
+
5534  nties[i] += dat[i].size();
+
5535 
+
5536  bool directed = agents->is_directed();
+
5537  for (size_t i = 0u; i < dat.size(); ++i)
+
5538  {
+
5539  if (nties[i] > 0)
+
5540  {
+
5541  non_isolates.push_back(i);
+
5542  if (directed)
+
5543  {
+
5544  weights.push_back(
+
5545  static_cast<epiworld_double>(nties[i])
+
5546  );
+
5547  nedges += static_cast<epiworld_double>(nties[i]);
+
5548  }
+
5549  else {
+
5550  weights.push_back(
+
5551  static_cast<epiworld_double>(nties[i])/2.0
+
5552  );
+
5553  nedges += static_cast<epiworld_double>(nties[i]) / 2.0;
+
5554  }
+
5555  }
+
5556  }
+
5557 
+
5558  if (non_isolates.size() == 0u)
+
5559  throw std::logic_error("The graph is completely disconnected.");
+
5560 
+
5561  // Cumulative probs
+
5562  weights[0u] /= nedges;
+
5563  for (epiworld_fast_uint i = 1u; i < non_isolates.size(); ++i)
+
5564  {
+
5565  weights[i] /= nedges;
+
5566  weights[i] += weights[i - 1u];
+
5567  }
+
5568 
+
5569  // Only swap if needed
+
5570  epiworld_fast_uint N = non_isolates.size();
+
5571  epiworld_double prob;
+
5572  int nrewires = floor(proportion * nedges / (
+
5573  agents->is_directed() ? 1.0 : 2.0
+
5574  ));
+
5575 
+
5576  while (nrewires-- > 0)
+
5577  {
+
5578 
+
5579  // Picking egos
+
5580  prob = model->runif();
+
5581  int id0 = N - 1;
+
5582  for (epiworld_fast_uint i = 0u; i < N; ++i)
+
5583  if (prob <= weights[i])
+
5584  {
+
5585  id0 = i;
+
5586  break;
+
5587  }
+
5588 
+
5589  prob = model->runif();
+
5590  int id1 = N - 1;
+
5591  for (epiworld_fast_uint i = 0u; i < N; ++i)
+
5592  if (prob <= weights[i])
+
5593  {
+
5594  id1 = i;
+
5595  break;
+
5596  }
+
5597 
+
5598  // Correcting for under or overflow.
+
5599  if (id1 == id0)
+
5600  id1++;
5601 
-
5602  std::map<int,int> & p01 = agents->get_dat()[id01];
-
5603  std::map<int,int> & p11 = agents->get_dat()[id11];
+
5602  if (id1 >= static_cast<int>(N))
+
5603  id1 = 0;
5604 
-
5605  std::swap(p01[id0], p11[id1]);
-
5606 
-
5607  }
-
5608 
-
5609  // Moving alter first
-
5610  std::swap(p0[id01], p1[id11]);
-
5611 
-
5612  }
-
5613 
-
5614  #ifdef EPI_DEBUG
-
5615  for (size_t _i = 0u; _i < _degree0.size(); ++_i)
-
5616  {
-
5617  if (_degree0[_i] != static_cast<int>(agents->get_dat()[_i].size()))
-
5618  throw std::logic_error(
-
5619  "[epi-debug] Degree does not match afted rewire_degseq. " +
-
5620  std::string("Expected: ") +
-
5621  std::to_string(_degree0[_i]) +
-
5622  std::string(", observed: ") +
-
5623  std::to_string(agents->get_dat()[_i].size())
-
5624  );
-
5625  }
-
5626  #endif
-
5627 
-
5628 
-
5629  return;
-
5630 
-
5631 }
-
5632 
-
5633 template<typename TSeq>
-
5634 inline AdjList rgraph_bernoulli(
-
5635  epiworld_fast_uint n,
-
5636  epiworld_double p,
-
5637  bool directed,
-
5638  Model<TSeq> & model
-
5639 ) {
-
5640 
-
5641  std::vector< int > source;
-
5642  std::vector< int > target;
+
5605  std::map<int,int> & p0 = agents->get_dat()[non_isolates[id0]];
+
5606  std::map<int,int> & p1 = agents->get_dat()[non_isolates[id1]];
+
5607 
+
5608  // Picking alters (relative location in their lists)
+
5609  // In this case, these are uniformly distributed within the list
+
5610  int id01 = std::floor(p0.size() * model->runif());
+
5611  int id11 = std::floor(p1.size() * model->runif());
+
5612 
+
5613  // Since it is a map, we need to find the actual ids (positions)
+
5614  // are not good enough.
+
5615  int count = 0;
+
5616  for (auto & n : p0)
+
5617  if (count++ == id01)
+
5618  id01 = n.first;
+
5619 
+
5620  count = 0;
+
5621  for (auto & n : p1)
+
5622  if (count++ == id11)
+
5623  id11 = n.first;
+
5624 
+
5625  // When rewiring, we need to flip the individuals from the other
+
5626  // end as well, since we are dealing withi an undirected graph
+
5627 
+
5628  // Finding what neighbour is id0
+
5629  if (!agents->is_directed())
+
5630  {
+
5631 
+
5632  std::map<int,int> & p01 = agents->get_dat()[id01];
+
5633  std::map<int,int> & p11 = agents->get_dat()[id11];
+
5634 
+
5635  std::swap(p01[id0], p11[id1]);
+
5636 
+
5637  }
+
5638 
+
5639  // Moving alter first
+
5640  std::swap(p0[id01], p1[id11]);
+
5641 
+
5642  }
5643 
-
5644  // Checking the density (how many)
-
5645  std::binomial_distribution<> d(
-
5646  n * (n - 1.0) / (directed ? 1.0 : 2.0),
-
5647  p
-
5648  );
-
5649 
-
5650  epiworld_fast_uint m = d(model.get_rand_endgine());
-
5651 
-
5652  source.resize(m);
-
5653  target.resize(m);
-
5654 
-
5655  epiworld_fast_uint a,b;
-
5656  for (epiworld_fast_uint i = 0u; i < m; ++i)
-
5657  {
-
5658  a = floor(model.runif() * n);
-
5659 
-
5660  if (!directed)
-
5661  b = floor(model.runif() * a);
-
5662  else
-
5663  {
-
5664  b = floor(model.runif() * n);
-
5665  if (b == a)
-
5666  b++;
-
5667 
-
5668  if (b >= n)
-
5669  b = 0u;
-
5670  }
-
5671 
-
5672  source[i] = static_cast<int>(a);
-
5673  target[i] = static_cast<int>(b);
-
5674 
-
5675  }
-
5676 
-
5677  AdjList al(source, target, static_cast<int>(n), directed);
-
5678 
-
5679  return al;
-
5680 
-
5681 }
-
5682 
-
5683 template<typename TSeq>
-
5684 inline AdjList rgraph_bernoulli2(
-
5685  epiworld_fast_uint n,
-
5686  epiworld_double p,
-
5687  bool directed,
-
5688  Model<TSeq> & model
-
5689 ) {
-
5690 
-
5691  std::vector< int > source;
-
5692  std::vector< int > target;
-
5693 
-
5694  // Checking the density (how many)
-
5695  std::binomial_distribution<> d(
-
5696  n * (n - 1.0) / (directed ? 1.0 : 2.0),
-
5697  p
-
5698  );
-
5699 
-
5700  // Need to compensate for the possible number of diagonal
-
5701  // elements sampled. If n * n, then each diag element has
-
5702  // 1/(n^2) chance of sampling
-
5703 
-
5704  epiworld_fast_uint m = d(model.get_rand_endgine());
-
5705 
-
5706  source.resize(m);
-
5707  target.resize(m);
+
5644  #ifdef EPI_DEBUG
+
5645  for (size_t _i = 0u; _i < _degree0.size(); ++_i)
+
5646  {
+
5647  if (_degree0[_i] != static_cast<int>(agents->get_dat()[_i].size()))
+
5648  throw std::logic_error(
+
5649  "[epi-debug] Degree does not match afted rewire_degseq. " +
+
5650  std::string("Expected: ") +
+
5651  std::to_string(_degree0[_i]) +
+
5652  std::string(", observed: ") +
+
5653  std::to_string(agents->get_dat()[_i].size())
+
5654  );
+
5655  }
+
5656  #endif
+
5657 
+
5658 
+
5659  return;
+
5660 
+
5661 }
+
5662 
+
5663 template<typename TSeq>
+
5664 inline AdjList rgraph_bernoulli(
+
5665  epiworld_fast_uint n,
+
5666  epiworld_double p,
+
5667  bool directed,
+
5668  Model<TSeq> & model
+
5669 ) {
+
5670 
+
5671  std::vector< int > source;
+
5672  std::vector< int > target;
+
5673 
+
5674  // Checking the density (how many)
+
5675  std::binomial_distribution<> d(
+
5676  n * (n - 1.0) / (directed ? 1.0 : 2.0),
+
5677  p
+
5678  );
+
5679 
+
5680  epiworld_fast_uint m = d(model.get_rand_endgine());
+
5681 
+
5682  source.resize(m);
+
5683  target.resize(m);
+
5684 
+
5685  epiworld_fast_uint a,b;
+
5686  for (epiworld_fast_uint i = 0u; i < m; ++i)
+
5687  {
+
5688  a = floor(model.runif() * n);
+
5689 
+
5690  if (!directed)
+
5691  b = floor(model.runif() * a);
+
5692  else
+
5693  {
+
5694  b = floor(model.runif() * n);
+
5695  if (b == a)
+
5696  b++;
+
5697 
+
5698  if (b >= n)
+
5699  b = 0u;
+
5700  }
+
5701 
+
5702  source[i] = static_cast<int>(a);
+
5703  target[i] = static_cast<int>(b);
+
5704 
+
5705  }
+
5706 
+
5707  AdjList al(source, target, static_cast<int>(n), directed);
5708 
-
5709  double n2 = static_cast<double>(n * n);
-
5710 
-
5711  int loc,row,col;
-
5712  for (epiworld_fast_uint i = 0u; i < m; ++i)
-
5713  {
-
5714  loc = floor(model.runif() * n2);
-
5715  col = floor(static_cast<double>(loc)/static_cast<double>(n));
-
5716  row = loc - row * n;
-
5717 
-
5718  // Undirected needs to swap
-
5719  if (!directed && (col > row))
-
5720  std::swap(col, row);
-
5721 
-
5722  source[i] = row;
-
5723  target[i] = col;
-
5724 
-
5725  }
-
5726 
-
5727  AdjList al(source, target, static_cast<int>(n), directed);
-
5728 
-
5729  return al;
-
5730 
-
5731 }
-
5732 
-
5733 inline AdjList rgraph_ring_lattice(
-
5734  epiworld_fast_uint n,
-
5735  epiworld_fast_uint k,
-
5736  bool directed = false
-
5737 ) {
+
5709  return al;
+
5710 
+
5711 }
+
5712 
+
5713 template<typename TSeq>
+
5714 inline AdjList rgraph_bernoulli2(
+
5715  epiworld_fast_uint n,
+
5716  epiworld_double p,
+
5717  bool directed,
+
5718  Model<TSeq> & model
+
5719 ) {
+
5720 
+
5721  std::vector< int > source;
+
5722  std::vector< int > target;
+
5723 
+
5724  // Checking the density (how many)
+
5725  std::binomial_distribution<> d(
+
5726  n * (n - 1.0) / (directed ? 1.0 : 2.0),
+
5727  p
+
5728  );
+
5729 
+
5730  // Need to compensate for the possible number of diagonal
+
5731  // elements sampled. If n * n, then each diag element has
+
5732  // 1/(n^2) chance of sampling
+
5733 
+
5734  epiworld_fast_uint m = d(model.get_rand_endgine());
+
5735 
+
5736  source.resize(m);
+
5737  target.resize(m);
5738 
-
5739  if ((n - 1u) < k)
-
5740  throw std::logic_error("k can be at most n - 1.");
-
5741 
-
5742  std::vector< int > source;
-
5743  std::vector< int > target;
-
5744 
-
5745  if (!directed)
-
5746  if (k > 1u) k = static_cast< size_t >(floor(k / 2.0));
+
5739  double n2 = static_cast<double>(n * n);
+
5740 
+
5741  int loc,row,col;
+
5742  for (epiworld_fast_uint i = 0u; i < m; ++i)
+
5743  {
+
5744  loc = floor(model.runif() * n2);
+
5745  col = floor(static_cast<double>(loc)/static_cast<double>(n));
+
5746  row = loc - row * n;
5747 
-
5748  for (size_t i = 0; i < n; ++i)
-
5749  {
-
5750 
-
5751  for (size_t j = 1u; j <= k; ++j)
-
5752  {
-
5753 
-
5754  // Next neighbor
-
5755  size_t l = i + j;
-
5756  if (l >= n) l = l - n;
-
5757 
-
5758  source.push_back(i);
-
5759  target.push_back(l);
-
5760 
-
5761  }
+
5748  // Undirected needs to swap
+
5749  if (!directed && (col > row))
+
5750  std::swap(col, row);
+
5751 
+
5752  source[i] = row;
+
5753  target[i] = col;
+
5754 
+
5755  }
+
5756 
+
5757  AdjList al(source, target, static_cast<int>(n), directed);
+
5758 
+
5759  return al;
+
5760 
+
5761 }
5762 
-
5763  }
-
5764 
-
5765  return AdjList(source, target, n, directed);
-
5766 
-
5767 }
+
5763 inline AdjList rgraph_ring_lattice(
+
5764  epiworld_fast_uint n,
+
5765  epiworld_fast_uint k,
+
5766  bool directed = false
+
5767 ) {
5768 
-
5780 template<typename TSeq>
-
5781 inline AdjList rgraph_smallworld(
-
5782  epiworld_fast_uint n,
-
5783  epiworld_fast_uint k,
-
5784  epiworld_double p,
-
5785  bool directed,
-
5786  Model<TSeq> & model
-
5787 ) {
-
5788 
-
5789  // Creating the ring lattice
-
5790  AdjList ring = rgraph_ring_lattice(n,k,directed);
-
5791 
-
5792  // Rewiring and returning
-
5793  if (k > 0u)
-
5794  rewire_degseq(&ring, &model, p);
-
5795 
-
5796  return ring;
-
5797 
-
5798 }
-
5799 
-
5813 template<typename TSeq>
-
5814 inline AdjList rgraph_blocked(
-
5815  epiworld_fast_uint n,
-
5816  epiworld_fast_uint blocksize,
-
5817  epiworld_fast_uint ncons,
-
5818  Model<TSeq>&
-
5819 ) {
-
5820 
-
5821  std::vector< int > source_;
-
5822  std::vector< int > target_;
-
5823 
-
5824  size_t i = 0u;
-
5825  size_t cum_node_count = 0u;
-
5826  while (i < n)
-
5827  {
-
5828 
-
5829  for (size_t j = 0; j < blocksize; ++j)
-
5830  {
-
5831 
-
5832  for (size_t k = 0; k < j; ++k)
-
5833  {
-
5834  // No loops
-
5835  if (k == j)
-
5836  continue;
-
5837 
-
5838  // Exists the loop in case there are no more
-
5839  // nodes available
-
5840  if ((i + k) >= n)
-
5841  break;
-
5842 
-
5843  source_.push_back(static_cast<int>(j + i));
-
5844  target_.push_back(static_cast<int>(k + i));
-
5845  }
-
5846 
-
5847  // No more nodes left to build connections
-
5848  if (++cum_node_count >= n)
-
5849  break;
-
5850 
-
5851  }
-
5852 
-
5853  // Connections between this and the previou sone
-
5854  if (i != 0)
-
5855  {
-
5856 
-
5857  size_t max_cons = std::min(ncons, n - cum_node_count);
+
5769  if ((n - 1u) < k)
+
5770  throw std::logic_error("k can be at most n - 1.");
+
5771 
+
5772  std::vector< int > source;
+
5773  std::vector< int > target;
+
5774 
+
5775  if (!directed)
+
5776  if (k > 1u) k = static_cast< size_t >(floor(k / 2.0));
+
5777 
+
5778  for (size_t i = 0; i < n; ++i)
+
5779  {
+
5780 
+
5781  for (size_t j = 1u; j <= k; ++j)
+
5782  {
+
5783 
+
5784  // Next neighbor
+
5785  size_t l = i + j;
+
5786  if (l >= n) l = l - n;
+
5787 
+
5788  source.push_back(i);
+
5789  target.push_back(l);
+
5790 
+
5791  }
+
5792 
+
5793  }
+
5794 
+
5795  return AdjList(source, target, n, directed);
+
5796 
+
5797 }
+
5798 
+
5810 template<typename TSeq>
+
5811 inline AdjList rgraph_smallworld(
+
5812  epiworld_fast_uint n,
+
5813  epiworld_fast_uint k,
+
5814  epiworld_double p,
+
5815  bool directed,
+
5816  Model<TSeq> & model
+
5817 ) {
+
5818 
+
5819  // Creating the ring lattice
+
5820  AdjList ring = rgraph_ring_lattice(n,k,directed);
+
5821 
+
5822  // Rewiring and returning
+
5823  if (k > 0u)
+
5824  rewire_degseq(&ring, &model, p);
+
5825 
+
5826  return ring;
+
5827 
+
5828 }
+
5829 
+
5843 template<typename TSeq>
+
5844 inline AdjList rgraph_blocked(
+
5845  epiworld_fast_uint n,
+
5846  epiworld_fast_uint blocksize,
+
5847  epiworld_fast_uint ncons,
+
5848  Model<TSeq>&
+
5849 ) {
+
5850 
+
5851  std::vector< int > source_;
+
5852  std::vector< int > target_;
+
5853 
+
5854  size_t i = 0u;
+
5855  size_t cum_node_count = 0u;
+
5856  while (i < n)
+
5857  {
5858 
-
5859  // Generating the connections
-
5860  for (size_t j = 0u; j < max_cons; ++j)
-
5861  {
-
5862 
-
5863  source_.push_back(static_cast<int>(i + j - blocksize));
-
5864  target_.push_back(static_cast<int>(i + j));
-
5865 
-
5866  }
-
5867  }
-
5868 
-
5869  i += blocksize;
-
5870 
-
5871  }
-
5872 
-
5873  return AdjList(source_, target_, n, false);
-
5874 
-
5875 }
+
5859  for (size_t j = 0; j < blocksize; ++j)
+
5860  {
+
5861 
+
5862  for (size_t k = 0; k < j; ++k)
+
5863  {
+
5864  // No loops
+
5865  if (k == j)
+
5866  continue;
+
5867 
+
5868  // Exists the loop in case there are no more
+
5869  // nodes available
+
5870  if ((i + k) >= n)
+
5871  break;
+
5872 
+
5873  source_.push_back(static_cast<int>(j + i));
+
5874  target_.push_back(static_cast<int>(k + i));
+
5875  }
5876 
-
5877 #endif
-
5878 /*//////////////////////////////////////////////////////////////////////////////
-
5880 
-
5881  End of -include/epiworld/randgraph.hpp-
+
5877  // No more nodes left to build connections
+
5878  if (++cum_node_count >= n)
+
5879  break;
+
5880 
+
5881  }
5882 
-
5885 
+
5883  // Connections between this and the previou sone
+
5884  if (i != 0)
+
5885  {
5886 
-
5887 
-
5888 /*//////////////////////////////////////////////////////////////////////////////
-
5890 
-
5891  Start of -include/epiworld/queue-bones.hpp-
+
5887  size_t max_cons = std::min(ncons, n - cum_node_count);
+
5888 
+
5889  // Generating the connections
+
5890  for (size_t j = 0u; j < max_cons; ++j)
+
5891  {
5892 
+
5893  source_.push_back(static_cast<int>(i + j - blocksize));
+
5894  target_.push_back(static_cast<int>(i + j));
5895 
-
5896 
-
5897 #ifndef EPIWORLD_QUEUE_BONES_HPP
-
5898 #define EPIWORLD_QUEUE_BONES_HPP
-
5899 
-
5910 template<typename TSeq>
-
5911 class Queue
-
5912 {
-
5913  friend class Model<TSeq>;
-
5914 
-
5915 private:
+
5896  }
+
5897  }
+
5898 
+
5899  i += blocksize;
+
5900 
+
5901  }
+
5902 
+
5903  return AdjList(source_, target_, n, false);
+
5904 
+
5905 }
+
5906 
+
5907 #endif
+
5908 /*//////////////////////////////////////////////////////////////////////////////
+
5910 
+
5911  End of -include/epiworld/randgraph.hpp-
+
5912 
+
5915 
5916 
-
5920  std::vector< epiworld_fast_int > active;
-
5921  Model<TSeq> * model = nullptr;
-
5922  int n_in_queue = 0;
-
5923 
-
5924  // Auxiliary variable that checks how many steps
-
5925  // left are there
-
5926  // int n_steps_left;
-
5927  // bool queuing_started = false;
-
5928 
-
5929 public:
-
5930 
-
5931  void operator+=(Agent<TSeq> * p);
-
5932  void operator-=(Agent<TSeq> * p);
-
5933  epiworld_fast_int & operator[](epiworld_fast_uint i);
-
5934 
-
5935  // void initialize(Model<TSeq> * m, Agent<TSeq> * p);
-
5936  void reset();
-
5937 
-
5938  bool operator==(const Queue<TSeq> & other) const;
-
5939  bool operator!=(const Queue<TSeq> & other) const {return !operator==(other);};
-
5940 
-
5941  static const int NoOne = 0;
-
5942  static const int OnlySelf = 1;
-
5943  static const int Everyone = 2;
+
5917 
+
5918 /*//////////////////////////////////////////////////////////////////////////////
+
5920 
+
5921  Start of -include/epiworld/queue-bones.hpp-
+
5922 
+
5925 
+
5926 
+
5927 #ifndef EPIWORLD_QUEUE_BONES_HPP
+
5928 #define EPIWORLD_QUEUE_BONES_HPP
+
5929 
+
5940 template<typename TSeq>
+
5941 class Queue
+
5942 {
+
5943  friend class Model<TSeq>;
5944 
-
5945 };
+
5945 private:
5946 
-
5947 template<typename TSeq>
-
5948 inline void Queue<TSeq>::operator+=(Agent<TSeq> * p)
-
5949 {
-
5950 
-
5951  if (++active[p->id] == 1)
-
5952  n_in_queue++;
+
5950  std::vector< epiworld_fast_int > active;
+
5951  Model<TSeq> * model = nullptr;
+
5952  int n_in_queue = 0;
5953 
-
5954  for (auto n : p->neighbors)
-
5955  {
-
5956 
-
5957  if (++active[n] == 1)
-
5958  n_in_queue++;
-
5959 
-
5960  }
-
5961 
-
5962 }
-
5963 
-
5964 template<typename TSeq>
-
5965 inline void Queue<TSeq>::operator-=(Agent<TSeq> * p)
-
5966 {
+
5954  // Auxiliary variable that checks how many steps
+
5955  // left are there
+
5956  // int n_steps_left;
+
5957  // bool queuing_started = false;
+
5958 
+
5959 public:
+
5960 
+
5961  void operator+=(Agent<TSeq> * p);
+
5962  void operator-=(Agent<TSeq> * p);
+
5963  epiworld_fast_int & operator[](epiworld_fast_uint i);
+
5964 
+
5965  // void initialize(Model<TSeq> * m, Agent<TSeq> * p);
+
5966  void reset();
5967 
-
5968  if (--active[p->id] == 0)
-
5969  n_in_queue--;
+
5968  bool operator==(const Queue<TSeq> & other) const;
+
5969  bool operator!=(const Queue<TSeq> & other) const {return !operator==(other);};
5970 
-
5971  for (auto n : p->neighbors)
-
5972  {
-
5973  if (--active[n] == 0)
-
5974  n_in_queue--;
-
5975  }
+
5971  static const int NoOne = 0;
+
5972  static const int OnlySelf = 1;
+
5973  static const int Everyone = 2;
+
5974 
+
5975 };
5976 
-
5977 }
-
5978 
-
5979 template<typename TSeq>
-
5980 inline epiworld_fast_int & Queue<TSeq>::operator[](epiworld_fast_uint i)
-
5981 {
-
5982  return active[i];
-
5983 }
-
5984 
-
5985 template<typename TSeq>
-
5986 inline void Queue<TSeq>::reset()
-
5987 {
-
5988 
-
5989  if (n_in_queue)
-
5990  {
+
5977 template<typename TSeq>
+
5978 inline void Queue<TSeq>::operator+=(Agent<TSeq> * p)
+
5979 {
+
5980 
+
5981  if (++active[p->id] == 1)
+
5982  n_in_queue++;
+
5983 
+
5984  for (auto n : p->neighbors)
+
5985  {
+
5986 
+
5987  if (++active[n] == 1)
+
5988  n_in_queue++;
+
5989 
+
5990  }
5991 
-
5992  for (auto & q : this->active)
-
5993  q = 0;
-
5994 
-
5995  n_in_queue = 0;
-
5996 
-
5997  }
-
5998 
-
5999  active.resize(model->size(), 0);
+
5992 }
+
5993 
+
5994 template<typename TSeq>
+
5995 inline void Queue<TSeq>::operator-=(Agent<TSeq> * p)
+
5996 {
+
5997 
+
5998  if (--active[p->id] == 0)
+
5999  n_in_queue--;
6000 
-
6001 }
-
6002 
-
6003 template<typename TSeq>
-
6004 inline bool Queue<TSeq>::operator==(const Queue<TSeq> & other) const
-
6005 {
-
6006  if (active.size() != other.active.size())
-
6007  return false;
+
6001  for (auto n : p->neighbors)
+
6002  {
+
6003  if (--active[n] == 0)
+
6004  n_in_queue--;
+
6005  }
+
6006 
+
6007 }
6008 
-
6009  for (size_t i = 0u; i < active.size(); ++i)
-
6010  {
-
6011  if (active[i] != other.active[i])
-
6012  return false;
-
6013  }
+
6009 template<typename TSeq>
+
6010 inline epiworld_fast_int & Queue<TSeq>::operator[](epiworld_fast_uint i)
+
6011 {
+
6012  return active[i];
+
6013 }
6014 
-
6015  return true;
-
6016 }
-
6017 
-
6018 #endif
-
6019 /*//////////////////////////////////////////////////////////////////////////////
+
6015 template<typename TSeq>
+
6016 inline void Queue<TSeq>::reset()
+
6017 {
+
6018 
+
6019  if (n_in_queue)
+
6020  {
6021 
-
6022  End of -include/epiworld/queue-bones.hpp-
-
6023 
-
6026 
-
6027 
+
6022  for (auto & q : this->active)
+
6023  q = 0;
+
6024 
+
6025  n_in_queue = 0;
+
6026 
+
6027  }
6028 
-
6029 /*//////////////////////////////////////////////////////////////////////////////
-
6031 
-
6032  Start of -include/epiworld/globalevent-bones.hpp-
-
6033 
-
6036 
-
6037 
-
6038 #ifndef EPIWORLD_GLOBALEVENT_BONES_HPP
-
6039 #define EPIWORLD_GLOBALEVENT_BONES_HPP
-
6040 
-
6041 // template<typename TSeq = EPI_DEFAULT_TSEQ>
-
6042 // using GlobalFun = std::function<void(Model<TSeq>*)>;
-
6043 
-
6050 template<typename TSeq>
-
6051 class GlobalEvent
-
6052 {
-
6053 private:
-
6054  GlobalFun<TSeq> fun = nullptr;
-
6055  std::string name = "A global action";
-
6056  int day = -99;
-
6057 public:
+
6029  active.resize(model->size(), 0);
+
6030 
+
6031 }
+
6032 
+
6033 template<typename TSeq>
+
6034 inline bool Queue<TSeq>::operator==(const Queue<TSeq> & other) const
+
6035 {
+
6036  if (active.size() != other.active.size())
+
6037  return false;
+
6038 
+
6039  for (size_t i = 0u; i < active.size(); ++i)
+
6040  {
+
6041  if (active[i] != other.active[i])
+
6042  return false;
+
6043  }
+
6044 
+
6045  return true;
+
6046 }
+
6047 
+
6048 #endif
+
6049 /*//////////////////////////////////////////////////////////////////////////////
+
6051 
+
6052  End of -include/epiworld/queue-bones.hpp-
+
6053 
+
6056 
+
6057 
6058 
-
6059  GlobalEvent() {};
-
6060 
-
6068  GlobalEvent(GlobalFun<TSeq> fun, std::string name, int day = -99);
-
6069 
-
6070  ~GlobalEvent() {};
-
6071 
-
6072  void operator()(Model<TSeq> * m, int day);
+
6059 /*//////////////////////////////////////////////////////////////////////////////
+
6061 
+
6062  Start of -include/epiworld/globalevent-bones.hpp-
+
6063 
+
6066 
+
6067 
+
6068 #ifndef EPIWORLD_GLOBALEVENT_BONES_HPP
+
6069 #define EPIWORLD_GLOBALEVENT_BONES_HPP
+
6070 
+
6071 // template<typename TSeq = EPI_DEFAULT_TSEQ>
+
6072 // using GlobalFun = std::function<void(Model<TSeq>*)>;
6073 
-
6074  void set_name(std::string name);
-
6075  std::string get_name() const;
-
6076 
-
6077  void set_day(int day);
-
6078  int get_day() const;
-
6079 
-
6080  void print() const;
-
6081 
-
6082  // Comparison operators
-
6083  bool operator==(const GlobalEvent<TSeq> & other) const;
-
6084  bool operator!=(const GlobalEvent<TSeq> & other) const;
-
6085 
-
6086 };
-
6087 
+
6080 template<typename TSeq>
+
6081 class GlobalEvent
+
6082 {
+
6083 private:
+
6084  GlobalFun<TSeq> fun = nullptr;
+
6085  std::string name = "A global action";
+
6086  int day = -99;
+
6087 public:
6088 
-
6089 
-
6090 #endif
-
6091 /*//////////////////////////////////////////////////////////////////////////////
-
6093 
-
6094  End of -include/epiworld/globalevent-bones.hpp-
-
6095 
-
6098 
-
6099 
-
6100 /*//////////////////////////////////////////////////////////////////////////////
-
6102 
-
6103  Start of -include/epiworld/globalevent-meat.hpp-
-
6104 
-
6107 
-
6108 
-
6109 #ifndef EPIWORLD_GLOBALEVENT_MEAT_HPP
-
6110 #define EPIWORLD_GLOBALEVENT_MEAT_HPP
+
6089  GlobalEvent() {};
+
6090 
+
6098  GlobalEvent(GlobalFun<TSeq> fun, std::string name, int day = -99);
+
6099 
+
6100  ~GlobalEvent() {};
+
6101 
+
6102  void operator()(Model<TSeq> * m, int day);
+
6103 
+
6104  void set_name(std::string name);
+
6105  std::string get_name() const;
+
6106 
+
6107  void set_day(int day);
+
6108  int get_day() const;
+
6109 
+
6110  void print() const;
6111 
-
6112 template<typename TSeq>
-
6113 inline GlobalEvent<TSeq>::GlobalEvent(
-
6114  GlobalFun<TSeq> fun,
-
6115  std::string name,
-
6116  int day
-
6117  )
-
6118 {
-
6119  this->fun = fun;
-
6120  this->name = name;
-
6121  this->day = day;
-
6122 }
+
6112  // Comparison operators
+
6113  bool operator==(const GlobalEvent<TSeq> & other) const;
+
6114  bool operator!=(const GlobalEvent<TSeq> & other) const;
+
6115 
+
6116 };
+
6117 
+
6118 
+
6119 
+
6120 #endif
+
6121 /*//////////////////////////////////////////////////////////////////////////////
6123 
-
6124 template<typename TSeq>
-
6125 inline void GlobalEvent<TSeq>::operator()(Model<TSeq> * m, int day)
-
6126 {
-
6127 
-
6128  if (this->fun == nullptr)
-
6129  return;
-
6130 
-
6131  // events apply if day is negative or if day is equal to the day of the action
-
6132  if (this->day < 0 || this->day == day)
-
6133  this->fun(m);
-
6134 
-
6135  return;
-
6136 
-
6137 }
+
6124  End of -include/epiworld/globalevent-bones.hpp-
+
6125 
+
6128 
+
6129 
+
6130 /*//////////////////////////////////////////////////////////////////////////////
+
6132 
+
6133  Start of -include/epiworld/globalevent-meat.hpp-
+
6134 
+
6137 
6138 
-
6139 template<typename TSeq>
-
6140 inline void GlobalEvent<TSeq>::set_name(std::string name)
-
6141 {
-
6142  this->name = name;
-
6143 }
-
6144 
-
6145 template<typename TSeq>
-
6146 inline std::string GlobalEvent<TSeq>::get_name() const
-
6147 {
-
6148  return this->name;
-
6149 }
-
6150 
-
6151 template<typename TSeq>
-
6152 inline void GlobalEvent<TSeq>::set_day(int day)
-
6153 {
-
6154  this->day = day;
-
6155 }
-
6156 
-
6157 template<typename TSeq>
-
6158 inline int GlobalEvent<TSeq>::get_day() const
-
6159 {
-
6160  return this->day;
-
6161 }
-
6162 
-
6163 template<typename TSeq>
-
6164 inline void GlobalEvent<TSeq>::print() const
-
6165 {
-
6166  printf_epiworld(
-
6167  "Global action: %s\n"
-
6168  " - Day: %i\n",
-
6169  this->name.c_str(),
-
6170  this->day
-
6171  );
-
6172 }
-
6173 
-
6174 template<typename TSeq>
-
6175 inline bool GlobalEvent<TSeq>::operator==(const GlobalEvent<TSeq> & other) const
-
6176 {
-
6177  return (this->name == other.name) && (this->day == other.day);
-
6178 }
-
6179 
-
6180 template<typename TSeq>
-
6181 inline bool GlobalEvent<TSeq>::operator!=(const GlobalEvent<TSeq> & other) const
-
6182 {
-
6183  return !(*this == other);
-
6184 }
-
6185 
-
6186 #endif
-
6187 /*//////////////////////////////////////////////////////////////////////////////
-
6189 
-
6190  End of -include/epiworld/globalevent-meat.hpp-
-
6191 
-
6194 
-
6195 
-
6196 
-
6197 /*//////////////////////////////////////////////////////////////////////////////
-
6199 
-
6200  Start of -include/epiworld/model-bones.hpp-
-
6201 
-
6204 
-
6205 
-
6206 #ifndef EPIWORLD_MODEL_HPP
-
6207 #define EPIWORLD_MODEL_HPP
-
6208 
-
6209 template<typename TSeq>
-
6210 class Agent;
-
6211 
-
6212 template<typename TSeq>
-
6213 class AgentsSample;
-
6214 
-
6215 template<typename TSeq>
-
6216 class Virus;
-
6217 
-
6218 template<typename TSeq>
-
6219 class Viruses;
-
6220 
-
6221 template<typename TSeq>
-
6222 class Viruses_const;
-
6223 
-
6224 template<typename TSeq>
-
6225 class Tool;
+
6139 #ifndef EPIWORLD_GLOBALEVENT_MEAT_HPP
+
6140 #define EPIWORLD_GLOBALEVENT_MEAT_HPP
+
6141 
+
6142 template<typename TSeq>
+
6143 inline GlobalEvent<TSeq>::GlobalEvent(
+
6144  GlobalFun<TSeq> fun,
+
6145  std::string name,
+
6146  int day
+
6147  )
+
6148 {
+
6149  this->fun = fun;
+
6150  this->name = name;
+
6151  this->day = day;
+
6152 }
+
6153 
+
6154 template<typename TSeq>
+
6155 inline void GlobalEvent<TSeq>::operator()(Model<TSeq> * m, int day)
+
6156 {
+
6157 
+
6158  if (this->fun == nullptr)
+
6159  return;
+
6160 
+
6161  // events apply if day is negative or if day is equal to the day of the action
+
6162  if (this->day < 0 || this->day == day)
+
6163  this->fun(m);
+
6164 
+
6165  return;
+
6166 
+
6167 }
+
6168 
+
6169 template<typename TSeq>
+
6170 inline void GlobalEvent<TSeq>::set_name(std::string name)
+
6171 {
+
6172  this->name = name;
+
6173 }
+
6174 
+
6175 template<typename TSeq>
+
6176 inline std::string GlobalEvent<TSeq>::get_name() const
+
6177 {
+
6178  return this->name;
+
6179 }
+
6180 
+
6181 template<typename TSeq>
+
6182 inline void GlobalEvent<TSeq>::set_day(int day)
+
6183 {
+
6184  this->day = day;
+
6185 }
+
6186 
+
6187 template<typename TSeq>
+
6188 inline int GlobalEvent<TSeq>::get_day() const
+
6189 {
+
6190  return this->day;
+
6191 }
+
6192 
+
6193 template<typename TSeq>
+
6194 inline void GlobalEvent<TSeq>::print() const
+
6195 {
+
6196  printf_epiworld(
+
6197  "Global action: %s\n"
+
6198  " - Day: %i\n",
+
6199  this->name.c_str(),
+
6200  this->day
+
6201  );
+
6202 }
+
6203 
+
6204 template<typename TSeq>
+
6205 inline bool GlobalEvent<TSeq>::operator==(const GlobalEvent<TSeq> & other) const
+
6206 {
+
6207  return (this->name == other.name) && (this->day == other.day);
+
6208 }
+
6209 
+
6210 template<typename TSeq>
+
6211 inline bool GlobalEvent<TSeq>::operator!=(const GlobalEvent<TSeq> & other) const
+
6212 {
+
6213  return !(*this == other);
+
6214 }
+
6215 
+
6216 #endif
+
6217 /*//////////////////////////////////////////////////////////////////////////////
+
6219 
+
6220  End of -include/epiworld/globalevent-meat.hpp-
+
6221 
+
6224 
+
6225 
6226 
-
6227 class AdjList;
-
6228 
-
6229 template<typename TSeq>
-
6230 class DataBase;
+
6227 /*//////////////////////////////////////////////////////////////////////////////
+
6229 
+
6230  Start of -include/epiworld/model-bones.hpp-
6231 
-
6232 template<typename TSeq>
-
6233 class Queue;
6234 
-
6235 template<typename TSeq>
-
6236 struct Event;
-
6237 
-
6238 template<typename TSeq>
-
6239 class GlobalEvent;
-
6240 
-
6241 template<typename TSeq>
-
6242 inline epiworld_double susceptibility_reduction_mixer_default(
-
6243  Agent<TSeq>* p,
-
6244  VirusPtr<TSeq> v,
-
6245  Model<TSeq>* m
-
6246  );
-
6247 template<typename TSeq>
-
6248 inline epiworld_double transmission_reduction_mixer_default(
-
6249  Agent<TSeq>* p,
-
6250  VirusPtr<TSeq> v,
-
6251  Model<TSeq>* m
-
6252  );
-
6253 template<typename TSeq>
-
6254 inline epiworld_double recovery_enhancer_mixer_default(
-
6255  Agent<TSeq>* p,
-
6256  VirusPtr<TSeq> v,
-
6257  Model<TSeq>* m
-
6258  );
+
6235 
+
6236 #ifndef EPIWORLD_MODEL_HPP
+
6237 #define EPIWORLD_MODEL_HPP
+
6238 
+
6239 template<typename TSeq>
+
6240 class Agent;
+
6241 
+
6242 template<typename TSeq>
+
6243 class AgentsSample;
+
6244 
+
6245 template<typename TSeq>
+
6246 class Virus;
+
6247 
+
6248 template<typename TSeq>
+
6249 class Viruses;
+
6250 
+
6251 template<typename TSeq>
+
6252 class Viruses_const;
+
6253 
+
6254 template<typename TSeq>
+
6255 class Tool;
+
6256 
+
6257 class AdjList;
+
6258 
6259 template<typename TSeq>
-
6260 inline epiworld_double death_reduction_mixer_default(
-
6261  Agent<TSeq>* p,
-
6262  VirusPtr<TSeq> v,
-
6263  Model<TSeq>* m
-
6264  );
-
6265 
-
6266 template<typename TSeq>
-
6267 inline std::function<void(size_t,Model<TSeq>*)> make_save_run(
-
6268  std::string fmt = "%03lu-episimulation.csv",
-
6269  bool total_hist = true,
-
6270  bool virus_info = false,
-
6271  bool virus_hist = false,
-
6272  bool tool_info = false,
-
6273  bool tool_hist = false,
-
6274  bool transmission = false,
-
6275  bool transition = false,
-
6276  bool reproductive = false,
-
6277  bool generation = false
-
6278  );
-
6279 
-
6280 // template<typename TSeq>
-
6281 // class VirusPtr;
-
6282 
-
6283 // template<typename TSeq>
-
6284 // class ToolPtr;
-
6285 
-
6295 template<typename TSeq>
-
6296 class Model {
-
6297  friend class Agent<TSeq>;
-
6298  friend class AgentsSample<TSeq>;
-
6299  friend class DataBase<TSeq>;
-
6300  friend class Queue<TSeq>;
-
6301 protected:
-
6302 
-
6303  std::string name = ""; ///< Name of the model
-
6304 
-
6305  DataBase<TSeq> db = DataBase<TSeq>(*this);
-
6306 
-
6307  std::vector< Agent<TSeq> > population = {};
-
6308 
-
6309  bool using_backup = true;
-
6310  std::vector< Agent<TSeq> > population_backup = {};
-
6311 
-
6321  std::vector< Agent<TSeq> * > sampled_population;
-
6322  size_t sampled_population_n = 0u;
-
6323  std::vector< size_t > population_left;
-
6324  size_t population_left_n = 0u;
-
6326 
-
6336  double * agents_data = nullptr;
-
6337  size_t agents_data_ncols = 0u;
-
6339 
-
6340  bool directed = false;
-
6341 
-
6342  std::vector< VirusPtr<TSeq> > viruses = {};
-
6343  std::vector< ToolPtr<TSeq> > tools = {};
-
6344 
-
6345  std::vector< Entity<TSeq> > entities = {};
-
6346  std::vector< Entity<TSeq> > entities_backup = {};
-
6347 
-
6348  std::shared_ptr< std::mt19937 > engine = std::make_shared< std::mt19937 >();
-
6349 
-
6350  std::uniform_real_distribution<> runifd =
-
6351  std::uniform_real_distribution<> (0.0, 1.0);
-
6352  std::normal_distribution<> rnormd =
-
6353  std::normal_distribution<>(0.0);
-
6354  std::gamma_distribution<> rgammad =
-
6355  std::gamma_distribution<>();
-
6356  std::lognormal_distribution<> rlognormald =
-
6357  std::lognormal_distribution<>();
-
6358  std::exponential_distribution<> rexpd =
-
6359  std::exponential_distribution<>();
-
6360  std::binomial_distribution<> rbinomd =
-
6361  std::binomial_distribution<>();
-
6362 
-
6363  std::function<void(std::vector<Agent<TSeq>>*,Model<TSeq>*,epiworld_double)> rewire_fun;
-
6364  epiworld_double rewire_prop = 0.0;
-
6365 
-
6366  std::map<std::string, epiworld_double > parameters;
-
6367  epiworld_fast_uint ndays = 0;
-
6368  Progress pb;
+
6260 class DataBase;
+
6261 
+
6262 template<typename TSeq>
+
6263 class Queue;
+
6264 
+
6265 template<typename TSeq>
+
6266 struct Event;
+
6267 
+
6268 template<typename TSeq>
+
6269 class GlobalEvent;
+
6270 
+
6271 template<typename TSeq>
+
6272 inline epiworld_double susceptibility_reduction_mixer_default(
+
6273  Agent<TSeq>* p,
+
6274  VirusPtr<TSeq> v,
+
6275  Model<TSeq>* m
+
6276  );
+
6277 template<typename TSeq>
+
6278 inline epiworld_double transmission_reduction_mixer_default(
+
6279  Agent<TSeq>* p,
+
6280  VirusPtr<TSeq> v,
+
6281  Model<TSeq>* m
+
6282  );
+
6283 template<typename TSeq>
+
6284 inline epiworld_double recovery_enhancer_mixer_default(
+
6285  Agent<TSeq>* p,
+
6286  VirusPtr<TSeq> v,
+
6287  Model<TSeq>* m
+
6288  );
+
6289 template<typename TSeq>
+
6290 inline epiworld_double death_reduction_mixer_default(
+
6291  Agent<TSeq>* p,
+
6292  VirusPtr<TSeq> v,
+
6293  Model<TSeq>* m
+
6294  );
+
6295 
+
6296 template<typename TSeq>
+
6297 inline std::function<void(size_t,Model<TSeq>*)> make_save_run(
+
6298  std::string fmt = "%03lu-episimulation.csv",
+
6299  bool total_hist = true,
+
6300  bool virus_info = false,
+
6301  bool virus_hist = false,
+
6302  bool tool_info = false,
+
6303  bool tool_hist = false,
+
6304  bool transmission = false,
+
6305  bool transition = false,
+
6306  bool reproductive = false,
+
6307  bool generation = false
+
6308  );
+
6309 
+
6310 // template<typename TSeq>
+
6311 // class VirusPtr;
+
6312 
+
6313 // template<typename TSeq>
+
6314 // class ToolPtr;
+
6315 
+
6325 template<typename TSeq>
+
6326 class Model {
+
6327  friend class Agent<TSeq>;
+
6328  friend class AgentsSample<TSeq>;
+
6329  friend class DataBase<TSeq>;
+
6330  friend class Queue<TSeq>;
+
6331 protected:
+
6332 
+
6333  std::string name = ""; ///< Name of the model
+
6334 
+
6335  DataBase<TSeq> db = DataBase<TSeq>(*this);
+
6336 
+
6337  std::vector< Agent<TSeq> > population = {};
+
6338 
+
6339  bool using_backup = true;
+
6340  std::vector< Agent<TSeq> > population_backup = {};
+
6341 
+
6351  std::vector< Agent<TSeq> * > sampled_population;
+
6352  size_t sampled_population_n = 0u;
+
6353  std::vector< size_t > population_left;
+
6354  size_t population_left_n = 0u;
+
6356 
+
6366  double * agents_data = nullptr;
+
6367  size_t agents_data_ncols = 0u;
6369 
-
6370  std::vector< UpdateFun<TSeq> > state_fun = {}; ///< Functions to update states
-
6371  std::vector< std::string > states_labels = {}; ///< Labels of the states
-
6372 
-
6374  std::function<void(Model<TSeq>*)> initial_states_fun = [](Model<TSeq> * /**/)
-
6375  -> void {};
-
6376 
-
6377  epiworld_fast_uint nstates = 0u;
-
6378 
-
6379  bool verbose = true;
-
6380  int current_date = 0;
-
6381 
-
6382  void dist_tools();
-
6383  void dist_virus();
-
6384  void dist_entities();
-
6385 
-
6386  std::chrono::time_point<std::chrono::steady_clock> time_start;
-
6387  std::chrono::time_point<std::chrono::steady_clock> time_end;
-
6388 
-
6389  // std::chrono::milliseconds
-
6390  std::chrono::duration<epiworld_double,std::micro> time_elapsed =
-
6391  std::chrono::duration<epiworld_double,std::micro>::zero();
-
6392  epiworld_fast_uint n_replicates = 0u;
-
6393  void chrono_start();
-
6394  void chrono_end();
-
6395 
-
6396  std::vector<GlobalEvent<TSeq>> globalevents;
-
6397 
-
6398  Queue<TSeq> queue;
-
6399  bool use_queuing = true;
-
6400 
-
6405  std::vector< Event<TSeq> > events = {};
-
6406  epiworld_fast_uint nactions = 0u;
-
6407 
-
6421  void events_add(
-
6422  Agent<TSeq> * agent_,
-
6423  VirusPtr<TSeq> virus_,
-
6424  ToolPtr<TSeq> tool_,
-
6425  Entity<TSeq> * entity_,
-
6426  epiworld_fast_int new_state_,
-
6427  epiworld_fast_int queue_,
-
6428  EventFun<TSeq> call_,
-
6429  int idx_agent_,
-
6430  int idx_object_
-
6431  );
-
6432 
-
6442  MixerFun<TSeq> susceptibility_reduction_mixer = susceptibility_reduction_mixer_default<TSeq>;
-
6443  MixerFun<TSeq> transmission_reduction_mixer = transmission_reduction_mixer_default<TSeq>;
-
6444  MixerFun<TSeq> recovery_enhancer_mixer = recovery_enhancer_mixer_default<TSeq>;
-
6445  MixerFun<TSeq> death_reduction_mixer = death_reduction_mixer_default<TSeq>;
-
6446 
-
6452  virtual Model<TSeq> * clone_ptr();
-
6453 
-
6454 public:
-
6455 
-
6456 
-
6457  std::vector<epiworld_double> array_double_tmp;
-
6458  std::vector<Virus<TSeq> * > array_virus_tmp;
-
6459  std::vector< int > array_int_tmp;
-
6460 
-
6461  Model();
-
6462  Model(const Model<TSeq> & m);
-
6463  Model(Model<TSeq> & m);
-
6464  Model(Model<TSeq> && m);
-
6465  Model<TSeq> & operator=(const Model<TSeq> & m);
-
6466 
-
6467  virtual ~Model() {};
-
6468 
-
6477  void set_backup();
-
6478  // void restore_backup();
-
6480 
-
6481  DataBase<TSeq> & get_db();
-
6482  const DataBase<TSeq> & get_db() const;
-
6483  epiworld_double & operator()(std::string pname);
-
6484 
-
6485  size_t size() const;
-
6486 
-
6494  void set_rand_engine(std::shared_ptr< std::mt19937 > & eng);
-
6495  std::shared_ptr< std::mt19937 > & get_rand_endgine();
-
6496  void seed(size_t s);
-
6497  void set_rand_norm(epiworld_double mean, epiworld_double sd);
-
6498  void set_rand_unif(epiworld_double a, epiworld_double b);
-
6499  void set_rand_exp(epiworld_double lambda);
-
6500  void set_rand_gamma(epiworld_double alpha, epiworld_double beta);
-
6501  void set_rand_lognormal(epiworld_double mean, epiworld_double shape);
-
6502  void set_rand_binom(int n, epiworld_double p);
-
6503  epiworld_double runif();
-
6504  epiworld_double runif(epiworld_double a, epiworld_double b);
-
6505  epiworld_double rnorm();
-
6506  epiworld_double rnorm(epiworld_double mean, epiworld_double sd);
-
6507  epiworld_double rgamma();
-
6508  epiworld_double rgamma(epiworld_double alpha, epiworld_double beta);
-
6509  epiworld_double rexp();
-
6510  epiworld_double rexp(epiworld_double lambda);
-
6511  epiworld_double rlognormal();
-
6512  epiworld_double rlognormal(epiworld_double mean, epiworld_double shape);
-
6513  int rbinom();
-
6514  int rbinom(int n, epiworld_double p);
+
6370  bool directed = false;
+
6371 
+
6372  std::vector< VirusPtr<TSeq> > viruses = {};
+
6373  std::vector< ToolPtr<TSeq> > tools = {};
+
6374 
+
6375  std::vector< Entity<TSeq> > entities = {};
+
6376  std::vector< Entity<TSeq> > entities_backup = {};
+
6377 
+
6378  std::shared_ptr< std::mt19937 > engine = std::make_shared< std::mt19937 >();
+
6379 
+
6380  std::uniform_real_distribution<> runifd =
+
6381  std::uniform_real_distribution<> (0.0, 1.0);
+
6382  std::normal_distribution<> rnormd =
+
6383  std::normal_distribution<>(0.0);
+
6384  std::gamma_distribution<> rgammad =
+
6385  std::gamma_distribution<>();
+
6386  std::lognormal_distribution<> rlognormald =
+
6387  std::lognormal_distribution<>();
+
6388  std::exponential_distribution<> rexpd =
+
6389  std::exponential_distribution<>();
+
6390  std::binomial_distribution<> rbinomd =
+
6391  std::binomial_distribution<>();
+
6392 
+
6393  std::function<void(std::vector<Agent<TSeq>>*,Model<TSeq>*,epiworld_double)> rewire_fun;
+
6394  epiworld_double rewire_prop = 0.0;
+
6395 
+
6396  std::map<std::string, epiworld_double > parameters;
+
6397  epiworld_fast_uint ndays = 0;
+
6398  Progress pb;
+
6399 
+
6400  std::vector< UpdateFun<TSeq> > state_fun = {}; ///< Functions to update states
+
6401  std::vector< std::string > states_labels = {}; ///< Labels of the states
+
6402 
+
6404  std::function<void(Model<TSeq>*)> initial_states_fun = [](Model<TSeq> * /**/)
+
6405  -> void {};
+
6406 
+
6407  epiworld_fast_uint nstates = 0u;
+
6408 
+
6409  bool verbose = true;
+
6410  int current_date = 0;
+
6411 
+
6412  void dist_tools();
+
6413  void dist_virus();
+
6414  void dist_entities();
+
6415 
+
6416  std::chrono::time_point<std::chrono::steady_clock> time_start;
+
6417  std::chrono::time_point<std::chrono::steady_clock> time_end;
+
6418 
+
6419  // std::chrono::milliseconds
+
6420  std::chrono::duration<epiworld_double,std::micro> time_elapsed =
+
6421  std::chrono::duration<epiworld_double,std::micro>::zero();
+
6422  epiworld_fast_uint n_replicates = 0u;
+
6423  void chrono_start();
+
6424  void chrono_end();
+
6425 
+
6426  std::vector<GlobalEvent<TSeq>> globalevents;
+
6427 
+
6428  Queue<TSeq> queue;
+
6429  bool use_queuing = true;
+
6430 
+
6435  std::vector< Event<TSeq> > events = {};
+
6436  epiworld_fast_uint nactions = 0u;
+
6437 
+
6451  void events_add(
+
6452  Agent<TSeq> * agent_,
+
6453  VirusPtr<TSeq> virus_,
+
6454  ToolPtr<TSeq> tool_,
+
6455  Entity<TSeq> * entity_,
+
6456  epiworld_fast_int new_state_,
+
6457  epiworld_fast_int queue_,
+
6458  EventFun<TSeq> call_,
+
6459  int idx_agent_,
+
6460  int idx_object_
+
6461  );
+
6462 
+
6472  MixerFun<TSeq> susceptibility_reduction_mixer = susceptibility_reduction_mixer_default<TSeq>;
+
6473  MixerFun<TSeq> transmission_reduction_mixer = transmission_reduction_mixer_default<TSeq>;
+
6474  MixerFun<TSeq> recovery_enhancer_mixer = recovery_enhancer_mixer_default<TSeq>;
+
6475  MixerFun<TSeq> death_reduction_mixer = death_reduction_mixer_default<TSeq>;
+
6476 
+
6482  virtual Model<TSeq> * clone_ptr();
+
6483 
+
6484 public:
+
6485 
+
6486 
+
6487  std::vector<epiworld_double> array_double_tmp;
+
6488  std::vector<Virus<TSeq> * > array_virus_tmp;
+
6489  std::vector< int > array_int_tmp;
+
6490 
+
6491  Model();
+
6492  Model(const Model<TSeq> & m);
+
6493  Model(Model<TSeq> & m);
+
6494  Model(Model<TSeq> && m);
+
6495  Model<TSeq> & operator=(const Model<TSeq> & m);
+
6496 
+
6497  virtual ~Model() {};
+
6498 
+
6507  void set_backup();
+
6508  // void restore_backup();
+
6510 
+
6511  DataBase<TSeq> & get_db();
+
6512  const DataBase<TSeq> & get_db() const;
+
6513  epiworld_double & operator()(std::string pname);
+
6514 
+
6515  size_t size() const;
6516 
-
6529  void add_virus(Virus<TSeq> & v);
-
6530  void add_tool(Tool<TSeq> & t);
-
6531  void add_entity(Entity<TSeq> e);
-
6532  void rm_virus(size_t virus_pos);
-
6533  void rm_tool(size_t tool_pos);
-
6534  void rm_entity(size_t entity_id);
-
6536 
-
6547  void load_agents_entities_ties(std::string fn, int skip);
-
6548 
-
6552  void load_agents_entities_ties(
-
6553  const std::vector<int> & agents_ids,
-
6554  const std::vector<int> & entities_ids
-
6555  );
-
6556 
-
6557  void load_agents_entities_ties(
-
6558  const int * agents_id,
-
6559  const int * entities_id,
-
6560  size_t n
-
6561  );
-
6562 
-
6573  void agents_from_adjlist(
-
6574  std::string fn,
-
6575  int size,
-
6576  int skip = 0,
-
6577  bool directed = false
-
6578  );
-
6579 
-
6580  void agents_from_edgelist(
-
6581  const std::vector< int > & source,
-
6582  const std::vector< int > & target,
-
6583  int size,
-
6584  bool directed
-
6585  );
+
6524  void set_rand_engine(std::shared_ptr< std::mt19937 > & eng);
+
6525  std::shared_ptr< std::mt19937 > & get_rand_endgine();
+
6526  void seed(size_t s);
+
6527  void set_rand_norm(epiworld_double mean, epiworld_double sd);
+
6528  void set_rand_unif(epiworld_double a, epiworld_double b);
+
6529  void set_rand_exp(epiworld_double lambda);
+
6530  void set_rand_gamma(epiworld_double alpha, epiworld_double beta);
+
6531  void set_rand_lognormal(epiworld_double mean, epiworld_double shape);
+
6532  void set_rand_binom(int n, epiworld_double p);
+
6533  epiworld_double runif();
+
6534  epiworld_double runif(epiworld_double a, epiworld_double b);
+
6535  epiworld_double rnorm();
+
6536  epiworld_double rnorm(epiworld_double mean, epiworld_double sd);
+
6537  epiworld_double rgamma();
+
6538  epiworld_double rgamma(epiworld_double alpha, epiworld_double beta);
+
6539  epiworld_double rexp();
+
6540  epiworld_double rexp(epiworld_double lambda);
+
6541  epiworld_double rlognormal();
+
6542  epiworld_double rlognormal(epiworld_double mean, epiworld_double shape);
+
6543  int rbinom();
+
6544  int rbinom(int n, epiworld_double p);
+
6546 
+
6559  void add_virus(Virus<TSeq> & v);
+
6560  void add_tool(Tool<TSeq> & t);
+
6561  void add_entity(Entity<TSeq> e);
+
6562  void rm_virus(size_t virus_pos);
+
6563  void rm_tool(size_t tool_pos);
+
6564  void rm_entity(size_t entity_id);
+
6566 
+
6577  void load_agents_entities_ties(std::string fn, int skip);
+
6578 
+
6582  void load_agents_entities_ties(
+
6583  const std::vector<int> & agents_ids,
+
6584  const std::vector<int> & entities_ids
+
6585  );
6586 
-
6587  void agents_from_adjlist(AdjList al);
-
6588 
-
6589  bool is_directed() const;
-
6590 
-
6591  std::vector< Agent<TSeq> > & get_agents();
+
6587  void load_agents_entities_ties(
+
6588  const int * agents_id,
+
6589  const int * entities_id,
+
6590  size_t n
+
6591  );
6592 
-
6593  Agent<TSeq> & get_agent(size_t i);
-
6594 
-
6595  std::vector< epiworld_fast_uint > get_agents_states() const;
-
6596 
-
6597  std::vector< Viruses_const<TSeq> > get_agents_viruses() const;
-
6598 
-
6599  std::vector< Viruses<TSeq> > get_agents_viruses();
-
6600 
-
6601  std::vector< Entity<TSeq> > & get_entities();
-
6602 
-
6603  Entity<TSeq> & get_entity(size_t entity_id, int * entity_pos = nullptr);
-
6604 
-
6605  Model<TSeq> & agents_smallworld(
-
6606  epiworld_fast_uint n = 1000,
-
6607  epiworld_fast_uint k = 5,
-
6608  bool d = false,
-
6609  epiworld_double p = .01
-
6610  );
-
6611  void agents_empty_graph(epiworld_fast_uint n = 1000);
-
6613 
-
6624  void update_state();
-
6625  void mutate_virus();
-
6626  void next();
-
6627  virtual Model<TSeq> & run(
-
6628  epiworld_fast_uint ndays,
-
6629  int seed = -1
-
6630  );
-
6631  void run_multiple(
-
6632  epiworld_fast_uint ndays,
-
6633  epiworld_fast_uint nexperiments,
-
6634  int seed_ = -1,
-
6635  std::function<void(size_t,Model<TSeq>*)> fun = make_save_run<TSeq>(),
-
6636  bool reset = true,
-
6637  bool verbose = true,
-
6638  int nthreads = 1
-
6639  );
-
6641 
-
6642  size_t get_n_viruses() const;
-
6643  size_t get_n_tools() const;
-
6644  epiworld_fast_uint get_ndays() const;
-
6645  epiworld_fast_uint get_n_replicates() const;
-
6646  void set_ndays(epiworld_fast_uint ndays);
-
6647  bool get_verbose() const;
-
6648  Model<TSeq> & verbose_off();
-
6649  Model<TSeq> & verbose_on();
-
6650  int today() const;
-
6651 
-
6664  void set_rewire_fun(std::function<void(std::vector<Agent<TSeq>>*,Model<TSeq>*,epiworld_double)> fun);
-
6665  void set_rewire_prop(epiworld_double prop);
-
6666  epiworld_double get_rewire_prop() const;
-
6667  void rewire();
-
6669 
-
6682  void write_data(
-
6683  std::string fn_virus_info,
-
6684  std::string fn_virus_hist,
-
6685  std::string fn_tool_info,
-
6686  std::string fn_tool_hist,
-
6687  std::string fn_total_hist,
-
6688  std::string fn_transmission,
-
6689  std::string fn_transition,
-
6690  std::string fn_reproductive_number,
-
6691  std::string fn_generation_time
-
6692  ) const;
-
6693 
-
6705  void write_edgelist(
-
6706  std::string fn
-
6707  ) const;
-
6708 
-
6709  void write_edgelist(
-
6710  std::vector< int > & source,
-
6711  std::vector< int > & target
-
6712  ) const;
-
6714 
-
6715  std::map<std::string, epiworld_double> & params();
-
6716 
-
6728  virtual void reset();
-
6729  const Model<TSeq> & print(bool lite = false) const;
-
6730 
-
6746  void add_state(std::string lab, UpdateFun<TSeq> fun = nullptr);
-
6747  const std::vector< std::string > & get_states() const;
-
6748  const std::vector< UpdateFun<TSeq> > & get_state_fun() const;
-
6749  void print_state_codes() const;
-
6751 
-
6760  virtual Model<TSeq> & initial_states(
-
6761  std::vector< double > /*proportions_*/,
-
6762  std::vector< int > /*queue_*/
-
6763  ) {return *this;};
-
6764 
-
6800  epiworld_double add_param(epiworld_double initial_val, std::string pname);
-
6801  void read_params(std::string fn);
-
6802  epiworld_double get_param(epiworld_fast_uint k);
-
6803  epiworld_double get_param(std::string pname);
-
6804  // void set_param(size_t k, epiworld_double val);
-
6805  void set_param(std::string pname, epiworld_double val);
-
6806  // epiworld_double par(epiworld_fast_uint k);
-
6807  epiworld_double par(std::string pname) const;
-
6809 
-
6810  void get_elapsed(
-
6811  std::string unit = "auto",
-
6812  epiworld_double * last_elapsed = nullptr,
-
6813  epiworld_double * total_elapsed = nullptr,
-
6814  std::string * unit_abbr = nullptr,
-
6815  bool print = true
-
6816  ) const;
-
6817 
-
6824  void set_user_data(std::vector< std::string > names);
-
6825  void add_user_data(epiworld_fast_uint j, epiworld_double x);
-
6826  void add_user_data(std::vector< epiworld_double > x);
-
6827  UserData<TSeq> & get_user_data();
-
6829 
-
6841  void add_globalevent(
-
6842  std::function<void(Model<TSeq>*)> fun,
-
6843  std::string name = "A global action",
-
6844  int date = -99
-
6845  );
-
6846 
-
6847  void add_globalevent(
-
6848  GlobalEvent<TSeq> action
-
6849  );
-
6850 
-
6851  GlobalEvent<TSeq> & get_globalevent(std::string name);
-
6852  GlobalEvent<TSeq> & get_globalevent(size_t i);
-
6853 
-
6854  void rm_globalevent(std::string name);
-
6855  void rm_globalevent(size_t i);
-
6856 
-
6857  void run_globalevents();
-
6858 
-
6859  void clear_state_set();
-
6860 
-
6869  void queuing_on();
-
6870  Model<TSeq> & queuing_off();
-
6871  bool is_queuing_on() const;
-
6872  Queue<TSeq> & get_queue();
-
6874 
-
6882  void set_susceptibility_reduction_mixer(MixerFun<TSeq> fun);
-
6883  void set_transmission_reduction_mixer(MixerFun<TSeq> fun);
-
6884  void set_recovery_enhancer_mixer(MixerFun<TSeq> fun);
-
6885  void set_death_reduction_mixer(MixerFun<TSeq> fun);
-
6887 
-
6888  const std::vector< VirusPtr<TSeq> > & get_viruses() const;
-
6889  const std::vector< ToolPtr<TSeq> > & get_tools() const;
-
6890  Virus<TSeq> & get_virus(size_t id);
-
6891  Tool<TSeq> & get_tool(size_t id);
-
6892 
-
6904  void set_agents_data(double * data_, size_t ncols_);
-
6905  double * get_agents_data();
-
6906  size_t get_agents_data_ncols() const;
-
6907 
-
6913  void set_name(std::string name);
-
6914  std::string get_name() const;
-
6915 
-
6916  bool operator==(const Model<TSeq> & other) const;
-
6917  bool operator!=(const Model<TSeq> & other) const {return !operator==(other);};
-
6918 
-
6924  void events_run();
-
6925 
-
6926 
-
6927 };
-
6928 
-
6929 #endif
-
6930 /*//////////////////////////////////////////////////////////////////////////////
-
6932 
-
6933  End of -include/epiworld/model-bones.hpp-
-
6934 
-
6937 
-
6938 
-
6939 /*//////////////////////////////////////////////////////////////////////////////
-
6941 
-
6942  Start of -include/epiworld/model-meat.hpp-
-
6943 
-
6946 
-
6947 
-
6948 #ifndef EPIWORLD_MODEL_MEAT_HPP
-
6949 #define EPIWORLD_MODEL_MEAT_HPP
-
6950 
-
6969 template<typename TSeq = int>
-
6970 inline std::function<void(size_t,Model<TSeq>*)> make_save_run(
-
6971  std::string fmt,
-
6972  bool total_hist,
-
6973  bool virus_info,
-
6974  bool virus_hist,
-
6975  bool tool_info,
-
6976  bool tool_hist,
-
6977  bool transmission,
-
6978  bool transition,
-
6979  bool reproductive,
-
6980  bool generation
-
6981  )
-
6982 {
-
6983 
-
6984  // Counting number of %
-
6985  int n_fmt = 0;
-
6986  for (auto & f : fmt)
-
6987  if (f == '%')
-
6988  n_fmt++;
-
6989 
-
6990  if (n_fmt != 1)
-
6991  throw std::logic_error("The -fmt- argument must have only one \"%\" symbol.");
-
6992 
-
6993  // Listting things to save
-
6994  std::vector< bool > what_to_save = {
-
6995  virus_info,
-
6996  virus_hist,
-
6997  tool_info,
-
6998  tool_hist,
-
6999  total_hist,
-
7000  transmission,
-
7001  transition,
-
7002  reproductive,
-
7003  generation
-
7004  };
-
7005 
-
7006  std::function<void(size_t,Model<TSeq>*)> saver = [fmt,what_to_save](
-
7007  size_t niter, Model<TSeq> * m
-
7008  ) -> void {
-
7009 
-
7010  std::string virus_info = "";
-
7011  std::string virus_hist = "";
-
7012  std::string tool_info = "";
-
7013  std::string tool_hist = "";
-
7014  std::string total_hist = "";
-
7015  std::string transmission = "";
-
7016  std::string transition = "";
-
7017  std::string reproductive = "";
-
7018  std::string generation = "";
+
6603  void agents_from_adjlist(
+
6604  std::string fn,
+
6605  int size,
+
6606  int skip = 0,
+
6607  bool directed = false
+
6608  );
+
6609 
+
6610  void agents_from_edgelist(
+
6611  const std::vector< int > & source,
+
6612  const std::vector< int > & target,
+
6613  int size,
+
6614  bool directed
+
6615  );
+
6616 
+
6617  void agents_from_adjlist(AdjList al);
+
6618 
+
6619  bool is_directed() const;
+
6620 
+
6621  std::vector< Agent<TSeq> > & get_agents();
+
6622 
+
6623  Agent<TSeq> & get_agent(size_t i);
+
6624 
+
6625  std::vector< epiworld_fast_uint > get_agents_states() const;
+
6626 
+
6627  std::vector< Viruses_const<TSeq> > get_agents_viruses() const;
+
6628 
+
6629  std::vector< Viruses<TSeq> > get_agents_viruses();
+
6630 
+
6631  std::vector< Entity<TSeq> > & get_entities();
+
6632 
+
6633  Entity<TSeq> & get_entity(size_t entity_id, int * entity_pos = nullptr);
+
6634 
+
6635  Model<TSeq> & agents_smallworld(
+
6636  epiworld_fast_uint n = 1000,
+
6637  epiworld_fast_uint k = 5,
+
6638  bool d = false,
+
6639  epiworld_double p = .01
+
6640  );
+
6641  void agents_empty_graph(epiworld_fast_uint n = 1000);
+
6643 
+
6654  void update_state();
+
6655  void mutate_virus();
+
6656  void next();
+
6657  virtual Model<TSeq> & run(
+
6658  epiworld_fast_uint ndays,
+
6659  int seed = -1
+
6660  );
+
6661  void run_multiple(
+
6662  epiworld_fast_uint ndays,
+
6663  epiworld_fast_uint nexperiments,
+
6664  int seed_ = -1,
+
6665  std::function<void(size_t,Model<TSeq>*)> fun = make_save_run<TSeq>(),
+
6666  bool reset = true,
+
6667  bool verbose = true,
+
6668  int nthreads = 1
+
6669  );
+
6671 
+
6672  size_t get_n_viruses() const;
+
6673  size_t get_n_tools() const;
+
6674  epiworld_fast_uint get_ndays() const;
+
6675  epiworld_fast_uint get_n_replicates() const;
+
6676  void set_ndays(epiworld_fast_uint ndays);
+
6677  bool get_verbose() const;
+
6678  Model<TSeq> & verbose_off();
+
6679  Model<TSeq> & verbose_on();
+
6680  int today() const;
+
6681 
+
6694  void set_rewire_fun(std::function<void(std::vector<Agent<TSeq>>*,Model<TSeq>*,epiworld_double)> fun);
+
6695  void set_rewire_prop(epiworld_double prop);
+
6696  epiworld_double get_rewire_prop() const;
+
6697  void rewire();
+
6699 
+
6712  void write_data(
+
6713  std::string fn_virus_info,
+
6714  std::string fn_virus_hist,
+
6715  std::string fn_tool_info,
+
6716  std::string fn_tool_hist,
+
6717  std::string fn_total_hist,
+
6718  std::string fn_transmission,
+
6719  std::string fn_transition,
+
6720  std::string fn_reproductive_number,
+
6721  std::string fn_generation_time
+
6722  ) const;
+
6723 
+
6735  void write_edgelist(
+
6736  std::string fn
+
6737  ) const;
+
6738 
+
6739  void write_edgelist(
+
6740  std::vector< int > & source,
+
6741  std::vector< int > & target
+
6742  ) const;
+
6744 
+
6745  std::map<std::string, epiworld_double> & params();
+
6746 
+
6758  virtual void reset();
+
6759  const Model<TSeq> & print(bool lite = false) const;
+
6760 
+
6776  void add_state(std::string lab, UpdateFun<TSeq> fun = nullptr);
+
6777  const std::vector< std::string > & get_states() const;
+
6778  const std::vector< UpdateFun<TSeq> > & get_state_fun() const;
+
6779  void print_state_codes() const;
+
6781 
+
6790  virtual Model<TSeq> & initial_states(
+
6791  std::vector< double > /*proportions_*/,
+
6792  std::vector< int > /*queue_*/
+
6793  ) {return *this;};
+
6794 
+
6830  epiworld_double add_param(epiworld_double initial_val, std::string pname);
+
6831  void read_params(std::string fn);
+
6832  epiworld_double get_param(epiworld_fast_uint k);
+
6833  epiworld_double get_param(std::string pname);
+
6834  // void set_param(size_t k, epiworld_double val);
+
6835  void set_param(std::string pname, epiworld_double val);
+
6836  // epiworld_double par(epiworld_fast_uint k);
+
6837  epiworld_double par(std::string pname) const;
+
6839 
+
6840  void get_elapsed(
+
6841  std::string unit = "auto",
+
6842  epiworld_double * last_elapsed = nullptr,
+
6843  epiworld_double * total_elapsed = nullptr,
+
6844  std::string * unit_abbr = nullptr,
+
6845  bool print = true
+
6846  ) const;
+
6847 
+
6854  void set_user_data(std::vector< std::string > names);
+
6855  void add_user_data(epiworld_fast_uint j, epiworld_double x);
+
6856  void add_user_data(std::vector< epiworld_double > x);
+
6857  UserData<TSeq> & get_user_data();
+
6859 
+
6871  void add_globalevent(
+
6872  std::function<void(Model<TSeq>*)> fun,
+
6873  std::string name = "A global action",
+
6874  int date = -99
+
6875  );
+
6876 
+
6877  void add_globalevent(
+
6878  GlobalEvent<TSeq> action
+
6879  );
+
6880 
+
6881  GlobalEvent<TSeq> & get_globalevent(std::string name);
+
6882  GlobalEvent<TSeq> & get_globalevent(size_t i);
+
6883 
+
6884  void rm_globalevent(std::string name);
+
6885  void rm_globalevent(size_t i);
+
6886 
+
6887  void run_globalevents();
+
6888 
+
6889  void clear_state_set();
+
6890 
+
6899  void queuing_on();
+
6900  Model<TSeq> & queuing_off();
+
6901  bool is_queuing_on() const;
+
6902  Queue<TSeq> & get_queue();
+
6904 
+
6912  void set_susceptibility_reduction_mixer(MixerFun<TSeq> fun);
+
6913  void set_transmission_reduction_mixer(MixerFun<TSeq> fun);
+
6914  void set_recovery_enhancer_mixer(MixerFun<TSeq> fun);
+
6915  void set_death_reduction_mixer(MixerFun<TSeq> fun);
+
6917 
+
6918  const std::vector< VirusPtr<TSeq> > & get_viruses() const;
+
6919  const std::vector< ToolPtr<TSeq> > & get_tools() const;
+
6920  Virus<TSeq> & get_virus(size_t id);
+
6921  Tool<TSeq> & get_tool(size_t id);
+
6922 
+
6934  void set_agents_data(double * data_, size_t ncols_);
+
6935  double * get_agents_data();
+
6936  size_t get_agents_data_ncols() const;
+
6937 
+
6943  void set_name(std::string name);
+
6944  std::string get_name() const;
+
6945 
+
6946  bool operator==(const Model<TSeq> & other) const;
+
6947  bool operator!=(const Model<TSeq> & other) const {return !operator==(other);};
+
6948 
+
6954  void events_run();
+
6955 
+
6956 
+
6957 };
+
6958 
+
6959 #endif
+
6960 /*//////////////////////////////////////////////////////////////////////////////
+
6962 
+
6963  End of -include/epiworld/model-bones.hpp-
+
6964 
+
6967 
+
6968 
+
6969 /*//////////////////////////////////////////////////////////////////////////////
+
6971 
+
6972  Start of -include/epiworld/model-meat.hpp-
+
6973 
+
6976 
+
6977 
+
6978 #ifndef EPIWORLD_MODEL_MEAT_HPP
+
6979 #define EPIWORLD_MODEL_MEAT_HPP
+
6980 
+
6999 template<typename TSeq = int>
+
7000 inline std::function<void(size_t,Model<TSeq>*)> make_save_run(
+
7001  std::string fmt,
+
7002  bool total_hist,
+
7003  bool virus_info,
+
7004  bool virus_hist,
+
7005  bool tool_info,
+
7006  bool tool_hist,
+
7007  bool transmission,
+
7008  bool transition,
+
7009  bool reproductive,
+
7010  bool generation
+
7011  )
+
7012 {
+
7013 
+
7014  // Counting number of %
+
7015  int n_fmt = 0;
+
7016  for (auto & f : fmt)
+
7017  if (f == '%')
+
7018  n_fmt++;
7019 
-
7020  char buff[1024u];
-
7021  if (what_to_save[0u])
-
7022  {
-
7023  virus_info = fmt + std::string("_virus_info.csv");
-
7024  snprintf(buff, sizeof(buff), virus_info.c_str(), niter);
-
7025  virus_info = buff;
-
7026  }
-
7027  if (what_to_save[1u])
-
7028  {
-
7029  virus_hist = fmt + std::string("_virus_hist.csv");
-
7030  snprintf(buff, sizeof(buff), virus_hist.c_str(), niter);
-
7031  virus_hist = buff;
-
7032  }
-
7033  if (what_to_save[2u])
-
7034  {
-
7035  tool_info = fmt + std::string("_tool_info.csv");
-
7036  snprintf(buff, sizeof(buff), tool_info.c_str(), niter);
-
7037  tool_info = buff;
-
7038  }
-
7039  if (what_to_save[3u])
-
7040  {
-
7041  tool_hist = fmt + std::string("_tool_hist.csv");
-
7042  snprintf(buff, sizeof(buff), tool_hist.c_str(), niter);
-
7043  tool_hist = buff;
-
7044  }
-
7045  if (what_to_save[4u])
-
7046  {
-
7047  total_hist = fmt + std::string("_total_hist.csv");
-
7048  snprintf(buff, sizeof(buff), total_hist.c_str(), niter);
-
7049  total_hist = buff;
-
7050  }
-
7051  if (what_to_save[5u])
+
7020  if (n_fmt != 1)
+
7021  throw std::logic_error("The -fmt- argument must have only one \"%\" symbol.");
+
7022 
+
7023  // Listting things to save
+
7024  std::vector< bool > what_to_save = {
+
7025  virus_info,
+
7026  virus_hist,
+
7027  tool_info,
+
7028  tool_hist,
+
7029  total_hist,
+
7030  transmission,
+
7031  transition,
+
7032  reproductive,
+
7033  generation
+
7034  };
+
7035 
+
7036  std::function<void(size_t,Model<TSeq>*)> saver = [fmt,what_to_save](
+
7037  size_t niter, Model<TSeq> * m
+
7038  ) -> void {
+
7039 
+
7040  std::string virus_info = "";
+
7041  std::string virus_hist = "";
+
7042  std::string tool_info = "";
+
7043  std::string tool_hist = "";
+
7044  std::string total_hist = "";
+
7045  std::string transmission = "";
+
7046  std::string transition = "";
+
7047  std::string reproductive = "";
+
7048  std::string generation = "";
+
7049 
+
7050  char buff[1024u];
+
7051  if (what_to_save[0u])
7052  {
-
7053  transmission = fmt + std::string("_transmission.csv");
-
7054  snprintf(buff, sizeof(buff), transmission.c_str(), niter);
-
7055  transmission = buff;
+
7053  virus_info = fmt + std::string("_virus_info.csv");
+
7054  snprintf(buff, sizeof(buff), virus_info.c_str(), niter);
+
7055  virus_info = buff;
7056  }
-
7057  if (what_to_save[6u])
+
7057  if (what_to_save[1u])
7058  {
-
7059  transition = fmt + std::string("_transition.csv");
-
7060  snprintf(buff, sizeof(buff), transition.c_str(), niter);
-
7061  transition = buff;
+
7059  virus_hist = fmt + std::string("_virus_hist.csv");
+
7060  snprintf(buff, sizeof(buff), virus_hist.c_str(), niter);
+
7061  virus_hist = buff;
7062  }
-
7063  if (what_to_save[7u])
+
7063  if (what_to_save[2u])
7064  {
-
7065 
-
7066  reproductive = fmt + std::string("_reproductive.csv");
-
7067  snprintf(buff, sizeof(buff), reproductive.c_str(), niter);
-
7068  reproductive = buff;
-
7069 
-
7070  }
-
7071  if (what_to_save[8u])
-
7072  {
-
7073 
-
7074  generation = fmt + std::string("_generation.csv");
-
7075  snprintf(buff, sizeof(buff), generation.c_str(), niter);
-
7076  generation = buff;
-
7077 
-
7078  }
-
7079 
-
7080 
-
7081  m->write_data(
-
7082  virus_info,
-
7083  virus_hist,
-
7084  tool_info,
-
7085  tool_hist,
-
7086  total_hist,
-
7087  transmission,
-
7088  transition,
-
7089  reproductive,
-
7090  generation
-
7091  );
-
7092 
-
7093  };
-
7094 
-
7095  return saver;
-
7096 }
-
7097 
-
7098 
-
7099 template<typename TSeq>
-
7100 inline void Model<TSeq>::events_add(
-
7101  Agent<TSeq> * agent_,
-
7102  VirusPtr<TSeq> virus_,
-
7103  ToolPtr<TSeq> tool_,
-
7104  Entity<TSeq> * entity_,
-
7105  epiworld_fast_int new_state_,
-
7106  epiworld_fast_int queue_,
-
7107  EventFun<TSeq> call_,
-
7108  int idx_agent_,
-
7109  int idx_object_
-
7110 ) {
-
7111 
-
7112  ++nactions;
-
7113 
-
7114  #ifdef EPI_DEBUG
-
7115  if (nactions == 0)
-
7116  throw std::logic_error("Events cannot be zero!!");
-
7117  #endif
-
7118 
-
7119  if (nactions > events.size())
-
7120  {
-
7121 
-
7122  events.emplace_back(
-
7123  Event<TSeq>(
-
7124  agent_, virus_, tool_, entity_, new_state_, queue_, call_,
-
7125  idx_agent_, idx_object_
-
7126  ));
+
7065  tool_info = fmt + std::string("_tool_info.csv");
+
7066  snprintf(buff, sizeof(buff), tool_info.c_str(), niter);
+
7067  tool_info = buff;
+
7068  }
+
7069  if (what_to_save[3u])
+
7070  {
+
7071  tool_hist = fmt + std::string("_tool_hist.csv");
+
7072  snprintf(buff, sizeof(buff), tool_hist.c_str(), niter);
+
7073  tool_hist = buff;
+
7074  }
+
7075  if (what_to_save[4u])
+
7076  {
+
7077  total_hist = fmt + std::string("_total_hist.csv");
+
7078  snprintf(buff, sizeof(buff), total_hist.c_str(), niter);
+
7079  total_hist = buff;
+
7080  }
+
7081  if (what_to_save[5u])
+
7082  {
+
7083  transmission = fmt + std::string("_transmission.csv");
+
7084  snprintf(buff, sizeof(buff), transmission.c_str(), niter);
+
7085  transmission = buff;
+
7086  }
+
7087  if (what_to_save[6u])
+
7088  {
+
7089  transition = fmt + std::string("_transition.csv");
+
7090  snprintf(buff, sizeof(buff), transition.c_str(), niter);
+
7091  transition = buff;
+
7092  }
+
7093  if (what_to_save[7u])
+
7094  {
+
7095 
+
7096  reproductive = fmt + std::string("_reproductive.csv");
+
7097  snprintf(buff, sizeof(buff), reproductive.c_str(), niter);
+
7098  reproductive = buff;
+
7099 
+
7100  }
+
7101  if (what_to_save[8u])
+
7102  {
+
7103 
+
7104  generation = fmt + std::string("_generation.csv");
+
7105  snprintf(buff, sizeof(buff), generation.c_str(), niter);
+
7106  generation = buff;
+
7107 
+
7108  }
+
7109 
+
7110 
+
7111  m->write_data(
+
7112  virus_info,
+
7113  virus_hist,
+
7114  tool_info,
+
7115  tool_hist,
+
7116  total_hist,
+
7117  transmission,
+
7118  transition,
+
7119  reproductive,
+
7120  generation
+
7121  );
+
7122 
+
7123  };
+
7124 
+
7125  return saver;
+
7126 }
7127 
-
7128  }
-
7129  else
-
7130  {
-
7131 
-
7132  Event<TSeq> & A = events.at(nactions - 1u);
-
7133 
-
7134  A.agent = agent_;
-
7135  A.virus = virus_;
-
7136  A.tool = tool_;
-
7137  A.entity = entity_;
-
7138  A.new_state = new_state_;
-
7139  A.queue = queue_;
-
7140  A.call = call_;
-
7141  A.idx_agent = idx_agent_;
-
7142  A.idx_object = idx_object_;
+
7128 
+
7129 template<typename TSeq>
+
7130 inline void Model<TSeq>::events_add(
+
7131  Agent<TSeq> * agent_,
+
7132  VirusPtr<TSeq> virus_,
+
7133  ToolPtr<TSeq> tool_,
+
7134  Entity<TSeq> * entity_,
+
7135  epiworld_fast_int new_state_,
+
7136  epiworld_fast_int queue_,
+
7137  EventFun<TSeq> call_,
+
7138  int idx_agent_,
+
7139  int idx_object_
+
7140 ) {
+
7141 
+
7142  ++nactions;
7143 
-
7144  }
-
7145 
-
7146  return;
-
7147 
-
7148 }
-
7149 
-
7150 template<typename TSeq>
-
7151 inline void Model<TSeq>::events_run()
-
7152 {
-
7153  // Making the call
-
7154  size_t nevents_tmp = 0;
-
7155  while (nevents_tmp < nactions)
-
7156  {
+
7144  #ifdef EPI_DEBUG
+
7145  if (nactions == 0)
+
7146  throw std::logic_error("Events cannot be zero!!");
+
7147  #endif
+
7148 
+
7149  if (nactions > events.size())
+
7150  {
+
7151 
+
7152  events.emplace_back(
+
7153  Event<TSeq>(
+
7154  agent_, virus_, tool_, entity_, new_state_, queue_, call_,
+
7155  idx_agent_, idx_object_
+
7156  ));
7157 
-
7158  Event<TSeq> & a = events[nevents_tmp++];
-
7159  Agent<TSeq> * p = a.agent;
-
7160 
-
7161  #ifdef EPI_DEBUG
-
7162  if (a.new_state >= static_cast<epiworld_fast_int>(nstates))
-
7163  throw std::range_error(
-
7164  "The proposed state " + std::to_string(a.new_state) + " is out of range. " +
-
7165  "The model currently has " + std::to_string(nstates - 1) + " states.");
-
7166 
-
7167  if (a.new_state < 0)
-
7168  throw std::range_error(
-
7169  "The proposed state " + std::to_string(a.new_state) + " is out of range. " +
-
7170  "The state cannot be negative.");
-
7171  #endif
-
7172 
-
7173  // Undoing the change in the transition matrix
-
7174  if ((p->state_last_changed == today()) && (static_cast<int>(p->state) != a.new_state))
-
7175  {
-
7176  // Undoing state change in the transition matrix
-
7177  // The previous state is already recorded
-
7178  db.update_state(p->state_prev, p->state, true);
+
7158  }
+
7159  else
+
7160  {
+
7161 
+
7162  Event<TSeq> & A = events.at(nactions - 1u);
+
7163 
+
7164  A.agent = agent_;
+
7165  A.virus = virus_;
+
7166  A.tool = tool_;
+
7167  A.entity = entity_;
+
7168  A.new_state = new_state_;
+
7169  A.queue = queue_;
+
7170  A.call = call_;
+
7171  A.idx_agent = idx_agent_;
+
7172  A.idx_object = idx_object_;
+
7173 
+
7174  }
+
7175 
+
7176  return;
+
7177 
+
7178 }
7179 
-
7180  } else
-
7181  p->state_prev = p->state; // Recording the previous state
-
7182 
-
7183  // Applying function after the fact. This way, if there were
-
7184  // updates, they can be recorded properly, before losing the information
-
7185  p->state = a.new_state;
-
7186  if (a.call)
-
7187  {
-
7188  a.call(a, this);
-
7189  }
+
7180 template<typename TSeq>
+
7181 inline void Model<TSeq>::events_run()
+
7182 {
+
7183  // Making the call
+
7184  size_t nevents_tmp = 0;
+
7185  while (nevents_tmp < nactions)
+
7186  {
+
7187 
+
7188  Event<TSeq> & a = events[nevents_tmp++];
+
7189  Agent<TSeq> * p = a.agent;
7190 
-
7191  // Registering that the last change was today
-
7192  p->state_last_changed = today();
-
7193 
-
7194  #ifdef EPI_DEBUG
-
7195  if (static_cast<int>(p->state) >= static_cast<int>(nstates))
-
7196  throw std::range_error(
-
7197  "The new state " + std::to_string(p->state) + " is out of range. " +
-
7198  "The model currently has " + std::to_string(nstates - 1) + " states.");
-
7199  #endif
-
7200 
-
7201  // Updating queue
-
7202  if (use_queuing)
-
7203  {
-
7204 
-
7205  if (a.queue == Queue<TSeq>::Everyone)
-
7206  queue += p;
-
7207  else if (a.queue == -Queue<TSeq>::Everyone)
-
7208  queue -= p;
-
7209  else if (a.queue == Queue<TSeq>::OnlySelf)
-
7210  queue[p->get_id()]++;
-
7211  else if (a.queue == -Queue<TSeq>::OnlySelf)
-
7212  queue[p->get_id()]--;
-
7213  else if (a.queue != Queue<TSeq>::NoOne)
-
7214  throw std::logic_error(
-
7215  "The proposed queue change is not valid. Queue values can be {-2, -1, 0, 1, 2}."
-
7216  );
-
7217 
-
7218  }
-
7219 
-
7220  }
-
7221 
-
7222  // Go back to square 1
-
7223  nactions = 0u;
-
7224 
-
7225  return;
-
7226 
-
7227 }
-
7228 
-
7237 template<typename TSeq>
-
7238 inline epiworld_double susceptibility_reduction_mixer_default(
-
7239  Agent<TSeq>* p,
-
7240  VirusPtr<TSeq> v,
-
7241  Model<TSeq> * m
-
7242 )
-
7243 {
-
7244  epiworld_double total = 1.0;
-
7245  for (auto & tool : p->get_tools())
-
7246  total *= (1.0 - tool->get_susceptibility_reduction(v, m));
-
7247 
-
7248  return 1.0 - total;
-
7249 
-
7250 }
+
7191  #ifdef EPI_DEBUG
+
7192  if (a.new_state >= static_cast<epiworld_fast_int>(nstates))
+
7193  throw std::range_error(
+
7194  "The proposed state " + std::to_string(a.new_state) + " is out of range. " +
+
7195  "The model currently has " + std::to_string(nstates - 1) + " states.");
+
7196 
+
7197  if (a.new_state < 0)
+
7198  throw std::range_error(
+
7199  "The proposed state " + std::to_string(a.new_state) + " is out of range. " +
+
7200  "The state cannot be negative.");
+
7201  #endif
+
7202 
+
7203  // Undoing the change in the transition matrix
+
7204  if ((p->state_last_changed == today()) && (static_cast<int>(p->state) != a.new_state))
+
7205  {
+
7206  // Undoing state change in the transition matrix
+
7207  // The previous state is already recorded
+
7208  db.update_state(p->state_prev, p->state, true);
+
7209 
+
7210  } else
+
7211  p->state_prev = p->state; // Recording the previous state
+
7212 
+
7213  // Applying function after the fact. This way, if there were
+
7214  // updates, they can be recorded properly, before losing the information
+
7215  p->state = a.new_state;
+
7216  if (a.call)
+
7217  {
+
7218  a.call(a, this);
+
7219  }
+
7220 
+
7221  // Registering that the last change was today
+
7222  p->state_last_changed = today();
+
7223 
+
7224  #ifdef EPI_DEBUG
+
7225  if (static_cast<int>(p->state) >= static_cast<int>(nstates))
+
7226  throw std::range_error(
+
7227  "The new state " + std::to_string(p->state) + " is out of range. " +
+
7228  "The model currently has " + std::to_string(nstates - 1) + " states.");
+
7229  #endif
+
7230 
+
7231  // Updating queue
+
7232  if (use_queuing)
+
7233  {
+
7234 
+
7235  if (a.queue == Queue<TSeq>::Everyone)
+
7236  queue += p;
+
7237  else if (a.queue == -Queue<TSeq>::Everyone)
+
7238  queue -= p;
+
7239  else if (a.queue == Queue<TSeq>::OnlySelf)
+
7240  queue[p->get_id()]++;
+
7241  else if (a.queue == -Queue<TSeq>::OnlySelf)
+
7242  queue[p->get_id()]--;
+
7243  else if (a.queue != Queue<TSeq>::NoOne)
+
7244  throw std::logic_error(
+
7245  "The proposed queue change is not valid. Queue values can be {-2, -1, 0, 1, 2}."
+
7246  );
+
7247 
+
7248  }
+
7249 
+
7250  }
7251 
-
7252 template<typename TSeq>
-
7253 inline epiworld_double transmission_reduction_mixer_default(
-
7254  Agent<TSeq>* p,
-
7255  VirusPtr<TSeq> v,
-
7256  Model<TSeq>* m
-
7257 )
-
7258 {
-
7259  epiworld_double total = 1.0;
-
7260  for (auto & tool : p->get_tools())
-
7261  total *= (1.0 - tool->get_transmission_reduction(v, m));
-
7262 
-
7263  return (1.0 - total);
-
7264 
-
7265 }
-
7266 
+
7252  // Go back to square 1
+
7253  nactions = 0u;
+
7254 
+
7255  return;
+
7256 
+
7257 }
+
7258 
7267 template<typename TSeq>
-
7268 inline epiworld_double recovery_enhancer_mixer_default(
+
7268 inline epiworld_double susceptibility_reduction_mixer_default(
7269  Agent<TSeq>* p,
7270  VirusPtr<TSeq> v,
-
7271  Model<TSeq>* m
+
7271  Model<TSeq> * m
7272 )
7273 {
7274  epiworld_double total = 1.0;
7275  for (auto & tool : p->get_tools())
-
7276  total *= (1.0 - tool->get_recovery_enhancer(v, m));
+
7276  total *= (1.0 - tool->get_susceptibility_reduction(v, m));
7277 
7278  return 1.0 - total;
7279 
7280 }
7281 
7282 template<typename TSeq>
-
7283 inline epiworld_double death_reduction_mixer_default(
+
7283 inline epiworld_double transmission_reduction_mixer_default(
7284  Agent<TSeq>* p,
7285  VirusPtr<TSeq> v,
7286  Model<TSeq>* m
-
7287 ) {
-
7288 
+
7287 )
+
7288 {
7289  epiworld_double total = 1.0;
7290  for (auto & tool : p->get_tools())
-
7291  {
-
7292  total *= (1.0 - tool->get_death_reduction(v, m));
-
7293  }
-
7294 
-
7295  return 1.0 - total;
-
7296 
-
7297 }
-
7299 
-
7300 template<typename TSeq>
-
7301 inline Model<TSeq> * Model<TSeq>::clone_ptr()
-
7302 {
-
7303  Model<TSeq> * ptr = new Model<TSeq>(*dynamic_cast<const Model<TSeq>*>(this));
-
7304 
-
7305  #ifdef EPI_DEBUG
-
7306  if (*this != *ptr)
-
7307  throw std::logic_error("Model::clone_ptr The copies of the model don't match.");
-
7308  #endif
-
7309 
-
7310  return ptr;
-
7311 }
-
7312 
-
7313 template<typename TSeq>
-
7314 inline Model<TSeq>::Model()
-
7315 {
-
7316  db.model = this;
-
7317  db.user_data = this;
-
7318  if (use_queuing)
-
7319  queue.model = this;
-
7320 }
-
7321 
-
7322 template<typename TSeq>
-
7323 inline Model<TSeq>::Model(const Model<TSeq> & model) :
-
7324  name(model.name),
-
7325  db(model.db),
-
7326  population(model.population),
-
7327  population_backup(model.population_backup),
-
7328  directed(model.directed),
-
7329  viruses(model.viruses),
-
7330  tools(model.tools),
-
7331  entities(model.entities),
-
7332  entities_backup(model.entities_backup),
-
7333  rewire_fun(model.rewire_fun),
-
7334  rewire_prop(model.rewire_prop),
-
7335  parameters(model.parameters),
-
7336  ndays(model.ndays),
-
7337  pb(model.pb),
-
7338  state_fun(model.state_fun),
-
7339  states_labels(model.states_labels),
-
7340  initial_states_fun(model.initial_states_fun),
-
7341  nstates(model.nstates),
-
7342  verbose(model.verbose),
-
7343  current_date(model.current_date),
-
7344  globalevents(model.globalevents),
-
7345  queue(model.queue),
-
7346  use_queuing(model.use_queuing),
-
7347  array_double_tmp(model.array_double_tmp.size()),
-
7348  array_virus_tmp(model.array_virus_tmp.size()),
-
7349  array_int_tmp(model.array_int_tmp.size())
-
7350 {
+
7291  total *= (1.0 - tool->get_transmission_reduction(v, m));
+
7292 
+
7293  return (1.0 - total);
+
7294 
+
7295 }
+
7296 
+
7297 template<typename TSeq>
+
7298 inline epiworld_double recovery_enhancer_mixer_default(
+
7299  Agent<TSeq>* p,
+
7300  VirusPtr<TSeq> v,
+
7301  Model<TSeq>* m
+
7302 )
+
7303 {
+
7304  epiworld_double total = 1.0;
+
7305  for (auto & tool : p->get_tools())
+
7306  total *= (1.0 - tool->get_recovery_enhancer(v, m));
+
7307 
+
7308  return 1.0 - total;
+
7309 
+
7310 }
+
7311 
+
7312 template<typename TSeq>
+
7313 inline epiworld_double death_reduction_mixer_default(
+
7314  Agent<TSeq>* p,
+
7315  VirusPtr<TSeq> v,
+
7316  Model<TSeq>* m
+
7317 ) {
+
7318 
+
7319  epiworld_double total = 1.0;
+
7320  for (auto & tool : p->get_tools())
+
7321  {
+
7322  total *= (1.0 - tool->get_death_reduction(v, m));
+
7323  }
+
7324 
+
7325  return 1.0 - total;
+
7326 
+
7327 }
+
7329 
+
7330 template<typename TSeq>
+
7331 inline Model<TSeq> * Model<TSeq>::clone_ptr()
+
7332 {
+
7333  Model<TSeq> * ptr = new Model<TSeq>(*dynamic_cast<const Model<TSeq>*>(this));
+
7334 
+
7335  #ifdef EPI_DEBUG
+
7336  if (*this != *ptr)
+
7337  throw std::logic_error("Model::clone_ptr The copies of the model don't match.");
+
7338  #endif
+
7339 
+
7340  return ptr;
+
7341 }
+
7342 
+
7343 template<typename TSeq>
+
7344 inline Model<TSeq>::Model()
+
7345 {
+
7346  db.model = this;
+
7347  db.user_data = this;
+
7348  if (use_queuing)
+
7349  queue.model = this;
+
7350 }
7351 
-
7352 
-
7353  // Removing old neighbors
-
7354  for (auto & p : population)
-
7355  p.model = this;
-
7356 
-
7357  if (population_backup.size() != 0u)
-
7358  for (auto & p : population_backup)
-
7359  p.model = this;
-
7360 
-
7361  // Pointing to the right place. This needs
-
7362  // to be done afterwards since the state zero is set as a function
-
7363  // of the population.
-
7364  db.model = this;
-
7365  db.user_data.model = this;
-
7366 
-
7367  if (use_queuing)
-
7368  queue.model = this;
-
7369 
-
7370  agents_data = model.agents_data;
-
7371  agents_data_ncols = model.agents_data_ncols;
-
7372 
-
7373 }
-
7374 
-
7375 template<typename TSeq>
-
7376 inline Model<TSeq>::Model(Model<TSeq> & model) :
-
7377  Model(dynamic_cast< const Model<TSeq> & >(model)) {}
-
7378 
-
7379 template<typename TSeq>
-
7380 inline Model<TSeq>::Model(Model<TSeq> && model) :
-
7381  name(std::move(model.name)),
-
7382  db(std::move(model.db)),
-
7383  population(std::move(model.population)),
-
7384  agents_data(std::move(model.agents_data)),
-
7385  agents_data_ncols(std::move(model.agents_data_ncols)),
-
7386  directed(std::move(model.directed)),
-
7387  // Virus
-
7388  viruses(std::move(model.viruses)),
-
7389  // Tools
-
7390  tools(std::move(model.tools)),
-
7391  // Entities
-
7392  entities(std::move(model.entities)),
-
7393  entities_backup(std::move(model.entities_backup)),
-
7394  // Pseudo-RNG
-
7395  engine(std::move(model.engine)),
-
7396  runifd(std::move(model.runifd)),
-
7397  rnormd(std::move(model.rnormd)),
-
7398  rgammad(std::move(model.rgammad)),
-
7399  rlognormald(std::move(model.rlognormald)),
-
7400  rexpd(std::move(model.rexpd)),
-
7401  // Rewiring
-
7402  rewire_fun(std::move(model.rewire_fun)),
-
7403  rewire_prop(std::move(model.rewire_prop)),
-
7404  parameters(std::move(model.parameters)),
-
7405  // Others
-
7406  ndays(model.ndays),
-
7407  pb(std::move(model.pb)),
-
7408  state_fun(std::move(model.state_fun)),
-
7409  states_labels(std::move(model.states_labels)),
-
7410  initial_states_fun(std::move(model.initial_states_fun)),
-
7411  nstates(model.nstates),
-
7412  verbose(model.verbose),
-
7413  current_date(std::move(model.current_date)),
-
7414  globalevents(std::move(model.globalevents)),
-
7415  queue(std::move(model.queue)),
-
7416  use_queuing(model.use_queuing),
-
7417  array_double_tmp(model.array_double_tmp.size()),
-
7418  array_virus_tmp(model.array_virus_tmp.size()),
-
7419  array_int_tmp(model.array_int_tmp.size())
-
7420 {
-
7421 
-
7422  db.model = this;
-
7423  db.user_data.model = this;
-
7424 
-
7425  if (use_queuing)
-
7426  queue.model = this;
-
7427 
-
7428 }
-
7429 
-
7430 template<typename TSeq>
-
7431 inline Model<TSeq> & Model<TSeq>::operator=(const Model<TSeq> & m)
-
7432 {
-
7433  name = m.name;
-
7434 
-
7435  population = m.population;
-
7436  population_backup = m.population_backup;
-
7437 
-
7438  for (auto & p : population)
-
7439  p.model = this;
-
7440 
-
7441  if (population_backup.size() != 0)
-
7442  for (auto & p : population_backup)
-
7443  p.model = this;
-
7444 
-
7445  db = m.db;
-
7446  db.model = this;
-
7447  db.user_data.model = this;
-
7448 
-
7449  directed = m.directed;
-
7450 
-
7451  viruses = m.viruses;
-
7452 
-
7453  tools = m.tools;
-
7454 
-
7455  entities = m.entities;
-
7456  entities_backup = m.entities_backup;
-
7457 
-
7458  rewire_fun = m.rewire_fun;
-
7459  rewire_prop = m.rewire_prop;
-
7460 
-
7461  parameters = m.parameters;
-
7462  ndays = m.ndays;
-
7463  pb = m.pb;
+
7352 template<typename TSeq>
+
7353 inline Model<TSeq>::Model(const Model<TSeq> & model) :
+
7354  name(model.name),
+
7355  db(model.db),
+
7356  population(model.population),
+
7357  population_backup(model.population_backup),
+
7358  directed(model.directed),
+
7359  viruses(model.viruses),
+
7360  tools(model.tools),
+
7361  entities(model.entities),
+
7362  entities_backup(model.entities_backup),
+
7363  rewire_fun(model.rewire_fun),
+
7364  rewire_prop(model.rewire_prop),
+
7365  parameters(model.parameters),
+
7366  ndays(model.ndays),
+
7367  pb(model.pb),
+
7368  state_fun(model.state_fun),
+
7369  states_labels(model.states_labels),
+
7370  initial_states_fun(model.initial_states_fun),
+
7371  nstates(model.nstates),
+
7372  verbose(model.verbose),
+
7373  current_date(model.current_date),
+
7374  globalevents(model.globalevents),
+
7375  queue(model.queue),
+
7376  use_queuing(model.use_queuing),
+
7377  array_double_tmp(model.array_double_tmp.size()),
+
7378  array_virus_tmp(model.array_virus_tmp.size()),
+
7379  array_int_tmp(model.array_int_tmp.size())
+
7380 {
+
7381 
+
7382 
+
7383  // Removing old neighbors
+
7384  for (auto & p : population)
+
7385  p.model = this;
+
7386 
+
7387  if (population_backup.size() != 0u)
+
7388  for (auto & p : population_backup)
+
7389  p.model = this;
+
7390 
+
7391  // Pointing to the right place. This needs
+
7392  // to be done afterwards since the state zero is set as a function
+
7393  // of the population.
+
7394  db.model = this;
+
7395  db.user_data.model = this;
+
7396 
+
7397  if (use_queuing)
+
7398  queue.model = this;
+
7399 
+
7400  agents_data = model.agents_data;
+
7401  agents_data_ncols = model.agents_data_ncols;
+
7402 
+
7403 }
+
7404 
+
7405 template<typename TSeq>
+
7406 inline Model<TSeq>::Model(Model<TSeq> & model) :
+
7407  Model(dynamic_cast< const Model<TSeq> & >(model)) {}
+
7408 
+
7409 template<typename TSeq>
+
7410 inline Model<TSeq>::Model(Model<TSeq> && model) :
+
7411  name(std::move(model.name)),
+
7412  db(std::move(model.db)),
+
7413  population(std::move(model.population)),
+
7414  agents_data(std::move(model.agents_data)),
+
7415  agents_data_ncols(std::move(model.agents_data_ncols)),
+
7416  directed(std::move(model.directed)),
+
7417  // Virus
+
7418  viruses(std::move(model.viruses)),
+
7419  // Tools
+
7420  tools(std::move(model.tools)),
+
7421  // Entities
+
7422  entities(std::move(model.entities)),
+
7423  entities_backup(std::move(model.entities_backup)),
+
7424  // Pseudo-RNG
+
7425  engine(std::move(model.engine)),
+
7426  runifd(std::move(model.runifd)),
+
7427  rnormd(std::move(model.rnormd)),
+
7428  rgammad(std::move(model.rgammad)),
+
7429  rlognormald(std::move(model.rlognormald)),
+
7430  rexpd(std::move(model.rexpd)),
+
7431  // Rewiring
+
7432  rewire_fun(std::move(model.rewire_fun)),
+
7433  rewire_prop(std::move(model.rewire_prop)),
+
7434  parameters(std::move(model.parameters)),
+
7435  // Others
+
7436  ndays(model.ndays),
+
7437  pb(std::move(model.pb)),
+
7438  state_fun(std::move(model.state_fun)),
+
7439  states_labels(std::move(model.states_labels)),
+
7440  initial_states_fun(std::move(model.initial_states_fun)),
+
7441  nstates(model.nstates),
+
7442  verbose(model.verbose),
+
7443  current_date(std::move(model.current_date)),
+
7444  globalevents(std::move(model.globalevents)),
+
7445  queue(std::move(model.queue)),
+
7446  use_queuing(model.use_queuing),
+
7447  array_double_tmp(model.array_double_tmp.size()),
+
7448  array_virus_tmp(model.array_virus_tmp.size()),
+
7449  array_int_tmp(model.array_int_tmp.size())
+
7450 {
+
7451 
+
7452  db.model = this;
+
7453  db.user_data.model = this;
+
7454 
+
7455  if (use_queuing)
+
7456  queue.model = this;
+
7457 
+
7458 }
+
7459 
+
7460 template<typename TSeq>
+
7461 inline Model<TSeq> & Model<TSeq>::operator=(const Model<TSeq> & m)
+
7462 {
+
7463  name = m.name;
7464 
-
7465  state_fun = m.state_fun;
-
7466  states_labels = m.states_labels;
-
7467  initial_states_fun = m.initial_states_fun;
-
7468  nstates = m.nstates;
-
7469 
-
7470  verbose = m.verbose;
-
7471 
-
7472  current_date = m.current_date;
-
7473 
-
7474  globalevents = m.globalevents;
-
7475 
-
7476  queue = m.queue;
-
7477  use_queuing = m.use_queuing;
+
7465  population = m.population;
+
7466  population_backup = m.population_backup;
+
7467 
+
7468  for (auto & p : population)
+
7469  p.model = this;
+
7470 
+
7471  if (population_backup.size() != 0)
+
7472  for (auto & p : population_backup)
+
7473  p.model = this;
+
7474 
+
7475  db = m.db;
+
7476  db.model = this;
+
7477  db.user_data.model = this;
7478 
-
7479  // Making sure population is passed correctly
-
7480  // Pointing to the right place
-
7481  db.model = this;
-
7482  db.user_data.model = this;
-
7483 
-
7484  agents_data = m.agents_data;
-
7485  agents_data_ncols = m.agents_data_ncols;
-
7486 
-
7487  // Figure out the queuing
-
7488  if (use_queuing)
-
7489  queue.model = this;
+
7479  directed = m.directed;
+
7480 
+
7481  viruses = m.viruses;
+
7482 
+
7483  tools = m.tools;
+
7484 
+
7485  entities = m.entities;
+
7486  entities_backup = m.entities_backup;
+
7487 
+
7488  rewire_fun = m.rewire_fun;
+
7489  rewire_prop = m.rewire_prop;
7490 
-
7491  array_double_tmp.resize(std::max(
-
7492  size(),
-
7493  static_cast<size_t>(1024 * 1024)
-
7494  ));
-
7495 
-
7496  array_virus_tmp.resize(1024u);
-
7497  array_int_tmp.resize(1024u * 1024);
-
7498 
-
7499  return *this;
-
7500 
-
7501 }
-
7502 
-
7503 template<typename TSeq>
-
7504 inline DataBase<TSeq> & Model<TSeq>::get_db()
-
7505 {
-
7506  return db;
-
7507 }
+
7491  parameters = m.parameters;
+
7492  ndays = m.ndays;
+
7493  pb = m.pb;
+
7494 
+
7495  state_fun = m.state_fun;
+
7496  states_labels = m.states_labels;
+
7497  initial_states_fun = m.initial_states_fun;
+
7498  nstates = m.nstates;
+
7499 
+
7500  verbose = m.verbose;
+
7501 
+
7502  current_date = m.current_date;
+
7503 
+
7504  globalevents = m.globalevents;
+
7505 
+
7506  queue = m.queue;
+
7507  use_queuing = m.use_queuing;
7508 
-
7509 template<typename TSeq>
-
7510 inline const DataBase<TSeq> & Model<TSeq>::get_db() const
-
7511 {
-
7512  return db;
-
7513 }
-
7514 
-
7515 
-
7516 template<typename TSeq>
-
7517 inline std::vector<Agent<TSeq>> & Model<TSeq>::get_agents()
-
7518 {
-
7519  return population;
-
7520 }
-
7521 
-
7522 template<typename TSeq>
-
7523 inline Agent<TSeq> & Model<TSeq>::get_agent(size_t i)
-
7524 {
-
7525  return population[i];
-
7526 }
-
7527 
-
7528 template<typename TSeq>
-
7529 inline std::vector< epiworld_fast_uint > Model<TSeq>::get_agents_states() const
-
7530 {
-
7531  std::vector< epiworld_fast_uint > states(population.size());
-
7532  for (size_t i = 0u; i < population.size(); ++i)
-
7533  states[i] = population[i].get_state();
-
7534 
-
7535  return states;
-
7536 }
-
7537 
-
7538 template<typename TSeq>
-
7539 inline std::vector< Viruses_const<TSeq> > Model<TSeq>::get_agents_viruses() const
-
7540 {
-
7541 
-
7542  std::vector< Viruses_const<TSeq> > viruses(population.size());
-
7543  for (size_t i = 0u; i < population.size(); ++i)
-
7544  viruses[i] = population[i].get_virus();
+
7509  // Making sure population is passed correctly
+
7510  // Pointing to the right place
+
7511  db.model = this;
+
7512  db.user_data.model = this;
+
7513 
+
7514  agents_data = m.agents_data;
+
7515  agents_data_ncols = m.agents_data_ncols;
+
7516 
+
7517  // Figure out the queuing
+
7518  if (use_queuing)
+
7519  queue.model = this;
+
7520 
+
7521  array_double_tmp.resize(std::max(
+
7522  size(),
+
7523  static_cast<size_t>(1024 * 1024)
+
7524  ));
+
7525 
+
7526  array_virus_tmp.resize(1024u);
+
7527  array_int_tmp.resize(1024u * 1024);
+
7528 
+
7529  return *this;
+
7530 
+
7531 }
+
7532 
+
7533 template<typename TSeq>
+
7534 inline DataBase<TSeq> & Model<TSeq>::get_db()
+
7535 {
+
7536  return db;
+
7537 }
+
7538 
+
7539 template<typename TSeq>
+
7540 inline const DataBase<TSeq> & Model<TSeq>::get_db() const
+
7541 {
+
7542  return db;
+
7543 }
+
7544 
7545 
-
7546  return viruses;
-
7547 
-
7548 }
-
7549 
-
7550 // Same as before, but the non const version
-
7551 template<typename TSeq>
-
7552 inline std::vector< Viruses<TSeq> > Model<TSeq>::get_agents_viruses()
-
7553 {
-
7554 
-
7555  std::vector< Viruses<TSeq> > viruses(population.size());
-
7556  for (size_t i = 0u; i < population.size(); ++i)
-
7557  viruses[i] = population[i].get_virus();
-
7558 
-
7559  return viruses;
-
7560 
-
7561 }
-
7562 
-
7563 template<typename TSeq>
-
7564 inline std::vector<Entity<TSeq>> & Model<TSeq>::get_entities()
-
7565 {
-
7566  return entities;
-
7567 }
-
7568 
-
7569 template<typename TSeq>
-
7570 inline Entity<TSeq> & Model<TSeq>::get_entity(size_t i, int * entity_pos)
-
7571 {
-
7572 
-
7573  for (size_t j = 0u; j < entities.size(); ++j)
-
7574  if (entities[j].get_id() == static_cast<int>(i))
-
7575  {
-
7576 
-
7577  if (entity_pos)
-
7578  *entity_pos = j;
+
7546 template<typename TSeq>
+
7547 inline std::vector<Agent<TSeq>> & Model<TSeq>::get_agents()
+
7548 {
+
7549  return population;
+
7550 }
+
7551 
+
7552 template<typename TSeq>
+
7553 inline Agent<TSeq> & Model<TSeq>::get_agent(size_t i)
+
7554 {
+
7555  return population[i];
+
7556 }
+
7557 
+
7558 template<typename TSeq>
+
7559 inline std::vector< epiworld_fast_uint > Model<TSeq>::get_agents_states() const
+
7560 {
+
7561  std::vector< epiworld_fast_uint > states(population.size());
+
7562  for (size_t i = 0u; i < population.size(); ++i)
+
7563  states[i] = population[i].get_state();
+
7564 
+
7565  return states;
+
7566 }
+
7567 
+
7568 template<typename TSeq>
+
7569 inline std::vector< Viruses_const<TSeq> > Model<TSeq>::get_agents_viruses() const
+
7570 {
+
7571 
+
7572  std::vector< Viruses_const<TSeq> > viruses(population.size());
+
7573  for (size_t i = 0u; i < population.size(); ++i)
+
7574  viruses[i] = population[i].get_virus();
+
7575 
+
7576  return viruses;
+
7577 
+
7578 }
7579 
-
7580  return entities[j];
-
7581 
-
7582  }
-
7583 
-
7584  throw std::range_error("The entity with id " + std::to_string(i) + " was not found.");
-
7585 
-
7586 }
-
7587 
-
7588 template<typename TSeq>
-
7589 inline Model<TSeq> & Model<TSeq>::agents_smallworld(
-
7590  epiworld_fast_uint n,
-
7591  epiworld_fast_uint k,
-
7592  bool d,
-
7593  epiworld_double p
-
7594 )
+
7580 // Same as before, but the non const version
+
7581 template<typename TSeq>
+
7582 inline std::vector< Viruses<TSeq> > Model<TSeq>::get_agents_viruses()
+
7583 {
+
7584 
+
7585  std::vector< Viruses<TSeq> > viruses(population.size());
+
7586  for (size_t i = 0u; i < population.size(); ++i)
+
7587  viruses[i] = population[i].get_virus();
+
7588 
+
7589  return viruses;
+
7590 
+
7591 }
+
7592 
+
7593 template<typename TSeq>
+
7594 inline std::vector<Entity<TSeq>> & Model<TSeq>::get_entities()
7595 {
-
7596  agents_from_adjlist(
-
7597  rgraph_smallworld(n, k, p, d, *this)
-
7598  );
-
7599 
-
7600  return *this;
-
7601 }
-
7602 
-
7603 template<typename TSeq>
-
7604 inline void Model<TSeq>::agents_empty_graph(
-
7605  epiworld_fast_uint n
-
7606 )
-
7607 {
-
7608 
-
7609  // Resizing the people
-
7610  population.clear();
-
7611  population.resize(n, Agent<TSeq>());
-
7612 
-
7613  // Filling the model and ids
-
7614  size_t i = 0u;
-
7615  for (auto & p : population)
-
7616  {
-
7617  p.id = i++;
-
7618  p.model = this;
-
7619  }
-
7620 
-
7621 
-
7622 }
-
7623 
-
7624 template<typename TSeq>
-
7625 inline void Model<TSeq>::set_rand_gamma(epiworld_double alpha, epiworld_double beta)
-
7626 {
-
7627  rgammad = std::gamma_distribution<>(alpha,beta);
-
7628 }
+
7596  return entities;
+
7597 }
+
7598 
+
7599 template<typename TSeq>
+
7600 inline Entity<TSeq> & Model<TSeq>::get_entity(size_t i, int * entity_pos)
+
7601 {
+
7602 
+
7603  for (size_t j = 0u; j < entities.size(); ++j)
+
7604  if (entities[j].get_id() == static_cast<int>(i))
+
7605  {
+
7606 
+
7607  if (entity_pos)
+
7608  *entity_pos = j;
+
7609 
+
7610  return entities[j];
+
7611 
+
7612  }
+
7613 
+
7614  throw std::range_error("The entity with id " + std::to_string(i) + " was not found.");
+
7615 
+
7616 }
+
7617 
+
7618 template<typename TSeq>
+
7619 inline Model<TSeq> & Model<TSeq>::agents_smallworld(
+
7620  epiworld_fast_uint n,
+
7621  epiworld_fast_uint k,
+
7622  bool d,
+
7623  epiworld_double p
+
7624 )
+
7625 {
+
7626  agents_from_adjlist(
+
7627  rgraph_smallworld(n, k, p, d, *this)
+
7628  );
7629 
-
7630 template<typename TSeq>
-
7631 inline void Model<TSeq>::set_rand_norm(epiworld_double mean, epiworld_double sd)
-
7632 {
-
7633  rnormd = std::normal_distribution<>(mean, sd);
-
7634 }
-
7635 
-
7636 template<typename TSeq>
-
7637 inline void Model<TSeq>::set_rand_unif(epiworld_double a, epiworld_double b)
-
7638 {
-
7639  runifd = std::uniform_real_distribution<>(a, b);
-
7640 }
-
7641 
-
7642 template<typename TSeq>
-
7643 inline void Model<TSeq>::set_rand_lognormal(epiworld_double mean, epiworld_double shape)
-
7644 {
-
7645  rlognormald = std::lognormal_distribution<>(mean, shape);
-
7646 }
-
7647 
-
7648 template<typename TSeq>
-
7649 inline void Model<TSeq>::set_rand_exp(epiworld_double lambda)
-
7650 {
-
7651  rexpd = std::exponential_distribution<>(lambda);
+
7630  return *this;
+
7631 }
+
7632 
+
7633 template<typename TSeq>
+
7634 inline void Model<TSeq>::agents_empty_graph(
+
7635  epiworld_fast_uint n
+
7636 )
+
7637 {
+
7638 
+
7639  // Resizing the people
+
7640  population.clear();
+
7641  population.resize(n, Agent<TSeq>());
+
7642 
+
7643  // Filling the model and ids
+
7644  size_t i = 0u;
+
7645  for (auto & p : population)
+
7646  {
+
7647  p.id = i++;
+
7648  p.model = this;
+
7649  }
+
7650 
+
7651 
7652 }
7653 
7654 template<typename TSeq>
-
7655 inline void Model<TSeq>::set_rand_binom(int n, epiworld_double p)
-
7656 {
-
7657  rbinomd = std::binomial_distribution<>(n, p);
+
7655 inline void Model<TSeq>::set_rand_gamma(epiworld_double alpha, epiworld_double beta)
+
7656 {
+
7657  rgammad = std::gamma_distribution<>(alpha,beta);
7658 }
7659 
7660 template<typename TSeq>
-
7661 inline epiworld_double & Model<TSeq>::operator()(std::string pname) {
-
7662 
-
7663  if (parameters.find(pname) == parameters.end())
-
7664  throw std::range_error("The parameter "+ pname + "is not in the model.");
+
7661 inline void Model<TSeq>::set_rand_norm(epiworld_double mean, epiworld_double sd)
+
7662 {
+
7663  rnormd = std::normal_distribution<>(mean, sd);
+
7664 }
7665 
-
7666  return parameters[pname];
-
7667 
-
7668 }
-
7669 
-
7670 template<typename TSeq>
-
7671 inline size_t Model<TSeq>::size() const {
-
7672  return population.size();
-
7673 }
-
7674 
-
7675 template<typename TSeq>
-
7676 inline void Model<TSeq>::dist_virus()
-
7677 {
-
7678 
-
7679  for (auto & v: viruses)
-
7680  {
-
7681 
-
7682  v->distribute(this);
+
7666 template<typename TSeq>
+
7667 inline void Model<TSeq>::set_rand_unif(epiworld_double a, epiworld_double b)
+
7668 {
+
7669  runifd = std::uniform_real_distribution<>(a, b);
+
7670 }
+
7671 
+
7672 template<typename TSeq>
+
7673 inline void Model<TSeq>::set_rand_lognormal(epiworld_double mean, epiworld_double shape)
+
7674 {
+
7675  rlognormald = std::lognormal_distribution<>(mean, shape);
+
7676 }
+
7677 
+
7678 template<typename TSeq>
+
7679 inline void Model<TSeq>::set_rand_exp(epiworld_double lambda)
+
7680 {
+
7681  rexpd = std::exponential_distribution<>(lambda);
+
7682 }
7683 
-
7684  // Apply the events
-
7685  events_run();
-
7686  }
-
7687 
+
7684 template<typename TSeq>
+
7685 inline void Model<TSeq>::set_rand_binom(int n, epiworld_double p)
+
7686 {
+
7687  rbinomd = std::binomial_distribution<>(n, p);
7688 }
7689 
7690 template<typename TSeq>
-
7691 inline void Model<TSeq>::dist_tools()
-
7692 {
-
7693 
-
7694  for (auto & tool: tools)
-
7695  {
-
7696 
-
7697  tool->distribute(this);
-
7698 
-
7699  // Apply the events
-
7700  events_run();
-
7701 
-
7702  }
-
7703 
-
7704 }
-
7705 
-
7706 template<typename TSeq>
-
7707 inline void Model<TSeq>::dist_entities()
-
7708 {
-
7709 
-
7710  for (auto & entity: entities)
-
7711  {
-
7712 
-
7713  entity.distribute(this);
-
7714 
-
7715  // Apply the events
-
7716  events_run();
+
7691 inline epiworld_double & Model<TSeq>::operator()(std::string pname) {
+
7692 
+
7693  if (parameters.find(pname) == parameters.end())
+
7694  throw std::range_error("The parameter '"+ pname + "' is not in the model.");
+
7695 
+
7696  return parameters[pname];
+
7697 
+
7698 }
+
7699 
+
7700 template<typename TSeq>
+
7701 inline size_t Model<TSeq>::size() const {
+
7702  return population.size();
+
7703 }
+
7704 
+
7705 template<typename TSeq>
+
7706 inline void Model<TSeq>::dist_virus()
+
7707 {
+
7708 
+
7709  for (auto & v: viruses)
+
7710  {
+
7711 
+
7712  v->distribute(this);
+
7713 
+
7714  // Apply the events
+
7715  events_run();
+
7716  }
7717 
-
7718  }
+
7718 }
7719 
-
7720 }
-
7721 
-
7722 template<typename TSeq>
-
7723 inline void Model<TSeq>::chrono_start() {
-
7724  time_start = std::chrono::steady_clock::now();
-
7725 }
+
7720 template<typename TSeq>
+
7721 inline void Model<TSeq>::dist_tools()
+
7722 {
+
7723 
+
7724  for (auto & tool: tools)
+
7725  {
7726 
-
7727 template<typename TSeq>
-
7728 inline void Model<TSeq>::chrono_end() {
-
7729  time_end = std::chrono::steady_clock::now();
-
7730  time_elapsed += (time_end - time_start);
-
7731  n_replicates++;
-
7732 }
+
7727  tool->distribute(this);
+
7728 
+
7729  // Apply the events
+
7730  events_run();
+
7731 
+
7732  }
7733 
-
7734 template<typename TSeq>
-
7735 inline void Model<TSeq>::set_backup()
-
7736 {
-
7737 
-
7738  if (population_backup.size() == 0u)
-
7739  population_backup = population;
-
7740 
-
7741  if (entities_backup.size() == 0u)
-
7742  entities_backup = entities;
-
7743 
-
7744 }
-
7745 
-
7746 // template<typename TSeq>
-
7747 // inline void Model<TSeq>::restore_backup()
-
7748 // {
+
7734 }
+
7735 
+
7736 template<typename TSeq>
+
7737 inline void Model<TSeq>::dist_entities()
+
7738 {
+
7739 
+
7740  for (auto & entity: entities)
+
7741  {
+
7742 
+
7743  entity.distribute(this);
+
7744 
+
7745  // Apply the events
+
7746  events_run();
+
7747 
+
7748  }
7749 
-
7750 // // Restoring the data
-
7751 // population = *population_backup;
-
7752 // entities = *entities_backup;
-
7753 
-
7754 // // And correcting the pointer
-
7755 // for (auto & p : population)
-
7756 // p.model = this;
-
7757 
-
7758 // for (auto & e : entities)
-
7759 // e.model = this;
-
7760 
-
7761 // }
-
7762 
-
7763 template<typename TSeq>
-
7764 inline std::shared_ptr< std::mt19937 > & Model<TSeq>::get_rand_endgine()
-
7765 {
-
7766  return engine;
-
7767 }
-
7768 
-
7769 template<typename TSeq>
-
7770 inline epiworld_double Model<TSeq>::runif() {
-
7771  // CHECK_INIT()
-
7772  return runifd(*engine);
-
7773 }
-
7774 
-
7775 template<typename TSeq>
-
7776 inline epiworld_double Model<TSeq>::runif(epiworld_double a, epiworld_double b) {
-
7777  // CHECK_INIT()
-
7778  return runifd(*engine) * (b - a) + a;
-
7779 }
-
7780 
-
7781 template<typename TSeq>
-
7782 inline epiworld_double Model<TSeq>::rnorm() {
-
7783  // CHECK_INIT()
-
7784  return rnormd(*engine);
-
7785 }
-
7786 
-
7787 template<typename TSeq>
-
7788 inline epiworld_double Model<TSeq>::rnorm(epiworld_double mean, epiworld_double sd) {
-
7789  // CHECK_INIT()
-
7790  return rnormd(*engine) * sd + mean;
-
7791 }
+
7750 }
+
7751 
+
7752 template<typename TSeq>
+
7753 inline void Model<TSeq>::chrono_start() {
+
7754  time_start = std::chrono::steady_clock::now();
+
7755 }
+
7756 
+
7757 template<typename TSeq>
+
7758 inline void Model<TSeq>::chrono_end() {
+
7759  time_end = std::chrono::steady_clock::now();
+
7760  time_elapsed += (time_end - time_start);
+
7761  n_replicates++;
+
7762 }
+
7763 
+
7764 template<typename TSeq>
+
7765 inline void Model<TSeq>::set_backup()
+
7766 {
+
7767 
+
7768  if (population_backup.size() == 0u)
+
7769  population_backup = population;
+
7770 
+
7771  if (entities_backup.size() == 0u)
+
7772  entities_backup = entities;
+
7773 
+
7774 }
+
7775 
+
7776 // template<typename TSeq>
+
7777 // inline void Model<TSeq>::restore_backup()
+
7778 // {
+
7779 
+
7780 // // Restoring the data
+
7781 // population = *population_backup;
+
7782 // entities = *entities_backup;
+
7783 
+
7784 // // And correcting the pointer
+
7785 // for (auto & p : population)
+
7786 // p.model = this;
+
7787 
+
7788 // for (auto & e : entities)
+
7789 // e.model = this;
+
7790 
+
7791 // }
7792 
7793 template<typename TSeq>
-
7794 inline epiworld_double Model<TSeq>::rgamma() {
-
7795  return rgammad(*engine);
-
7796 }
-
7797 
-
7798 template<typename TSeq>
-
7799 inline epiworld_double Model<TSeq>::rgamma(epiworld_double alpha, epiworld_double beta) {
-
7800  auto old_param = rgammad.param();
-
7801  rgammad.param(std::gamma_distribution<>::param_type(alpha, beta));
-
7802  epiworld_double ans = rgammad(*engine);
-
7803  rgammad.param(old_param);
-
7804  return ans;
-
7805 }
-
7806 
-
7807 template<typename TSeq>
-
7808 inline epiworld_double Model<TSeq>::rexp() {
-
7809  return rexpd(*engine);
-
7810 }
-
7811 
-
7812 template<typename TSeq>
-
7813 inline epiworld_double Model<TSeq>::rexp(epiworld_double lambda) {
-
7814  auto old_param = rexpd.param();
-
7815  rexpd.param(std::exponential_distribution<>::param_type(lambda));
-
7816  epiworld_double ans = rexpd(*engine);
-
7817  rexpd.param(old_param);
-
7818  return ans;
-
7819 }
-
7820 
-
7821 template<typename TSeq>
-
7822 inline epiworld_double Model<TSeq>::rlognormal() {
-
7823  return rlognormald(*engine);
-
7824 }
-
7825 
-
7826 template<typename TSeq>
-
7827 inline epiworld_double Model<TSeq>::rlognormal(epiworld_double mean, epiworld_double shape) {
-
7828  auto old_param = rlognormald.param();
-
7829  rlognormald.param(std::lognormal_distribution<>::param_type(mean, shape));
-
7830  epiworld_double ans = rlognormald(*engine);
-
7831  rlognormald.param(old_param);
-
7832  return ans;
-
7833 }
-
7834 
-
7835 template<typename TSeq>
-
7836 inline int Model<TSeq>::rbinom() {
-
7837  return rbinomd(*engine);
-
7838 }
-
7839 
-
7840 template<typename TSeq>
-
7841 inline int Model<TSeq>::rbinom(int n, epiworld_double p) {
-
7842  auto old_param = rbinomd.param();
-
7843  rbinomd.param(std::binomial_distribution<>::param_type(n, p));
-
7844  epiworld_double ans = rbinomd(*engine);
-
7845  rbinomd.param(old_param);
-
7846  return ans;
-
7847 }
-
7848 
-
7849 template<typename TSeq>
-
7850 inline void Model<TSeq>::seed(size_t s) {
-
7851  this->engine->seed(s);
-
7852 }
-
7853 
-
7854 template<typename TSeq>
-
7855 inline void Model<TSeq>::add_virus(
-
7856  Virus<TSeq> & v
-
7857  )
-
7858 {
-
7859 
-
7860  // Checking the state
-
7861  epiworld_fast_int init_, post_, rm_;
-
7862  v.get_state(&init_, &post_, &rm_);
-
7863 
-
7864  if (init_ == -99)
-
7865  throw std::logic_error(
-
7866  "The virus \"" + v.get_name() + "\" has no -init- state."
-
7867  );
-
7868  else if (post_ == -99)
-
7869  throw std::logic_error(
-
7870  "The virus \"" + v.get_name() + "\" has no -post- state."
-
7871  );
-
7872 
-
7873  // Recording the variant
-
7874  db.record_virus(v);
-
7875 
-
7876  // Adding new virus
-
7877  viruses.push_back(std::make_shared< Virus<TSeq> >(v));
+
7794 inline std::shared_ptr< std::mt19937 > & Model<TSeq>::get_rand_endgine()
+
7795 {
+
7796  return engine;
+
7797 }
+
7798 
+
7799 template<typename TSeq>
+
7800 inline epiworld_double Model<TSeq>::runif() {
+
7801  // CHECK_INIT()
+
7802  return runifd(*engine);
+
7803 }
+
7804 
+
7805 template<typename TSeq>
+
7806 inline epiworld_double Model<TSeq>::runif(epiworld_double a, epiworld_double b) {
+
7807  // CHECK_INIT()
+
7808  return runifd(*engine) * (b - a) + a;
+
7809 }
+
7810 
+
7811 template<typename TSeq>
+
7812 inline epiworld_double Model<TSeq>::rnorm() {
+
7813  // CHECK_INIT()
+
7814  return rnormd(*engine);
+
7815 }
+
7816 
+
7817 template<typename TSeq>
+
7818 inline epiworld_double Model<TSeq>::rnorm(epiworld_double mean, epiworld_double sd) {
+
7819  // CHECK_INIT()
+
7820  return rnormd(*engine) * sd + mean;
+
7821 }
+
7822 
+
7823 template<typename TSeq>
+
7824 inline epiworld_double Model<TSeq>::rgamma() {
+
7825  return rgammad(*engine);
+
7826 }
+
7827 
+
7828 template<typename TSeq>
+
7829 inline epiworld_double Model<TSeq>::rgamma(epiworld_double alpha, epiworld_double beta) {
+
7830  auto old_param = rgammad.param();
+
7831  rgammad.param(std::gamma_distribution<>::param_type(alpha, beta));
+
7832  epiworld_double ans = rgammad(*engine);
+
7833  rgammad.param(old_param);
+
7834  return ans;
+
7835 }
+
7836 
+
7837 template<typename TSeq>
+
7838 inline epiworld_double Model<TSeq>::rexp() {
+
7839  return rexpd(*engine);
+
7840 }
+
7841 
+
7842 template<typename TSeq>
+
7843 inline epiworld_double Model<TSeq>::rexp(epiworld_double lambda) {
+
7844  auto old_param = rexpd.param();
+
7845  rexpd.param(std::exponential_distribution<>::param_type(lambda));
+
7846  epiworld_double ans = rexpd(*engine);
+
7847  rexpd.param(old_param);
+
7848  return ans;
+
7849 }
+
7850 
+
7851 template<typename TSeq>
+
7852 inline epiworld_double Model<TSeq>::rlognormal() {
+
7853  return rlognormald(*engine);
+
7854 }
+
7855 
+
7856 template<typename TSeq>
+
7857 inline epiworld_double Model<TSeq>::rlognormal(epiworld_double mean, epiworld_double shape) {
+
7858  auto old_param = rlognormald.param();
+
7859  rlognormald.param(std::lognormal_distribution<>::param_type(mean, shape));
+
7860  epiworld_double ans = rlognormald(*engine);
+
7861  rlognormald.param(old_param);
+
7862  return ans;
+
7863 }
+
7864 
+
7865 template<typename TSeq>
+
7866 inline int Model<TSeq>::rbinom() {
+
7867  return rbinomd(*engine);
+
7868 }
+
7869 
+
7870 template<typename TSeq>
+
7871 inline int Model<TSeq>::rbinom(int n, epiworld_double p) {
+
7872  auto old_param = rbinomd.param();
+
7873  rbinomd.param(std::binomial_distribution<>::param_type(n, p));
+
7874  epiworld_double ans = rbinomd(*engine);
+
7875  rbinomd.param(old_param);
+
7876  return ans;
+
7877 }
7878 
-
7879 }
-
7880 
-
7881 template<typename TSeq>
-
7882 inline void Model<TSeq>::add_tool(Tool<TSeq> & t)
-
7883 {
-
7884 
-
7885 
-
7886  db.record_tool(t);
-
7887 
-
7888  // Adding the tool to the model (and database.)
-
7889  tools.push_back(std::make_shared< Tool<TSeq> >(t));
-
7890 
-
7891 }
-
7892 
-
7893 template<typename TSeq>
-
7894 inline void Model<TSeq>::add_entity(Entity<TSeq> e)
-
7895 {
-
7896 
-
7897  e.id = entities.size();
-
7898  entities.push_back(e);
-
7899 
-
7900 }
-
7901 
-
7902 template<typename TSeq>
-
7903 inline void Model<TSeq>::rm_entity(size_t entity_id)
-
7904 {
+
7879 template<typename TSeq>
+
7880 inline void Model<TSeq>::seed(size_t s) {
+
7881  this->engine->seed(s);
+
7882 }
+
7883 
+
7884 template<typename TSeq>
+
7885 inline void Model<TSeq>::add_virus(
+
7886  Virus<TSeq> & v
+
7887  )
+
7888 {
+
7889 
+
7890  // Checking the state
+
7891  epiworld_fast_int init_, post_, rm_;
+
7892  v.get_state(&init_, &post_, &rm_);
+
7893 
+
7894  if (init_ == -99)
+
7895  throw std::logic_error(
+
7896  "The virus \"" + v.get_name() + "\" has no -init- state."
+
7897  );
+
7898  else if (post_ == -99)
+
7899  throw std::logic_error(
+
7900  "The virus \"" + v.get_name() + "\" has no -post- state."
+
7901  );
+
7902 
+
7903  // Recording the variant
+
7904  db.record_virus(v);
7905 
-
7906  int entity_pos = 0;
-
7907  auto & entity = this->get_entity(entity_id, &entity_pos);
+
7906  // Adding new virus
+
7907  viruses.push_back(std::make_shared< Virus<TSeq> >(v));
7908 
-
7909  // First, resetting the entity
-
7910  entity.reset();
-
7911 
-
7912  // How should
-
7913  if (entity_pos != (static_cast<int>(entities.size()) - 1))
-
7914  std::swap(entities[entity_pos], entities[entities.size() - 1]);
-
7915 
-
7916  entities.pop_back();
-
7917 }
-
7918 
-
7919 template<typename TSeq>
-
7920 inline void Model<TSeq>::rm_virus(size_t virus_pos)
-
7921 {
+
7909 }
+
7910 
+
7911 template<typename TSeq>
+
7912 inline void Model<TSeq>::add_tool(Tool<TSeq> & t)
+
7913 {
+
7914 
+
7915 
+
7916  db.record_tool(t);
+
7917 
+
7918  // Adding the tool to the model (and database.)
+
7919  tools.push_back(std::make_shared< Tool<TSeq> >(t));
+
7920 
+
7921 }
7922 
-
7923  if (viruses.size() <= virus_pos)
-
7924  throw std::range_error(
-
7925  std::string("The specified virus (") +
-
7926  std::to_string(virus_pos) +
-
7927  std::string(") is out of range. ") +
-
7928  std::string("There are only ") +
-
7929  std::to_string(viruses.size()) +
-
7930  std::string(" viruses.")
-
7931  );
-
7932 
-
7933  // Flipping with the last one
-
7934  std::swap(viruses[virus_pos], viruses[viruses.size() - 1]);
-
7935  viruses.pop_back();
-
7936 
-
7937  return;
+
7923 template<typename TSeq>
+
7924 inline void Model<TSeq>::add_entity(Entity<TSeq> e)
+
7925 {
+
7926 
+
7927  e.id = entities.size();
+
7928  entities.push_back(e);
+
7929 
+
7930 }
+
7931 
+
7932 template<typename TSeq>
+
7933 inline void Model<TSeq>::rm_entity(size_t entity_id)
+
7934 {
+
7935 
+
7936  int entity_pos = 0;
+
7937  auto & entity = this->get_entity(entity_id, &entity_pos);
7938 
-
7939 }
-
7940 
-
7941 template<typename TSeq>
-
7942 inline void Model<TSeq>::rm_tool(size_t tool_pos)
-
7943 {
-
7944 
-
7945  if (tools.size() <= tool_pos)
-
7946  throw std::range_error(
-
7947  std::string("The specified tool (") +
-
7948  std::to_string(tool_pos) +
-
7949  std::string(") is out of range. ") +
-
7950  std::string("There are only ") +
-
7951  std::to_string(tools.size()) +
-
7952  std::string(" tools.")
-
7953  );
-
7954 
-
7955  // Flipping with the last one
-
7956  std::swap(tools[tool_pos], tools[tools.size() - 1]);
-
7957 
-
7958  /* There's an error on windows:
-
7959  https://github.com/UofUEpiBio/epiworldR/actions/runs/4801482395/jobs/8543744180#step:6:84
-
7960 
-
7961  More clear here:
-
7962  https://stackoverflow.com/questions/58660207/why-doesnt-stdswap-work-on-vectorbool-elements-under-clang-win
-
7963  */
-
7964 
-
7965  tools.pop_back();
-
7966 
-
7967  return;
-
7968 
-
7969 }
-
7970 
-
7971 template<typename TSeq>
-
7972 inline void Model<TSeq>::load_agents_entities_ties(
-
7973  std::string fn,
-
7974  int skip
-
7975  )
-
7976 {
-
7977 
-
7978  int i,j;
-
7979  std::ifstream filei(fn);
-
7980 
-
7981  if (!filei)
-
7982  throw std::logic_error("The file " + fn + " was not found.");
-
7983 
-
7984  int linenum = 0;
-
7985  std::vector< std::vector< epiworld_fast_uint > > target_(entities.size());
-
7986 
-
7987  target_.reserve(1e5);
-
7988 
-
7989  while (!filei.eof())
-
7990  {
-
7991 
-
7992  if (linenum++ < skip)
-
7993  continue;
+
7939  // First, resetting the entity
+
7940  entity.reset();
+
7941 
+
7942  // How should
+
7943  if (entity_pos != (static_cast<int>(entities.size()) - 1))
+
7944  std::swap(entities[entity_pos], entities[entities.size() - 1]);
+
7945 
+
7946  entities.pop_back();
+
7947 }
+
7948 
+
7949 template<typename TSeq>
+
7950 inline void Model<TSeq>::rm_virus(size_t virus_pos)
+
7951 {
+
7952 
+
7953  if (viruses.size() <= virus_pos)
+
7954  throw std::range_error(
+
7955  std::string("The specified virus (") +
+
7956  std::to_string(virus_pos) +
+
7957  std::string(") is out of range. ") +
+
7958  std::string("There are only ") +
+
7959  std::to_string(viruses.size()) +
+
7960  std::string(" viruses.")
+
7961  );
+
7962 
+
7963  // Flipping with the last one
+
7964  std::swap(viruses[virus_pos], viruses[viruses.size() - 1]);
+
7965  viruses.pop_back();
+
7966 
+
7967  return;
+
7968 
+
7969 }
+
7970 
+
7971 template<typename TSeq>
+
7972 inline void Model<TSeq>::rm_tool(size_t tool_pos)
+
7973 {
+
7974 
+
7975  if (tools.size() <= tool_pos)
+
7976  throw std::range_error(
+
7977  std::string("The specified tool (") +
+
7978  std::to_string(tool_pos) +
+
7979  std::string(") is out of range. ") +
+
7980  std::string("There are only ") +
+
7981  std::to_string(tools.size()) +
+
7982  std::string(" tools.")
+
7983  );
+
7984 
+
7985  // Flipping with the last one
+
7986  std::swap(tools[tool_pos], tools[tools.size() - 1]);
+
7987 
+
7988  /* There's an error on windows:
+
7989  https://github.com/UofUEpiBio/epiworldR/actions/runs/4801482395/jobs/8543744180#step:6:84
+
7990 
+
7991  More clear here:
+
7992  https://stackoverflow.com/questions/58660207/why-doesnt-stdswap-work-on-vectorbool-elements-under-clang-win
+
7993  */
7994 
-
7995  filei >> i >> j;
+
7995  tools.pop_back();
7996 
-
7997  // Looking for exceptions
-
7998  if (filei.bad())
-
7999  throw std::logic_error(
-
8000  "I/O error while reading the file " +
-
8001  fn
-
8002  );
-
8003 
-
8004  if (filei.fail())
-
8005  break;
-
8006 
-
8007  if (i >= static_cast<int>(this->size()))
-
8008  throw std::range_error(
-
8009  "The agent["+std::to_string(linenum)+"] = " + std::to_string(i) +
-
8010  " is above the max id " + std::to_string(this->size() - 1)
-
8011  );
-
8012 
-
8013  if (j >= static_cast<int>(this->entities.size()))
-
8014  throw std::range_error(
-
8015  "The entity["+std::to_string(linenum)+"] = " + std::to_string(j) +
-
8016  " is above the max id " + std::to_string(this->entities.size() - 1)
-
8017  );
+
7997  return;
+
7998 
+
7999 }
+
8000 
+
8001 template<typename TSeq>
+
8002 inline void Model<TSeq>::load_agents_entities_ties(
+
8003  std::string fn,
+
8004  int skip
+
8005  )
+
8006 {
+
8007 
+
8008  int i,j;
+
8009  std::ifstream filei(fn);
+
8010 
+
8011  if (!filei)
+
8012  throw std::logic_error("The file " + fn + " was not found.");
+
8013 
+
8014  int linenum = 0;
+
8015  std::vector< std::vector< epiworld_fast_uint > > target_(entities.size());
+
8016 
+
8017  target_.reserve(1e5);
8018 
-
8019  target_[j].push_back(i);
-
8020 
-
8021  population[i].add_entity(entities[j], nullptr);
-
8022 
-
8023  }
+
8019  while (!filei.eof())
+
8020  {
+
8021 
+
8022  if (linenum++ < skip)
+
8023  continue;
8024 
-
8025  return;
+
8025  filei >> i >> j;
8026 
-
8027 }
-
8028 
-
8029 template<typename TSeq>
-
8030 inline void Model<TSeq>::load_agents_entities_ties(
-
8031  const std::vector< int > & agents_ids,
-
8032  const std::vector< int > & entities_ids
-
8033 ) {
-
8034 
-
8035  // Checking the size
-
8036  if (agents_ids.size() != entities_ids.size())
-
8037  throw std::length_error(
-
8038  std::string("The size of agents_ids (") +
-
8039  std::to_string(agents_ids.size()) +
-
8040  std::string(") and entities_ids (") +
-
8041  std::to_string(entities_ids.size()) +
-
8042  std::string(") must be the same.")
-
8043  );
-
8044 
-
8045  return this->load_agents_entities_ties(
-
8046  agents_ids.data(),
-
8047  entities_ids.data(),
-
8048  agents_ids.size()
-
8049  );
+
8027  // Looking for exceptions
+
8028  if (filei.bad())
+
8029  throw std::logic_error(
+
8030  "I/O error while reading the file " +
+
8031  fn
+
8032  );
+
8033 
+
8034  if (filei.fail())
+
8035  break;
+
8036 
+
8037  if (i >= static_cast<int>(this->size()))
+
8038  throw std::range_error(
+
8039  "The agent["+std::to_string(linenum)+"] = " + std::to_string(i) +
+
8040  " is above the max id " + std::to_string(this->size() - 1)
+
8041  );
+
8042 
+
8043  if (j >= static_cast<int>(this->entities.size()))
+
8044  throw std::range_error(
+
8045  "The entity["+std::to_string(linenum)+"] = " + std::to_string(j) +
+
8046  " is above the max id " + std::to_string(this->entities.size() - 1)
+
8047  );
+
8048 
+
8049  target_[j].push_back(i);
8050 
-
8051 }
+
8051  population[i].add_entity(entities[j], nullptr);
8052 
-
8053 template<typename TSeq>
-
8054 inline void Model<TSeq>::load_agents_entities_ties(
-
8055  const int * agents_ids,
-
8056  const int * entities_ids,
-
8057  size_t n
-
8058 ) {
-
8059 
-
8060  auto get_agent = [agents_ids](int i) -> int {
-
8061  return *(agents_ids + i);
-
8062  };
-
8063 
-
8064  auto get_entity = [entities_ids](int i) -> int {
-
8065  return *(entities_ids + i);
-
8066  };
-
8067 
-
8068  for (size_t i = 0u; i < n; ++i)
-
8069  {
-
8070 
-
8071  if (get_agent(i) < 0)
-
8072  throw std::length_error(
-
8073  std::string("agents_ids[") +
-
8074  std::to_string(i) +
-
8075  std::string("] = ") +
-
8076  std::to_string(get_agent(i)) +
-
8077  std::string(" is negative.")
-
8078  );
-
8079 
-
8080  if (get_entity(i) < 0)
-
8081  throw std::length_error(
-
8082  std::string("entities_ids[") +
-
8083  std::to_string(i) +
-
8084  std::string("] = ") +
-
8085  std::to_string(get_entity(i)) +
-
8086  std::string(" is negative.")
-
8087  );
-
8088 
-
8089  int pop_size = static_cast<int>(this->population.size());
-
8090  if (get_agent(i) >= pop_size)
-
8091  throw std::length_error(
-
8092  std::string("agents_ids[") +
-
8093  std::to_string(i) +
-
8094  std::string("] = ") +
-
8095  std::to_string(get_agent(i)) +
-
8096  std::string(" is out of range (population size: ") +
-
8097  std::to_string(pop_size) +
-
8098  std::string(").")
-
8099  );
+
8053  }
+
8054 
+
8055  return;
+
8056 
+
8057 }
+
8058 
+
8059 template<typename TSeq>
+
8060 inline void Model<TSeq>::load_agents_entities_ties(
+
8061  const std::vector< int > & agents_ids,
+
8062  const std::vector< int > & entities_ids
+
8063 ) {
+
8064 
+
8065  // Checking the size
+
8066  if (agents_ids.size() != entities_ids.size())
+
8067  throw std::length_error(
+
8068  std::string("The size of agents_ids (") +
+
8069  std::to_string(agents_ids.size()) +
+
8070  std::string(") and entities_ids (") +
+
8071  std::to_string(entities_ids.size()) +
+
8072  std::string(") must be the same.")
+
8073  );
+
8074 
+
8075  return this->load_agents_entities_ties(
+
8076  agents_ids.data(),
+
8077  entities_ids.data(),
+
8078  agents_ids.size()
+
8079  );
+
8080 
+
8081 }
+
8082 
+
8083 template<typename TSeq>
+
8084 inline void Model<TSeq>::load_agents_entities_ties(
+
8085  const int * agents_ids,
+
8086  const int * entities_ids,
+
8087  size_t n
+
8088 ) {
+
8089 
+
8090  auto get_agent = [agents_ids](int i) -> int {
+
8091  return *(agents_ids + i);
+
8092  };
+
8093 
+
8094  auto get_entity = [entities_ids](int i) -> int {
+
8095  return *(entities_ids + i);
+
8096  };
+
8097 
+
8098  for (size_t i = 0u; i < n; ++i)
+
8099  {
8100 
-
8101  int ent_size = static_cast<int>(this->entities.size());
-
8102  if (get_entity(i) >= ent_size)
-
8103  throw std::length_error(
-
8104  std::string("entities_ids[") +
-
8105  std::to_string(i) +
-
8106  std::string("] = ") +
-
8107  std::to_string(get_entity(i)) +
-
8108  std::string(" is out of range (entities size: ") +
-
8109  std::to_string(ent_size) +
-
8110  std::string(").")
-
8111  );
-
8112 
-
8113  // Adding the entity to the agent
-
8114  this->population[get_agent(i)].add_entity(
-
8115  this->entities[get_entity(i)],
-
8116  nullptr /* Immediately add it to the agent */
-
8117  );
+
8101  if (get_agent(i) < 0)
+
8102  throw std::length_error(
+
8103  std::string("agents_ids[") +
+
8104  std::to_string(i) +
+
8105  std::string("] = ") +
+
8106  std::to_string(get_agent(i)) +
+
8107  std::string(" is negative.")
+
8108  );
+
8109 
+
8110  if (get_entity(i) < 0)
+
8111  throw std::length_error(
+
8112  std::string("entities_ids[") +
+
8113  std::to_string(i) +
+
8114  std::string("] = ") +
+
8115  std::to_string(get_entity(i)) +
+
8116  std::string(" is negative.")
+
8117  );
8118 
-
8119  }
-
8120 
-
8121  return;
-
8122 
-
8123 
-
8124 }
-
8125 
-
8126 template<typename TSeq>
-
8127 inline void Model<TSeq>::agents_from_adjlist(
-
8128  std::string fn,
-
8129  int size,
-
8130  int skip,
-
8131  bool directed
-
8132  ) {
-
8133 
-
8134  AdjList al;
-
8135  al.read_edgelist(fn, size, skip, directed);
-
8136  this->agents_from_adjlist(al);
-
8137 
-
8138 }
-
8139 
-
8140 template<typename TSeq>
-
8141 inline void Model<TSeq>::agents_from_edgelist(
-
8142  const std::vector< int > & source,
-
8143  const std::vector< int > & target,
-
8144  int size,
-
8145  bool directed
-
8146 ) {
-
8147 
-
8148  AdjList al(source, target, size, directed);
-
8149  agents_from_adjlist(al);
+
8119  int pop_size = static_cast<int>(this->population.size());
+
8120  if (get_agent(i) >= pop_size)
+
8121  throw std::length_error(
+
8122  std::string("agents_ids[") +
+
8123  std::to_string(i) +
+
8124  std::string("] = ") +
+
8125  std::to_string(get_agent(i)) +
+
8126  std::string(" is out of range (population size: ") +
+
8127  std::to_string(pop_size) +
+
8128  std::string(").")
+
8129  );
+
8130 
+
8131  int ent_size = static_cast<int>(this->entities.size());
+
8132  if (get_entity(i) >= ent_size)
+
8133  throw std::length_error(
+
8134  std::string("entities_ids[") +
+
8135  std::to_string(i) +
+
8136  std::string("] = ") +
+
8137  std::to_string(get_entity(i)) +
+
8138  std::string(" is out of range (entities size: ") +
+
8139  std::to_string(ent_size) +
+
8140  std::string(").")
+
8141  );
+
8142 
+
8143  // Adding the entity to the agent
+
8144  this->population[get_agent(i)].add_entity(
+
8145  this->entities[get_entity(i)],
+
8146  nullptr /* Immediately add it to the agent */
+
8147  );
+
8148 
+
8149  }
8150 
-
8151 }
+
8151  return;
8152 
-
8153 template<typename TSeq>
-
8154 inline void Model<TSeq>::agents_from_adjlist(AdjList al) {
+
8153 
+
8154 }
8155 
-
8156  // Resizing the people
-
8157  agents_empty_graph(al.vcount());
-
8158 
-
8159  const auto & tmpdat = al.get_dat();
-
8160 
-
8161  for (size_t i = 0u; i < tmpdat.size(); ++i)
-
8162  {
+
8156 template<typename TSeq>
+
8157 inline void Model<TSeq>::agents_from_adjlist(
+
8158  std::string fn,
+
8159  int size,
+
8160  int skip,
+
8161  bool directed
+
8162  ) {
8163 
-
8164  // population[i].id = i;
-
8165  population[i].model = this;
-
8166 
-
8167  for (const auto & link: tmpdat[i])
-
8168  {
+
8164  AdjList al;
+
8165  al.read_edgelist(fn, size, skip, directed);
+
8166  this->agents_from_adjlist(al);
+
8167 
+
8168 }
8169 
-
8170  population[i].add_neighbor(
-
8171  population[link.first],
-
8172  true, true
-
8173  );
-
8174 
-
8175  }
-
8176 
-
8177  }
-
8178 
-
8179  #ifdef EPI_DEBUG
-
8180  for (auto & p: population)
-
8181  {
-
8182  if (p.id >= static_cast<int>(al.vcount()))
-
8183  throw std::logic_error(
-
8184  "Agent's id cannot be negative above or equal to the number of agents!");
-
8185  }
-
8186  #endif
-
8187 
-
8188 }
-
8189 
-
8190 template<typename TSeq>
-
8191 inline bool Model<TSeq>::is_directed() const
-
8192 {
-
8193  if (population.size() == 0u)
-
8194  throw std::logic_error("The population hasn't been initialized.");
-
8195 
-
8196  return directed;
-
8197 }
-
8198 
-
8199 template<typename TSeq>
-
8200 inline int Model<TSeq>::today() const {
-
8201 
-
8202  if (ndays == 0)
-
8203  return 0;
+
8170 template<typename TSeq>
+
8171 inline void Model<TSeq>::agents_from_edgelist(
+
8172  const std::vector< int > & source,
+
8173  const std::vector< int > & target,
+
8174  int size,
+
8175  bool directed
+
8176 ) {
+
8177 
+
8178  AdjList al(source, target, size, directed);
+
8179  agents_from_adjlist(al);
+
8180 
+
8181 }
+
8182 
+
8183 template<typename TSeq>
+
8184 inline void Model<TSeq>::agents_from_adjlist(AdjList al) {
+
8185 
+
8186  // Resizing the people
+
8187  agents_empty_graph(al.vcount());
+
8188 
+
8189  const auto & tmpdat = al.get_dat();
+
8190 
+
8191  for (size_t i = 0u; i < tmpdat.size(); ++i)
+
8192  {
+
8193 
+
8194  // population[i].id = i;
+
8195  population[i].model = this;
+
8196 
+
8197  for (const auto & link: tmpdat[i])
+
8198  {
+
8199 
+
8200  population[i].add_neighbor(
+
8201  population[link.first],
+
8202  true, true
+
8203  );
8204 
-
8205  return this->current_date;
-
8206 }
-
8207 
-
8208 template<typename TSeq>
-
8209 inline void Model<TSeq>::next() {
-
8210 
-
8211  db.record();
-
8212  ++this->current_date;
-
8213 
-
8214  // Advancing the progress bar
-
8215  if ((this->current_date >= 1) && verbose)
-
8216  pb.next();
+
8205  }
+
8206 
+
8207  }
+
8208 
+
8209  #ifdef EPI_DEBUG
+
8210  for (auto & p: population)
+
8211  {
+
8212  if (p.id >= static_cast<int>(al.vcount()))
+
8213  throw std::logic_error(
+
8214  "Agent's id cannot be negative above or equal to the number of agents!");
+
8215  }
+
8216  #endif
8217 
-
8218  return ;
-
8219 }
-
8220 
-
8221 template<typename TSeq>
-
8222 inline Model<TSeq> & Model<TSeq>::run(
-
8223  epiworld_fast_uint ndays,
-
8224  int seed
-
8225 )
-
8226 {
-
8227 
-
8228  if (size() == 0u)
-
8229  throw std::logic_error("There's no agents in this model!");
-
8230 
-
8231  if (nstates == 0u)
-
8232  throw std::logic_error(
-
8233  std::string("No states registered in this model. ") +
-
8234  std::string("At least one state should be included. See the function -Model::add_state()-")
-
8235  );
-
8236 
-
8237  // Setting up the number of steps
-
8238  this->ndays = ndays;
-
8239 
-
8240  if (seed >= 0)
-
8241  engine->seed(seed);
-
8242 
-
8243  array_double_tmp.resize(std::max(
-
8244  size(),
-
8245  static_cast<size_t>(1024 * 1024)
-
8246  ));
+
8218 }
+
8219 
+
8220 template<typename TSeq>
+
8221 inline bool Model<TSeq>::is_directed() const
+
8222 {
+
8223  if (population.size() == 0u)
+
8224  throw std::logic_error("The population hasn't been initialized.");
+
8225 
+
8226  return directed;
+
8227 }
+
8228 
+
8229 template<typename TSeq>
+
8230 inline int Model<TSeq>::today() const {
+
8231 
+
8232  if (ndays == 0)
+
8233  return 0;
+
8234 
+
8235  return this->current_date;
+
8236 }
+
8237 
+
8238 template<typename TSeq>
+
8239 inline void Model<TSeq>::next() {
+
8240 
+
8241  db.record();
+
8242  ++this->current_date;
+
8243 
+
8244  // Advancing the progress bar
+
8245  if ((this->current_date >= 1) && verbose)
+
8246  pb.next();
8247 
-
8248 
-
8249  array_virus_tmp.resize(1024);
-
8250  array_int_tmp.resize(1024 * 1024);
-
8251 
-
8252  // Checking whether the proposed state in/out/removed
-
8253  // are valid
-
8254  epiworld_fast_int _init, _end, _removed;
-
8255  int nstate_int = static_cast<int>(nstates);
-
8256  for (auto & v : viruses)
-
8257  {
-
8258  v->get_state(&_init, &_end, &_removed);
-
8259 
-
8260  // Negative unspecified state
-
8261  if (((_init != -99) && (_init < 0)) || (_init >= nstate_int))
-
8262  throw std::range_error("States must be between 0 and " +
-
8263  std::to_string(nstates - 1));
-
8264 
-
8265  // Negative unspecified state
-
8266  if (((_end != -99) && (_end < 0)) || (_end >= nstate_int))
-
8267  throw std::range_error("States must be between 0 and " +
-
8268  std::to_string(nstates - 1));
+
8248  return ;
+
8249 }
+
8250 
+
8251 template<typename TSeq>
+
8252 inline Model<TSeq> & Model<TSeq>::run(
+
8253  epiworld_fast_uint ndays,
+
8254  int seed
+
8255 )
+
8256 {
+
8257 
+
8258  if (size() == 0u)
+
8259  throw std::logic_error("There's no agents in this model!");
+
8260 
+
8261  if (nstates == 0u)
+
8262  throw std::logic_error(
+
8263  std::string("No states registered in this model. ") +
+
8264  std::string("At least one state should be included. See the function -Model::add_state()-")
+
8265  );
+
8266 
+
8267  // Setting up the number of steps
+
8268  this->ndays = ndays;
8269 
-
8270  if (((_removed != -99) && (_removed < 0)) || (_removed >= nstate_int))
-
8271  throw std::range_error("States must be between 0 and " +
-
8272  std::to_string(nstates - 1));
-
8273 
-
8274  }
-
8275 
-
8276  for (auto & t : tools)
-
8277  {
-
8278  t->get_state(&_init, &_end);
-
8279 
-
8280  // Negative unspecified state
-
8281  if (((_init != -99) && (_init < 0)) || (_init >= nstate_int))
-
8282  throw std::range_error("States must be between 0 and " +
-
8283  std::to_string(nstates - 1));
-
8284 
-
8285  // Negative unspecified state
-
8286  if (((_end != -99) && (_end < 0)) || (_end >= nstate_int))
-
8287  throw std::range_error("States must be between 0 and " +
-
8288  std::to_string(nstates - 1));
-
8289 
-
8290  }
-
8291 
-
8292  // Starting first infection and tools
-
8293  reset();
+
8270  if (seed >= 0)
+
8271  engine->seed(seed);
+
8272 
+
8273  array_double_tmp.resize(std::max(
+
8274  size(),
+
8275  static_cast<size_t>(1024 * 1024)
+
8276  ));
+
8277 
+
8278 
+
8279  array_virus_tmp.resize(1024);
+
8280  array_int_tmp.resize(1024 * 1024);
+
8281 
+
8282  // Checking whether the proposed state in/out/removed
+
8283  // are valid
+
8284  epiworld_fast_int _init, _end, _removed;
+
8285  int nstate_int = static_cast<int>(nstates);
+
8286  for (auto & v : viruses)
+
8287  {
+
8288  v->get_state(&_init, &_end, &_removed);
+
8289 
+
8290  // Negative unspecified state
+
8291  if (((_init != -99) && (_init < 0)) || (_init >= nstate_int))
+
8292  throw std::range_error("States must be between 0 and " +
+
8293  std::to_string(nstates - 1));
8294 
-
8295  // Initializing the simulation
-
8296  chrono_start();
-
8297  EPIWORLD_RUN((*this))
-
8298  {
+
8295  // Negative unspecified state
+
8296  if (((_end != -99) && (_end < 0)) || (_end >= nstate_int))
+
8297  throw std::range_error("States must be between 0 and " +
+
8298  std::to_string(nstates - 1));
8299 
-
8300  #ifdef EPI_DEBUG
-
8301  db.n_transmissions_potential = 0;
-
8302  db.n_transmissions_today = 0;
-
8303  #endif
-
8304 
-
8305  // We can execute these components in whatever order the
-
8306  // user needs.
-
8307  this->update_state();
-
8308 
-
8309  // We start with the Global events
-
8310  this->run_globalevents();
-
8311 
-
8312  // In this case we are applying degree sequence rewiring
-
8313  // to change the network just a bit.
-
8314  this->rewire();
-
8315 
-
8316  // This locks all the changes
-
8317  this->next();
-
8318 
-
8319  // Mutation must happen at the very end of all
-
8320  this->mutate_virus();
+
8300  if (((_removed != -99) && (_removed < 0)) || (_removed >= nstate_int))
+
8301  throw std::range_error("States must be between 0 and " +
+
8302  std::to_string(nstates - 1));
+
8303 
+
8304  }
+
8305 
+
8306  for (auto & t : tools)
+
8307  {
+
8308  t->get_state(&_init, &_end);
+
8309 
+
8310  // Negative unspecified state
+
8311  if (((_init != -99) && (_init < 0)) || (_init >= nstate_int))
+
8312  throw std::range_error("States must be between 0 and " +
+
8313  std::to_string(nstates - 1));
+
8314 
+
8315  // Negative unspecified state
+
8316  if (((_end != -99) && (_end < 0)) || (_end >= nstate_int))
+
8317  throw std::range_error("States must be between 0 and " +
+
8318  std::to_string(nstates - 1));
+
8319 
+
8320  }
8321 
-
8322  }
-
8323 
-
8324  // The last reaches the end...
-
8325  this->current_date--;
-
8326 
-
8327  chrono_end();
-
8328 
-
8329  return *this;
-
8330 
-
8331 }
-
8332 
-
8333 template<typename TSeq>
-
8334 inline void Model<TSeq>::run_multiple(
-
8335  epiworld_fast_uint ndays,
-
8336  epiworld_fast_uint nexperiments,
-
8337  int seed_,
-
8338  std::function<void(size_t,Model<TSeq>*)> fun,
-
8339  bool reset,
-
8340  bool verbose,
-
8341  #ifdef _OPENMP
-
8342  int nthreads
-
8343  #else
-
8344  int
-
8345  #endif
-
8346 )
-
8347 {
+
8322  // Starting first infection and tools
+
8323  reset();
+
8324 
+
8325  // Initializing the simulation
+
8326  chrono_start();
+
8327  EPIWORLD_RUN((*this))
+
8328  {
+
8329 
+
8330  #ifdef EPI_DEBUG
+
8331  db.n_transmissions_potential = 0;
+
8332  db.n_transmissions_today = 0;
+
8333  #endif
+
8334 
+
8335  // We can execute these components in whatever order the
+
8336  // user needs.
+
8337  this->update_state();
+
8338 
+
8339  // We start with the Global events
+
8340  this->run_globalevents();
+
8341 
+
8342  // In this case we are applying degree sequence rewiring
+
8343  // to change the network just a bit.
+
8344  this->rewire();
+
8345 
+
8346  // This locks all the changes
+
8347  this->next();
8348 
-
8349  if (seed_ >= 0)
-
8350  this->seed(seed_);
+
8349  // Mutation must happen at the very end of all
+
8350  this->mutate_virus();
8351 
-
8352  // Seeds will be reproducible by default
-
8353  std::vector< int > seeds_n(nexperiments);
-
8354  for (auto & s : seeds_n)
-
8355  {
-
8356  s = static_cast<int>(
-
8357  std::floor(
-
8358  runif() * static_cast<double>(std::numeric_limits<int>::max())
-
8359  )
-
8360  );
-
8361  }
-
8362  // #endif
-
8363 
-
8364  EPI_DEBUG_NOTIFY_ACTIVE()
-
8365 
-
8366  bool old_verb = this->verbose;
-
8367  verbose_off();
-
8368 
-
8369  // Setting up backup
-
8370  if (reset)
-
8371  set_backup();
-
8372 
-
8373  #ifdef _OPENMP
-
8374 
-
8375  omp_set_num_threads(nthreads);
-
8376 
-
8377  // Generating copies of the model
-
8378  std::vector< Model<TSeq> * > these;
-
8379  for (size_t i = 0; i < static_cast<size_t>(std::max(nthreads - 1, 0)); ++i)
-
8380  these.push_back(clone_ptr());
+
8352  }
+
8353 
+
8354  // The last reaches the end...
+
8355  this->current_date--;
+
8356 
+
8357  chrono_end();
+
8358 
+
8359  return *this;
+
8360 
+
8361 }
+
8362 
+
8363 template<typename TSeq>
+
8364 inline void Model<TSeq>::run_multiple(
+
8365  epiworld_fast_uint ndays,
+
8366  epiworld_fast_uint nexperiments,
+
8367  int seed_,
+
8368  std::function<void(size_t,Model<TSeq>*)> fun,
+
8369  bool reset,
+
8370  bool verbose,
+
8371  #ifdef _OPENMP
+
8372  int nthreads
+
8373  #else
+
8374  int
+
8375  #endif
+
8376 )
+
8377 {
+
8378 
+
8379  if (seed_ >= 0)
+
8380  this->seed(seed_);
8381 
-
8382  // Figuring out how many replicates
-
8383  std::vector< size_t > nreplicates(nthreads, 0);
-
8384  std::vector< size_t > nreplicates_csum(nthreads, 0);
-
8385  size_t sums = 0u;
-
8386  for (int i = 0; i < nthreads; ++i)
-
8387  {
-
8388  nreplicates[i] = static_cast<epiworld_fast_uint>(
-
8389  std::floor(nexperiments/nthreads)
-
8390  );
-
8391 
-
8392  // This takes the cumsum
-
8393  nreplicates_csum[i] = sums;
-
8394 
-
8395  sums += nreplicates[i];
-
8396 
-
8397  }
+
8382  // Seeds will be reproducible by default
+
8383  std::vector< int > seeds_n(nexperiments);
+
8384  for (auto & s : seeds_n)
+
8385  {
+
8386  s = static_cast<int>(
+
8387  std::floor(
+
8388  runif() * static_cast<double>(std::numeric_limits<int>::max())
+
8389  )
+
8390  );
+
8391  }
+
8392  // #endif
+
8393 
+
8394  EPI_DEBUG_NOTIFY_ACTIVE()
+
8395 
+
8396  bool old_verb = this->verbose;
+
8397  verbose_off();
8398 
-
8399  if (sums < nexperiments)
-
8400  nreplicates[nthreads - 1] += (nexperiments - sums);
-
8401 
-
8402  Progress pb_multiple(
-
8403  nreplicates[0u],
-
8404  EPIWORLD_PROGRESS_BAR_WIDTH
-
8405  );
+
8399  // Setting up backup
+
8400  if (reset)
+
8401  set_backup();
+
8402 
+
8403  #ifdef _OPENMP
+
8404 
+
8405  omp_set_num_threads(nthreads);
8406 
-
8407  if (verbose)
-
8408  {
-
8409 
-
8410  printf_epiworld(
-
8411  "Starting multiple runs (%i) using %i thread(s)\n",
-
8412  static_cast<int>(nexperiments),
-
8413  static_cast<int>(nthreads)
-
8414  );
-
8415 
-
8416  pb_multiple.start();
-
8417 
-
8418  }
-
8419 
-
8420  #ifdef EPI_DEBUG
-
8421  // Checking the initial state of all the models. Throw an
-
8422  // exception if they are not the same.
-
8423  for (size_t i = 1; i < static_cast<size_t>(std::max(nthreads - 1, 0)); ++i)
-
8424  {
-
8425 
-
8426  if (db != these[i]->db)
-
8427  {
-
8428  throw std::runtime_error(
-
8429  "The initial state of the models is not the same"
-
8430  );
-
8431  }
-
8432  }
-
8433  #endif
-
8434 
-
8435  #pragma omp parallel shared(these, nreplicates, nreplicates_csum, seeds_n) \
-
8436  firstprivate(nexperiments, nthreads, fun, reset, verbose, pb_multiple, ndays) \
-
8437  default(shared)
+
8407  // Generating copies of the model
+
8408  std::vector< Model<TSeq> * > these;
+
8409  for (size_t i = 0; i < static_cast<size_t>(std::max(nthreads - 1, 0)); ++i)
+
8410  these.push_back(clone_ptr());
+
8411 
+
8412  // Figuring out how many replicates
+
8413  std::vector< size_t > nreplicates(nthreads, 0);
+
8414  std::vector< size_t > nreplicates_csum(nthreads, 0);
+
8415  size_t sums = 0u;
+
8416  for (int i = 0; i < nthreads; ++i)
+
8417  {
+
8418  nreplicates[i] = static_cast<epiworld_fast_uint>(
+
8419  std::floor(nexperiments/nthreads)
+
8420  );
+
8421 
+
8422  // This takes the cumsum
+
8423  nreplicates_csum[i] = sums;
+
8424 
+
8425  sums += nreplicates[i];
+
8426 
+
8427  }
+
8428 
+
8429  if (sums < nexperiments)
+
8430  nreplicates[nthreads - 1] += (nexperiments - sums);
+
8431 
+
8432  Progress pb_multiple(
+
8433  nreplicates[0u],
+
8434  EPIWORLD_PROGRESS_BAR_WIDTH
+
8435  );
+
8436 
+
8437  if (verbose)
8438  {
8439 
-
8440  auto iam = omp_get_thread_num();
-
8441 
-
8442  for (size_t n = 0u; n < nreplicates[iam]; ++n)
-
8443  {
-
8444  size_t sim_id = nreplicates_csum[iam] + n;
-
8445  if (iam == 0)
-
8446  {
+
8440  printf_epiworld(
+
8441  "Starting multiple runs (%i) using %i thread(s)\n",
+
8442  static_cast<int>(nexperiments),
+
8443  static_cast<int>(nthreads)
+
8444  );
+
8445 
+
8446  pb_multiple.start();
8447 
-
8448  // Initializing the seed
-
8449  run(ndays, seeds_n[sim_id]);
-
8450 
-
8451  if (fun)
-
8452  fun(n, this);
-
8453 
-
8454  // Only the first one prints
-
8455  if (verbose)
-
8456  pb_multiple.next();
-
8457 
-
8458  } else {
-
8459 
-
8460  // Initializing the seed
-
8461  these[iam - 1]->run(ndays, seeds_n[sim_id]);
-
8462 
-
8463  if (fun)
-
8464  fun(sim_id, these[iam - 1]);
-
8465 
-
8466  }
-
8467 
-
8468  }
-
8469 
-
8470  }
+
8448  }
+
8449 
+
8450  #ifdef EPI_DEBUG
+
8451  // Checking the initial state of all the models. Throw an
+
8452  // exception if they are not the same.
+
8453  for (size_t i = 1; i < static_cast<size_t>(std::max(nthreads - 1, 0)); ++i)
+
8454  {
+
8455 
+
8456  if (db != these[i]->db)
+
8457  {
+
8458  throw std::runtime_error(
+
8459  "The initial state of the models is not the same"
+
8460  );
+
8461  }
+
8462  }
+
8463  #endif
+
8464 
+
8465  #pragma omp parallel shared(these, nreplicates, nreplicates_csum, seeds_n) \
+
8466  firstprivate(nexperiments, nthreads, fun, reset, verbose, pb_multiple, ndays) \
+
8467  default(shared)
+
8468  {
+
8469 
+
8470  auto iam = omp_get_thread_num();
8471 
-
8472  // Adjusting the number of replicates
-
8473  n_replicates += (nexperiments - nreplicates[0u]);
-
8474 
-
8475  for (auto & ptr : these)
-
8476  delete ptr;
+
8472  for (size_t n = 0u; n < nreplicates[iam]; ++n)
+
8473  {
+
8474  size_t sim_id = nreplicates_csum[iam] + n;
+
8475  if (iam == 0)
+
8476  {
8477 
-
8478  #else
-
8479  // if (reset)
-
8480  // set_backup();
-
8481 
-
8482  Progress pb_multiple(
-
8483  nexperiments,
-
8484  EPIWORLD_PROGRESS_BAR_WIDTH
-
8485  )
-
8486  ;
-
8487  if (verbose)
-
8488  {
+
8478  // Initializing the seed
+
8479  run(ndays, seeds_n[sim_id]);
+
8480 
+
8481  if (fun)
+
8482  fun(n, this);
+
8483 
+
8484  // Only the first one prints
+
8485  if (verbose)
+
8486  pb_multiple.next();
+
8487 
+
8488  } else {
8489 
-
8490  printf_epiworld(
-
8491  "Starting multiple runs (%i)\n",
-
8492  static_cast<int>(nexperiments)
-
8493  );
-
8494 
-
8495  pb_multiple.start();
-
8496 
-
8497  }
-
8498 
-
8499  for (size_t n = 0u; n < nexperiments; ++n)
-
8500  {
+
8490  // Initializing the seed
+
8491  these[iam - 1]->run(ndays, seeds_n[sim_id]);
+
8492 
+
8493  if (fun)
+
8494  fun(sim_id, these[iam - 1]);
+
8495 
+
8496  }
+
8497 
+
8498  }
+
8499 
+
8500  }
8501 
-
8502  run(ndays, seeds_n[n]);
-
8503 
-
8504  if (fun)
-
8505  fun(n, this);
-
8506 
-
8507  if (verbose)
-
8508  pb_multiple.next();
-
8509 
-
8510  }
-
8511  #endif
-
8512 
-
8513  if (verbose)
-
8514  pb_multiple.end();
-
8515 
-
8516  if (old_verb)
-
8517  verbose_on();
-
8518 
-
8519  return;
-
8520 
-
8521 }
-
8522 
-
8523 template<typename TSeq>
-
8524 inline void Model<TSeq>::update_state() {
-
8525 
-
8526  // Next state
-
8527  if (use_queuing)
-
8528  {
-
8529  int i = -1;
-
8530  for (auto & p: population)
-
8531  if (queue[++i] > 0)
-
8532  {
-
8533  if (state_fun[p.state])
-
8534  state_fun[p.state](&p, this);
-
8535  }
+
8502  // Adjusting the number of replicates
+
8503  n_replicates += (nexperiments - nreplicates[0u]);
+
8504 
+
8505  for (auto & ptr : these)
+
8506  delete ptr;
+
8507 
+
8508  #else
+
8509  // if (reset)
+
8510  // set_backup();
+
8511 
+
8512  Progress pb_multiple(
+
8513  nexperiments,
+
8514  EPIWORLD_PROGRESS_BAR_WIDTH
+
8515  )
+
8516  ;
+
8517  if (verbose)
+
8518  {
+
8519 
+
8520  printf_epiworld(
+
8521  "Starting multiple runs (%i)\n",
+
8522  static_cast<int>(nexperiments)
+
8523  );
+
8524 
+
8525  pb_multiple.start();
+
8526 
+
8527  }
+
8528 
+
8529  for (size_t n = 0u; n < nexperiments; ++n)
+
8530  {
+
8531 
+
8532  run(ndays, seeds_n[n]);
+
8533 
+
8534  if (fun)
+
8535  fun(n, this);
8536 
-
8537  }
-
8538  else
-
8539  {
-
8540 
-
8541  for (auto & p: population)
-
8542  if (state_fun[p.state])
-
8543  state_fun[p.state](&p, this);
-
8544 
-
8545  }
-
8546 
-
8547  events_run();
-
8548 
-
8549 }
+
8537  if (verbose)
+
8538  pb_multiple.next();
+
8539 
+
8540  }
+
8541  #endif
+
8542 
+
8543  if (verbose)
+
8544  pb_multiple.end();
+
8545 
+
8546  if (old_verb)
+
8547  verbose_on();
+
8548 
+
8549  return;
8550 
-
8551 
+
8551 }
8552 
8553 template<typename TSeq>
-
8554 inline void Model<TSeq>::mutate_virus() {
+
8554 inline void Model<TSeq>::update_state() {
8555 
-
8556  // Checking if any virus has mutation
-
8557  size_t nmutates = 0u;
-
8558  for (const auto & v: viruses)
-
8559  if (v->mutation_fun)
-
8560  nmutates++;
-
8561 
-
8562  if (nmutates == 0u)
-
8563  return;
-
8564 
-
8565  if (use_queuing)
-
8566  {
-
8567 
-
8568  int i = -1;
-
8569  for (auto & p: population)
-
8570  {
-
8571 
-
8572  if (queue[++i] == 0)
-
8573  continue;
+
8556  // Next state
+
8557  if (use_queuing)
+
8558  {
+
8559  int i = -1;
+
8560  for (auto & p: population)
+
8561  if (queue[++i] > 0)
+
8562  {
+
8563  if (state_fun[p.state])
+
8564  state_fun[p.state](&p, this);
+
8565  }
+
8566 
+
8567  }
+
8568  else
+
8569  {
+
8570 
+
8571  for (auto & p: population)
+
8572  if (state_fun[p.state])
+
8573  state_fun[p.state](&p, this);
8574 
-
8575  if (p.virus != nullptr)
-
8576  p.virus->mutate(this);
-
8577 
-
8578  }
-
8579 
-
8580  }
-
8581  else
-
8582  {
-
8583 
-
8584  for (auto & p: population)
-
8585  {
-
8586 
-
8587  if (p.virus != nullptr)
-
8588  p.virus->mutate(this);
-
8589 
-
8590  }
+
8575  }
+
8576 
+
8577  events_run();
+
8578 
+
8579 }
+
8580 
+
8581 
+
8582 
+
8583 template<typename TSeq>
+
8584 inline void Model<TSeq>::mutate_virus() {
+
8585 
+
8586  // Checking if any virus has mutation
+
8587  size_t nmutates = 0u;
+
8588  for (const auto & v: viruses)
+
8589  if (v->mutation_fun)
+
8590  nmutates++;
8591 
-
8592  }
-
8593 
+
8592  if (nmutates == 0u)
+
8593  return;
8594 
-
8595 }
-
8596 
-
8597 template<typename TSeq>
-
8598 inline size_t Model<TSeq>::get_n_viruses() const {
-
8599  return db.size();
-
8600 }
+
8595  if (use_queuing)
+
8596  {
+
8597 
+
8598  int i = -1;
+
8599  for (auto & p: population)
+
8600  {
8601 
-
8602 template<typename TSeq>
-
8603 inline size_t Model<TSeq>::get_n_tools() const {
-
8604  return tools.size();
-
8605 }
-
8606 
-
8607 template<typename TSeq>
-
8608 inline epiworld_fast_uint Model<TSeq>::get_ndays() const {
-
8609  return ndays;
-
8610 }
-
8611 
-
8612 template<typename TSeq>
-
8613 inline epiworld_fast_uint Model<TSeq>::get_n_replicates() const
-
8614 {
-
8615  return n_replicates;
-
8616 }
-
8617 
-
8618 template<typename TSeq>
-
8619 inline void Model<TSeq>::set_ndays(epiworld_fast_uint ndays) {
-
8620  this->ndays = ndays;
-
8621 }
-
8622 
-
8623 template<typename TSeq>
-
8624 inline bool Model<TSeq>::get_verbose() const {
-
8625  return verbose;
-
8626 }
-
8627 
-
8628 template<typename TSeq>
-
8629 inline Model<TSeq> & Model<TSeq>::verbose_on() {
-
8630  verbose = true;
-
8631  return *this;
-
8632 }
-
8633 
-
8634 template<typename TSeq>
-
8635 inline Model<TSeq> & Model<TSeq>::verbose_off() {
-
8636  verbose = false;
-
8637  return *this;
-
8638 }
-
8639 
-
8640 template<typename TSeq>
-
8641 inline void Model<TSeq>::set_rewire_fun(
-
8642  std::function<void(std::vector<Agent<TSeq>>*,Model<TSeq>*,epiworld_double)> fun
-
8643  ) {
-
8644  rewire_fun = fun;
-
8645 }
-
8646 
-
8647 template<typename TSeq>
-
8648 inline void Model<TSeq>::set_rewire_prop(epiworld_double prop)
-
8649 {
-
8650 
-
8651  if (prop < 0.0)
-
8652  throw std::range_error("Proportions cannot be negative.");
-
8653 
-
8654  if (prop > 1.0)
-
8655  throw std::range_error("Proportions cannot be above 1.0.");
-
8656 
-
8657  rewire_prop = prop;
-
8658 }
-
8659 
-
8660 template<typename TSeq>
-
8661 inline epiworld_double Model<TSeq>::get_rewire_prop() const {
-
8662  return rewire_prop;
-
8663 }
-
8664 
-
8665 template<typename TSeq>
-
8666 inline void Model<TSeq>::rewire() {
-
8667 
-
8668  if (rewire_fun)
-
8669  rewire_fun(&population, this, rewire_prop);
-
8670 }
-
8671 
-
8672 
-
8673 template<typename TSeq>
-
8674 inline void Model<TSeq>::write_data(
-
8675  std::string fn_virus_info,
-
8676  std::string fn_virus_hist,
-
8677  std::string fn_tool_info,
-
8678  std::string fn_tool_hist,
-
8679  std::string fn_total_hist,
-
8680  std::string fn_transmission,
-
8681  std::string fn_transition,
-
8682  std::string fn_reproductive_number,
-
8683  std::string fn_generation_time
-
8684  ) const
-
8685 {
+
8602  if (queue[++i] == 0)
+
8603  continue;
+
8604 
+
8605  if (p.virus != nullptr)
+
8606  p.virus->mutate(this);
+
8607 
+
8608  }
+
8609 
+
8610  }
+
8611  else
+
8612  {
+
8613 
+
8614  for (auto & p: population)
+
8615  {
+
8616 
+
8617  if (p.virus != nullptr)
+
8618  p.virus->mutate(this);
+
8619 
+
8620  }
+
8621 
+
8622  }
+
8623 
+
8624 
+
8625 }
+
8626 
+
8627 template<typename TSeq>
+
8628 inline size_t Model<TSeq>::get_n_viruses() const {
+
8629  return db.size();
+
8630 }
+
8631 
+
8632 template<typename TSeq>
+
8633 inline size_t Model<TSeq>::get_n_tools() const {
+
8634  return tools.size();
+
8635 }
+
8636 
+
8637 template<typename TSeq>
+
8638 inline epiworld_fast_uint Model<TSeq>::get_ndays() const {
+
8639  return ndays;
+
8640 }
+
8641 
+
8642 template<typename TSeq>
+
8643 inline epiworld_fast_uint Model<TSeq>::get_n_replicates() const
+
8644 {
+
8645  return n_replicates;
+
8646 }
+
8647 
+
8648 template<typename TSeq>
+
8649 inline void Model<TSeq>::set_ndays(epiworld_fast_uint ndays) {
+
8650  this->ndays = ndays;
+
8651 }
+
8652 
+
8653 template<typename TSeq>
+
8654 inline bool Model<TSeq>::get_verbose() const {
+
8655  return verbose;
+
8656 }
+
8657 
+
8658 template<typename TSeq>
+
8659 inline Model<TSeq> & Model<TSeq>::verbose_on() {
+
8660  verbose = true;
+
8661  return *this;
+
8662 }
+
8663 
+
8664 template<typename TSeq>
+
8665 inline Model<TSeq> & Model<TSeq>::verbose_off() {
+
8666  verbose = false;
+
8667  return *this;
+
8668 }
+
8669 
+
8670 template<typename TSeq>
+
8671 inline void Model<TSeq>::set_rewire_fun(
+
8672  std::function<void(std::vector<Agent<TSeq>>*,Model<TSeq>*,epiworld_double)> fun
+
8673  ) {
+
8674  rewire_fun = fun;
+
8675 }
+
8676 
+
8677 template<typename TSeq>
+
8678 inline void Model<TSeq>::set_rewire_prop(epiworld_double prop)
+
8679 {
+
8680 
+
8681  if (prop < 0.0)
+
8682  throw std::range_error("Proportions cannot be negative.");
+
8683 
+
8684  if (prop > 1.0)
+
8685  throw std::range_error("Proportions cannot be above 1.0.");
8686 
-
8687  db.write_data(
-
8688  fn_virus_info, fn_virus_hist,
-
8689  fn_tool_info, fn_tool_hist,
-
8690  fn_total_hist, fn_transmission, fn_transition,
-
8691  fn_reproductive_number, fn_generation_time
-
8692  );
-
8693 
-
8694 }
-
8695 
-
8696 template<typename TSeq>
-
8697 inline void Model<TSeq>::write_edgelist(
-
8698  std::string fn
-
8699  ) const
-
8700 {
+
8687  rewire_prop = prop;
+
8688 }
+
8689 
+
8690 template<typename TSeq>
+
8691 inline epiworld_double Model<TSeq>::get_rewire_prop() const {
+
8692  return rewire_prop;
+
8693 }
+
8694 
+
8695 template<typename TSeq>
+
8696 inline void Model<TSeq>::rewire() {
+
8697 
+
8698  if (rewire_fun)
+
8699  rewire_fun(&population, this, rewire_prop);
+
8700 }
8701 
-
8702  // Figuring out the writing sequence
-
8703  std::vector< const Agent<TSeq> * > wseq(size());
-
8704  for (const auto & p: population)
-
8705  wseq[p.id] = &p;
-
8706 
-
8707  std::ofstream efile(fn, std::ios_base::out);
-
8708  efile << "source target\n";
-
8709  if (this->is_directed())
-
8710  {
-
8711 
-
8712  for (const auto & p : wseq)
-
8713  {
-
8714  for (auto & n : p->neighbors)
-
8715  efile << p->id << " " << n << "\n";
-
8716  }
-
8717 
-
8718  } else {
-
8719 
-
8720  for (const auto & p : wseq)
-
8721  {
-
8722  for (auto & n : p->neighbors)
-
8723  if (static_cast<int>(p->id) <= static_cast<int>(n))
-
8724  efile << p->id << " " << n << "\n";
-
8725  }
-
8726 
-
8727  }
-
8728 
-
8729 }
-
8730 
-
8731 template<typename TSeq>
-
8732 inline void Model<TSeq>::write_edgelist(
-
8733 std::vector< int > & source,
-
8734 std::vector< int > & target
-
8735 ) const {
+
8702 
+
8703 template<typename TSeq>
+
8704 inline void Model<TSeq>::write_data(
+
8705  std::string fn_virus_info,
+
8706  std::string fn_virus_hist,
+
8707  std::string fn_tool_info,
+
8708  std::string fn_tool_hist,
+
8709  std::string fn_total_hist,
+
8710  std::string fn_transmission,
+
8711  std::string fn_transition,
+
8712  std::string fn_reproductive_number,
+
8713  std::string fn_generation_time
+
8714  ) const
+
8715 {
+
8716 
+
8717  db.write_data(
+
8718  fn_virus_info, fn_virus_hist,
+
8719  fn_tool_info, fn_tool_hist,
+
8720  fn_total_hist, fn_transmission, fn_transition,
+
8721  fn_reproductive_number, fn_generation_time
+
8722  );
+
8723 
+
8724 }
+
8725 
+
8726 template<typename TSeq>
+
8727 inline void Model<TSeq>::write_edgelist(
+
8728  std::string fn
+
8729  ) const
+
8730 {
+
8731 
+
8732  // Figuring out the writing sequence
+
8733  std::vector< const Agent<TSeq> * > wseq(size());
+
8734  for (const auto & p: population)
+
8735  wseq[p.id] = &p;
8736 
-
8737  // Figuring out the writing sequence
-
8738  std::vector< const Agent<TSeq> * > wseq(size());
-
8739  for (const auto & p: population)
-
8740  wseq[p.id] = &p;
+
8737  std::ofstream efile(fn, std::ios_base::out);
+
8738  efile << "source target\n";
+
8739  if (this->is_directed())
+
8740  {
8741 
-
8742  if (this->is_directed())
-
8743  {
-
8744 
-
8745  for (const auto & p : wseq)
-
8746  {
-
8747  for (auto & n : p->neighbors)
-
8748  {
-
8749  source.push_back(static_cast<int>(p->id));
-
8750  target.push_back(static_cast<int>(n));
-
8751  }
-
8752  }
-
8753 
-
8754  } else {
-
8755 
-
8756  for (const auto & p : wseq)
-
8757  {
-
8758  for (auto & n : p->neighbors) {
-
8759  if (static_cast<int>(p->id) <= static_cast<int>(n)) {
-
8760  source.push_back(static_cast<int>(p->id));
-
8761  target.push_back(static_cast<int>(n));
-
8762  }
-
8763  }
-
8764  }
-
8765 
-
8766  }
-
8767 
-
8768 
-
8769 }
-
8770 
-
8771 template<typename TSeq>
-
8772 inline std::map<std::string,epiworld_double> & Model<TSeq>::params()
-
8773 {
-
8774  return parameters;
-
8775 }
-
8776 
-
8777 template<typename TSeq>
-
8778 inline void Model<TSeq>::reset() {
-
8779 
-
8780  // Restablishing people
-
8781  pb = Progress(ndays, 80);
-
8782 
-
8783  if (population_backup.size() != 0u)
-
8784  {
-
8785  population = population_backup;
-
8786 
-
8787  #ifdef EPI_DEBUG
-
8788  for (size_t i = 0; i < population.size(); ++i)
-
8789  {
-
8790 
-
8791  if (population[i] != population_backup[i])
-
8792  throw std::logic_error("Model::reset population doesn't match.");
-
8793 
+
8742  for (const auto & p : wseq)
+
8743  {
+
8744  for (auto & n : p->neighbors)
+
8745  efile << p->id << " " << n << "\n";
+
8746  }
+
8747 
+
8748  } else {
+
8749 
+
8750  for (const auto & p : wseq)
+
8751  {
+
8752  for (auto & n : p->neighbors)
+
8753  if (static_cast<int>(p->id) <= static_cast<int>(n))
+
8754  efile << p->id << " " << n << "\n";
+
8755  }
+
8756 
+
8757  }
+
8758 
+
8759 }
+
8760 
+
8761 template<typename TSeq>
+
8762 inline void Model<TSeq>::write_edgelist(
+
8763 std::vector< int > & source,
+
8764 std::vector< int > & target
+
8765 ) const {
+
8766 
+
8767  // Figuring out the writing sequence
+
8768  std::vector< const Agent<TSeq> * > wseq(size());
+
8769  for (const auto & p: population)
+
8770  wseq[p.id] = &p;
+
8771 
+
8772  if (this->is_directed())
+
8773  {
+
8774 
+
8775  for (const auto & p : wseq)
+
8776  {
+
8777  for (auto & n : p->neighbors)
+
8778  {
+
8779  source.push_back(static_cast<int>(p->id));
+
8780  target.push_back(static_cast<int>(n));
+
8781  }
+
8782  }
+
8783 
+
8784  } else {
+
8785 
+
8786  for (const auto & p : wseq)
+
8787  {
+
8788  for (auto & n : p->neighbors) {
+
8789  if (static_cast<int>(p->id) <= static_cast<int>(n)) {
+
8790  source.push_back(static_cast<int>(p->id));
+
8791  target.push_back(static_cast<int>(n));
+
8792  }
+
8793  }
8794  }
-
8795  #endif
-
8796 
-
8797  }
+
8795 
+
8796  }
+
8797 
8798 
-
8799  for (auto & p : population)
-
8800  p.reset();
-
8801 
-
8802  #ifdef EPI_DEBUG
-
8803  for (auto & a: population)
-
8804  {
-
8805  if (a.get_state() != 0u)
-
8806  throw std::logic_error("Model::reset population doesn't match."
-
8807  "Some agents are not in the baseline state.");
-
8808  }
-
8809  #endif
-
8810 
-
8811  if (entities_backup.size() != 0)
-
8812  {
-
8813  entities = entities_backup;
-
8814 
-
8815  #ifdef EPI_DEBUG
-
8816  for (size_t i = 0; i < entities.size(); ++i)
-
8817  {
-
8818 
-
8819  if (entities[i] != entities_backup[i])
-
8820  throw std::logic_error("Model::reset entities don't match.");
-
8821 
-
8822  }
-
8823  #endif
-
8824 
-
8825  }
+
8799 }
+
8800 
+
8801 template<typename TSeq>
+
8802 inline std::map<std::string,epiworld_double> & Model<TSeq>::params()
+
8803 {
+
8804  return parameters;
+
8805 }
+
8806 
+
8807 template<typename TSeq>
+
8808 inline void Model<TSeq>::reset() {
+
8809 
+
8810  // Restablishing people
+
8811  pb = Progress(ndays, 80);
+
8812 
+
8813  if (population_backup.size() != 0u)
+
8814  {
+
8815  population = population_backup;
+
8816 
+
8817  #ifdef EPI_DEBUG
+
8818  for (size_t i = 0; i < population.size(); ++i)
+
8819  {
+
8820 
+
8821  if (population[i] != population_backup[i])
+
8822  throw std::logic_error("Model::reset population doesn't match.");
+
8823 
+
8824  }
+
8825  #endif
8826 
-
8827  for (auto & e: entities)
-
8828  e.reset();
-
8829 
-
8830  current_date = 0;
+
8827  }
+
8828 
+
8829  for (auto & p : population)
+
8830  p.reset();
8831 
-
8832  db.reset();
-
8833 
-
8834  // This also clears the queue
-
8835  if (use_queuing)
-
8836  queue.reset();
-
8837 
-
8838  // Re distributing tools and virus
-
8839  dist_virus();
-
8840  dist_tools();
-
8841  dist_entities();
-
8842 
-
8843  // Distributing initial state, if specified
-
8844  initial_states_fun(this);
-
8845 
-
8846  // Recording the original state (at time 0) and advancing
-
8847  // to time 1
-
8848  next();
-
8849 
-
8850 
-
8851 }
-
8852 
-
8853 // Too big to keep here
-
8854 /*//////////////////////////////////////////////////////////////////////////////
-
8856 
-
8857  Start of -include/epiworld//model-meat-print.hpp-
-
8858 
-
8861 
-
8862 
-
8863 #ifndef EPIWORLD_MODEL_MEAT_PRINT_HPP
-
8864 #define EPIWORLD_MODEL_MEAT_PRINT_HPP
-
8865 
-
8866 template<typename TSeq>
-
8867 inline const Model<TSeq> & Model<TSeq>::print(bool lite) const
-
8868 {
-
8869 
-
8870  // Horizontal line
-
8871  std::string line = "";
-
8872  for (epiworld_fast_uint i = 0u; i < 80u; ++i)
-
8873  line += "_";
-
8874 
-
8875  // Prints a message if debugging is on
-
8876  EPI_DEBUG_NOTIFY_ACTIVE()
-
8877 
-
8878  printf_epiworld("%s\n",line.c_str());
-
8879 
-
8880  if (lite)
-
8881  {
-
8882  // Printing the name of the model
-
8883  printf_epiworld("%s", name.c_str());
-
8884 
-
8885  // Printing the number of agents, viruses, and tools
-
8886  printf_epiworld(
-
8887  "\nIt features %i agents, %i virus(es), and %i tool(s).\n",
-
8888  static_cast<int>(size()),
-
8889  static_cast<int>(get_n_viruses()),
-
8890  static_cast<int>(get_n_tools())
-
8891  );
+
8832  #ifdef EPI_DEBUG
+
8833  for (auto & a: population)
+
8834  {
+
8835  if (a.get_state() != 0u)
+
8836  throw std::logic_error("Model::reset population doesn't match."
+
8837  "Some agents are not in the baseline state.");
+
8838  }
+
8839  #endif
+
8840 
+
8841  if (entities_backup.size() != 0)
+
8842  {
+
8843  entities = entities_backup;
+
8844 
+
8845  #ifdef EPI_DEBUG
+
8846  for (size_t i = 0; i < entities.size(); ++i)
+
8847  {
+
8848 
+
8849  if (entities[i] != entities_backup[i])
+
8850  throw std::logic_error("Model::reset entities don't match.");
+
8851 
+
8852  }
+
8853  #endif
+
8854 
+
8855  }
+
8856 
+
8857  for (auto & e: entities)
+
8858  e.reset();
+
8859 
+
8860  current_date = 0;
+
8861 
+
8862  db.reset();
+
8863 
+
8864  // This also clears the queue
+
8865  if (use_queuing)
+
8866  queue.reset();
+
8867 
+
8868  // Re distributing tools and virus
+
8869  dist_virus();
+
8870  dist_tools();
+
8871  dist_entities();
+
8872 
+
8873  // Distributing initial state, if specified
+
8874  initial_states_fun(this);
+
8875 
+
8876  // Recording the original state (at time 0) and advancing
+
8877  // to time 1
+
8878  next();
+
8879 
+
8880 
+
8881 }
+
8882 
+
8883 // Too big to keep here
+
8884 /*//////////////////////////////////////////////////////////////////////////////
+
8886 
+
8887  Start of -include/epiworld//model-meat-print.hpp-
+
8888 
+
8891 
8892 
-
8893  printf_epiworld(
-
8894  "The model has %i states.",
-
8895  static_cast<int>(nstates)
-
8896  );
-
8897 
-
8898  if (today() != 0)
-
8899  {
-
8900  printf_epiworld(
-
8901  "\nThe final distribution is: "
-
8902  );
-
8903 
-
8904  int nstate_int = static_cast<int>(nstates);
-
8905 
-
8906  for (int i = 0u; i < nstate_int; ++i)
-
8907  {
-
8908  printf_epiworld(
-
8909  "%i %s%s",
-
8910  static_cast<int>(db.today_total[ i ]),
-
8911  states_labels[i].c_str(),
-
8912  (
-
8913  i == (nstate_int - 2)
-
8914  ) ? ", and " : (
-
8915  (i == (nstate_int - 1)) ? ".\n" : ", "
-
8916  )
-
8917  );
-
8918  }
-
8919  } else {
-
8920  printf_epiworld(" The model hasn't been run yet.\n");
-
8921  }
+
8893 #ifndef EPIWORLD_MODEL_MEAT_PRINT_HPP
+
8894 #define EPIWORLD_MODEL_MEAT_PRINT_HPP
+
8895 
+
8896 template<typename TSeq>
+
8897 inline const Model<TSeq> & Model<TSeq>::print(bool lite) const
+
8898 {
+
8899 
+
8900  // Horizontal line
+
8901  std::string line = "";
+
8902  for (epiworld_fast_uint i = 0u; i < 80u; ++i)
+
8903  line += "_";
+
8904 
+
8905  // Prints a message if debugging is on
+
8906  EPI_DEBUG_NOTIFY_ACTIVE()
+
8907 
+
8908  printf_epiworld("%s\n",line.c_str());
+
8909 
+
8910  if (lite)
+
8911  {
+
8912  // Printing the name of the model
+
8913  printf_epiworld("%s", name.c_str());
+
8914 
+
8915  // Printing the number of agents, viruses, and tools
+
8916  printf_epiworld(
+
8917  "\nIt features %i agents, %i virus(es), and %i tool(s).\n",
+
8918  static_cast<int>(size()),
+
8919  static_cast<int>(get_n_viruses()),
+
8920  static_cast<int>(get_n_tools())
+
8921  );
8922 
-
8923  return *this;
-
8924  }
-
8925 
-
8926  printf_epiworld("%s\n%s\n\n",line.c_str(), "SIMULATION STUDY");
+
8923  printf_epiworld(
+
8924  "The model has %i states.",
+
8925  static_cast<int>(nstates)
+
8926  );
8927 
-
8928  printf_epiworld("Name of the model : %s\n", (this->name == "") ? std::string("(none)").c_str() : name.c_str());
-
8929  printf_epiworld("Population size : %i\n", static_cast<int>(size()));
-
8930 
-
8931  auto ncols = get_agents_data_ncols();
-
8932 
-
8933  if (ncols > 0)
-
8934  {
-
8935  printf_epiworld("Agents' data loaded : yes (%i columns/features)\n", static_cast<int>(ncols));
-
8936  }
-
8937  else
-
8938  {
-
8939  printf_epiworld("Agents' data : (none)\n");
-
8940  }
-
8941 
-
8942  printf_epiworld("Number of entities : %i\n", static_cast<int>(entities.size()));
-
8943  printf_epiworld("Days (duration) : %i (of %i)\n", today(), static_cast<int>(ndays));
-
8944  printf_epiworld("Number of viruses : %i\n", static_cast<int>(db.get_n_viruses()));
-
8945  if (n_replicates > 0u)
-
8946  {
-
8947  std::string abbr;
-
8948  epiworld_double elapsed;
-
8949  epiworld_double total;
-
8950  get_elapsed("auto", &elapsed, &total, &abbr, false);
-
8951  printf_epiworld("Last run elapsed t : %.2f%s\n", elapsed, abbr.c_str());
-
8952  if (n_replicates > 1u)
-
8953  {
-
8954  printf_epiworld("Total elapsed t : %.2f%s (%i runs)\n", total, abbr.c_str(), static_cast<int>(n_replicates));
-
8955  }
-
8956 
-
8957  // Elapsed time in speed
-
8958  get_elapsed("microseconds", &elapsed, &total, &abbr, false);
-
8959  printf_epiworld("Last run speed : %.2f million agents x day / second\n",
-
8960  static_cast<double>(this->size()) *
-
8961  static_cast<double>(this->get_ndays()) /
-
8962  static_cast<double>(elapsed)
-
8963  );
-
8964  if (n_replicates > 1u)
-
8965  {
-
8966  printf_epiworld("Average run speed : %.2f million agents x day / second\n",
-
8967  static_cast<double>(this->size()) *
-
8968  static_cast<double>(this->get_ndays()) *
-
8969  static_cast<double>(n_replicates) /
-
8970  static_cast<double>(total)
-
8971  );
-
8972  }
-
8973 
-
8974  } else {
-
8975  printf_epiworld("Last run elapsed t : -\n");
-
8976  }
-
8977 
-
8978 
-
8979  if (rewire_fun)
-
8980  {
-
8981  printf_epiworld("Rewiring : on (%.2f)\n\n", rewire_prop);
-
8982  } else {
-
8983  printf_epiworld("Rewiring : off\n\n");
-
8984  }
-
8985 
-
8986  // Printing Global events
-
8987  printf_epiworld("Global events:\n");
-
8988  for (auto & a : globalevents)
-
8989  {
-
8990  if (a.get_day() < 0)
-
8991  {
-
8992  printf_epiworld(" - %s (runs daily)\n", a.get_name().c_str());
-
8993  } else {
-
8994  printf_epiworld(" - %s (day %i)\n", a.get_name().c_str(), a.get_day());
-
8995  }
-
8996  }
-
8997 
-
8998  if (globalevents.size() == 0u)
-
8999  {
-
9000  printf_epiworld(" (none)\n");
-
9001  }
-
9002 
-
9003  printf_epiworld("\nVirus(es):\n");
-
9004  size_t n_viruses_model = viruses.size();
-
9005  for (size_t i = 0u; i < n_viruses_model; ++i)
-
9006  {
-
9007 
-
9008 
-
9009  const auto & virus = viruses[i];
-
9010  if ((n_viruses_model > 10) && (i >= 10))
-
9011  {
-
9012  printf_epiworld(" ...and %i more viruses...\n",
-
9013  static_cast<int>(n_viruses_model) -
-
9014  static_cast<int>(i)
-
9015  );
-
9016  break;
-
9017  }
-
9018 
-
9019  if (i < n_viruses_model)
-
9020  {
-
9021 
-
9022  printf_epiworld(
-
9023  " - %s\n",
-
9024  virus->get_name().c_str()
-
9025  );
-
9026 
-
9027  } else {
-
9028 
-
9029  printf_epiworld(
-
9030  " - %s (originated in the model...)\n",
-
9031  virus->get_name().c_str()
-
9032  );
-
9033 
-
9034  }
-
9035 
-
9036  }
+
8928  if (today() != 0)
+
8929  {
+
8930  printf_epiworld(
+
8931  "\nThe final distribution is: "
+
8932  );
+
8933 
+
8934  int nstate_int = static_cast<int>(nstates);
+
8935 
+
8936  for (int i = 0u; i < nstate_int; ++i)
+
8937  {
+
8938  printf_epiworld(
+
8939  "%i %s%s",
+
8940  static_cast<int>(db.today_total[ i ]),
+
8941  states_labels[i].c_str(),
+
8942  (
+
8943  i == (nstate_int - 2)
+
8944  ) ? ", and " : (
+
8945  (i == (nstate_int - 1)) ? ".\n" : ", "
+
8946  )
+
8947  );
+
8948  }
+
8949  } else {
+
8950  printf_epiworld(" The model hasn't been run yet.\n");
+
8951  }
+
8952 
+
8953  return *this;
+
8954  }
+
8955 
+
8956  printf_epiworld("%s\n%s\n\n",line.c_str(), "SIMULATION STUDY");
+
8957 
+
8958  printf_epiworld("Name of the model : %s\n", (this->name == "") ? std::string("(none)").c_str() : name.c_str());
+
8959  printf_epiworld("Population size : %i\n", static_cast<int>(size()));
+
8960 
+
8961  auto ncols = get_agents_data_ncols();
+
8962 
+
8963  if (ncols > 0)
+
8964  {
+
8965  printf_epiworld("Agents' data loaded : yes (%i columns/features)\n", static_cast<int>(ncols));
+
8966  }
+
8967  else
+
8968  {
+
8969  printf_epiworld("Agents' data : (none)\n");
+
8970  }
+
8971 
+
8972  printf_epiworld("Number of entities : %i\n", static_cast<int>(entities.size()));
+
8973  printf_epiworld("Days (duration) : %i (of %i)\n", today(), static_cast<int>(ndays));
+
8974  printf_epiworld("Number of viruses : %i\n", static_cast<int>(db.get_n_viruses()));
+
8975  if (n_replicates > 0u)
+
8976  {
+
8977  std::string abbr;
+
8978  epiworld_double elapsed;
+
8979  epiworld_double total;
+
8980  get_elapsed("auto", &elapsed, &total, &abbr, false);
+
8981  printf_epiworld("Last run elapsed t : %.2f%s\n", elapsed, abbr.c_str());
+
8982  if (n_replicates > 1u)
+
8983  {
+
8984  printf_epiworld("Total elapsed t : %.2f%s (%i runs)\n", total, abbr.c_str(), static_cast<int>(n_replicates));
+
8985  }
+
8986 
+
8987  // Elapsed time in speed
+
8988  get_elapsed("microseconds", &elapsed, &total, &abbr, false);
+
8989  printf_epiworld("Last run speed : %.2f million agents x day / second\n",
+
8990  static_cast<double>(this->size()) *
+
8991  static_cast<double>(this->get_ndays()) /
+
8992  static_cast<double>(elapsed)
+
8993  );
+
8994  if (n_replicates > 1u)
+
8995  {
+
8996  printf_epiworld("Average run speed : %.2f million agents x day / second\n",
+
8997  static_cast<double>(this->size()) *
+
8998  static_cast<double>(this->get_ndays()) *
+
8999  static_cast<double>(n_replicates) /
+
9000  static_cast<double>(total)
+
9001  );
+
9002  }
+
9003 
+
9004  } else {
+
9005  printf_epiworld("Last run elapsed t : -\n");
+
9006  }
+
9007 
+
9008 
+
9009  if (rewire_fun)
+
9010  {
+
9011  printf_epiworld("Rewiring : on (%.2f)\n\n", rewire_prop);
+
9012  } else {
+
9013  printf_epiworld("Rewiring : off\n\n");
+
9014  }
+
9015 
+
9016  // Printing Global events
+
9017  printf_epiworld("Global events:\n");
+
9018  for (auto & a : globalevents)
+
9019  {
+
9020  if (a.get_day() < 0)
+
9021  {
+
9022  printf_epiworld(" - %s (runs daily)\n", a.get_name().c_str());
+
9023  } else {
+
9024  printf_epiworld(" - %s (day %i)\n", a.get_name().c_str(), a.get_day());
+
9025  }
+
9026  }
+
9027 
+
9028  if (globalevents.size() == 0u)
+
9029  {
+
9030  printf_epiworld(" (none)\n");
+
9031  }
+
9032 
+
9033  printf_epiworld("\nVirus(es):\n");
+
9034  size_t n_viruses_model = viruses.size();
+
9035  for (size_t i = 0u; i < n_viruses_model; ++i)
+
9036  {
9037 
-
9038  auto nvariants = db.get_n_viruses() - n_viruses_model;
-
9039  if (nvariants > 0)
-
9040  {
-
9041 
-
9042  printf_epiworld(" ...and %i more variants...\n", static_cast<int>(nvariants));
-
9043 
-
9044  }
-
9045 
-
9046  if (viruses.size() == 0u)
-
9047  {
-
9048  printf_epiworld(" (none)\n");
-
9049  }
-
9050 
-
9051  printf_epiworld("\nTool(s):\n");
-
9052  size_t n_tools_model = tools.size();
-
9053  for (size_t i = 0u; i < tools.size(); ++i)
-
9054  {
-
9055  const auto & tool = tools[i];
+
9038 
+
9039  const auto & virus = viruses[i];
+
9040  if ((n_viruses_model > 10) && (i >= 10))
+
9041  {
+
9042  printf_epiworld(" ...and %i more viruses...\n",
+
9043  static_cast<int>(n_viruses_model) -
+
9044  static_cast<int>(i)
+
9045  );
+
9046  break;
+
9047  }
+
9048 
+
9049  if (i < n_viruses_model)
+
9050  {
+
9051 
+
9052  printf_epiworld(
+
9053  " - %s\n",
+
9054  virus->get_name().c_str()
+
9055  );
9056 
-
9057  if ((n_tools_model > 10) && (i >= 10))
-
9058  {
+
9057  } else {
+
9058 
9059  printf_epiworld(
-
9060  " ...and %i more tools...\n",
-
9061  static_cast<int>(n_tools_model) - static_cast<int>(i)
-
9062  );
-
9063  break;
+
9060  " - %s (originated in the model...)\n",
+
9061  virus->get_name().c_str()
+
9062  );
+
9063 
9064  }
9065 
-
9066  if (i < n_tools_model)
-
9067  {
-
9068  printf_epiworld(
-
9069  " - %s\n",
-
9070  tool->get_name().c_str()
-
9071  );
-
9072 
+
9066  }
+
9067 
+
9068  auto nvariants = db.get_n_viruses() - n_viruses_model;
+
9069  if (nvariants > 0)
+
9070  {
+
9071 
+
9072  printf_epiworld(" ...and %i more variants...\n", static_cast<int>(nvariants));
9073 
-
9074  } else {
+
9074  }
9075 
-
9076  printf_epiworld(
-
9077  " - %s (originated in the model...)\n",
-
9078  tool->get_name().c_str()
-
9079  );
+
9076  if (viruses.size() == 0u)
+
9077  {
+
9078  printf_epiworld(" (none)\n");
+
9079  }
9080 
-
9081  }
-
9082 
-
9083 
-
9084  }
-
9085 
-
9086  if (tools.size() == 0u)
-
9087  {
-
9088  printf_epiworld(" (none)\n");
-
9089  }
-
9090 
-
9091  // Information about the parameters included
-
9092  printf_epiworld("\nModel parameters:\n");
-
9093  epiworld_fast_uint nchar = 0u;
-
9094  for (auto & p : parameters)
-
9095  if (p.first.length() > nchar)
-
9096  nchar = p.first.length();
-
9097 
-
9098  std::string fmt = " - %-" + std::to_string(nchar + 1) + "s: ";
-
9099  for (auto & p : parameters)
-
9100  {
-
9101  std::string fmt_tmp = fmt;
-
9102  if (std::fabs(p.second) < 0.0001)
-
9103  fmt_tmp += "%.1e\n";
-
9104  else
-
9105  fmt_tmp += "%.4f\n";
-
9106 
-
9107  printf_epiworld(
-
9108  fmt_tmp.c_str(),
-
9109  p.first.c_str(),
-
9110  p.second
-
9111  );
+
9081  printf_epiworld("\nTool(s):\n");
+
9082  size_t n_tools_model = tools.size();
+
9083  for (size_t i = 0u; i < tools.size(); ++i)
+
9084  {
+
9085  const auto & tool = tools[i];
+
9086 
+
9087  if ((n_tools_model > 10) && (i >= 10))
+
9088  {
+
9089  printf_epiworld(
+
9090  " ...and %i more tools...\n",
+
9091  static_cast<int>(n_tools_model) - static_cast<int>(i)
+
9092  );
+
9093  break;
+
9094  }
+
9095 
+
9096  if (i < n_tools_model)
+
9097  {
+
9098  printf_epiworld(
+
9099  " - %s\n",
+
9100  tool->get_name().c_str()
+
9101  );
+
9102 
+
9103 
+
9104  } else {
+
9105 
+
9106  printf_epiworld(
+
9107  " - %s (originated in the model...)\n",
+
9108  tool->get_name().c_str()
+
9109  );
+
9110 
+
9111  }
9112 
-
9113  }
-
9114 
-
9115  if (parameters.size() == 0u)
-
9116  {
-
9117  printf_epiworld(" (none)\n");
-
9118  }
-
9119 
-
9120  nchar = 0u;
-
9121  for (auto & p : states_labels)
-
9122  if (p.length() > nchar)
-
9123  nchar = p.length();
-
9124 
-
9125 
-
9126 
-
9127  if (today() != 0)
-
9128  {
-
9129  fmt =
-
9130  std::string(" - (%") +
-
9131  std::to_string(std::to_string(nstates).length()) +
-
9132  std::string("d) %-") + std::to_string(nchar) +
-
9133  std::string("s : %") +
-
9134  std::to_string(std::to_string(size()).length()) +
-
9135  std::string("i -> %i\n");
-
9136  } else {
-
9137  fmt =
-
9138  std::string(" - (%") +
-
9139  std::to_string(std::to_string(nstates).length()) +
-
9140  std::string("d) %-") + std::to_string(nchar) +
-
9141  std::string("s : %i\n");
-
9142  }
-
9143 
-
9144  if (today() != 0)
-
9145  {
-
9146  printf_epiworld("\nDistribution of the population at time %i:\n", today());
-
9147  for (size_t s = 0u; s < nstates; ++s)
-
9148  {
+
9113 
+
9114  }
+
9115 
+
9116  if (tools.size() == 0u)
+
9117  {
+
9118  printf_epiworld(" (none)\n");
+
9119  }
+
9120 
+
9121  // Information about the parameters included
+
9122  printf_epiworld("\nModel parameters:\n");
+
9123  epiworld_fast_uint nchar = 0u;
+
9124  for (auto & p : parameters)
+
9125  if (p.first.length() > nchar)
+
9126  nchar = p.first.length();
+
9127 
+
9128  std::string fmt = " - %-" + std::to_string(nchar + 1) + "s: ";
+
9129  for (auto & p : parameters)
+
9130  {
+
9131  std::string fmt_tmp = fmt;
+
9132  if (std::fabs(p.second) < 0.0001)
+
9133  fmt_tmp += "%.1e\n";
+
9134  else
+
9135  fmt_tmp += "%.4f\n";
+
9136 
+
9137  printf_epiworld(
+
9138  fmt_tmp.c_str(),
+
9139  p.first.c_str(),
+
9140  p.second
+
9141  );
+
9142 
+
9143  }
+
9144 
+
9145  if (parameters.size() == 0u)
+
9146  {
+
9147  printf_epiworld(" (none)\n");
+
9148  }
9149 
-
9150  printf_epiworld(
-
9151  fmt.c_str(),
-
9152  s,
-
9153  states_labels[s].c_str(),
-
9154  db.hist_total_counts[s],
-
9155  db.today_total[ s ]
-
9156  );
-
9157 
-
9158  }
-
9159  // else
-
9160  // {
-
9161 
-
9162  // printf_epiworld(
-
9163  // fmt.c_str(),
-
9164  // s,
-
9165  // states_labels[s].c_str(),
-
9166  // db.today_total[ s ]
-
9167  // );
-
9168 
-
9169  // }
-
9170  }
-
9171 
-
9172  if (today() != 0)
-
9173  (void) db.transition_probability(true);
-
9174 
-
9175  return *this;
-
9176 
-
9177 }
-
9178 
-
9179 #endif
-
9180 /*//////////////////////////////////////////////////////////////////////////////
-
9182 
-
9183  End of -include/epiworld//model-meat-print.hpp-
-
9184 
+
9150  nchar = 0u;
+
9151  for (auto & p : states_labels)
+
9152  if (p.length() > nchar)
+
9153  nchar = p.length();
+
9154 
+
9155 
+
9156 
+
9157  if (today() != 0)
+
9158  {
+
9159  fmt =
+
9160  std::string(" - (%") +
+
9161  std::to_string(std::to_string(nstates).length()) +
+
9162  std::string("d) %-") + std::to_string(nchar) +
+
9163  std::string("s : %") +
+
9164  std::to_string(std::to_string(size()).length()) +
+
9165  std::string("i -> %i\n");
+
9166  } else {
+
9167  fmt =
+
9168  std::string(" - (%") +
+
9169  std::to_string(std::to_string(nstates).length()) +
+
9170  std::string("d) %-") + std::to_string(nchar) +
+
9171  std::string("s : %i\n");
+
9172  }
+
9173 
+
9174  if (today() != 0)
+
9175  {
+
9176  printf_epiworld("\nDistribution of the population at time %i:\n", today());
+
9177  for (size_t s = 0u; s < nstates; ++s)
+
9178  {
+
9179 
+
9180  printf_epiworld(
+
9181  fmt.c_str(),
+
9182  s,
+
9183  states_labels[s].c_str(),
+
9184  db.hist_total_counts[s],
+
9185  db.today_total[ s ]
+
9186  );
9187 
-
9188 
-
9189 
-
9190 
-
9191 template<typename TSeq>
-
9192 inline void Model<TSeq>::add_state(
-
9193  std::string lab,
-
9194  UpdateFun<TSeq> fun
-
9195 )
-
9196 {
-
9197 
-
9198  // Checking it doesn't match
-
9199  for (auto & s : states_labels)
-
9200  if (s == lab)
-
9201  throw std::logic_error("state \"" + s + "\" already registered.");
-
9202 
-
9203  states_labels.push_back(lab);
-
9204  state_fun.push_back(fun);
-
9205  nstates++;
+
9188  }
+
9189  // else
+
9190  // {
+
9191 
+
9192  // printf_epiworld(
+
9193  // fmt.c_str(),
+
9194  // s,
+
9195  // states_labels[s].c_str(),
+
9196  // db.today_total[ s ]
+
9197  // );
+
9198 
+
9199  // }
+
9200  }
+
9201 
+
9202  if (today() != 0)
+
9203  (void) db.transition_probability(true);
+
9204 
+
9205  return *this;
9206 
9207 }
9208 
-
9209 
-
9210 template<typename TSeq>
-
9211 inline const std::vector< std::string > &
-
9212 Model<TSeq>::get_states() const
-
9213 {
-
9214  return states_labels;
-
9215 }
-
9216 
-
9217 template<typename TSeq>
-
9218 inline const std::vector< UpdateFun<TSeq> > &
-
9219 Model<TSeq>::get_state_fun() const
-
9220 {
-
9221  return state_fun;
-
9222 }
-
9223 
-
9224 template<typename TSeq>
-
9225 inline void Model<TSeq>::print_state_codes() const
+
9209 #endif
+
9210 /*//////////////////////////////////////////////////////////////////////////////
+
9212 
+
9213  End of -include/epiworld//model-meat-print.hpp-
+
9214 
+
9217 
+
9218 
+
9219 
+
9220 
+
9221 template<typename TSeq>
+
9222 inline void Model<TSeq>::add_state(
+
9223  std::string lab,
+
9224  UpdateFun<TSeq> fun
+
9225 )
9226 {
9227 
-
9228  // Horizontal line
-
9229  std::string line = "";
-
9230  for (epiworld_fast_uint i = 0u; i < 80u; ++i)
-
9231  line += "_";
+
9228  // Checking it doesn't match
+
9229  for (auto & s : states_labels)
+
9230  if (s == lab)
+
9231  throw std::logic_error("state \"" + s + "\" already registered.");
9232 
-
9233  printf_epiworld("\n%s\nstates CODES\n\n", line.c_str());
-
9234 
-
9235  epiworld_fast_uint nchar = 0u;
-
9236  for (auto & p : states_labels)
-
9237  if (p.length() > nchar)
-
9238  nchar = p.length();
-
9239 
-
9240  std::string fmt = " %2i = %-" + std::to_string(nchar + 1 + 4) + "s\n";
-
9241  for (epiworld_fast_uint i = 0u; i < nstates; ++i)
-
9242  {
-
9243 
-
9244  printf_epiworld(
-
9245  fmt.c_str(),
-
9246  i,
-
9247  (states_labels[i] + " (S)").c_str()
-
9248  );
-
9249 
-
9250  }
-
9251 
+
9233  states_labels.push_back(lab);
+
9234  state_fun.push_back(fun);
+
9235  nstates++;
+
9236 
+
9237 }
+
9238 
+
9239 
+
9240 template<typename TSeq>
+
9241 inline const std::vector< std::string > &
+
9242 Model<TSeq>::get_states() const
+
9243 {
+
9244  return states_labels;
+
9245 }
+
9246 
+
9247 template<typename TSeq>
+
9248 inline const std::vector< UpdateFun<TSeq> > &
+
9249 Model<TSeq>::get_state_fun() const
+
9250 {
+
9251  return state_fun;
9252 }
9253 
-
9254 
-
9255 
-
9256 template<typename TSeq>
-
9257 inline epiworld_double Model<TSeq>::add_param(
-
9258  epiworld_double initial_value,
-
9259  std::string pname
-
9260  ) {
-
9261 
-
9262  if (parameters.find(pname) == parameters.end())
-
9263  parameters[pname] = initial_value;
-
9264 
-
9265  return initial_value;
-
9266 
-
9267 }
-
9268 
-
9269 template<typename TSeq>
-
9270 inline void Model<TSeq>::read_params(std::string fn)
-
9271 {
-
9272 
-
9273  std::ifstream paramsfile(fn);
-
9274 
-
9275  if (!paramsfile)
-
9276  throw std::logic_error("The file " + fn + " was not found.");
-
9277 
-
9278  std::regex pattern("^([^:]+)\\s*[:]\\s*([0-9]+|[0-9]*\\.[0-9]+)?\\s*$");
+
9254 template<typename TSeq>
+
9255 inline void Model<TSeq>::print_state_codes() const
+
9256 {
+
9257 
+
9258  // Horizontal line
+
9259  std::string line = "";
+
9260  for (epiworld_fast_uint i = 0u; i < 80u; ++i)
+
9261  line += "_";
+
9262 
+
9263  printf_epiworld("\n%s\nstates CODES\n\n", line.c_str());
+
9264 
+
9265  epiworld_fast_uint nchar = 0u;
+
9266  for (auto & p : states_labels)
+
9267  if (p.length() > nchar)
+
9268  nchar = p.length();
+
9269 
+
9270  std::string fmt = " %2i = %-" + std::to_string(nchar + 1 + 4) + "s\n";
+
9271  for (epiworld_fast_uint i = 0u; i < nstates; ++i)
+
9272  {
+
9273 
+
9274  printf_epiworld(
+
9275  fmt.c_str(),
+
9276  i,
+
9277  (states_labels[i] + " (S)").c_str()
+
9278  );
9279 
-
9280  std::string line;
-
9281  std::smatch match;
-
9282  auto empty = std::sregex_iterator();
+
9280  }
+
9281 
+
9282 }
9283 
-
9284  while (std::getline(paramsfile, line))
-
9285  {
-
9286 
-
9287  // Is it a comment or an empty line?
-
9288  if (std::regex_match(line, std::regex("^([*].+|//.+|#.+|\\s*)$")))
-
9289  continue;
-
9290 
-
9291  // Finding the patter, if it doesn't match, then error
-
9292  std::regex_match(line, match, pattern);
-
9293 
-
9294  if (match.empty())
-
9295  throw std::logic_error("The line does not match parameters:\n" + line);
+
9284 
+
9285 
+
9286 template<typename TSeq>
+
9287 inline epiworld_double Model<TSeq>::add_param(
+
9288  epiworld_double initial_value,
+
9289  std::string pname
+
9290  ) {
+
9291 
+
9292  if (parameters.find(pname) == parameters.end())
+
9293  parameters[pname] = initial_value;
+
9294 
+
9295  return initial_value;
9296 
-
9297  // Capturing the number
-
9298  std::string anumber = match[2u].str() + match[3u].str();
-
9299  epiworld_double tmp_num = static_cast<epiworld_double>(
-
9300  std::strtod(anumber.c_str(), nullptr)
-
9301  );
+
9297 }
+
9298 
+
9299 template<typename TSeq>
+
9300 inline void Model<TSeq>::read_params(std::string fn)
+
9301 {
9302 
-
9303  add_param(
-
9304  tmp_num,
-
9305  std::regex_replace(
-
9306  match[1u].str(),
-
9307  std::regex("^\\s+|\\s+$"),
-
9308  "")
-
9309  );
-
9310 
-
9311  }
-
9312 
-
9313 }
-
9314 
-
9315 template<typename TSeq>
-
9316 inline epiworld_double Model<TSeq>::get_param(std::string pname)
-
9317 {
-
9318  if (parameters.find(pname) == parameters.end())
-
9319  throw std::logic_error("The parameter " + pname + " does not exists.");
+
9303  std::ifstream paramsfile(fn);
+
9304 
+
9305  if (!paramsfile)
+
9306  throw std::logic_error("The file " + fn + " was not found.");
+
9307 
+
9308  std::regex pattern("^([^:]+)\\s*[:]\\s*([0-9]+|[0-9]*\\.[0-9]+)?\\s*$");
+
9309 
+
9310  std::string line;
+
9311  std::smatch match;
+
9312  auto empty = std::sregex_iterator();
+
9313 
+
9314  while (std::getline(paramsfile, line))
+
9315  {
+
9316 
+
9317  // Is it a comment or an empty line?
+
9318  if (std::regex_match(line, std::regex("^([*].+|//.+|#.+|\\s*)$")))
+
9319  continue;
9320 
-
9321  return parameters[pname];
-
9322 }
+
9321  // Finding the patter, if it doesn't match, then error
+
9322  std::regex_match(line, match, pattern);
9323 
-
9324 template<typename TSeq>
-
9325 inline void Model<TSeq>::set_param(std::string pname, epiworld_double value)
-
9326 {
-
9327  if (parameters.find(pname) == parameters.end())
-
9328  throw std::logic_error("The parameter " + pname + " does not exists.");
-
9329 
-
9330  parameters[pname] = value;
-
9331 
-
9332  return;
-
9333 
-
9334 }
-
9335 
-
9336 // // Same as before but using the size_t method
-
9337 // template<typename TSeq>
-
9338 // inline void Model<TSeq>::set_param(size_t k, epiworld_double value)
-
9339 // {
-
9340 // if (k >= parameters.size())
-
9341 // throw std::logic_error("The parameter index " + std::to_string(k) + " does not exists.");
+
9324  if (match.empty())
+
9325  throw std::logic_error("The line does not match parameters:\n" + line);
+
9326 
+
9327  // Capturing the number
+
9328  std::string anumber = match[2u].str() + match[3u].str();
+
9329  epiworld_double tmp_num = static_cast<epiworld_double>(
+
9330  std::strtod(anumber.c_str(), nullptr)
+
9331  );
+
9332 
+
9333  add_param(
+
9334  tmp_num,
+
9335  std::regex_replace(
+
9336  match[1u].str(),
+
9337  std::regex("^\\s+|\\s+$"),
+
9338  "")
+
9339  );
+
9340 
+
9341  }
9342 
-
9343 // // Access the k-th element of the std::unordered_map parameters
+
9343 }
9344 
-
9345 
-
9346 // *(parameters.begin() + k) = value;
-
9347 
-
9348 // return;
-
9349 // }
+
9345 template<typename TSeq>
+
9346 inline epiworld_double Model<TSeq>::get_param(std::string pname)
+
9347 {
+
9348  if (parameters.find(pname) == parameters.end())
+
9349  throw std::logic_error("The parameter " + pname + " does not exists.");
9350 
-
9351 template<typename TSeq>
-
9352 inline epiworld_double Model<TSeq>::par(std::string pname) const
-
9353 {
-
9354  const auto iter = parameters.find(pname);
-
9355  if (iter == parameters.end())
-
9356  throw std::logic_error("The parameter " + pname + " does not exists.");
-
9357  return iter->second;
-
9358 }
+
9351  return parameters[pname];
+
9352 }
+
9353 
+
9354 template<typename TSeq>
+
9355 inline void Model<TSeq>::set_param(std::string pname, epiworld_double value)
+
9356 {
+
9357  if (parameters.find(pname) == parameters.end())
+
9358  throw std::logic_error("The parameter " + pname + " does not exists.");
9359 
-
9360 #define DURCAST(tunit,txtunit) {\
-
9361  elapsed = std::chrono::duration_cast<std::chrono:: tunit>(\
-
9362  time_end - time_start).count(); \
-
9363  elapsed_total = std::chrono::duration_cast<std::chrono:: tunit>(time_elapsed).count(); \
-
9364  abbr_unit = txtunit;}
+
9360  parameters[pname] = value;
+
9361 
+
9362  return;
+
9363 
+
9364 }
9365 
-
9366 template<typename TSeq>
-
9367 inline void Model<TSeq>::get_elapsed(
-
9368  std::string unit,
-
9369  epiworld_double * last_elapsed,
-
9370  epiworld_double * total_elapsed,
-
9371  std::string * unit_abbr,
-
9372  bool print
-
9373 ) const {
+
9366 // // Same as before but using the size_t method
+
9367 // template<typename TSeq>
+
9368 // inline void Model<TSeq>::set_param(size_t k, epiworld_double value)
+
9369 // {
+
9370 // if (k >= parameters.size())
+
9371 // throw std::logic_error("The parameter index " + std::to_string(k) + " does not exists.");
+
9372 
+
9373 // // Access the k-th element of the std::unordered_map parameters
9374 
-
9375  // Preparing the result
-
9376  epiworld_double elapsed, elapsed_total;
-
9377  std::string abbr_unit;
-
9378 
-
9379  // Figuring out the length
-
9380  if (unit == "auto")
-
9381  {
-
9382 
-
9383  size_t tlength = std::to_string(
-
9384  static_cast<int>(floor(time_elapsed.count()))
-
9385  ).length();
-
9386 
-
9387  if (tlength <= 1)
-
9388  unit = "nanoseconds";
-
9389  else if (tlength <= 3)
-
9390  unit = "microseconds";
-
9391  else if (tlength <= 6)
-
9392  unit = "milliseconds";
-
9393  else if (tlength <= 8)
-
9394  unit = "seconds";
-
9395  else if (tlength <= 9)
-
9396  unit = "minutes";
-
9397  else
-
9398  unit = "hours";
-
9399 
-
9400  }
-
9401 
-
9402  if (unit == "nanoseconds") DURCAST(nanoseconds,"ns")
-
9403  else if (unit == "microseconds") DURCAST(microseconds,"\xC2\xB5s")
-
9404  else if (unit == "milliseconds") DURCAST(milliseconds,"ms")
-
9405  else if (unit == "seconds") DURCAST(seconds,"s")
-
9406  else if (unit == "minutes") DURCAST(minutes,"m")
-
9407  else if (unit == "hours") DURCAST(hours,"h")
-
9408  else
-
9409  throw std::range_error("The time unit " + unit + " is not supported.");
-
9410 
-
9411 
-
9412  if (last_elapsed != nullptr)
-
9413  *last_elapsed = elapsed;
-
9414  if (total_elapsed != nullptr)
-
9415  *total_elapsed = elapsed_total;
-
9416  if (unit_abbr != nullptr)
-
9417  *unit_abbr = abbr_unit;
-
9418 
-
9419  if (!print)
-
9420  return;
-
9421 
-
9422  if (n_replicates > 1u)
-
9423  {
-
9424  printf_epiworld("last run elapsed time : %.2f%s\n",
-
9425  elapsed, abbr_unit.c_str());
-
9426  printf_epiworld("total elapsed time : %.2f%s\n",
-
9427  elapsed_total, abbr_unit.c_str());
-
9428  printf_epiworld("total runs : %i\n",
-
9429  static_cast<int>(n_replicates));
-
9430  printf_epiworld("mean run elapsed time : %.2f%s\n",
-
9431  elapsed_total/static_cast<epiworld_double>(n_replicates), abbr_unit.c_str());
-
9432 
-
9433  } else {
-
9434  printf_epiworld("last run elapsed time : %.2f%s.\n", elapsed, abbr_unit.c_str());
-
9435  }
-
9436 }
-
9437 
-
9438 template<typename TSeq>
-
9439 inline void Model<TSeq>::set_user_data(std::vector< std::string > names)
-
9440 {
-
9441  db.set_user_data(names);
-
9442 }
-
9443 
-
9444 template<typename TSeq>
-
9445 inline void Model<TSeq>::add_user_data(epiworld_fast_uint j, epiworld_double x)
-
9446 {
-
9447  db.add_user_data(j, x);
-
9448 }
-
9449 
-
9450 template<typename TSeq>
-
9451 inline void Model<TSeq>::add_user_data(std::vector<epiworld_double> x)
-
9452 {
-
9453  db.add_user_data(x);
-
9454 }
-
9455 
-
9456 template<typename TSeq>
-
9457 inline UserData<TSeq> & Model<TSeq>::get_user_data()
-
9458 {
-
9459  return db.get_user_data();
-
9460 }
-
9461 
-
9462 template<typename TSeq>
-
9463 inline void Model<TSeq>::add_globalevent(
-
9464  std::function<void(Model<TSeq>*)> fun,
-
9465  std::string name,
-
9466  int date
-
9467 )
-
9468 {
-
9469 
-
9470  globalevents.push_back(
-
9471  GlobalEvent<TSeq>(
-
9472  fun,
-
9473  name,
-
9474  date
-
9475  )
-
9476  );
-
9477 
+
9375 
+
9376 // *(parameters.begin() + k) = value;
+
9377 
+
9378 // return;
+
9379 // }
+
9380 
+
9381 template<typename TSeq>
+
9382 inline epiworld_double Model<TSeq>::par(std::string pname) const
+
9383 {
+
9384  const auto iter = parameters.find(pname);
+
9385  if (iter == parameters.end())
+
9386  throw std::logic_error("The parameter " + pname + " does not exists.");
+
9387  return iter->second;
+
9388 }
+
9389 
+
9390 #define DURCAST(tunit,txtunit) {\
+
9391  elapsed = std::chrono::duration_cast<std::chrono:: tunit>(\
+
9392  time_end - time_start).count(); \
+
9393  elapsed_total = std::chrono::duration_cast<std::chrono:: tunit>(time_elapsed).count(); \
+
9394  abbr_unit = txtunit;}
+
9395 
+
9396 template<typename TSeq>
+
9397 inline void Model<TSeq>::get_elapsed(
+
9398  std::string unit,
+
9399  epiworld_double * last_elapsed,
+
9400  epiworld_double * total_elapsed,
+
9401  std::string * unit_abbr,
+
9402  bool print
+
9403 ) const {
+
9404 
+
9405  // Preparing the result
+
9406  epiworld_double elapsed, elapsed_total;
+
9407  std::string abbr_unit;
+
9408 
+
9409  // Figuring out the length
+
9410  if (unit == "auto")
+
9411  {
+
9412 
+
9413  size_t tlength = std::to_string(
+
9414  static_cast<int>(floor(time_elapsed.count()))
+
9415  ).length();
+
9416 
+
9417  if (tlength <= 1)
+
9418  unit = "nanoseconds";
+
9419  else if (tlength <= 3)
+
9420  unit = "microseconds";
+
9421  else if (tlength <= 6)
+
9422  unit = "milliseconds";
+
9423  else if (tlength <= 8)
+
9424  unit = "seconds";
+
9425  else if (tlength <= 9)
+
9426  unit = "minutes";
+
9427  else
+
9428  unit = "hours";
+
9429 
+
9430  }
+
9431 
+
9432  if (unit == "nanoseconds") DURCAST(nanoseconds,"ns")
+
9433  else if (unit == "microseconds") DURCAST(microseconds,"\xC2\xB5s")
+
9434  else if (unit == "milliseconds") DURCAST(milliseconds,"ms")
+
9435  else if (unit == "seconds") DURCAST(seconds,"s")
+
9436  else if (unit == "minutes") DURCAST(minutes,"m")
+
9437  else if (unit == "hours") DURCAST(hours,"h")
+
9438  else
+
9439  throw std::range_error("The time unit " + unit + " is not supported.");
+
9440 
+
9441 
+
9442  if (last_elapsed != nullptr)
+
9443  *last_elapsed = elapsed;
+
9444  if (total_elapsed != nullptr)
+
9445  *total_elapsed = elapsed_total;
+
9446  if (unit_abbr != nullptr)
+
9447  *unit_abbr = abbr_unit;
+
9448 
+
9449  if (!print)
+
9450  return;
+
9451 
+
9452  if (n_replicates > 1u)
+
9453  {
+
9454  printf_epiworld("last run elapsed time : %.2f%s\n",
+
9455  elapsed, abbr_unit.c_str());
+
9456  printf_epiworld("total elapsed time : %.2f%s\n",
+
9457  elapsed_total, abbr_unit.c_str());
+
9458  printf_epiworld("total runs : %i\n",
+
9459  static_cast<int>(n_replicates));
+
9460  printf_epiworld("mean run elapsed time : %.2f%s\n",
+
9461  elapsed_total/static_cast<epiworld_double>(n_replicates), abbr_unit.c_str());
+
9462 
+
9463  } else {
+
9464  printf_epiworld("last run elapsed time : %.2f%s.\n", elapsed, abbr_unit.c_str());
+
9465  }
+
9466 }
+
9467 
+
9468 template<typename TSeq>
+
9469 inline void Model<TSeq>::set_user_data(std::vector< std::string > names)
+
9470 {
+
9471  db.set_user_data(names);
+
9472 }
+
9473 
+
9474 template<typename TSeq>
+
9475 inline void Model<TSeq>::add_user_data(epiworld_fast_uint j, epiworld_double x)
+
9476 {
+
9477  db.add_user_data(j, x);
9478 }
9479 
9480 template<typename TSeq>
-
9481 inline void Model<TSeq>::add_globalevent(
-
9482  GlobalEvent<TSeq> action
-
9483 )
-
9484 {
-
9485  globalevents.push_back(action);
-
9486 }
-
9487 
-
9488 template<typename TSeq>
-
9489 GlobalEvent<TSeq> & Model<TSeq>::get_globalevent(
-
9490  std::string name
-
9491 )
-
9492 {
-
9493 
-
9494  for (auto & a : globalevents)
-
9495  if (a.name == name)
-
9496  return a;
-
9497 
-
9498  throw std::logic_error("The global action " + name + " was not found.");
+
9481 inline void Model<TSeq>::add_user_data(std::vector<epiworld_double> x)
+
9482 {
+
9483  db.add_user_data(x);
+
9484 }
+
9485 
+
9486 template<typename TSeq>
+
9487 inline UserData<TSeq> & Model<TSeq>::get_user_data()
+
9488 {
+
9489  return db.get_user_data();
+
9490 }
+
9491 
+
9492 template<typename TSeq>
+
9493 inline void Model<TSeq>::add_globalevent(
+
9494  std::function<void(Model<TSeq>*)> fun,
+
9495  std::string name,
+
9496  int date
+
9497 )
+
9498 {
9499 
-
9500 }
-
9501 
-
9502 template<typename TSeq>
-
9503 GlobalEvent<TSeq> & Model<TSeq>::get_globalevent(
-
9504  size_t index
-
9505 )
-
9506 {
+
9500  globalevents.push_back(
+
9501  GlobalEvent<TSeq>(
+
9502  fun,
+
9503  name,
+
9504  date
+
9505  )
+
9506  );
9507 
-
9508  if (index >= globalevents.size())
-
9509  throw std::range_error("The index " + std::to_string(index) + " is out of range.");
-
9510 
-
9511  return globalevents[index];
-
9512 
-
9513 }
-
9514 
-
9515 // Remove implementation
-
9516 template<typename TSeq>
-
9517 inline void Model<TSeq>::rm_globalevent(
-
9518  std::string name
-
9519 )
-
9520 {
-
9521 
-
9522  for (auto it = globalevents.begin(); it != globalevents.end(); ++it)
-
9523  {
-
9524  if (it->get_name() == name)
-
9525  {
-
9526  globalevents.erase(it);
-
9527  return;
-
9528  }
-
9529  }
-
9530 
-
9531  throw std::logic_error("The global action " + name + " was not found.");
-
9532 
-
9533 }
-
9534 
-
9535 // Same as above, but the index implementation
-
9536 template<typename TSeq>
-
9537 inline void Model<TSeq>::rm_globalevent(
-
9538  size_t index
-
9539 )
-
9540 {
-
9541 
-
9542  if (index >= globalevents.size())
-
9543  throw std::range_error("The index " + std::to_string(index) + " is out of range.");
+
9508 }
+
9509 
+
9510 template<typename TSeq>
+
9511 inline void Model<TSeq>::add_globalevent(
+
9512  GlobalEvent<TSeq> action
+
9513 )
+
9514 {
+
9515  globalevents.push_back(action);
+
9516 }
+
9517 
+
9518 template<typename TSeq>
+
9519 GlobalEvent<TSeq> & Model<TSeq>::get_globalevent(
+
9520  std::string name
+
9521 )
+
9522 {
+
9523 
+
9524  for (auto & a : globalevents)
+
9525  if (a.name == name)
+
9526  return a;
+
9527 
+
9528  throw std::logic_error("The global action " + name + " was not found.");
+
9529 
+
9530 }
+
9531 
+
9532 template<typename TSeq>
+
9533 GlobalEvent<TSeq> & Model<TSeq>::get_globalevent(
+
9534  size_t index
+
9535 )
+
9536 {
+
9537 
+
9538  if (index >= globalevents.size())
+
9539  throw std::range_error("The index " + std::to_string(index) + " is out of range.");
+
9540 
+
9541  return globalevents[index];
+
9542 
+
9543 }
9544 
-
9545  globalevents.erase(globalevents.begin() + index);
-
9546 
-
9547 }
-
9548 
-
9549 template<typename TSeq>
-
9550 inline void Model<TSeq>::run_globalevents()
-
9551 {
-
9552 
-
9553  for (auto & action: globalevents)
-
9554  {
-
9555  action(this, today());
-
9556  events_run();
-
9557  }
-
9558 
-
9559 }
+
9545 // Remove implementation
+
9546 template<typename TSeq>
+
9547 inline void Model<TSeq>::rm_globalevent(
+
9548  std::string name
+
9549 )
+
9550 {
+
9551 
+
9552  for (auto it = globalevents.begin(); it != globalevents.end(); ++it)
+
9553  {
+
9554  if (it->get_name() == name)
+
9555  {
+
9556  globalevents.erase(it);
+
9557  return;
+
9558  }
+
9559  }
9560 
-
9561 template<typename TSeq>
-
9562 inline void Model<TSeq>::queuing_on()
-
9563 {
-
9564  use_queuing = true;
-
9565 }
-
9566 
-
9567 template<typename TSeq>
-
9568 inline Model<TSeq> & Model<TSeq>::queuing_off()
-
9569 {
-
9570  use_queuing = false;
-
9571  return *this;
-
9572 }
-
9573 
-
9574 template<typename TSeq>
-
9575 inline bool Model<TSeq>::is_queuing_on() const
-
9576 {
-
9577  return use_queuing;
-
9578 }
-
9579 
-
9580 template<typename TSeq>
-
9581 inline Queue<TSeq> & Model<TSeq>::get_queue()
-
9582 {
-
9583  return queue;
-
9584 }
-
9585 
-
9586 template<typename TSeq>
-
9587 inline const std::vector< VirusPtr<TSeq> > & Model<TSeq>::get_viruses() const
-
9588 {
-
9589  return viruses;
-
9590 }
-
9591 
-
9592 template<typename TSeq>
-
9593 const std::vector< ToolPtr<TSeq> > & Model<TSeq>::get_tools() const
-
9594 {
-
9595  return tools;
-
9596 }
-
9597 
-
9598 template<typename TSeq>
-
9599 inline Virus<TSeq> & Model<TSeq>::get_virus(size_t id)
-
9600 {
-
9601 
-
9602  if (viruses.size() <= id)
-
9603  throw std::length_error("The specified id for the virus is out of range");
-
9604 
-
9605  return *viruses[id];
-
9606 
-
9607 }
-
9608 
-
9609 template<typename TSeq>
-
9610 inline Tool<TSeq> & Model<TSeq>::get_tool(size_t id)
-
9611 {
-
9612 
-
9613  if (tools.size() <= id)
-
9614  throw std::length_error("The specified id for the tools is out of range");
+
9561  throw std::logic_error("The global action " + name + " was not found.");
+
9562 
+
9563 }
+
9564 
+
9565 // Same as above, but the index implementation
+
9566 template<typename TSeq>
+
9567 inline void Model<TSeq>::rm_globalevent(
+
9568  size_t index
+
9569 )
+
9570 {
+
9571 
+
9572  if (index >= globalevents.size())
+
9573  throw std::range_error("The index " + std::to_string(index) + " is out of range.");
+
9574 
+
9575  globalevents.erase(globalevents.begin() + index);
+
9576 
+
9577 }
+
9578 
+
9579 template<typename TSeq>
+
9580 inline void Model<TSeq>::run_globalevents()
+
9581 {
+
9582 
+
9583  for (auto & action: globalevents)
+
9584  {
+
9585  action(this, today());
+
9586  events_run();
+
9587  }
+
9588 
+
9589 }
+
9590 
+
9591 template<typename TSeq>
+
9592 inline void Model<TSeq>::queuing_on()
+
9593 {
+
9594  use_queuing = true;
+
9595 }
+
9596 
+
9597 template<typename TSeq>
+
9598 inline Model<TSeq> & Model<TSeq>::queuing_off()
+
9599 {
+
9600  use_queuing = false;
+
9601  return *this;
+
9602 }
+
9603 
+
9604 template<typename TSeq>
+
9605 inline bool Model<TSeq>::is_queuing_on() const
+
9606 {
+
9607  return use_queuing;
+
9608 }
+
9609 
+
9610 template<typename TSeq>
+
9611 inline Queue<TSeq> & Model<TSeq>::get_queue()
+
9612 {
+
9613  return queue;
+
9614 }
9615 
-
9616  return *tools[id];
-
9617 
-
9618 }
-
9619 
-
9620 
-
9621 template<typename TSeq>
-
9622 inline void Model<TSeq>::set_agents_data(double * data_, size_t ncols_)
-
9623 {
-
9624  agents_data = data_;
-
9625  agents_data_ncols = ncols_;
+
9616 template<typename TSeq>
+
9617 inline const std::vector< VirusPtr<TSeq> > & Model<TSeq>::get_viruses() const
+
9618 {
+
9619  return viruses;
+
9620 }
+
9621 
+
9622 template<typename TSeq>
+
9623 const std::vector< ToolPtr<TSeq> > & Model<TSeq>::get_tools() const
+
9624 {
+
9625  return tools;
9626 }
9627 
9628 template<typename TSeq>
-
9629 inline double * Model<TSeq>::get_agents_data() {
-
9630  return this->agents_data;
-
9631 }
-
9632 
-
9633 template<typename TSeq>
-
9634 inline size_t Model<TSeq>::get_agents_data_ncols() const {
-
9635  return this->agents_data_ncols;
-
9636 }
-
9637 
+
9629 inline Virus<TSeq> & Model<TSeq>::get_virus(size_t id)
+
9630 {
+
9631 
+
9632  if (viruses.size() <= id)
+
9633  throw std::length_error("The specified id for the virus is out of range");
+
9634 
+
9635  return *viruses[id];
+
9636 
+
9637 }
9638 
9639 template<typename TSeq>
-
9640 inline void Model<TSeq>::set_name(std::string name)
+
9640 inline Tool<TSeq> & Model<TSeq>::get_tool(size_t id)
9641 {
-
9642  this->name = name;
-
9643 }
-
9644 
-
9645 template<typename TSeq>
-
9646 inline std::string Model<TSeq>::get_name() const
-
9647 {
-
9648  return this->name;
-
9649 }
+
9642 
+
9643  if (tools.size() <= id)
+
9644  throw std::length_error("The specified id for the tools is out of range");
+
9645 
+
9646  return *tools[id];
+
9647 
+
9648 }
+
9649 
9650 
-
9651 #define VECT_MATCH(a, b, c) \
-
9652  EPI_DEBUG_FAIL_AT_TRUE(a.size() != b.size(), c) \
-
9653  for (size_t __i = 0u; __i < a.size(); ++__i) \
-
9654  {\
-
9655  EPI_DEBUG_FAIL_AT_TRUE(a[__i] != b[__i], c) \
-
9656  }
+
9651 template<typename TSeq>
+
9652 inline void Model<TSeq>::set_agents_data(double * data_, size_t ncols_)
+
9653 {
+
9654  agents_data = data_;
+
9655  agents_data_ncols = ncols_;
+
9656 }
9657 
9658 template<typename TSeq>
-
9659 inline bool Model<TSeq>::operator==(const Model<TSeq> & other) const
-
9660 {
-
9661  EPI_DEBUG_FAIL_AT_TRUE(name != other.name, "names don't match")
-
9662  EPI_DEBUG_FAIL_AT_TRUE(db != other.db, "database don't match")
-
9663 
-
9664  VECT_MATCH(population, other.population, "population doesn't match")
-
9665 
-
9666  EPI_DEBUG_FAIL_AT_TRUE(
-
9667  using_backup != other.using_backup,
-
9668  "Model:: using_backup don't match"
-
9669  )
-
9670 
-
9671  if ((population_backup.size() != 0) & (other.population_backup.size() != 0))
-
9672  {
-
9673 
-
9674  // False is population_backup.size() != other.population_backup.size()
-
9675  if (population_backup.size() != other.population_backup.size())
-
9676  return false;
-
9677 
-
9678  for (size_t i = 0u; i < population_backup.size(); ++i)
-
9679  {
-
9680  if (population_backup[i] != other.population_backup[i])
-
9681  return false;
-
9682  }
-
9683 
-
9684  } else if ((population_backup.size() == 0) & (other.population_backup.size() != 0)) {
-
9685  return false;
-
9686  } else if ((population_backup.size() != 0) & (other.population_backup.size() == 0))
-
9687  {
-
9688  return false;
-
9689  }
-
9690 
-
9691  EPI_DEBUG_FAIL_AT_TRUE(
-
9692  agents_data != other.agents_data,
-
9693  "Model:: agents_data don't match"
-
9694  )
+
9659 inline double * Model<TSeq>::get_agents_data() {
+
9660  return this->agents_data;
+
9661 }
+
9662 
+
9663 template<typename TSeq>
+
9664 inline size_t Model<TSeq>::get_agents_data_ncols() const {
+
9665  return this->agents_data_ncols;
+
9666 }
+
9667 
+
9668 
+
9669 template<typename TSeq>
+
9670 inline void Model<TSeq>::set_name(std::string name)
+
9671 {
+
9672  this->name = name;
+
9673 }
+
9674 
+
9675 template<typename TSeq>
+
9676 inline std::string Model<TSeq>::get_name() const
+
9677 {
+
9678  return this->name;
+
9679 }
+
9680 
+
9681 #define VECT_MATCH(a, b, c) \
+
9682  EPI_DEBUG_FAIL_AT_TRUE(a.size() != b.size(), c) \
+
9683  for (size_t __i = 0u; __i < a.size(); ++__i) \
+
9684  {\
+
9685  EPI_DEBUG_FAIL_AT_TRUE(a[__i] != b[__i], c) \
+
9686  }
+
9687 
+
9688 template<typename TSeq>
+
9689 inline bool Model<TSeq>::operator==(const Model<TSeq> & other) const
+
9690 {
+
9691  EPI_DEBUG_FAIL_AT_TRUE(name != other.name, "names don't match")
+
9692  EPI_DEBUG_FAIL_AT_TRUE(db != other.db, "database don't match")
+
9693 
+
9694  VECT_MATCH(population, other.population, "population doesn't match")
9695 
9696  EPI_DEBUG_FAIL_AT_TRUE(
-
9697  agents_data_ncols != other.agents_data_ncols,
-
9698  "Model:: agents_data_ncols don't match"
-
9699  )
-
9700 
-
9701  EPI_DEBUG_FAIL_AT_TRUE(
-
9702  directed != other.directed,
-
9703  "Model:: directed don't match"
-
9704  )
-
9705 
-
9706  // Viruses -----------------------------------------------------------------
-
9707  EPI_DEBUG_FAIL_AT_TRUE(
-
9708  viruses.size() != other.viruses.size(),
-
9709  "Model:: viruses.size() don't match"
-
9710  )
-
9711 
-
9712  for (size_t i = 0u; i < viruses.size(); ++i)
-
9713  {
-
9714  EPI_DEBUG_FAIL_AT_TRUE(
-
9715  *viruses[i] != *other.viruses[i],
-
9716  "Model:: *viruses[i] don't match"
-
9717  )
-
9718 
+
9697  using_backup != other.using_backup,
+
9698  "Model:: using_backup don't match"
+
9699  )
+
9700 
+
9701  if ((population_backup.size() != 0) & (other.population_backup.size() != 0))
+
9702  {
+
9703 
+
9704  // False is population_backup.size() != other.population_backup.size()
+
9705  if (population_backup.size() != other.population_backup.size())
+
9706  return false;
+
9707 
+
9708  for (size_t i = 0u; i < population_backup.size(); ++i)
+
9709  {
+
9710  if (population_backup[i] != other.population_backup[i])
+
9711  return false;
+
9712  }
+
9713 
+
9714  } else if ((population_backup.size() == 0) & (other.population_backup.size() != 0)) {
+
9715  return false;
+
9716  } else if ((population_backup.size() != 0) & (other.population_backup.size() == 0))
+
9717  {
+
9718  return false;
9719  }
-
9720 
-
9721  // Tools -------------------------------------------------------------------
-
9722  EPI_DEBUG_FAIL_AT_TRUE(
-
9723  tools.size() != other.tools.size(),
-
9724  "Model:: tools.size() don't match"
-
9725  )
-
9726 
-
9727  for (size_t i = 0u; i < tools.size(); ++i)
-
9728  {
-
9729  EPI_DEBUG_FAIL_AT_TRUE(
-
9730  *tools[i] != *other.tools[i],
-
9731  "Model:: *tools[i] don't match"
-
9732  )
-
9733 
-
9734  }
+
9720 
+
9721  EPI_DEBUG_FAIL_AT_TRUE(
+
9722  agents_data != other.agents_data,
+
9723  "Model:: agents_data don't match"
+
9724  )
+
9725 
+
9726  EPI_DEBUG_FAIL_AT_TRUE(
+
9727  agents_data_ncols != other.agents_data_ncols,
+
9728  "Model:: agents_data_ncols don't match"
+
9729  )
+
9730 
+
9731  EPI_DEBUG_FAIL_AT_TRUE(
+
9732  directed != other.directed,
+
9733  "Model:: directed don't match"
+
9734  )
9735 
-
9736  VECT_MATCH(
-
9737  entities,
-
9738  other.entities,
-
9739  "entities don't match"
-
9740  )
+
9736  // Viruses -----------------------------------------------------------------
+
9737  EPI_DEBUG_FAIL_AT_TRUE(
+
9738  viruses.size() != other.viruses.size(),
+
9739  "Model:: viruses.size() don't match"
+
9740  )
9741 
-
9742  if ((entities_backup.size() != 0) & (other.entities_backup.size() != 0))
+
9742  for (size_t i = 0u; i < viruses.size(); ++i)
9743  {
-
9744 
-
9745  for (size_t i = 0u; i < entities_backup.size(); ++i)
-
9746  {
-
9747 
-
9748  EPI_DEBUG_FAIL_AT_TRUE(
-
9749  entities_backup[i] != other.entities_backup[i],
-
9750  "Model:: entities_backup[i] don't match"
-
9751  )
-
9752 
-
9753  }
-
9754 
-
9755  } else if ((entities_backup.size() == 0) & (other.entities_backup.size() != 0)) {
-
9756  EPI_DEBUG_FAIL_AT_TRUE(true, "entities_backup don't match")
-
9757  } else if ((entities_backup.size() != 0) & (other.entities_backup.size() == 0))
+
9744  EPI_DEBUG_FAIL_AT_TRUE(
+
9745  *viruses[i] != *other.viruses[i],
+
9746  "Model:: *viruses[i] don't match"
+
9747  )
+
9748 
+
9749  }
+
9750 
+
9751  // Tools -------------------------------------------------------------------
+
9752  EPI_DEBUG_FAIL_AT_TRUE(
+
9753  tools.size() != other.tools.size(),
+
9754  "Model:: tools.size() don't match"
+
9755  )
+
9756 
+
9757  for (size_t i = 0u; i < tools.size(); ++i)
9758  {
-
9759  EPI_DEBUG_FAIL_AT_TRUE(true, "entities_backup don't match")
-
9760  }
-
9761 
-
9762  EPI_DEBUG_FAIL_AT_TRUE(
-
9763  rewire_prop != other.rewire_prop,
-
9764  "Model:: rewire_prop don't match"
-
9765  )
-
9766 
-
9767  EPI_DEBUG_FAIL_AT_TRUE(
-
9768  parameters.size() != other.parameters.size(),
-
9769  "Model:: () don't match"
+
9759  EPI_DEBUG_FAIL_AT_TRUE(
+
9760  *tools[i] != *other.tools[i],
+
9761  "Model:: *tools[i] don't match"
+
9762  )
+
9763 
+
9764  }
+
9765 
+
9766  VECT_MATCH(
+
9767  entities,
+
9768  other.entities,
+
9769  "entities don't match"
9770  )
9771 
-
9772  EPI_DEBUG_FAIL_AT_TRUE(
-
9773  parameters != other.parameters,
-
9774  "Model:: parameters don't match"
-
9775  )
-
9776 
-
9777  EPI_DEBUG_FAIL_AT_TRUE(
-
9778  ndays != other.ndays,
-
9779  "Model:: ndays don't match"
-
9780  )
-
9781 
-
9782  VECT_MATCH(
-
9783  states_labels,
-
9784  other.states_labels,
-
9785  "state labels don't match"
-
9786  )
-
9787 
-
9788  EPI_DEBUG_FAIL_AT_TRUE(
-
9789  nstates != other.nstates,
-
9790  "Model:: nstates don't match"
-
9791  )
-
9792 
-
9793  EPI_DEBUG_FAIL_AT_TRUE(
-
9794  verbose != other.verbose,
-
9795  "Model:: verbose don't match"
-
9796  )
-
9797 
-
9798  EPI_DEBUG_FAIL_AT_TRUE(
-
9799  current_date != other.current_date,
-
9800  "Model:: current_date don't match"
-
9801  )
-
9802 
-
9803  VECT_MATCH(globalevents, other.globalevents, "global action don't match");
-
9804 
-
9805  EPI_DEBUG_FAIL_AT_TRUE(
-
9806  queue != other.queue,
-
9807  "Model:: queue don't match"
-
9808  )
-
9809 
-
9810 
-
9811  EPI_DEBUG_FAIL_AT_TRUE(
-
9812  use_queuing != other.use_queuing,
-
9813  "Model:: use_queuing don't match"
-
9814  )
-
9815 
-
9816  return true;
+
9772  if ((entities_backup.size() != 0) & (other.entities_backup.size() != 0))
+
9773  {
+
9774 
+
9775  for (size_t i = 0u; i < entities_backup.size(); ++i)
+
9776  {
+
9777 
+
9778  EPI_DEBUG_FAIL_AT_TRUE(
+
9779  entities_backup[i] != other.entities_backup[i],
+
9780  "Model:: entities_backup[i] don't match"
+
9781  )
+
9782 
+
9783  }
+
9784 
+
9785  } else if ((entities_backup.size() == 0) & (other.entities_backup.size() != 0)) {
+
9786  EPI_DEBUG_FAIL_AT_TRUE(true, "entities_backup don't match")
+
9787  } else if ((entities_backup.size() != 0) & (other.entities_backup.size() == 0))
+
9788  {
+
9789  EPI_DEBUG_FAIL_AT_TRUE(true, "entities_backup don't match")
+
9790  }
+
9791 
+
9792  EPI_DEBUG_FAIL_AT_TRUE(
+
9793  rewire_prop != other.rewire_prop,
+
9794  "Model:: rewire_prop don't match"
+
9795  )
+
9796 
+
9797  EPI_DEBUG_FAIL_AT_TRUE(
+
9798  parameters.size() != other.parameters.size(),
+
9799  "Model:: () don't match"
+
9800  )
+
9801 
+
9802  EPI_DEBUG_FAIL_AT_TRUE(
+
9803  parameters != other.parameters,
+
9804  "Model:: parameters don't match"
+
9805  )
+
9806 
+
9807  EPI_DEBUG_FAIL_AT_TRUE(
+
9808  ndays != other.ndays,
+
9809  "Model:: ndays don't match"
+
9810  )
+
9811 
+
9812  VECT_MATCH(
+
9813  states_labels,
+
9814  other.states_labels,
+
9815  "state labels don't match"
+
9816  )
9817 
-
9818 }
-
9819 
-
9820 #undef VECT_MATCH
-
9821 #undef DURCAST
-
9822 #undef CASES_PAR
-
9823 #undef CASE_PAR
-
9824 #undef CHECK_INIT
-
9825 #endif
-
9826 /*//////////////////////////////////////////////////////////////////////////////
-
9828 
-
9829  End of -include/epiworld/model-meat.hpp-
-
9830 
-
9833 
+
9818  EPI_DEBUG_FAIL_AT_TRUE(
+
9819  nstates != other.nstates,
+
9820  "Model:: nstates don't match"
+
9821  )
+
9822 
+
9823  EPI_DEBUG_FAIL_AT_TRUE(
+
9824  verbose != other.verbose,
+
9825  "Model:: verbose don't match"
+
9826  )
+
9827 
+
9828  EPI_DEBUG_FAIL_AT_TRUE(
+
9829  current_date != other.current_date,
+
9830  "Model:: current_date don't match"
+
9831  )
+
9832 
+
9833  VECT_MATCH(globalevents, other.globalevents, "global action don't match");
9834 
-
9835 
-
9836 /*//////////////////////////////////////////////////////////////////////////////
-
9838 
-
9839  Start of -include/epiworld/viruses-bones.hpp-
+
9835  EPI_DEBUG_FAIL_AT_TRUE(
+
9836  queue != other.queue,
+
9837  "Model:: queue don't match"
+
9838  )
+
9839 
9840 
-
9843 
-
9844 
-
9845 #ifndef EPIWORLD_VIRUSES_BONES_HPP
-
9846 #define EPIWORLD_VIRUSES_BONES_HPP
+
9841  EPI_DEBUG_FAIL_AT_TRUE(
+
9842  use_queuing != other.use_queuing,
+
9843  "Model:: use_queuing don't match"
+
9844  )
+
9845 
+
9846  return true;
9847 
-
9848 template<typename TSeq>
-
9849 class Virus;
-
9850 
-
9851 template<typename TSeq>
-
9852 class Agent;
-
9853 
-
9859 template<typename TSeq>
-
9860 class Viruses {
-
9861  friend class Virus<TSeq>;
-
9862  friend class Agent<TSeq>;
-
9863 private:
-
9864  std::vector< VirusPtr<TSeq> > * dat;
-
9865  const epiworld_fast_uint * n_viruses;
-
9866 
-
9867 public:
+
9848 }
+
9849 
+
9850 #undef VECT_MATCH
+
9851 #undef DURCAST
+
9852 #undef CASES_PAR
+
9853 #undef CASE_PAR
+
9854 #undef CHECK_INIT
+
9855 #endif
+
9856 /*//////////////////////////////////////////////////////////////////////////////
+
9858 
+
9859  End of -include/epiworld/model-meat.hpp-
+
9860 
+
9863 
+
9864 
+
9865 
+
9866 /*//////////////////////////////////////////////////////////////////////////////
9868 
-
9869  Viruses() = delete;
-
9870  Viruses(Agent<TSeq> & p) : dat(&p.viruses), n_viruses(&p.n_viruses) {};
-
9871 
-
9872  typename std::vector< VirusPtr<TSeq> >::iterator begin();
-
9873  typename std::vector< VirusPtr<TSeq> >::iterator end();
+
9869  Start of -include/epiworld/viruses-bones.hpp-
+
9870 
+
9873 
9874 
-
9875  VirusPtr<TSeq> & operator()(size_t i);
-
9876  VirusPtr<TSeq> & operator[](size_t i);
+
9875 #ifndef EPIWORLD_VIRUSES_BONES_HPP
+
9876 #define EPIWORLD_VIRUSES_BONES_HPP
9877 
-
9878  size_t size() const noexcept;
-
9879 
-
9880  void print() const noexcept;
-
9881 
-
9882 };
+
9878 template<typename TSeq>
+
9879 class Virus;
+
9880 
+
9881 template<typename TSeq>
+
9882 class Agent;
9883 
-
9884 template<typename TSeq>
-
9885 inline typename std::vector< VirusPtr<TSeq> >::iterator Viruses<TSeq>::begin()
-
9886 {
-
9887 
-
9888  if (*n_viruses == 0u)
-
9889  return dat->end();
-
9890 
-
9891  return dat->begin();
-
9892 }
-
9893 
-
9894 template<typename TSeq>
-
9895 inline typename std::vector< VirusPtr<TSeq> >::iterator Viruses<TSeq>::end()
-
9896 {
-
9897 
-
9898  #ifdef EPI_DEBUG
-
9899  if (dat->size() < *n_viruses)
-
9900  throw EPI_DEBUG_ERROR(std::logic_error, "Viruses:: The end of the virus is out of range");
-
9901  #endif
-
9902 
-
9903  return begin() + *n_viruses;
-
9904 }
-
9905 
-
9906 template<typename TSeq>
-
9907 inline VirusPtr<TSeq> & Viruses<TSeq>::operator()(size_t i)
-
9908 {
+
9889 template<typename TSeq>
+
9890 class Viruses {
+
9891  friend class Virus<TSeq>;
+
9892  friend class Agent<TSeq>;
+
9893 private:
+
9894  std::vector< VirusPtr<TSeq> > * dat;
+
9895  const epiworld_fast_uint * n_viruses;
+
9896 
+
9897 public:
+
9898 
+
9899  Viruses() = delete;
+
9900  Viruses(Agent<TSeq> & p) : dat(&p.viruses), n_viruses(&p.n_viruses) {};
+
9901 
+
9902  typename std::vector< VirusPtr<TSeq> >::iterator begin();
+
9903  typename std::vector< VirusPtr<TSeq> >::iterator end();
+
9904 
+
9905  VirusPtr<TSeq> & operator()(size_t i);
+
9906  VirusPtr<TSeq> & operator[](size_t i);
+
9907 
+
9908  size_t size() const noexcept;
9909 
-
9910  if (i >= *n_viruses)
-
9911  throw std::range_error("Virus index out of range.");
-
9912 
-
9913  return dat->operator[](i);
-
9914 
-
9915 }
-
9916 
-
9917 template<typename TSeq>
-
9918 inline VirusPtr<TSeq> & Viruses<TSeq>::operator[](size_t i)
-
9919 {
-
9920 
-
9921  return dat->operator[](i);
-
9922 
-
9923 }
-
9924 
-
9925 template<typename TSeq>
-
9926 inline size_t Viruses<TSeq>::size() const noexcept
-
9927 {
-
9928  return *n_viruses;
-
9929 }
-
9930 
-
9931 template<typename TSeq>
-
9932 inline void Viruses<TSeq>::print() const noexcept
-
9933 {
-
9934 
-
9935  if (*n_viruses == 0u)
-
9936  {
-
9937  printf_epiworld("List of viruses (none)\n");
-
9938  return;
-
9939  }
-
9940 
-
9941  printf_epiworld("List of viruses (%i): ", *n_viruses);
+
9910  void print() const noexcept;
+
9911 
+
9912 };
+
9913 
+
9914 template<typename TSeq>
+
9915 inline typename std::vector< VirusPtr<TSeq> >::iterator Viruses<TSeq>::begin()
+
9916 {
+
9917 
+
9918  if (*n_viruses == 0u)
+
9919  return dat->end();
+
9920 
+
9921  return dat->begin();
+
9922 }
+
9923 
+
9924 template<typename TSeq>
+
9925 inline typename std::vector< VirusPtr<TSeq> >::iterator Viruses<TSeq>::end()
+
9926 {
+
9927 
+
9928  #ifdef EPI_DEBUG
+
9929  if (dat->size() < *n_viruses)
+
9930  throw EPI_DEBUG_ERROR(std::logic_error, "Viruses:: The end of the virus is out of range");
+
9931  #endif
+
9932 
+
9933  return begin() + *n_viruses;
+
9934 }
+
9935 
+
9936 template<typename TSeq>
+
9937 inline VirusPtr<TSeq> & Viruses<TSeq>::operator()(size_t i)
+
9938 {
+
9939 
+
9940  if (i >= *n_viruses)
+
9941  throw std::range_error("Virus index out of range.");
9942 
-
9943  // Printing the name of each virus separated by a comma
-
9944  for (size_t i = 0u; i < *n_viruses; ++i)
-
9945  {
-
9946  if (i == *n_viruses - 1u)
-
9947  {
-
9948  printf_epiworld("%s", dat->operator[](i)->get_name().c_str());
-
9949  } else
-
9950  {
-
9951  printf_epiworld("%s, ", dat->operator[](i)->get_name().c_str());
-
9952  }
-
9953  }
-
9954 
-
9955  printf_epiworld("\n");
-
9956 
-
9957 }
-
9958 
-
9964 template<typename TSeq>
-
9965 class Viruses_const {
-
9966  friend class Virus<TSeq>;
-
9967  friend class Agent<TSeq>;
-
9968 private:
-
9969  const std::vector< VirusPtr<TSeq> > * dat;
-
9970  const epiworld_fast_uint * n_viruses;
-
9971 
-
9972 public:
-
9973 
-
9974  Viruses_const() = delete;
-
9975  Viruses_const(const Agent<TSeq> & p) : dat(&p.viruses), n_viruses(&p.n_viruses) {};
-
9976 
-
9977  typename std::vector< VirusPtr<TSeq> >::const_iterator begin() const;
-
9978  typename std::vector< VirusPtr<TSeq> >::const_iterator end() const;
-
9979 
-
9980  const VirusPtr<TSeq> & operator()(size_t i);
-
9981  const VirusPtr<TSeq> & operator[](size_t i);
-
9982 
-
9983  size_t size() const noexcept;
-
9984 
-
9985  void print() const noexcept;
+
9943  return dat->operator[](i);
+
9944 
+
9945 }
+
9946 
+
9947 template<typename TSeq>
+
9948 inline VirusPtr<TSeq> & Viruses<TSeq>::operator[](size_t i)
+
9949 {
+
9950 
+
9951  return dat->operator[](i);
+
9952 
+
9953 }
+
9954 
+
9955 template<typename TSeq>
+
9956 inline size_t Viruses<TSeq>::size() const noexcept
+
9957 {
+
9958  return *n_viruses;
+
9959 }
+
9960 
+
9961 template<typename TSeq>
+
9962 inline void Viruses<TSeq>::print() const noexcept
+
9963 {
+
9964 
+
9965  if (*n_viruses == 0u)
+
9966  {
+
9967  printf_epiworld("List of viruses (none)\n");
+
9968  return;
+
9969  }
+
9970 
+
9971  printf_epiworld("List of viruses (%i): ", *n_viruses);
+
9972 
+
9973  // Printing the name of each virus separated by a comma
+
9974  for (size_t i = 0u; i < *n_viruses; ++i)
+
9975  {
+
9976  if (i == *n_viruses - 1u)
+
9977  {
+
9978  printf_epiworld("%s", dat->operator[](i)->get_name().c_str());
+
9979  } else
+
9980  {
+
9981  printf_epiworld("%s, ", dat->operator[](i)->get_name().c_str());
+
9982  }
+
9983  }
+
9984 
+
9985  printf_epiworld("\n");
9986 
-
9987 };
+
9987 }
9988 
-
9989 template<typename TSeq>
-
9990 inline typename std::vector< VirusPtr<TSeq> >::const_iterator Viruses_const<TSeq>::begin() const {
-
9991 
-
9992  if (*n_viruses == 0u)
-
9993  return dat->end();
-
9994 
-
9995  return dat->begin();
-
9996 }
-
9997 
-
9998 template<typename TSeq>
-
9999 inline typename std::vector< VirusPtr<TSeq> >::const_iterator Viruses_const<TSeq>::end() const {
-
10000 
-
10001  #ifdef EPI_DEBUG
-
10002  if (dat->size() < *n_viruses)
-
10003  throw EPI_DEBUG_ERROR(std::logic_error, "Viruses_const:: The end of the virus is out of range");
-
10004  #endif
-
10005  return begin() + *n_viruses;
-
10006 }
-
10007 
-
10008 template<typename TSeq>
-
10009 inline const VirusPtr<TSeq> & Viruses_const<TSeq>::operator()(size_t i)
-
10010 {
-
10011 
-
10012  if (i >= *n_viruses)
-
10013  throw std::range_error("Virus index out of range.");
+
9994 template<typename TSeq>
+
9995 class Viruses_const {
+
9996  friend class Virus<TSeq>;
+
9997  friend class Agent<TSeq>;
+
9998 private:
+
9999  const std::vector< VirusPtr<TSeq> > * dat;
+
10000  const epiworld_fast_uint * n_viruses;
+
10001 
+
10002 public:
+
10003 
+
10004  Viruses_const() = delete;
+
10005  Viruses_const(const Agent<TSeq> & p) : dat(&p.viruses), n_viruses(&p.n_viruses) {};
+
10006 
+
10007  typename std::vector< VirusPtr<TSeq> >::const_iterator begin() const;
+
10008  typename std::vector< VirusPtr<TSeq> >::const_iterator end() const;
+
10009 
+
10010  const VirusPtr<TSeq> & operator()(size_t i);
+
10011  const VirusPtr<TSeq> & operator[](size_t i);
+
10012 
+
10013  size_t size() const noexcept;
10014 
-
10015  return dat->operator[](i);
+
10015  void print() const noexcept;
10016 
-
10017 }
+
10017 };
10018 
10019 template<typename TSeq>
-
10020 inline const VirusPtr<TSeq> & Viruses_const<TSeq>::operator[](size_t i)
-
10021 {
-
10022 
-
10023  return dat->operator[](i);
-
10024 
-
10025 }
-
10026 
-
10027 template<typename TSeq>
-
10028 inline size_t Viruses_const<TSeq>::size() const noexcept
-
10029 {
-
10030  return *n_viruses;
-
10031 }
-
10032 
-
10033 template<typename TSeq>
-
10034 inline void Viruses_const<TSeq>::print() const noexcept
-
10035 {
-
10036 
-
10037  if (*n_viruses == 0u)
-
10038  {
-
10039  printf_epiworld("List of viruses (none)\n");
-
10040  return;
-
10041  }
-
10042 
-
10043  printf_epiworld("List of viruses (%i): ", *n_viruses);
+
10020 inline typename std::vector< VirusPtr<TSeq> >::const_iterator Viruses_const<TSeq>::begin() const {
+
10021 
+
10022  if (*n_viruses == 0u)
+
10023  return dat->end();
+
10024 
+
10025  return dat->begin();
+
10026 }
+
10027 
+
10028 template<typename TSeq>
+
10029 inline typename std::vector< VirusPtr<TSeq> >::const_iterator Viruses_const<TSeq>::end() const {
+
10030 
+
10031  #ifdef EPI_DEBUG
+
10032  if (dat->size() < *n_viruses)
+
10033  throw EPI_DEBUG_ERROR(std::logic_error, "Viruses_const:: The end of the virus is out of range");
+
10034  #endif
+
10035  return begin() + *n_viruses;
+
10036 }
+
10037 
+
10038 template<typename TSeq>
+
10039 inline const VirusPtr<TSeq> & Viruses_const<TSeq>::operator()(size_t i)
+
10040 {
+
10041 
+
10042  if (i >= *n_viruses)
+
10043  throw std::range_error("Virus index out of range.");
10044 
-
10045  // Printing the name of each virus separated by a comma
-
10046  for (size_t i = 0u; i < *n_viruses; ++i)
-
10047  {
-
10048  if (i == *n_viruses - 1u)
-
10049  {
-
10050  printf_epiworld("%s", dat->operator[](i)->get_name().c_str());
-
10051  } else
-
10052  {
-
10053  printf_epiworld("%s, ", dat->operator[](i)->get_name().c_str());
-
10054  }
-
10055  }
-
10056 
-
10057  printf_epiworld("\n");
-
10058 
-
10059 }
-
10060 
-
10061 
-
10062 #endif
-
10063 /*//////////////////////////////////////////////////////////////////////////////
-
10065 
-
10066  End of -include/epiworld/viruses-bones.hpp-
-
10067 
-
10070 
-
10071 
+
10045  return dat->operator[](i);
+
10046 
+
10047 }
+
10048 
+
10049 template<typename TSeq>
+
10050 inline const VirusPtr<TSeq> & Viruses_const<TSeq>::operator[](size_t i)
+
10051 {
+
10052 
+
10053  return dat->operator[](i);
+
10054 
+
10055 }
+
10056 
+
10057 template<typename TSeq>
+
10058 inline size_t Viruses_const<TSeq>::size() const noexcept
+
10059 {
+
10060  return *n_viruses;
+
10061 }
+
10062 
+
10063 template<typename TSeq>
+
10064 inline void Viruses_const<TSeq>::print() const noexcept
+
10065 {
+
10066 
+
10067  if (*n_viruses == 0u)
+
10068  {
+
10069  printf_epiworld("List of viruses (none)\n");
+
10070  return;
+
10071  }
10072 
-
10073 /*//////////////////////////////////////////////////////////////////////////////
-
10075 
-
10076  Start of -include/epiworld/virus-bones.hpp-
-
10077 
-
10080 
-
10081 
-
10082 #ifndef EPIWORLD_VIRUS_HPP
-
10083 #define EPIWORLD_VIRUS_HPP
-
10084 
-
10085 template<typename TSeq>
-
10086 class Agent;
-
10087 
-
10088 template<typename TSeq>
-
10089 class Virus;
+
10073  printf_epiworld("List of viruses (%i): ", *n_viruses);
+
10074 
+
10075  // Printing the name of each virus separated by a comma
+
10076  for (size_t i = 0u; i < *n_viruses; ++i)
+
10077  {
+
10078  if (i == *n_viruses - 1u)
+
10079  {
+
10080  printf_epiworld("%s", dat->operator[](i)->get_name().c_str());
+
10081  } else
+
10082  {
+
10083  printf_epiworld("%s, ", dat->operator[](i)->get_name().c_str());
+
10084  }
+
10085  }
+
10086 
+
10087  printf_epiworld("\n");
+
10088 
+
10089 }
10090 
-
10091 template<typename TSeq>
-
10092 class Model;
-
10093 
-
10104 template<typename TSeq>
-
10105 class Virus {
-
10106  friend class Agent<TSeq>;
-
10107  friend class Model<TSeq>;
-
10108  friend class DataBase<TSeq>;
-
10109  friend void default_add_virus<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
10110  friend void default_rm_virus<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
10111 private:
-
10112 
-
10113  Agent<TSeq> * agent = nullptr;
+
10091 
+
10092 #endif
+
10093 /*//////////////////////////////////////////////////////////////////////////////
+
10095 
+
10096  End of -include/epiworld/viruses-bones.hpp-
+
10097 
+
10100 
+
10101 
+
10102 
+
10103 /*//////////////////////////////////////////////////////////////////////////////
+
10105 
+
10106  Start of -include/epiworld/virus-bones.hpp-
+
10107 
+
10110 
+
10111 
+
10112 #ifndef EPIWORLD_VIRUS_HPP
+
10113 #define EPIWORLD_VIRUS_HPP
10114 
-
10115  std::shared_ptr<TSeq> baseline_sequence = nullptr;
-
10116  std::shared_ptr<std::string> virus_name = nullptr;
-
10117  int date = -99;
-
10118  int id = -99;
-
10119  bool active = true;
-
10120  MutFun<TSeq> mutation_fun = nullptr;
-
10121  PostRecoveryFun<TSeq> post_recovery_fun = nullptr;
-
10122  VirusFun<TSeq> probability_of_infecting_fun = nullptr;
-
10123  VirusFun<TSeq> probability_of_recovery_fun = nullptr;
-
10124  VirusFun<TSeq> probability_of_death_fun = nullptr;
-
10125  VirusFun<TSeq> incubation_fun = nullptr;
-
10126 
-
10127  // Setup parameters
-
10128  std::vector< epiworld_double > data = {};
-
10129 
-
10130  epiworld_fast_int state_init = -99; ///< Change of state when added to agent.
-
10131  epiworld_fast_int state_post = -99; ///< Change of state when removed from agent.
-
10132  epiworld_fast_int state_removed = -99; ///< Change of state when agent is removed
-
10133 
-
10134  epiworld_fast_int queue_init = Queue<TSeq>::Everyone; ///< Change of state when added to agent.
-
10135  epiworld_fast_int queue_post = -Queue<TSeq>::Everyone; ///< Change of state when removed from agent.
-
10136  epiworld_fast_int queue_removed = -99; ///< Change of state when agent is removed
-
10137 
-
10138  // Information about how distribution works
-
10139  VirusToAgentFun<TSeq> dist_fun = nullptr;
-
10140 
-
10141 public:
-
10142  Virus(std::string name = "unknown virus");
-
10143 
-
10144  Virus(
-
10145  std::string name,
-
10146  epiworld_double prevalence,
-
10147  bool as_proportion
-
10148  );
-
10149 
-
10150  void mutate(Model<TSeq> * model);
-
10151  void set_mutation(MutFun<TSeq> fun);
-
10152 
-
10153  std::shared_ptr<TSeq> get_sequence();
-
10154  void set_sequence(TSeq sequence);
-
10155 
-
10156  Agent<TSeq> * get_agent();
-
10157  void set_agent(Agent<TSeq> * p);
-
10158 
-
10159  void set_date(int d);
-
10160  int get_date() const;
-
10161 
-
10162  void set_id(int idx);
-
10163  int get_id() const;
-
10164 
-
10174  epiworld_double get_prob_infecting(Model<TSeq> * model);
-
10175  epiworld_double get_prob_recovery(Model<TSeq> * model);
-
10176  epiworld_double get_prob_death(Model<TSeq> * model);
-
10177  epiworld_double get_incubation(Model<TSeq> * model);
-
10178 
-
10179  void post_recovery(Model<TSeq> * model);
-
10180  void set_post_recovery(PostRecoveryFun<TSeq> fun);
-
10181  void set_post_immunity(epiworld_double prob);
-
10182  void set_post_immunity(epiworld_double * prob);
-
10183 
-
10184  void set_prob_infecting_fun(VirusFun<TSeq> fun);
-
10185  void set_prob_recovery_fun(VirusFun<TSeq> fun);
-
10186  void set_prob_death_fun(VirusFun<TSeq> fun);
-
10187  void set_incubation_fun(VirusFun<TSeq> fun);
+
10115 template<typename TSeq>
+
10116 class Agent;
+
10117 
+
10118 template<typename TSeq>
+
10119 class Virus;
+
10120 
+
10121 template<typename TSeq>
+
10122 class Model;
+
10123 
+
10134 template<typename TSeq>
+
10135 class Virus {
+
10136  friend class Agent<TSeq>;
+
10137  friend class Model<TSeq>;
+
10138  friend class DataBase<TSeq>;
+
10139  friend void default_add_virus<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
10140  friend void default_rm_virus<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
10141 private:
+
10142 
+
10143  Agent<TSeq> * agent = nullptr;
+
10144 
+
10145  std::shared_ptr<TSeq> baseline_sequence = nullptr;
+
10146  std::shared_ptr<std::string> virus_name = nullptr;
+
10147  int date = -99;
+
10148  int id = -99;
+
10149  bool active = true;
+
10150  MutFun<TSeq> mutation_fun = nullptr;
+
10151  PostRecoveryFun<TSeq> post_recovery_fun = nullptr;
+
10152  VirusFun<TSeq> probability_of_infecting_fun = nullptr;
+
10153  VirusFun<TSeq> probability_of_recovery_fun = nullptr;
+
10154  VirusFun<TSeq> probability_of_death_fun = nullptr;
+
10155  VirusFun<TSeq> incubation_fun = nullptr;
+
10156 
+
10157  // Setup parameters
+
10158  std::vector< epiworld_double > data = {};
+
10159 
+
10160  epiworld_fast_int state_init = -99; ///< Change of state when added to agent.
+
10161  epiworld_fast_int state_post = -99; ///< Change of state when removed from agent.
+
10162  epiworld_fast_int state_removed = -99; ///< Change of state when agent is removed
+
10163 
+
10164  epiworld_fast_int queue_init = Queue<TSeq>::Everyone; ///< Change of state when added to agent.
+
10165  epiworld_fast_int queue_post = -Queue<TSeq>::Everyone; ///< Change of state when removed from agent.
+
10166  epiworld_fast_int queue_removed = -99; ///< Change of state when agent is removed
+
10167 
+
10168  // Information about how distribution works
+
10169  VirusToAgentFun<TSeq> dist_fun = nullptr;
+
10170 
+
10171 public:
+
10172  Virus(std::string name = "unknown virus");
+
10173 
+
10174  Virus(
+
10175  std::string name,
+
10176  epiworld_double prevalence,
+
10177  bool as_proportion
+
10178  );
+
10179 
+
10180  void mutate(Model<TSeq> * model);
+
10181  void set_mutation(MutFun<TSeq> fun);
+
10182 
+
10183  std::shared_ptr<TSeq> get_sequence();
+
10184  void set_sequence(TSeq sequence);
+
10185 
+
10186  Agent<TSeq> * get_agent();
+
10187  void set_agent(Agent<TSeq> * p);
10188 
-
10189  void set_prob_infecting(const epiworld_double * prob);
-
10190  void set_prob_recovery(const epiworld_double * prob);
-
10191  void set_prob_death(const epiworld_double * prob);
-
10192  void set_incubation(const epiworld_double * prob);
-
10193 
-
10194  void set_prob_infecting(epiworld_double prob);
-
10195  void set_prob_recovery(epiworld_double prob);
-
10196  void set_prob_death(epiworld_double prob);
-
10197  void set_incubation(epiworld_double prob);
-
10199 
-
10200 
-
10201  void set_name(std::string name);
-
10202  std::string get_name() const;
-
10203 
-
10204  std::vector< epiworld_double > & get_data();
-
10205 
-
10219  void set_state(
-
10220  epiworld_fast_int init,
-
10221  epiworld_fast_int end,
-
10222  epiworld_fast_int removed = -99
-
10223  );
-
10224 
-
10225  void set_queue(
-
10226  epiworld_fast_int init,
-
10227  epiworld_fast_int end,
-
10228  epiworld_fast_int removed = -99
-
10229  );
+
10189  void set_date(int d);
+
10190  int get_date() const;
+
10191 
+
10192  void set_id(int idx);
+
10193  int get_id() const;
+
10194 
+
10204  epiworld_double get_prob_infecting(Model<TSeq> * model);
+
10205  epiworld_double get_prob_recovery(Model<TSeq> * model);
+
10206  epiworld_double get_prob_death(Model<TSeq> * model);
+
10207  epiworld_double get_incubation(Model<TSeq> * model);
+
10208 
+
10209  void post_recovery(Model<TSeq> * model);
+
10210  void set_post_recovery(PostRecoveryFun<TSeq> fun);
+
10211  void set_post_immunity(epiworld_double prob);
+
10212  void set_post_immunity(epiworld_double * prob);
+
10213 
+
10214  void set_prob_infecting_fun(VirusFun<TSeq> fun);
+
10215  void set_prob_recovery_fun(VirusFun<TSeq> fun);
+
10216  void set_prob_death_fun(VirusFun<TSeq> fun);
+
10217  void set_incubation_fun(VirusFun<TSeq> fun);
+
10218 
+
10219  void set_prob_infecting(const epiworld_double * prob);
+
10220  void set_prob_recovery(const epiworld_double * prob);
+
10221  void set_prob_death(const epiworld_double * prob);
+
10222  void set_incubation(const epiworld_double * prob);
+
10223 
+
10224  void set_prob_infecting(epiworld_double prob);
+
10225  void set_prob_recovery(epiworld_double prob);
+
10226  void set_prob_death(epiworld_double prob);
+
10227  void set_incubation(epiworld_double prob);
+
10229 
10230 
-
10231  void get_state(
-
10232  epiworld_fast_int * init,
-
10233  epiworld_fast_int * end,
-
10234  epiworld_fast_int * removed = nullptr
-
10235  );
-
10236 
-
10237  void get_queue(
-
10238  epiworld_fast_int * init,
-
10239  epiworld_fast_int * end,
-
10240  epiworld_fast_int * removed = nullptr
-
10241  );
-
10243 
-
10244  bool operator==(const Virus<TSeq> & other) const;
-
10245  bool operator!=(const Virus<TSeq> & other) const {return !operator==(other);};
-
10246 
-
10247  void print() const;
-
10248 
-
10253  void distribute(Model<TSeq> * model);
-
10254  void set_distribution(VirusToAgentFun<TSeq> fun);
-
10256 
-
10257 
-
10258 };
-
10259 
-
10260 #endif
-
10261 /*//////////////////////////////////////////////////////////////////////////////
-
10263 
-
10264  End of -include/epiworld/virus-bones.hpp-
-
10265 
-
10268 
-
10269 
-
10270 /*//////////////////////////////////////////////////////////////////////////////
-
10272 
-
10273  Start of -include/epiworld/virus-distribute-meat.hpp-
-
10274 
-
10277 
+
10231  void set_name(std::string name);
+
10232  std::string get_name() const;
+
10233 
+
10234  std::vector< epiworld_double > & get_data();
+
10235 
+
10249  void set_state(
+
10250  epiworld_fast_int init,
+
10251  epiworld_fast_int end,
+
10252  epiworld_fast_int removed = -99
+
10253  );
+
10254 
+
10255  void set_queue(
+
10256  epiworld_fast_int init,
+
10257  epiworld_fast_int end,
+
10258  epiworld_fast_int removed = -99
+
10259  );
+
10260 
+
10261  void get_state(
+
10262  epiworld_fast_int * init,
+
10263  epiworld_fast_int * end,
+
10264  epiworld_fast_int * removed = nullptr
+
10265  );
+
10266 
+
10267  void get_queue(
+
10268  epiworld_fast_int * init,
+
10269  epiworld_fast_int * end,
+
10270  epiworld_fast_int * removed = nullptr
+
10271  );
+
10273 
+
10274  bool operator==(const Virus<TSeq> & other) const;
+
10275  bool operator!=(const Virus<TSeq> & other) const {return !operator==(other);};
+
10276 
+
10277  void print() const;
10278 
-
10279 #ifndef EPIWORLD_VIRUS_DISTRIBUTE_MEAT_HPP
-
10280 #define EPIWORLD_VIRUS_DISTRIBUTE_MEAT_HPP
-
10281 
-
10294 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
10295 inline VirusToAgentFun<TSeq> distribute_virus_to_set(
-
10296  std::vector< size_t > agents_ids
-
10297 ) {
+
10283  void distribute(Model<TSeq> * model);
+
10284  void set_distribution(VirusToAgentFun<TSeq> fun);
+
10286 
+
10287 
+
10288 };
+
10289 
+
10290 #endif
+
10291 /*//////////////////////////////////////////////////////////////////////////////
+
10293 
+
10294  End of -include/epiworld/virus-bones.hpp-
+
10295 
10298 
-
10299  return [agents_ids](
-
10300  Virus<TSeq> & virus, Model<TSeq> * model
-
10301  ) -> void
-
10302  {
-
10303  // Adding action
-
10304  for (auto i: agents_ids)
-
10305  {
-
10306  model->get_agent(i).set_virus(
-
10307  virus,
-
10308  const_cast<Model<TSeq> * >(model)
-
10309  );
-
10310  }
-
10311  };
-
10312 
-
10313 }
-
10314 
-
10325 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
10326 inline VirusToAgentFun<TSeq> distribute_virus_randomly(
-
10327  epiworld_double prevalence,
-
10328  bool prevalence_as_proportion = true
-
10329 ) {
-
10330 
-
10331  return [prevalence,prevalence_as_proportion](
-
10332  Virus<TSeq> & virus, Model<TSeq> * model
-
10333  ) -> void
-
10334  {
-
10335 
-
10336  // Figuring out how what agents are available
-
10337  std::vector< size_t > idx;
-
10338  for (const auto & agent: model->get_agents())
-
10339  if (agent.get_virus() == nullptr)
-
10340  idx.push_back(agent.get_id());
-
10341 
-
10342  // Picking how many
-
10343  size_t n = model->size();
-
10344  int n_available = static_cast<int>(idx.size());
-
10345  int n_to_sample;
-
10346  if (prevalence_as_proportion)
-
10347  {
-
10348  n_to_sample = static_cast<int>(std::floor(prevalence * n));
-
10349 
-
10350  if (n_to_sample == static_cast<int>(n))
-
10351  n_to_sample--;
-
10352  }
-
10353  else
-
10354  {
-
10355  n_to_sample = static_cast<int>(prevalence);
-
10356  }
-
10357 
-
10358  if (n_to_sample > n_available)
-
10359  throw std::range_error(
-
10360  "There are only " + std::to_string(n_available) +
-
10361  " individuals with no virus in the population. " +
-
10362  "Cannot add the virus to " +
-
10363  std::to_string(n_to_sample)
-
10364  );
+
10299 
+
10300 /*//////////////////////////////////////////////////////////////////////////////
+
10302 
+
10303  Start of -include/epiworld/virus-distribute-meat.hpp-
+
10304 
+
10307 
+
10308 
+
10309 #ifndef EPIWORLD_VIRUS_DISTRIBUTE_MEAT_HPP
+
10310 #define EPIWORLD_VIRUS_DISTRIBUTE_MEAT_HPP
+
10311 
+
10324 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
10325 inline VirusToAgentFun<TSeq> distribute_virus_to_set(
+
10326  std::vector< size_t > agents_ids
+
10327 ) {
+
10328 
+
10329  return [agents_ids](
+
10330  Virus<TSeq> & virus, Model<TSeq> * model
+
10331  ) -> void
+
10332  {
+
10333  // Adding action
+
10334  for (auto i: agents_ids)
+
10335  {
+
10336  model->get_agent(i).set_virus(
+
10337  virus,
+
10338  const_cast<Model<TSeq> * >(model)
+
10339  );
+
10340  }
+
10341  };
+
10342 
+
10343 }
+
10344 
+
10355 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
10356 inline VirusToAgentFun<TSeq> distribute_virus_randomly(
+
10357  epiworld_double prevalence,
+
10358  bool prevalence_as_proportion = true
+
10359 ) {
+
10360 
+
10361  return [prevalence,prevalence_as_proportion](
+
10362  Virus<TSeq> & virus, Model<TSeq> * model
+
10363  ) -> void
+
10364  {
10365 
-
10366  auto & population = model->get_agents();
-
10367  for (int i = 0; i < n_to_sample; ++i)
-
10368  {
-
10369 
-
10370  int loc = static_cast<epiworld_fast_uint>(
-
10371  floor(model->runif() * (n_available--))
-
10372  );
-
10373 
-
10374  // Correcting for possible overflow
-
10375  if ((loc > 0) && (loc >= n_available))
-
10376  loc = n_available - 1;
-
10377 
-
10378  Agent<TSeq> & agent = population[idx[loc]];
-
10379 
-
10380  // Adding action
-
10381  agent.set_virus(
-
10382  virus,
-
10383  const_cast<Model<TSeq> * >(model)
-
10384  );
-
10385 
-
10386  // Adjusting sample
-
10387  std::swap(idx[loc], idx[n_available]);
-
10388 
-
10389  }
-
10390 
-
10391  };
-
10392 
-
10393 }
-
10394 
-
10395 #endif
-
10396 /*//////////////////////////////////////////////////////////////////////////////
-
10398 
-
10399  End of -include/epiworld/virus-distribute-meat.hpp-
-
10400 
+
10366  // Figuring out how what agents are available
+
10367  std::vector< size_t > idx;
+
10368  for (const auto & agent: model->get_agents())
+
10369  if (agent.get_virus() == nullptr)
+
10370  idx.push_back(agent.get_id());
+
10371 
+
10372  // Picking how many
+
10373  size_t n = model->size();
+
10374  int n_available = static_cast<int>(idx.size());
+
10375  int n_to_sample;
+
10376  if (prevalence_as_proportion)
+
10377  {
+
10378  n_to_sample = static_cast<int>(std::floor(prevalence * n));
+
10379 
+
10380  if (n_to_sample == static_cast<int>(n))
+
10381  n_to_sample--;
+
10382  }
+
10383  else
+
10384  {
+
10385  n_to_sample = static_cast<int>(prevalence);
+
10386  }
+
10387 
+
10388  if (n_to_sample > n_available)
+
10389  throw std::range_error(
+
10390  "There are only " + std::to_string(n_available) +
+
10391  " individuals with no virus in the population. " +
+
10392  "Cannot add the virus to " +
+
10393  std::to_string(n_to_sample)
+
10394  );
+
10395 
+
10396  auto & population = model->get_agents();
+
10397  for (int i = 0; i < n_to_sample; ++i)
+
10398  {
+
10399 
+
10400  int loc = static_cast<epiworld_fast_uint>(
+
10401  floor(model->runif() * (n_available--))
+
10402  );
10403 
-
10404 
-
10405 /*//////////////////////////////////////////////////////////////////////////////
+
10404  // Correcting for possible overflow
+
10405  if ((loc > 0) && (loc >= n_available))
+
10406  loc = n_available - 1;
10407 
-
10408  Start of -include/epiworld/virus-meat.hpp-
-
10409 
-
10412 
-
10413 
-
10414 #ifndef EPIWORLD_VIRUS_MEAT_HPP
-
10415 #define EPIWORLD_VIRUS_MEAT_HPP
-
10416 
-
10425 template<typename TSeq>
-
10426 inline VirusFun<TSeq> virus_fun_logit(
-
10427  std::vector< int > vars,
-
10428  std::vector< double > coefs,
-
10429  Model<TSeq> * model,
-
10430  bool logit = true
-
10431 ) {
-
10432 
-
10433  // Checking that there are features
-
10434  if (coefs.size() == 0u)
-
10435  throw std::logic_error(
-
10436  "The -coefs- argument should feature at least one element."
-
10437  );
-
10438 
-
10439  if (coefs.size() != vars.size())
-
10440  throw std::length_error(
-
10441  std::string("The length of -coef- (") +
-
10442  std::to_string(coefs.size()) +
-
10443  std::string(") and -vars- (") +
-
10444  std::to_string(vars.size()) +
-
10445  std::string(") should match. ")
-
10446  );
-
10447 
-
10448  // Checking that there are variables in the model
-
10449  if (model != nullptr)
-
10450  {
-
10451 
-
10452  size_t K = model->get_agents_data_ncols();
-
10453  for (const auto & var: vars)
-
10454  {
-
10455  if ((var >= static_cast<int>(K)) | (var < 0))
-
10456  throw std::range_error(
-
10457  std::string("The variable ") +
-
10458  std::to_string(var) +
-
10459  std::string(" is out of range.") +
-
10460  std::string(" The agents only feature ") +
-
10461  std::to_string(K) +
-
10462  std::string("variables (features).")
-
10463  );
-
10464  }
-
10465 
-
10466  }
-
10467 
-
10468  std::vector< epiworld_double > coefs_f;
-
10469  for (auto c: coefs)
-
10470  coefs_f.push_back(static_cast<epiworld_double>(c));
-
10471 
-
10472  VirusFun<TSeq> fun_infect = [coefs_f,vars](
-
10473  Agent<TSeq> * agent,
-
10474  Virus<TSeq> &,
-
10475  Model<TSeq> *
-
10476  ) -> epiworld_double {
+
10408  Agent<TSeq> & agent = population[idx[loc]];
+
10409 
+
10410  // Adding action
+
10411  agent.set_virus(
+
10412  virus,
+
10413  const_cast<Model<TSeq> * >(model)
+
10414  );
+
10415 
+
10416  // Adjusting sample
+
10417  std::swap(idx[loc], idx[n_available]);
+
10418 
+
10419  }
+
10420 
+
10421  };
+
10422 
+
10423 }
+
10424 
+
10425 #endif
+
10426 /*//////////////////////////////////////////////////////////////////////////////
+
10428 
+
10429  End of -include/epiworld/virus-distribute-meat.hpp-
+
10430 
+
10433 
+
10434 
+
10435 /*//////////////////////////////////////////////////////////////////////////////
+
10437 
+
10438  Start of -include/epiworld/virus-meat.hpp-
+
10439 
+
10442 
+
10443 
+
10444 #ifndef EPIWORLD_VIRUS_MEAT_HPP
+
10445 #define EPIWORLD_VIRUS_MEAT_HPP
+
10446 
+
10455 template<typename TSeq>
+
10456 inline VirusFun<TSeq> virus_fun_logit(
+
10457  std::vector< int > vars,
+
10458  std::vector< double > coefs,
+
10459  Model<TSeq> * model,
+
10460  bool logit = true
+
10461 ) {
+
10462 
+
10463  // Checking that there are features
+
10464  if (coefs.size() == 0u)
+
10465  throw std::logic_error(
+
10466  "The -coefs- argument should feature at least one element."
+
10467  );
+
10468 
+
10469  if (coefs.size() != vars.size())
+
10470  throw std::length_error(
+
10471  std::string("The length of -coef- (") +
+
10472  std::to_string(coefs.size()) +
+
10473  std::string(") and -vars- (") +
+
10474  std::to_string(vars.size()) +
+
10475  std::string(") should match. ")
+
10476  );
10477 
-
10478  size_t K = coefs_f.size();
-
10479  epiworld_double res = 0.0;
-
10480 
-
10481  #if defined(__OPENMP) || defined(_OPENMP)
-
10482  #pragma omp simd reduction(+:res)
-
10483  #endif
-
10484  for (size_t i = 0u; i < K; ++i)
-
10485  res += agent->operator[](vars.at(i)) * coefs_f.at(i);
-
10486 
-
10487  return 1.0/(1.0 + std::exp(-res));
-
10488 
-
10489  };
-
10490 
-
10491  return fun_infect;
-
10492 
-
10493 }
-
10494 
-
10495 template<typename TSeq>
-
10496 inline Virus<TSeq>::Virus(
-
10497  std::string name
-
10498  ) {
-
10499  set_name(name);
-
10500 }
+
10478  // Checking that there are variables in the model
+
10479  if (model != nullptr)
+
10480  {
+
10481 
+
10482  size_t K = model->get_agents_data_ncols();
+
10483  for (const auto & var: vars)
+
10484  {
+
10485  if ((var >= static_cast<int>(K)) | (var < 0))
+
10486  throw std::range_error(
+
10487  std::string("The variable ") +
+
10488  std::to_string(var) +
+
10489  std::string(" is out of range.") +
+
10490  std::string(" The agents only feature ") +
+
10491  std::to_string(K) +
+
10492  std::string("variables (features).")
+
10493  );
+
10494  }
+
10495 
+
10496  }
+
10497 
+
10498  std::vector< epiworld_double > coefs_f;
+
10499  for (auto c: coefs)
+
10500  coefs_f.push_back(static_cast<epiworld_double>(c));
10501 
-
10502 template<typename TSeq>
-
10503 inline Virus<TSeq>::Virus(
-
10504  std::string name,
-
10505  epiworld_double prevalence,
-
10506  bool prevalence_as_proportion
-
10507  ) {
-
10508  set_name(name);
-
10509  set_distribution(
-
10510  distribute_virus_randomly<TSeq>(
-
10511  prevalence,
-
10512  prevalence_as_proportion
-
10513  )
-
10514  );
-
10515 }
+
10502  VirusFun<TSeq> fun_infect = [coefs_f,vars](
+
10503  Agent<TSeq> * agent,
+
10504  Virus<TSeq> &,
+
10505  Model<TSeq> *
+
10506  ) -> epiworld_double {
+
10507 
+
10508  size_t K = coefs_f.size();
+
10509  epiworld_double res = 0.0;
+
10510 
+
10511  #if defined(__OPENMP) || defined(_OPENMP)
+
10512  #pragma omp simd reduction(+:res)
+
10513  #endif
+
10514  for (size_t i = 0u; i < K; ++i)
+
10515  res += agent->operator[](vars.at(i)) * coefs_f.at(i);
10516 
-
10517 template<typename TSeq>
-
10518 inline void Virus<TSeq>::mutate(
-
10519  Model<TSeq> * model
-
10520 ) {
-
10521 
-
10522  if (mutation_fun)
-
10523  if (mutation_fun(agent, *this, model))
-
10524  model->get_db().record_virus(*this);
-
10525 
-
10526  return;
-
10527 
-
10528 }
-
10529 
-
10530 template<typename TSeq>
-
10531 inline void Virus<TSeq>::set_mutation(
-
10532  MutFun<TSeq> fun
-
10533 ) {
-
10534  mutation_fun = MutFun<TSeq>(fun);
-
10535 }
-
10536 
-
10537 template<typename TSeq>
-
10538 inline std::shared_ptr<TSeq> Virus<TSeq>::get_sequence()
-
10539 {
-
10540 
-
10541  return baseline_sequence;
-
10542 
-
10543 }
-
10544 
-
10545 template<typename TSeq>
-
10546 inline void Virus<TSeq>::set_sequence(TSeq sequence)
-
10547 {
-
10548 
-
10549  baseline_sequence = std::make_shared<TSeq>(sequence);
-
10550  return;
+
10517  return 1.0/(1.0 + std::exp(-res));
+
10518 
+
10519  };
+
10520 
+
10521  return fun_infect;
+
10522 
+
10523 }
+
10524 
+
10525 template<typename TSeq>
+
10526 inline Virus<TSeq>::Virus(
+
10527  std::string name
+
10528  ) {
+
10529  set_name(name);
+
10530 }
+
10531 
+
10532 template<typename TSeq>
+
10533 inline Virus<TSeq>::Virus(
+
10534  std::string name,
+
10535  epiworld_double prevalence,
+
10536  bool prevalence_as_proportion
+
10537  ) {
+
10538  set_name(name);
+
10539  set_distribution(
+
10540  distribute_virus_randomly<TSeq>(
+
10541  prevalence,
+
10542  prevalence_as_proportion
+
10543  )
+
10544  );
+
10545 }
+
10546 
+
10547 template<typename TSeq>
+
10548 inline void Virus<TSeq>::mutate(
+
10549  Model<TSeq> * model
+
10550 ) {
10551 
-
10552 }
-
10553 
-
10554 template<typename TSeq>
-
10555 inline Agent<TSeq> * Virus<TSeq>::get_agent()
-
10556 {
-
10557 
-
10558  return agent;
+
10552  if (mutation_fun)
+
10553  if (mutation_fun(agent, *this, model))
+
10554  model->get_db().record_virus(*this);
+
10555 
+
10556  return;
+
10557 
+
10558 }
10559 
-
10560 }
-
10561 
-
10562 template<typename TSeq>
-
10563 inline void Virus<TSeq>::set_agent(Agent<TSeq> * p)
-
10564 {
-
10565  agent = p;
-
10566 }
-
10567 
-
10568 template<typename TSeq>
-
10569 inline void Virus<TSeq>::set_id(int idx)
-
10570 {
-
10571 
-
10572  id = idx;
-
10573  return;
+
10560 template<typename TSeq>
+
10561 inline void Virus<TSeq>::set_mutation(
+
10562  MutFun<TSeq> fun
+
10563 ) {
+
10564  mutation_fun = MutFun<TSeq>(fun);
+
10565 }
+
10566 
+
10567 template<typename TSeq>
+
10568 inline std::shared_ptr<TSeq> Virus<TSeq>::get_sequence()
+
10569 {
+
10570 
+
10571  return baseline_sequence;
+
10572 
+
10573 }
10574 
-
10575 }
-
10576 
-
10577 template<typename TSeq>
-
10578 inline int Virus<TSeq>::get_id() const
-
10579 {
-
10580 
-
10581  return id;
-
10582 
-
10583 }
-
10584 
-
10585 template<typename TSeq>
-
10586 inline void Virus<TSeq>::set_date(int d)
-
10587 {
-
10588 
-
10589  date = d;
-
10590  return;
+
10575 template<typename TSeq>
+
10576 inline void Virus<TSeq>::set_sequence(TSeq sequence)
+
10577 {
+
10578 
+
10579  baseline_sequence = std::make_shared<TSeq>(sequence);
+
10580  return;
+
10581 
+
10582 }
+
10583 
+
10584 template<typename TSeq>
+
10585 inline Agent<TSeq> * Virus<TSeq>::get_agent()
+
10586 {
+
10587 
+
10588  return agent;
+
10589 
+
10590 }
10591 
-
10592 }
-
10593 
-
10594 template<typename TSeq>
-
10595 inline int Virus<TSeq>::get_date() const
-
10596 {
-
10597 
-
10598  return date;
-
10599 
-
10600 }
+
10592 template<typename TSeq>
+
10593 inline void Virus<TSeq>::set_agent(Agent<TSeq> * p)
+
10594 {
+
10595  agent = p;
+
10596 }
+
10597 
+
10598 template<typename TSeq>
+
10599 inline void Virus<TSeq>::set_id(int idx)
+
10600 {
10601 
-
10602 template<typename TSeq>
-
10603 inline epiworld_double Virus<TSeq>::get_prob_infecting(
-
10604  Model<TSeq> * model
-
10605 )
-
10606 {
-
10607 
-
10608  if (probability_of_infecting_fun)
-
10609  return probability_of_infecting_fun(agent, *this, model);
-
10610 
-
10611  return EPI_DEFAULT_VIRUS_PROB_INFECTION;
+
10602  id = idx;
+
10603  return;
+
10604 
+
10605 }
+
10606 
+
10607 template<typename TSeq>
+
10608 inline int Virus<TSeq>::get_id() const
+
10609 {
+
10610 
+
10611  return id;
10612 
10613 }
10614 
-
10615 
-
10616 
-
10617 template<typename TSeq>
-
10618 inline epiworld_double Virus<TSeq>::get_prob_recovery(
-
10619  Model<TSeq> * model
-
10620 )
-
10621 {
-
10622 
-
10623  if (probability_of_recovery_fun)
-
10624  return probability_of_recovery_fun(agent, *this, model);
-
10625 
-
10626  return EPI_DEFAULT_VIRUS_PROB_RECOVERY;
-
10627 
-
10628 }
-
10629 
-
10630 
+
10615 template<typename TSeq>
+
10616 inline void Virus<TSeq>::set_date(int d)
+
10617 {
+
10618 
+
10619  date = d;
+
10620  return;
+
10621 
+
10622 }
+
10623 
+
10624 template<typename TSeq>
+
10625 inline int Virus<TSeq>::get_date() const
+
10626 {
+
10627 
+
10628  return date;
+
10629 
+
10630 }
10631 
10632 template<typename TSeq>
-
10633 inline epiworld_double Virus<TSeq>::get_prob_death(
+
10633 inline epiworld_double Virus<TSeq>::get_prob_infecting(
10634  Model<TSeq> * model
10635 )
10636 {
10637 
-
10638  if (probability_of_death_fun)
-
10639  return probability_of_death_fun(agent, *this, model);
+
10638  if (probability_of_infecting_fun)
+
10639  return probability_of_infecting_fun(agent, *this, model);
10640 
-
10641  return EPI_DEFAULT_VIRUS_PROB_DEATH;
+
10641  return EPI_DEFAULT_VIRUS_PROB_INFECTION;
10642 
10643 }
10644 
-
10645 template<typename TSeq>
-
10646 inline epiworld_double Virus<TSeq>::get_incubation(
-
10647  Model<TSeq> * model
-
10648 )
-
10649 {
-
10650 
-
10651  if (incubation_fun)
-
10652  return incubation_fun(agent, *this, model);
-
10653 
-
10654  return EPI_DEFAULT_INCUBATION_DAYS;
-
10655 
-
10656 }
+
10645 
+
10646 
+
10647 template<typename TSeq>
+
10648 inline epiworld_double Virus<TSeq>::get_prob_recovery(
+
10649  Model<TSeq> * model
+
10650 )
+
10651 {
+
10652 
+
10653  if (probability_of_recovery_fun)
+
10654  return probability_of_recovery_fun(agent, *this, model);
+
10655 
+
10656  return EPI_DEFAULT_VIRUS_PROB_RECOVERY;
10657 
-
10658 template<typename TSeq>
-
10659 inline void Virus<TSeq>::set_prob_infecting_fun(VirusFun<TSeq> fun)
-
10660 {
-
10661  probability_of_infecting_fun = fun;
-
10662 }
-
10663 
-
10664 template<typename TSeq>
-
10665 inline void Virus<TSeq>::set_prob_recovery_fun(VirusFun<TSeq> fun)
+
10658 }
+
10659 
+
10660 
+
10661 
+
10662 template<typename TSeq>
+
10663 inline epiworld_double Virus<TSeq>::get_prob_death(
+
10664  Model<TSeq> * model
+
10665 )
10666 {
-
10667  probability_of_recovery_fun = fun;
-
10668 }
-
10669 
-
10670 template<typename TSeq>
-
10671 inline void Virus<TSeq>::set_prob_death_fun(VirusFun<TSeq> fun)
-
10672 {
-
10673  probability_of_death_fun = fun;
-
10674 }
-
10675 
-
10676 template<typename TSeq>
-
10677 inline void Virus<TSeq>::set_incubation_fun(VirusFun<TSeq> fun)
-
10678 {
-
10679  incubation_fun = fun;
-
10680 }
-
10681 
-
10682 template<typename TSeq>
-
10683 inline void Virus<TSeq>::set_prob_infecting(const epiworld_double * prob)
-
10684 {
-
10685  VirusFun<TSeq> tmpfun =
-
10686  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
-
10687  {
-
10688  return *prob;
-
10689  };
-
10690 
-
10691  probability_of_infecting_fun = tmpfun;
+
10667 
+
10668  if (probability_of_death_fun)
+
10669  return probability_of_death_fun(agent, *this, model);
+
10670 
+
10671  return EPI_DEFAULT_VIRUS_PROB_DEATH;
+
10672 
+
10673 }
+
10674 
+
10675 template<typename TSeq>
+
10676 inline epiworld_double Virus<TSeq>::get_incubation(
+
10677  Model<TSeq> * model
+
10678 )
+
10679 {
+
10680 
+
10681  if (incubation_fun)
+
10682  return incubation_fun(agent, *this, model);
+
10683 
+
10684  return EPI_DEFAULT_INCUBATION_DAYS;
+
10685 
+
10686 }
+
10687 
+
10688 template<typename TSeq>
+
10689 inline void Virus<TSeq>::set_prob_infecting_fun(VirusFun<TSeq> fun)
+
10690 {
+
10691  probability_of_infecting_fun = fun;
10692 }
10693 
10694 template<typename TSeq>
-
10695 inline void Virus<TSeq>::set_prob_recovery(const epiworld_double * prob)
+
10695 inline void Virus<TSeq>::set_prob_recovery_fun(VirusFun<TSeq> fun)
10696 {
-
10697  VirusFun<TSeq> tmpfun =
-
10698  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
-
10699  {
-
10700  return *prob;
-
10701  };
-
10702 
-
10703  probability_of_recovery_fun = tmpfun;
+
10697  probability_of_recovery_fun = fun;
+
10698 }
+
10699 
+
10700 template<typename TSeq>
+
10701 inline void Virus<TSeq>::set_prob_death_fun(VirusFun<TSeq> fun)
+
10702 {
+
10703  probability_of_death_fun = fun;
10704 }
10705 
10706 template<typename TSeq>
-
10707 inline void Virus<TSeq>::set_prob_death(const epiworld_double * prob)
+
10707 inline void Virus<TSeq>::set_incubation_fun(VirusFun<TSeq> fun)
10708 {
-
10709  VirusFun<TSeq> tmpfun =
-
10710  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
-
10711  {
-
10712  return *prob;
-
10713  };
-
10714 
-
10715  probability_of_death_fun = tmpfun;
-
10716 }
-
10717 
-
10718 template<typename TSeq>
-
10719 inline void Virus<TSeq>::set_incubation(const epiworld_double * prob)
-
10720 {
-
10721  VirusFun<TSeq> tmpfun =
-
10722  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
-
10723  {
-
10724  return *prob;
-
10725  };
-
10726 
-
10727  incubation_fun = tmpfun;
-
10728 }
-
10729 
-
10730 template<typename TSeq>
-
10731 inline void Virus<TSeq>::set_prob_infecting(epiworld_double prob)
-
10732 {
-
10733  VirusFun<TSeq> tmpfun =
-
10734  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
-
10735  {
-
10736  return prob;
-
10737  };
-
10738 
-
10739  probability_of_infecting_fun = tmpfun;
-
10740 }
-
10741 
-
10742 template<typename TSeq>
-
10743 inline void Virus<TSeq>::set_prob_recovery(epiworld_double prob)
-
10744 {
-
10745  VirusFun<TSeq> tmpfun =
-
10746  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
-
10747  {
-
10748  return prob;
-
10749  };
-
10750 
-
10751  probability_of_recovery_fun = tmpfun;
-
10752 }
-
10753 
-
10754 template<typename TSeq>
-
10755 inline void Virus<TSeq>::set_prob_death(epiworld_double prob)
-
10756 {
-
10757  VirusFun<TSeq> tmpfun =
-
10758  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
-
10759  {
-
10760  return prob;
-
10761  };
-
10762 
-
10763  probability_of_death_fun = tmpfun;
-
10764 }
-
10765 
-
10766 template<typename TSeq>
-
10767 inline void Virus<TSeq>::set_incubation(epiworld_double prob)
-
10768 {
-
10769  VirusFun<TSeq> tmpfun =
-
10770  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
-
10771  {
-
10772  return prob;
-
10773  };
-
10774 
-
10775  incubation_fun = tmpfun;
-
10776 }
-
10777 
-
10778 template<typename TSeq>
-
10779 inline void Virus<TSeq>::set_post_recovery(PostRecoveryFun<TSeq> fun)
-
10780 {
-
10781  if (post_recovery_fun)
-
10782  {
-
10783  printf_epiworld(
-
10784  "Warning: a PostRecoveryFun is alreay in place (overwriting)."
-
10785  );
-
10786  }
-
10787 
-
10788  post_recovery_fun = fun;
-
10789 }
-
10790 
-
10791 template<typename TSeq>
-
10792 inline void Virus<TSeq>::post_recovery(
-
10793  Model<TSeq> * model
-
10794 )
-
10795 {
-
10796 
-
10797  if (post_recovery_fun)
-
10798  post_recovery_fun(agent, *this, model);
-
10799 
-
10800  return;
-
10801 
-
10802 }
-
10803 
-
10804 template<typename TSeq>
-
10805 inline void Virus<TSeq>::set_post_immunity(
-
10806  epiworld_double prob
-
10807 )
-
10808 {
-
10809 
-
10810  if (post_recovery_fun)
-
10811  {
-
10812 
-
10813  std::string msg =
-
10814  std::string(
-
10815  "You cannot set post immunity when a post_recovery "
-
10816  ) +
-
10817  std::string(
-
10818  "function is already in place. Redesign the post_recovery function."
-
10819  );
+
10709  incubation_fun = fun;
+
10710 }
+
10711 
+
10712 template<typename TSeq>
+
10713 inline void Virus<TSeq>::set_prob_infecting(const epiworld_double * prob)
+
10714 {
+
10715  VirusFun<TSeq> tmpfun =
+
10716  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
+
10717  {
+
10718  return *prob;
+
10719  };
+
10720 
+
10721  probability_of_infecting_fun = tmpfun;
+
10722 }
+
10723 
+
10724 template<typename TSeq>
+
10725 inline void Virus<TSeq>::set_prob_recovery(const epiworld_double * prob)
+
10726 {
+
10727  VirusFun<TSeq> tmpfun =
+
10728  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
+
10729  {
+
10730  return *prob;
+
10731  };
+
10732 
+
10733  probability_of_recovery_fun = tmpfun;
+
10734 }
+
10735 
+
10736 template<typename TSeq>
+
10737 inline void Virus<TSeq>::set_prob_death(const epiworld_double * prob)
+
10738 {
+
10739  VirusFun<TSeq> tmpfun =
+
10740  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
+
10741  {
+
10742  return *prob;
+
10743  };
+
10744 
+
10745  probability_of_death_fun = tmpfun;
+
10746 }
+
10747 
+
10748 template<typename TSeq>
+
10749 inline void Virus<TSeq>::set_incubation(const epiworld_double * prob)
+
10750 {
+
10751  VirusFun<TSeq> tmpfun =
+
10752  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
+
10753  {
+
10754  return *prob;
+
10755  };
+
10756 
+
10757  incubation_fun = tmpfun;
+
10758 }
+
10759 
+
10760 template<typename TSeq>
+
10761 inline void Virus<TSeq>::set_prob_infecting(epiworld_double prob)
+
10762 {
+
10763  VirusFun<TSeq> tmpfun =
+
10764  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
+
10765  {
+
10766  return prob;
+
10767  };
+
10768 
+
10769  probability_of_infecting_fun = tmpfun;
+
10770 }
+
10771 
+
10772 template<typename TSeq>
+
10773 inline void Virus<TSeq>::set_prob_recovery(epiworld_double prob)
+
10774 {
+
10775  VirusFun<TSeq> tmpfun =
+
10776  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
+
10777  {
+
10778  return prob;
+
10779  };
+
10780 
+
10781  probability_of_recovery_fun = tmpfun;
+
10782 }
+
10783 
+
10784 template<typename TSeq>
+
10785 inline void Virus<TSeq>::set_prob_death(epiworld_double prob)
+
10786 {
+
10787  VirusFun<TSeq> tmpfun =
+
10788  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
+
10789  {
+
10790  return prob;
+
10791  };
+
10792 
+
10793  probability_of_death_fun = tmpfun;
+
10794 }
+
10795 
+
10796 template<typename TSeq>
+
10797 inline void Virus<TSeq>::set_incubation(epiworld_double prob)
+
10798 {
+
10799  VirusFun<TSeq> tmpfun =
+
10800  [prob](Agent<TSeq> *, Virus<TSeq> &, Model<TSeq> *)
+
10801  {
+
10802  return prob;
+
10803  };
+
10804 
+
10805  incubation_fun = tmpfun;
+
10806 }
+
10807 
+
10808 template<typename TSeq>
+
10809 inline void Virus<TSeq>::set_post_recovery(PostRecoveryFun<TSeq> fun)
+
10810 {
+
10811  if (post_recovery_fun)
+
10812  {
+
10813  printf_epiworld(
+
10814  "Warning: a PostRecoveryFun is alreay in place (overwriting)."
+
10815  );
+
10816  }
+
10817 
+
10818  post_recovery_fun = fun;
+
10819 }
10820 
-
10821  throw std::logic_error(msg);
-
10822 
-
10823  }
-
10824 
-
10825  // To make sure that we keep registering the virus
-
10826  ToolPtr<TSeq> __no_reinfect = std::make_shared<Tool<TSeq>>(
-
10827  "Immunity (" + *virus_name + ")"
-
10828  );
+
10821 template<typename TSeq>
+
10822 inline void Virus<TSeq>::post_recovery(
+
10823  Model<TSeq> * model
+
10824 )
+
10825 {
+
10826 
+
10827  if (post_recovery_fun)
+
10828  post_recovery_fun(agent, *this, model);
10829 
-
10830  __no_reinfect->set_susceptibility_reduction(prob);
-
10831  __no_reinfect->set_death_reduction(0.0);
-
10832  __no_reinfect->set_transmission_reduction(0.0);
-
10833  __no_reinfect->set_recovery_enhancer(0.0);
-
10834 
-
10835  PostRecoveryFun<TSeq> tmpfun =
-
10836  [__no_reinfect](
-
10837  Agent<TSeq> * p, Virus<TSeq> &, Model<TSeq> * m
-
10838  )
-
10839  {
-
10840 
-
10841  // Have we registered the tool?
-
10842  if (__no_reinfect->get_id() == -99)
-
10843  m->get_db().record_tool(*__no_reinfect);
-
10844 
-
10845  p->add_tool(__no_reinfect, m);
-
10846 
-
10847  return;
-
10848 
-
10849  };
+
10830  return;
+
10831 
+
10832 }
+
10833 
+
10834 template<typename TSeq>
+
10835 inline void Virus<TSeq>::set_post_immunity(
+
10836  epiworld_double prob
+
10837 )
+
10838 {
+
10839 
+
10840  if (post_recovery_fun)
+
10841  {
+
10842 
+
10843  std::string msg =
+
10844  std::string(
+
10845  "You cannot set post immunity when a post_recovery "
+
10846  ) +
+
10847  std::string(
+
10848  "function is already in place. Redesign the post_recovery function."
+
10849  );
10850 
-
10851  post_recovery_fun = tmpfun;
-
10852 
-
10853 }
+
10851  throw std::logic_error(msg);
+
10852 
+
10853  }
10854 
-
10855 template<typename TSeq>
-
10856 inline void Virus<TSeq>::set_post_immunity(
-
10857  epiworld_double * prob
-
10858 )
-
10859 {
-
10860 
-
10861  if (post_recovery_fun)
-
10862  {
-
10863 
-
10864  std::string msg =
-
10865  std::string(
-
10866  "You cannot set post immunity when a post_recovery "
-
10867  ) +
-
10868  std::string(
-
10869  "function is already in place. Redesign the post_recovery function."
-
10870  );
-
10871 
-
10872  throw std::logic_error(msg);
-
10873 
-
10874  }
-
10875 
-
10876  // To make sure that we keep registering the virus
-
10877  ToolPtr<TSeq> __no_reinfect = std::make_shared<Tool<TSeq>>(
-
10878  "Immunity (" + *virus_name + ")"
-
10879  );
+
10855  // To make sure that we keep registering the virus
+
10856  ToolPtr<TSeq> __no_reinfect = std::make_shared<Tool<TSeq>>(
+
10857  "Immunity (" + *virus_name + ")"
+
10858  );
+
10859 
+
10860  __no_reinfect->set_susceptibility_reduction(prob);
+
10861  __no_reinfect->set_death_reduction(0.0);
+
10862  __no_reinfect->set_transmission_reduction(0.0);
+
10863  __no_reinfect->set_recovery_enhancer(0.0);
+
10864 
+
10865  PostRecoveryFun<TSeq> tmpfun =
+
10866  [__no_reinfect](
+
10867  Agent<TSeq> * p, Virus<TSeq> &, Model<TSeq> * m
+
10868  )
+
10869  {
+
10870 
+
10871  // Have we registered the tool?
+
10872  if (__no_reinfect->get_id() == -99)
+
10873  m->get_db().record_tool(*__no_reinfect);
+
10874 
+
10875  p->add_tool(__no_reinfect, m);
+
10876 
+
10877  return;
+
10878 
+
10879  };
10880 
-
10881  __no_reinfect->set_susceptibility_reduction(prob);
-
10882  __no_reinfect->set_death_reduction(0.0);
-
10883  __no_reinfect->set_transmission_reduction(0.0);
-
10884  __no_reinfect->set_recovery_enhancer(0.0);
-
10885 
-
10886  PostRecoveryFun<TSeq> tmpfun =
-
10887  [__no_reinfect](Agent<TSeq> * p, Virus<TSeq> &, Model<TSeq> * m)
-
10888  {
-
10889 
-
10890  // Have we registered the tool?
-
10891  if (__no_reinfect->get_id() == -99)
-
10892  m->get_db().record_tool(*__no_reinfect);
+
10881  post_recovery_fun = tmpfun;
+
10882 
+
10883 }
+
10884 
+
10885 template<typename TSeq>
+
10886 inline void Virus<TSeq>::set_post_immunity(
+
10887  epiworld_double * prob
+
10888 )
+
10889 {
+
10890 
+
10891  if (post_recovery_fun)
+
10892  {
10893 
-
10894  p->add_tool(__no_reinfect, m);
-
10895 
-
10896  return;
-
10897 
-
10898  };
-
10899 
-
10900  post_recovery_fun = tmpfun;
+
10894  std::string msg =
+
10895  std::string(
+
10896  "You cannot set post immunity when a post_recovery "
+
10897  ) +
+
10898  std::string(
+
10899  "function is already in place. Redesign the post_recovery function."
+
10900  );
10901 
-
10902 }
+
10902  throw std::logic_error(msg);
10903 
-
10904 template<typename TSeq>
-
10905 inline void Virus<TSeq>::set_name(std::string name)
-
10906 {
-
10907 
-
10908  if (name == "")
-
10909  virus_name = nullptr;
-
10910  else
-
10911  virus_name = std::make_shared<std::string>(name);
-
10912 
-
10913 }
-
10914 
-
10915 template<typename TSeq>
-
10916 inline std::string Virus<TSeq>::get_name() const
-
10917 {
-
10918 
-
10919  if (virus_name)
-
10920  return *virus_name;
-
10921 
-
10922  return "unknown virus";
+
10904  }
+
10905 
+
10906  // To make sure that we keep registering the virus
+
10907  ToolPtr<TSeq> __no_reinfect = std::make_shared<Tool<TSeq>>(
+
10908  "Immunity (" + *virus_name + ")"
+
10909  );
+
10910 
+
10911  __no_reinfect->set_susceptibility_reduction(prob);
+
10912  __no_reinfect->set_death_reduction(0.0);
+
10913  __no_reinfect->set_transmission_reduction(0.0);
+
10914  __no_reinfect->set_recovery_enhancer(0.0);
+
10915 
+
10916  PostRecoveryFun<TSeq> tmpfun =
+
10917  [__no_reinfect](Agent<TSeq> * p, Virus<TSeq> &, Model<TSeq> * m)
+
10918  {
+
10919 
+
10920  // Have we registered the tool?
+
10921  if (__no_reinfect->get_id() == -99)
+
10922  m->get_db().record_tool(*__no_reinfect);
10923 
-
10924 }
+
10924  p->add_tool(__no_reinfect, m);
10925 
-
10926 template<typename TSeq>
-
10927 inline std::vector< epiworld_double > & Virus<TSeq>::get_data() {
-
10928  return data;
-
10929 }
-
10930 
-
10931 template<typename TSeq>
-
10932 inline void Virus<TSeq>::set_state(
-
10933  epiworld_fast_int init,
-
10934  epiworld_fast_int end,
-
10935  epiworld_fast_int removed
-
10936 )
-
10937 {
-
10938  state_init = init;
-
10939  state_post = end;
-
10940  state_removed = removed;
-
10941 }
+
10926  return;
+
10927 
+
10928  };
+
10929 
+
10930  post_recovery_fun = tmpfun;
+
10931 
+
10932 }
+
10933 
+
10934 template<typename TSeq>
+
10935 inline void Virus<TSeq>::set_name(std::string name)
+
10936 {
+
10937 
+
10938  if (name == "")
+
10939  virus_name = nullptr;
+
10940  else
+
10941  virus_name = std::make_shared<std::string>(name);
10942 
-
10943 template<typename TSeq>
-
10944 inline void Virus<TSeq>::set_queue(
-
10945  epiworld_fast_int init,
-
10946  epiworld_fast_int end,
-
10947  epiworld_fast_int removed
-
10948 )
-
10949 {
-
10950 
-
10951  queue_init = init;
-
10952  queue_post = end;
-
10953  queue_removed = removed;
-
10954 
-
10955 }
-
10956 
-
10957 template<typename TSeq>
-
10958 inline void Virus<TSeq>::get_state(
-
10959  epiworld_fast_int * init,
-
10960  epiworld_fast_int * end,
-
10961  epiworld_fast_int * removed
-
10962 )
-
10963 {
-
10964 
-
10965  if (init != nullptr)
-
10966  *init = state_init;
-
10967 
-
10968  if (end != nullptr)
-
10969  *end = state_post;
-
10970 
-
10971  if (removed != nullptr)
-
10972  *removed = state_removed;
-
10973 
-
10974 }
-
10975 
-
10976 template<typename TSeq>
-
10977 inline void Virus<TSeq>::get_queue(
-
10978  epiworld_fast_int * init,
-
10979  epiworld_fast_int * end,
-
10980  epiworld_fast_int * removed
-
10981 )
-
10982 {
-
10983 
-
10984  if (init != nullptr)
-
10985  *init = queue_init;
+
10943 }
+
10944 
+
10945 template<typename TSeq>
+
10946 inline std::string Virus<TSeq>::get_name() const
+
10947 {
+
10948 
+
10949  if (virus_name)
+
10950  return *virus_name;
+
10951 
+
10952  return "unknown virus";
+
10953 
+
10954 }
+
10955 
+
10956 template<typename TSeq>
+
10957 inline std::vector< epiworld_double > & Virus<TSeq>::get_data() {
+
10958  return data;
+
10959 }
+
10960 
+
10961 template<typename TSeq>
+
10962 inline void Virus<TSeq>::set_state(
+
10963  epiworld_fast_int init,
+
10964  epiworld_fast_int end,
+
10965  epiworld_fast_int removed
+
10966 )
+
10967 {
+
10968  state_init = init;
+
10969  state_post = end;
+
10970  state_removed = removed;
+
10971 }
+
10972 
+
10973 template<typename TSeq>
+
10974 inline void Virus<TSeq>::set_queue(
+
10975  epiworld_fast_int init,
+
10976  epiworld_fast_int end,
+
10977  epiworld_fast_int removed
+
10978 )
+
10979 {
+
10980 
+
10981  queue_init = init;
+
10982  queue_post = end;
+
10983  queue_removed = removed;
+
10984 
+
10985 }
10986 
-
10987  if (end != nullptr)
-
10988  *end = queue_post;
-
10989 
-
10990  if (removed != nullptr)
-
10991  *removed = queue_removed;
-
10992 
-
10993 }
+
10987 template<typename TSeq>
+
10988 inline void Virus<TSeq>::get_state(
+
10989  epiworld_fast_int * init,
+
10990  epiworld_fast_int * end,
+
10991  epiworld_fast_int * removed
+
10992 )
+
10993 {
10994 
-
10995 template<>
-
10996 inline bool Virus<std::vector<int>>::operator==(
-
10997  const Virus<std::vector<int>> & other
-
10998  ) const
-
10999 {
-
11000 
-
11001 
-
11002  EPI_DEBUG_FAIL_AT_TRUE(
-
11003  baseline_sequence->size() != other.baseline_sequence->size(),
-
11004  "Virus:: baseline_sequence don't match"
-
11005  )
-
11006 
-
11007  for (size_t i = 0u; i < baseline_sequence->size(); ++i)
-
11008  {
-
11009 
-
11010  EPI_DEBUG_FAIL_AT_TRUE(
-
11011  baseline_sequence->operator[](i) != other.baseline_sequence->operator[](i),
-
11012  "Virus:: baseline_sequence[i] don't match"
-
11013  )
-
11014 
-
11015  }
+
10995  if (init != nullptr)
+
10996  *init = state_init;
+
10997 
+
10998  if (end != nullptr)
+
10999  *end = state_post;
+
11000 
+
11001  if (removed != nullptr)
+
11002  *removed = state_removed;
+
11003 
+
11004 }
+
11005 
+
11006 template<typename TSeq>
+
11007 inline void Virus<TSeq>::get_queue(
+
11008  epiworld_fast_int * init,
+
11009  epiworld_fast_int * end,
+
11010  epiworld_fast_int * removed
+
11011 )
+
11012 {
+
11013 
+
11014  if (init != nullptr)
+
11015  *init = queue_init;
11016 
-
11017  EPI_DEBUG_FAIL_AT_TRUE(
-
11018  virus_name != other.virus_name,
-
11019  "Virus:: virus_name don't match"
-
11020  )
-
11021 
-
11022  EPI_DEBUG_FAIL_AT_TRUE(
-
11023  state_init != other.state_init,
-
11024  "Virus:: state_init don't match"
-
11025  )
-
11026 
-
11027  EPI_DEBUG_FAIL_AT_TRUE(
-
11028  state_post != other.state_post,
-
11029  "Virus:: state_post don't match"
-
11030  )
+
11017  if (end != nullptr)
+
11018  *end = queue_post;
+
11019 
+
11020  if (removed != nullptr)
+
11021  *removed = queue_removed;
+
11022 
+
11023 }
+
11024 
+
11025 template<>
+
11026 inline bool Virus<std::vector<int>>::operator==(
+
11027  const Virus<std::vector<int>> & other
+
11028  ) const
+
11029 {
+
11030 
11031 
11032  EPI_DEBUG_FAIL_AT_TRUE(
-
11033  state_removed != other.state_removed,
-
11034  "Virus:: state_removed don't match"
+
11033  baseline_sequence->size() != other.baseline_sequence->size(),
+
11034  "Virus:: baseline_sequence don't match"
11035  )
11036 
-
11037  EPI_DEBUG_FAIL_AT_TRUE(
-
11038  queue_init != other.queue_init,
-
11039  "Virus:: queue_init don't match"
-
11040  )
-
11041 
-
11042  EPI_DEBUG_FAIL_AT_TRUE(
-
11043  queue_post != other.queue_post,
-
11044  "Virus:: queue_post don't match"
-
11045  )
+
11037  for (size_t i = 0u; i < baseline_sequence->size(); ++i)
+
11038  {
+
11039 
+
11040  EPI_DEBUG_FAIL_AT_TRUE(
+
11041  baseline_sequence->operator[](i) != other.baseline_sequence->operator[](i),
+
11042  "Virus:: baseline_sequence[i] don't match"
+
11043  )
+
11044 
+
11045  }
11046 
11047  EPI_DEBUG_FAIL_AT_TRUE(
-
11048  queue_removed != other.queue_removed,
-
11049  "Virus:: queue_removed don't match"
+
11048  virus_name != other.virus_name,
+
11049  "Virus:: virus_name don't match"
11050  )
-
11051 
-
11052  return true;
-
11053 
-
11054 }
-
11055 
-
11056 template<typename TSeq>
-
11057 inline bool Virus<TSeq>::operator==(const Virus<TSeq> & other) const
-
11058 {
-
11059 
-
11060  EPI_DEBUG_FAIL_AT_TRUE(
-
11061  *baseline_sequence != *other.baseline_sequence,
-
11062  "Virus:: baseline_sequence don't match"
-
11063  )
-
11064 
-
11065  EPI_DEBUG_FAIL_AT_TRUE(
-
11066  virus_name != other.virus_name,
-
11067  "Virus:: virus_name don't match"
-
11068  )
-
11069 
-
11070  EPI_DEBUG_FAIL_AT_TRUE(
-
11071  state_init != other.state_init,
-
11072  "Virus:: state_init don't match"
-
11073  )
-
11074 
-
11075  EPI_DEBUG_FAIL_AT_TRUE(
-
11076  state_post != other.state_post,
-
11077  "Virus:: state_post don't match"
-
11078  )
-
11079 
-
11080  EPI_DEBUG_FAIL_AT_TRUE(
-
11081  state_removed != other.state_removed,
-
11082  "Virus:: state_removed don't match"
-
11083  )
-
11084 
-
11085  EPI_DEBUG_FAIL_AT_TRUE(
-
11086  queue_init != other.queue_init,
-
11087  "Virus:: queue_init don't match"
-
11088  )
-
11089 
+
11051 
+
11052  EPI_DEBUG_FAIL_AT_TRUE(
+
11053  state_init != other.state_init,
+
11054  "Virus:: state_init don't match"
+
11055  )
+
11056 
+
11057  EPI_DEBUG_FAIL_AT_TRUE(
+
11058  state_post != other.state_post,
+
11059  "Virus:: state_post don't match"
+
11060  )
+
11061 
+
11062  EPI_DEBUG_FAIL_AT_TRUE(
+
11063  state_removed != other.state_removed,
+
11064  "Virus:: state_removed don't match"
+
11065  )
+
11066 
+
11067  EPI_DEBUG_FAIL_AT_TRUE(
+
11068  queue_init != other.queue_init,
+
11069  "Virus:: queue_init don't match"
+
11070  )
+
11071 
+
11072  EPI_DEBUG_FAIL_AT_TRUE(
+
11073  queue_post != other.queue_post,
+
11074  "Virus:: queue_post don't match"
+
11075  )
+
11076 
+
11077  EPI_DEBUG_FAIL_AT_TRUE(
+
11078  queue_removed != other.queue_removed,
+
11079  "Virus:: queue_removed don't match"
+
11080  )
+
11081 
+
11082  return true;
+
11083 
+
11084 }
+
11085 
+
11086 template<typename TSeq>
+
11087 inline bool Virus<TSeq>::operator==(const Virus<TSeq> & other) const
+
11088 {
+
11089 
11090  EPI_DEBUG_FAIL_AT_TRUE(
-
11091  queue_post != other.queue_post,
-
11092  "Virus:: queue_post don't match"
+
11091  *baseline_sequence != *other.baseline_sequence,
+
11092  "Virus:: baseline_sequence don't match"
11093  )
11094 
11095  EPI_DEBUG_FAIL_AT_TRUE(
-
11096  queue_removed != other.queue_removed,
-
11097  "Virus:: queue_removed don't match"
+
11096  virus_name != other.virus_name,
+
11097  "Virus:: virus_name don't match"
11098  )
-
11099 
-
11100  return true;
-
11101 
-
11102 }
-
11103 
-
11104 template<typename TSeq>
-
11105 inline void Virus<TSeq>::print() const
-
11106 {
-
11107 
-
11108  printf_epiworld("Virus : %s\n", virus_name->c_str());
-
11109  printf_epiworld("Id : %s\n", (id < 0)? std::string("(empty)").c_str() : std::to_string(id).c_str());
-
11110  printf_epiworld("state_init : %i\n", static_cast<int>(state_init));
-
11111  printf_epiworld("state_post : %i\n", static_cast<int>(state_post));
-
11112  printf_epiworld("state_removed : %i\n", static_cast<int>(state_removed));
-
11113  printf_epiworld("queue_init : %i\n", static_cast<int>(queue_init));
-
11114  printf_epiworld("queue_post : %i\n", static_cast<int>(queue_post));
-
11115  printf_epiworld("queue_removed : %i\n", static_cast<int>(queue_removed));
-
11116 
-
11117 }
-
11118 
-
11119 template<typename TSeq>
-
11120 inline void Virus<TSeq>::distribute(Model<TSeq> * model)
-
11121 {
-
11122 
-
11123  if (dist_fun)
-
11124  {
-
11125 
-
11126  dist_fun(*this, model);
-
11127 
-
11128  }
+
11099 
+
11100  EPI_DEBUG_FAIL_AT_TRUE(
+
11101  state_init != other.state_init,
+
11102  "Virus:: state_init don't match"
+
11103  )
+
11104 
+
11105  EPI_DEBUG_FAIL_AT_TRUE(
+
11106  state_post != other.state_post,
+
11107  "Virus:: state_post don't match"
+
11108  )
+
11109 
+
11110  EPI_DEBUG_FAIL_AT_TRUE(
+
11111  state_removed != other.state_removed,
+
11112  "Virus:: state_removed don't match"
+
11113  )
+
11114 
+
11115  EPI_DEBUG_FAIL_AT_TRUE(
+
11116  queue_init != other.queue_init,
+
11117  "Virus:: queue_init don't match"
+
11118  )
+
11119 
+
11120  EPI_DEBUG_FAIL_AT_TRUE(
+
11121  queue_post != other.queue_post,
+
11122  "Virus:: queue_post don't match"
+
11123  )
+
11124 
+
11125  EPI_DEBUG_FAIL_AT_TRUE(
+
11126  queue_removed != other.queue_removed,
+
11127  "Virus:: queue_removed don't match"
+
11128  )
11129 
-
11130 }
+
11130  return true;
11131 
-
11132 template<typename TSeq>
-
11133 inline void Virus<TSeq>::set_distribution(VirusToAgentFun<TSeq> fun)
-
11134 {
-
11135  dist_fun = fun;
-
11136 }
+
11132 }
+
11133 
+
11134 template<typename TSeq>
+
11135 inline void Virus<TSeq>::print() const
+
11136 {
11137 
-
11138 #endif
-
11139 /*//////////////////////////////////////////////////////////////////////////////
-
11141 
-
11142  End of -include/epiworld/virus-meat.hpp-
-
11143 
+
11138  printf_epiworld("Virus : %s\n", virus_name->c_str());
+
11139  printf_epiworld("Id : %s\n", (id < 0)? std::string("(empty)").c_str() : std::to_string(id).c_str());
+
11140  printf_epiworld("state_init : %i\n", static_cast<int>(state_init));
+
11141  printf_epiworld("state_post : %i\n", static_cast<int>(state_post));
+
11142  printf_epiworld("state_removed : %i\n", static_cast<int>(state_removed));
+
11143  printf_epiworld("queue_init : %i\n", static_cast<int>(queue_init));
+
11144  printf_epiworld("queue_post : %i\n", static_cast<int>(queue_post));
+
11145  printf_epiworld("queue_removed : %i\n", static_cast<int>(queue_removed));
11146 
-
11147 
-
11148 
-
11149 /*//////////////////////////////////////////////////////////////////////////////
-
11151 
-
11152  Start of -include/epiworld/tools-bones.hpp-
-
11153 
-
11156 
+
11147 }
+
11148 
+
11149 template<typename TSeq>
+
11150 inline void Virus<TSeq>::distribute(Model<TSeq> * model)
+
11151 {
+
11152 
+
11153  if (dist_fun)
+
11154  {
+
11155 
+
11156  dist_fun(*this, model);
11157 
-
11158 #ifndef EPIWORLD_TOOLS_BONES_HPP
-
11159 #define EPIWORLD_TOOLS_BONES_HPP
-
11160 
-
11161 template<typename TSeq>
-
11162 class Tool;
-
11163 
-
11164 template<typename TSeq>
-
11165 class Agent;
-
11166 
-
11167 // #define ToolPtr<TSeq> std::shared_ptr< Tool<TSeq> >
-
11168 
-
11174 template<typename TSeq>
-
11175 class Tools {
-
11176  friend class Tool<TSeq>;
-
11177  friend class Agent<TSeq>;
-
11178 private:
-
11179  std::vector< ToolPtr<TSeq> > * dat;
-
11180  const epiworld_fast_uint * n_tools;
+
11158  }
+
11159 
+
11160 }
+
11161 
+
11162 template<typename TSeq>
+
11163 inline void Virus<TSeq>::set_distribution(VirusToAgentFun<TSeq> fun)
+
11164 {
+
11165  dist_fun = fun;
+
11166 }
+
11167 
+
11168 #endif
+
11169 /*//////////////////////////////////////////////////////////////////////////////
+
11171 
+
11172  End of -include/epiworld/virus-meat.hpp-
+
11173 
+
11176 
+
11177 
+
11178 
+
11179 /*//////////////////////////////////////////////////////////////////////////////
11181 
-
11182 public:
+
11182  Start of -include/epiworld/tools-bones.hpp-
11183 
-
11184  Tools() = delete;
-
11185  Tools(Agent<TSeq> & p) : dat(&p.tools), n_tools(&p.n_tools) {};
11186 
-
11187  typename std::vector< ToolPtr<TSeq> >::iterator begin();
-
11188  typename std::vector< ToolPtr<TSeq> >::iterator end();
-
11189 
-
11190  ToolPtr<TSeq> & operator()(size_t i);
-
11191  ToolPtr<TSeq> & operator[](size_t i);
-
11192 
-
11193  size_t size() const noexcept;
-
11194 
-
11195  void print() const noexcept;
+
11187 
+
11188 #ifndef EPIWORLD_TOOLS_BONES_HPP
+
11189 #define EPIWORLD_TOOLS_BONES_HPP
+
11190 
+
11191 template<typename TSeq>
+
11192 class Tool;
+
11193 
+
11194 template<typename TSeq>
+
11195 class Agent;
11196 
-
11197 };
+
11197 // #define ToolPtr<TSeq> std::shared_ptr< Tool<TSeq> >
11198 
-
11199 template<typename TSeq>
-
11200 inline typename std::vector< ToolPtr<TSeq> >::iterator Tools<TSeq>::begin()
-
11201 {
-
11202 
-
11203  if (*n_tools == 0u)
-
11204  return dat->end();
-
11205 
-
11206  return dat->begin();
-
11207 }
-
11208 
-
11209 template<typename TSeq>
-
11210 inline typename std::vector< ToolPtr<TSeq> >::iterator Tools<TSeq>::end()
-
11211 {
-
11212 
-
11213  return begin() + *n_tools;
-
11214 }
-
11215 
-
11216 template<typename TSeq>
-
11217 inline ToolPtr<TSeq> & Tools<TSeq>::operator()(size_t i)
-
11218 {
+
11204 template<typename TSeq>
+
11205 class Tools {
+
11206  friend class Tool<TSeq>;
+
11207  friend class Agent<TSeq>;
+
11208 private:
+
11209  std::vector< ToolPtr<TSeq> > * dat;
+
11210  const epiworld_fast_uint * n_tools;
+
11211 
+
11212 public:
+
11213 
+
11214  Tools() = delete;
+
11215  Tools(Agent<TSeq> & p) : dat(&p.tools), n_tools(&p.n_tools) {};
+
11216 
+
11217  typename std::vector< ToolPtr<TSeq> >::iterator begin();
+
11218  typename std::vector< ToolPtr<TSeq> >::iterator end();
11219 
-
11220  if (i >= *n_tools)
-
11221  throw std::range_error("Tool index out of range.");
+
11220  ToolPtr<TSeq> & operator()(size_t i);
+
11221  ToolPtr<TSeq> & operator[](size_t i);
11222 
-
11223  return dat->operator[](i);
+
11223  size_t size() const noexcept;
11224 
-
11225 }
+
11225  void print() const noexcept;
11226 
-
11227 template<typename TSeq>
-
11228 inline ToolPtr<TSeq> & Tools<TSeq>::operator[](size_t i)
-
11229 {
-
11230 
-
11231  return dat->operator[](i);
+
11227 };
+
11228 
+
11229 template<typename TSeq>
+
11230 inline typename std::vector< ToolPtr<TSeq> >::iterator Tools<TSeq>::begin()
+
11231 {
11232 
-
11233 }
-
11234 
-
11235 template<typename TSeq>
-
11236 inline size_t Tools<TSeq>::size() const noexcept
-
11237 {
-
11238  return *n_tools;
-
11239 }
-
11240 
-
11241 template<typename TSeq>
-
11242 inline void Tools<TSeq>::print() const noexcept
-
11243 {
-
11244  if (*n_tools == 0u)
-
11245  {
-
11246  printf_epiworld("List of tools (none)\n");
-
11247  return;
-
11248  }
+
11233  if (*n_tools == 0u)
+
11234  return dat->end();
+
11235 
+
11236  return dat->begin();
+
11237 }
+
11238 
+
11239 template<typename TSeq>
+
11240 inline typename std::vector< ToolPtr<TSeq> >::iterator Tools<TSeq>::end()
+
11241 {
+
11242 
+
11243  return begin() + *n_tools;
+
11244 }
+
11245 
+
11246 template<typename TSeq>
+
11247 inline ToolPtr<TSeq> & Tools<TSeq>::operator()(size_t i)
+
11248 {
11249 
-
11250  printf_epiworld("List of tools (%i): ", static_cast<int>(*n_tools));
-
11251 
-
11252  // Printing the name of each virus separated by a comma
-
11253  for (size_t i = 0u; i < *n_tools; ++i)
-
11254  {
-
11255  if (i == *n_tools - 1u)
-
11256  {
-
11257  printf_epiworld("%s", dat->operator[](i)->get_name().c_str());
-
11258  } else
-
11259  {
-
11260  printf_epiworld("%s, ", dat->operator[](i)->get_name().c_str());
-
11261  }
-
11262  }
-
11263 
-
11264  printf_epiworld("\n");
-
11265 
-
11266 }
-
11267 
-
11273 template<typename TSeq>
-
11274 class Tools_const {
-
11275  friend class Tool<TSeq>;
-
11276  friend class Agent<TSeq>;
-
11277 private:
-
11278  const std::vector< ToolPtr<TSeq> > * dat;
-
11279  const epiworld_fast_uint * n_tools;
-
11280 
-
11281 public:
-
11282 
-
11283  Tools_const() = delete;
-
11284  Tools_const(const Agent<TSeq> & p) : dat(&p.tools), n_tools(&p.n_tools) {};
-
11285 
-
11286  typename std::vector< ToolPtr<TSeq> >::const_iterator begin() const;
-
11287  typename std::vector< ToolPtr<TSeq> >::const_iterator end() const;
-
11288 
-
11289  const ToolPtr<TSeq> & operator()(size_t i);
-
11290  const ToolPtr<TSeq> & operator[](size_t i);
-
11291 
-
11292  size_t size() const noexcept;
-
11293 
-
11294  void print() const noexcept;
+
11250  if (i >= *n_tools)
+
11251  throw std::range_error("Tool index out of range.");
+
11252 
+
11253  return dat->operator[](i);
+
11254 
+
11255 }
+
11256 
+
11257 template<typename TSeq>
+
11258 inline ToolPtr<TSeq> & Tools<TSeq>::operator[](size_t i)
+
11259 {
+
11260 
+
11261  return dat->operator[](i);
+
11262 
+
11263 }
+
11264 
+
11265 template<typename TSeq>
+
11266 inline size_t Tools<TSeq>::size() const noexcept
+
11267 {
+
11268  return *n_tools;
+
11269 }
+
11270 
+
11271 template<typename TSeq>
+
11272 inline void Tools<TSeq>::print() const noexcept
+
11273 {
+
11274  if (*n_tools == 0u)
+
11275  {
+
11276  printf_epiworld("List of tools (none)\n");
+
11277  return;
+
11278  }
+
11279 
+
11280  printf_epiworld("List of tools (%i): ", static_cast<int>(*n_tools));
+
11281 
+
11282  // Printing the name of each virus separated by a comma
+
11283  for (size_t i = 0u; i < *n_tools; ++i)
+
11284  {
+
11285  if (i == *n_tools - 1u)
+
11286  {
+
11287  printf_epiworld("%s", dat->operator[](i)->get_name().c_str());
+
11288  } else
+
11289  {
+
11290  printf_epiworld("%s, ", dat->operator[](i)->get_name().c_str());
+
11291  }
+
11292  }
+
11293 
+
11294  printf_epiworld("\n");
11295 
-
11296 };
+
11296 }
11297 
-
11298 template<typename TSeq>
-
11299 inline typename std::vector< ToolPtr<TSeq> >::const_iterator Tools_const<TSeq>::begin() const {
-
11300 
-
11301  if (*n_tools == 0u)
-
11302  return dat->end();
-
11303 
-
11304  return dat->begin();
-
11305 }
-
11306 
-
11307 template<typename TSeq>
-
11308 inline typename std::vector< ToolPtr<TSeq> >::const_iterator Tools_const<TSeq>::end() const {
-
11309 
-
11310  return begin() + *n_tools;
-
11311 }
+
11303 template<typename TSeq>
+
11304 class Tools_const {
+
11305  friend class Tool<TSeq>;
+
11306  friend class Agent<TSeq>;
+
11307 private:
+
11308  const std::vector< ToolPtr<TSeq> > * dat;
+
11309  const epiworld_fast_uint * n_tools;
+
11310 
+
11311 public:
11312 
-
11313 template<typename TSeq>
-
11314 inline const ToolPtr<TSeq> & Tools_const<TSeq>::operator()(size_t i)
-
11315 {
-
11316 
-
11317  if (i >= *n_tools)
-
11318  throw std::range_error("Tool index out of range.");
-
11319 
-
11320  return dat->operator[](i);
+
11313  Tools_const() = delete;
+
11314  Tools_const(const Agent<TSeq> & p) : dat(&p.tools), n_tools(&p.n_tools) {};
+
11315 
+
11316  typename std::vector< ToolPtr<TSeq> >::const_iterator begin() const;
+
11317  typename std::vector< ToolPtr<TSeq> >::const_iterator end() const;
+
11318 
+
11319  const ToolPtr<TSeq> & operator()(size_t i);
+
11320  const ToolPtr<TSeq> & operator[](size_t i);
11321 
-
11322 }
+
11322  size_t size() const noexcept;
11323 
-
11324 template<typename TSeq>
-
11325 inline const ToolPtr<TSeq> & Tools_const<TSeq>::operator[](size_t i)
-
11326 {
+
11324  void print() const noexcept;
+
11325 
+
11326 };
11327 
-
11328  return dat->operator[](i);
-
11329 
-
11330 }
-
11331 
-
11332 template<typename TSeq>
-
11333 inline size_t Tools_const<TSeq>::size() const noexcept
-
11334 {
-
11335  return *n_tools;
-
11336 }
-
11337 
-
11338 template<typename TSeq>
-
11339 inline void Tools_const<TSeq>::print() const noexcept
-
11340 {
-
11341  if (*n_tools == 0u)
-
11342  {
-
11343  printf_epiworld("List of tools (none)\n");
-
11344  return;
-
11345  }
+
11328 template<typename TSeq>
+
11329 inline typename std::vector< ToolPtr<TSeq> >::const_iterator Tools_const<TSeq>::begin() const {
+
11330 
+
11331  if (*n_tools == 0u)
+
11332  return dat->end();
+
11333 
+
11334  return dat->begin();
+
11335 }
+
11336 
+
11337 template<typename TSeq>
+
11338 inline typename std::vector< ToolPtr<TSeq> >::const_iterator Tools_const<TSeq>::end() const {
+
11339 
+
11340  return begin() + *n_tools;
+
11341 }
+
11342 
+
11343 template<typename TSeq>
+
11344 inline const ToolPtr<TSeq> & Tools_const<TSeq>::operator()(size_t i)
+
11345 {
11346 
-
11347  printf_epiworld("List of tools (%i): ", *n_tools);
-
11348 
-
11349  // Printing the name of each virus separated by a comma
-
11350  for (size_t i = 0u; i < *n_tools; ++i)
-
11351  {
-
11352  if (i == *n_tools - 1u)
-
11353  {
-
11354  printf_epiworld("%s", dat->operator[](i)->get_name().c_str());
-
11355  } else
-
11356  {
-
11357  printf_epiworld("%s, ", dat->operator[](i)->get_name().c_str());
-
11358  }
-
11359  }
-
11360 
-
11361  printf_epiworld("\n");
-
11362 
-
11363 }
-
11364 
-
11365 
-
11366 
-
11367 #endif
-
11368 /*//////////////////////////////////////////////////////////////////////////////
-
11370 
-
11371  End of -include/epiworld/tools-bones.hpp-
-
11372 
-
11375 
+
11347  if (i >= *n_tools)
+
11348  throw std::range_error("Tool index out of range.");
+
11349 
+
11350  return dat->operator[](i);
+
11351 
+
11352 }
+
11353 
+
11354 template<typename TSeq>
+
11355 inline const ToolPtr<TSeq> & Tools_const<TSeq>::operator[](size_t i)
+
11356 {
+
11357 
+
11358  return dat->operator[](i);
+
11359 
+
11360 }
+
11361 
+
11362 template<typename TSeq>
+
11363 inline size_t Tools_const<TSeq>::size() const noexcept
+
11364 {
+
11365  return *n_tools;
+
11366 }
+
11367 
+
11368 template<typename TSeq>
+
11369 inline void Tools_const<TSeq>::print() const noexcept
+
11370 {
+
11371  if (*n_tools == 0u)
+
11372  {
+
11373  printf_epiworld("List of tools (none)\n");
+
11374  return;
+
11375  }
11376 
-
11377 
-
11378 /*//////////////////////////////////////////////////////////////////////////////
-
11380 
-
11381  Start of -include/epiworld/tool-bones.hpp-
-
11382 
-
11385 
-
11386 
-
11387 
-
11388 #ifndef EPIWORLD_TOOL_BONES_HPP
-
11389 #define EPIWORLD_TOOL_BONES_HPP
-
11390 
-
11391 template<typename TSeq>
-
11392 class Virus;
-
11393 
-
11394 template<typename TSeq>
-
11395 class Agent;
+
11377  printf_epiworld("List of tools (%i): ", *n_tools);
+
11378 
+
11379  // Printing the name of each virus separated by a comma
+
11380  for (size_t i = 0u; i < *n_tools; ++i)
+
11381  {
+
11382  if (i == *n_tools - 1u)
+
11383  {
+
11384  printf_epiworld("%s", dat->operator[](i)->get_name().c_str());
+
11385  } else
+
11386  {
+
11387  printf_epiworld("%s, ", dat->operator[](i)->get_name().c_str());
+
11388  }
+
11389  }
+
11390 
+
11391  printf_epiworld("\n");
+
11392 
+
11393 }
+
11394 
+
11395 
11396 
-
11397 template<typename TSeq>
-
11398 class Model;
-
11399 
-
11400 template<typename TSeq>
-
11401 class Tool;
+
11397 #endif
+
11398 /*//////////////////////////////////////////////////////////////////////////////
+
11400 
+
11401  End of -include/epiworld/tools-bones.hpp-
11402 
-
11408 template<typename TSeq>
-
11409 class Tool {
-
11410  friend class Agent<TSeq>;
-
11411  friend class Model<TSeq>;
-
11412  friend void default_add_tool<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
11413  friend void default_rm_tool<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
11414 private:
+
11405 
+
11406 
+
11407 
+
11408 /*//////////////////////////////////////////////////////////////////////////////
+
11410 
+
11411  Start of -include/epiworld/tool-bones.hpp-
+
11412 
11415 
-
11416  Agent<TSeq> * agent = nullptr;
-
11417  int pos_in_agent = -99; ///< Location in the agent
-
11418 
-
11419  int date = -99;
-
11420  int id = -99;
-
11421  std::shared_ptr<std::string> tool_name = nullptr;
-
11422  std::shared_ptr<TSeq> sequence = nullptr;
-
11423  ToolFun<TSeq> susceptibility_reduction_fun = nullptr;
-
11424  ToolFun<TSeq> transmission_reduction_fun = nullptr;
-
11425  ToolFun<TSeq> recovery_enhancer_fun = nullptr;
-
11426  ToolFun<TSeq> death_reduction_fun = nullptr;
-
11427 
-
11428  // Setup parameters
-
11429  std::vector< epiworld_double * > params;
-
11430 
-
11431  epiworld_fast_int state_init = -99;
-
11432  epiworld_fast_int state_post = -99;
-
11433 
-
11434  epiworld_fast_int queue_init = Queue<TSeq>::NoOne; ///< Change of state when added to agent.
-
11435  epiworld_fast_int queue_post = Queue<TSeq>::NoOne; ///< Change of state when removed from agent.
-
11436 
-
11437  void set_agent(Agent<TSeq> * p, size_t idx);
-
11438 
-
11439  ToolToAgentFun<TSeq> dist_fun = nullptr;
-
11440 
-
11441 public:
-
11442  Tool(std::string name = "unknown tool");
-
11443  Tool(
-
11444  std::string name,
-
11445  epiworld_double prevalence,
-
11446  bool as_proportion
-
11447  );
+
11416 
+
11417 
+
11418 #ifndef EPIWORLD_TOOL_BONES_HPP
+
11419 #define EPIWORLD_TOOL_BONES_HPP
+
11420 
+
11421 template<typename TSeq>
+
11422 class Virus;
+
11423 
+
11424 template<typename TSeq>
+
11425 class Agent;
+
11426 
+
11427 template<typename TSeq>
+
11428 class Model;
+
11429 
+
11430 template<typename TSeq>
+
11431 class Tool;
+
11432 
+
11438 template<typename TSeq>
+
11439 class Tool {
+
11440  friend class Agent<TSeq>;
+
11441  friend class Model<TSeq>;
+
11442  friend void default_add_tool<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
11443  friend void default_rm_tool<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
11444 private:
+
11445 
+
11446  Agent<TSeq> * agent = nullptr;
+
11447  int pos_in_agent = -99; ///< Location in the agent
11448 
-
11449  void set_sequence(TSeq d);
-
11450  void set_sequence(std::shared_ptr<TSeq> d);
-
11451  std::shared_ptr<TSeq> get_sequence();
-
11452 
-
11462  epiworld_double get_susceptibility_reduction(VirusPtr<TSeq> v, Model<TSeq> * model);
-
11463  epiworld_double get_transmission_reduction(VirusPtr<TSeq> v, Model<TSeq> * model);
-
11464  epiworld_double get_recovery_enhancer(VirusPtr<TSeq> v, Model<TSeq> * model);
-
11465  epiworld_double get_death_reduction(VirusPtr<TSeq> v, Model<TSeq> * model);
-
11466 
-
11467  void set_susceptibility_reduction_fun(ToolFun<TSeq> fun);
-
11468  void set_transmission_reduction_fun(ToolFun<TSeq> fun);
-
11469  void set_recovery_enhancer_fun(ToolFun<TSeq> fun);
-
11470  void set_death_reduction_fun(ToolFun<TSeq> fun);
-
11471 
-
11472  void set_susceptibility_reduction(epiworld_double * prob);
-
11473  void set_transmission_reduction(epiworld_double * prob);
-
11474  void set_recovery_enhancer(epiworld_double * prob);
-
11475  void set_death_reduction(epiworld_double * prob);
-
11476 
-
11477  void set_susceptibility_reduction(epiworld_double prob);
-
11478  void set_transmission_reduction(epiworld_double prob);
-
11479  void set_recovery_enhancer(epiworld_double prob);
-
11480  void set_death_reduction(epiworld_double prob);
+
11449  int date = -99;
+
11450  int id = -99;
+
11451  std::shared_ptr<std::string> tool_name = nullptr;
+
11452  std::shared_ptr<TSeq> sequence = nullptr;
+
11453  ToolFun<TSeq> susceptibility_reduction_fun = nullptr;
+
11454  ToolFun<TSeq> transmission_reduction_fun = nullptr;
+
11455  ToolFun<TSeq> recovery_enhancer_fun = nullptr;
+
11456  ToolFun<TSeq> death_reduction_fun = nullptr;
+
11457 
+
11458  // Setup parameters
+
11459  std::vector< epiworld_double * > params;
+
11460 
+
11461  epiworld_fast_int state_init = -99;
+
11462  epiworld_fast_int state_post = -99;
+
11463 
+
11464  epiworld_fast_int queue_init = Queue<TSeq>::NoOne; ///< Change of state when added to agent.
+
11465  epiworld_fast_int queue_post = Queue<TSeq>::NoOne; ///< Change of state when removed from agent.
+
11466 
+
11467  void set_agent(Agent<TSeq> * p, size_t idx);
+
11468 
+
11469  ToolToAgentFun<TSeq> dist_fun = nullptr;
+
11470 
+
11471 public:
+
11472  Tool(std::string name = "unknown tool");
+
11473  Tool(
+
11474  std::string name,
+
11475  epiworld_double prevalence,
+
11476  bool as_proportion
+
11477  );
+
11478 
+
11479  void set_sequence(TSeq d);
+
11480  void set_sequence(std::shared_ptr<TSeq> d);
+
11481  std::shared_ptr<TSeq> get_sequence();
11482 
-
11483  void set_name(std::string name);
-
11484  std::string get_name() const;
-
11485 
-
11486  Agent<TSeq> * get_agent();
-
11487  int get_id() const;
-
11488  void set_id(int id);
-
11489  void set_date(int d);
-
11490  int get_date() const;
-
11491 
-
11492  void set_state(epiworld_fast_int init, epiworld_fast_int post);
-
11493  void set_queue(epiworld_fast_int init, epiworld_fast_int post);
-
11494  void get_state(epiworld_fast_int * init, epiworld_fast_int * post);
-
11495  void get_queue(epiworld_fast_int * init, epiworld_fast_int * post);
-
11496 
-
11497  bool operator==(const Tool<TSeq> & other) const;
-
11498  bool operator!=(const Tool<TSeq> & other) const {return !operator==(other);};
-
11499 
-
11500  void print() const;
+
11492  epiworld_double get_susceptibility_reduction(VirusPtr<TSeq> v, Model<TSeq> * model);
+
11493  epiworld_double get_transmission_reduction(VirusPtr<TSeq> v, Model<TSeq> * model);
+
11494  epiworld_double get_recovery_enhancer(VirusPtr<TSeq> v, Model<TSeq> * model);
+
11495  epiworld_double get_death_reduction(VirusPtr<TSeq> v, Model<TSeq> * model);
+
11496 
+
11497  void set_susceptibility_reduction_fun(ToolFun<TSeq> fun);
+
11498  void set_transmission_reduction_fun(ToolFun<TSeq> fun);
+
11499  void set_recovery_enhancer_fun(ToolFun<TSeq> fun);
+
11500  void set_death_reduction_fun(ToolFun<TSeq> fun);
11501 
-
11502  void distribute(Model<TSeq> * model);
-
11503  void set_distribution(ToolToAgentFun<TSeq> fun);
-
11504 
-
11505 };
+
11502  void set_susceptibility_reduction(epiworld_double * prob);
+
11503  void set_transmission_reduction(epiworld_double * prob);
+
11504  void set_recovery_enhancer(epiworld_double * prob);
+
11505  void set_death_reduction(epiworld_double * prob);
11506 
-
11507 #endif
-
11508 /*//////////////////////////////////////////////////////////////////////////////
-
11510 
-
11511  End of -include/epiworld/tool-bones.hpp-
+
11507  void set_susceptibility_reduction(epiworld_double prob);
+
11508  void set_transmission_reduction(epiworld_double prob);
+
11509  void set_recovery_enhancer(epiworld_double prob);
+
11510  void set_death_reduction(epiworld_double prob);
11512 
+
11513  void set_name(std::string name);
+
11514  std::string get_name() const;
11515 
-
11516 
-
11517 /*//////////////////////////////////////////////////////////////////////////////
-
11519 
-
11520  Start of -include/epiworld/tool-distribute-meat.hpp-
+
11516  Agent<TSeq> * get_agent();
+
11517  int get_id() const;
+
11518  void set_id(int id);
+
11519  void set_date(int d);
+
11520  int get_date() const;
11521 
-
11524 
-
11525 
-
11526 #ifndef TOOL_DISTRIBUTE_MEAT_HPP
-
11527 #define TOOL_DISTRIBUTE_MEAT_HPP
-
11528 
-
11544 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
11545 inline ToolToAgentFun<TSeq> distribute_tool_to_set(
-
11546  std::vector< size_t > agents_ids
-
11547 ) {
-
11548 
-
11549  return [agents_ids](
-
11550  Tool<TSeq> & tool, Model<TSeq> * model
-
11551  ) -> void
-
11552  {
-
11553  // Adding action
-
11554  for (auto i: agents_ids)
-
11555  {
-
11556  model->get_agent(i).add_tool(
-
11557  tool,
-
11558  const_cast<Model<TSeq> * >(model)
-
11559  );
-
11560  }
-
11561  };
-
11562 
-
11563 }
-
11564 
-
11575 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
11576 inline ToolToAgentFun<TSeq> distribute_tool_randomly(
-
11577  epiworld_double prevalence,
-
11578  bool as_proportion = true
-
11579 ) {
-
11580 
-
11581  return [prevalence, as_proportion](
-
11582  Tool<TSeq> & tool, Model<TSeq> * model
-
11583  ) -> void {
-
11584 
-
11585  // Picking how many
-
11586  int n_to_distribute;
-
11587  int n = model->size();
-
11588  if (as_proportion)
-
11589  {
-
11590  n_to_distribute = static_cast<int>(std::floor(prevalence * n));
-
11591 
-
11592  if (n_to_distribute == n)
-
11593  n_to_distribute--;
-
11594  }
-
11595  else
-
11596  {
-
11597  n_to_distribute = static_cast<int>(prevalence);
-
11598  }
-
11599 
-
11600  if (n_to_distribute > n)
-
11601  throw std::range_error("There are only " + std::to_string(n) +
-
11602  " individuals in the population. Cannot add the tool to " + std::to_string(n_to_distribute));
-
11603 
-
11604  std::vector< int > idx(n);
-
11605  std::iota(idx.begin(), idx.end(), 0);
-
11606  auto & population = model->get_agents();
-
11607  for (int i = 0u; i < n_to_distribute; ++i)
-
11608  {
-
11609  int loc = static_cast<epiworld_fast_uint>(
-
11610  floor(model->runif() * n--)
-
11611  );
-
11612 
-
11613  if ((loc > 0) && (loc == n))
-
11614  loc--;
-
11615 
-
11616  population[idx[loc]].add_tool(
-
11617  tool,
-
11618  const_cast< Model<TSeq> * >(model)
-
11619  );
-
11620 
-
11621  std::swap(idx[loc], idx[n]);
-
11622 
-
11623  }
-
11624 
-
11625  };
-
11626 
-
11627 }
-
11628 #endif
-
11629 /*//////////////////////////////////////////////////////////////////////////////
-
11631 
-
11632  End of -include/epiworld/tool-distribute-meat.hpp-
-
11633 
-
11636 
-
11637 
-
11638 /*//////////////////////////////////////////////////////////////////////////////
-
11640 
-
11641  Start of -include/epiworld/tool-meat.hpp-
+
11522  void set_state(epiworld_fast_int init, epiworld_fast_int post);
+
11523  void set_queue(epiworld_fast_int init, epiworld_fast_int post);
+
11524  void get_state(epiworld_fast_int * init, epiworld_fast_int * post);
+
11525  void get_queue(epiworld_fast_int * init, epiworld_fast_int * post);
+
11526 
+
11527  bool operator==(const Tool<TSeq> & other) const;
+
11528  bool operator!=(const Tool<TSeq> & other) const {return !operator==(other);};
+
11529 
+
11530  void print() const;
+
11531 
+
11532  void distribute(Model<TSeq> * model);
+
11533  void set_distribution(ToolToAgentFun<TSeq> fun);
+
11534 
+
11535 };
+
11536 
+
11537 #endif
+
11538 /*//////////////////////////////////////////////////////////////////////////////
+
11540 
+
11541  End of -include/epiworld/tool-bones.hpp-
+
11542 
+
11545 
+
11546 
+
11547 /*//////////////////////////////////////////////////////////////////////////////
+
11549 
+
11550  Start of -include/epiworld/tool-distribute-meat.hpp-
+
11551 
+
11554 
+
11555 
+
11556 #ifndef TOOL_DISTRIBUTE_MEAT_HPP
+
11557 #define TOOL_DISTRIBUTE_MEAT_HPP
+
11558 
+
11574 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
11575 inline ToolToAgentFun<TSeq> distribute_tool_to_set(
+
11576  std::vector< size_t > agents_ids
+
11577 ) {
+
11578 
+
11579  return [agents_ids](
+
11580  Tool<TSeq> & tool, Model<TSeq> * model
+
11581  ) -> void
+
11582  {
+
11583  // Adding action
+
11584  for (auto i: agents_ids)
+
11585  {
+
11586  model->get_agent(i).add_tool(
+
11587  tool,
+
11588  const_cast<Model<TSeq> * >(model)
+
11589  );
+
11590  }
+
11591  };
+
11592 
+
11593 }
+
11594 
+
11605 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
11606 inline ToolToAgentFun<TSeq> distribute_tool_randomly(
+
11607  epiworld_double prevalence,
+
11608  bool as_proportion = true
+
11609 ) {
+
11610 
+
11611  return [prevalence, as_proportion](
+
11612  Tool<TSeq> & tool, Model<TSeq> * model
+
11613  ) -> void {
+
11614 
+
11615  // Picking how many
+
11616  int n_to_distribute;
+
11617  int n = model->size();
+
11618  if (as_proportion)
+
11619  {
+
11620  n_to_distribute = static_cast<int>(std::floor(prevalence * n));
+
11621 
+
11622  if (n_to_distribute == n)
+
11623  n_to_distribute--;
+
11624  }
+
11625  else
+
11626  {
+
11627  n_to_distribute = static_cast<int>(prevalence);
+
11628  }
+
11629 
+
11630  if (n_to_distribute > n)
+
11631  throw std::range_error("There are only " + std::to_string(n) +
+
11632  " individuals in the population. Cannot add the tool to " + std::to_string(n_to_distribute));
+
11633 
+
11634  std::vector< int > idx(n);
+
11635  std::iota(idx.begin(), idx.end(), 0);
+
11636  auto & population = model->get_agents();
+
11637  for (int i = 0u; i < n_to_distribute; ++i)
+
11638  {
+
11639  int loc = static_cast<epiworld_fast_uint>(
+
11640  floor(model->runif() * n--)
+
11641  );
11642 
-
11645 
-
11646 
-
11647 
-
11648 #ifndef EPIWORLD_TOOLS_MEAT_HPP
-
11649 #define EPIWORLD_TOOLS_MEAT_HPP
-
11650 
-
11659 template<typename TSeq>
-
11660 inline ToolFun<TSeq> tool_fun_logit(
-
11661  std::vector< int > vars,
-
11662  std::vector< double > coefs,
-
11663  Model<TSeq> * model
-
11664 ) {
-
11665 
-
11666  // Checking that there are features
-
11667  if (coefs.size() == 0u)
-
11668  throw std::logic_error(
-
11669  "The -coefs- argument should feature at least one element."
-
11670  );
-
11671 
-
11672  if (coefs.size() != vars.size())
-
11673  throw std::length_error(
-
11674  std::string("The length of -coef- (") +
-
11675  std::to_string(coefs.size()) +
-
11676  std::string(") and -vars- (") +
-
11677  std::to_string(vars.size()) +
-
11678  std::string(") should match. ")
-
11679  );
+
11643  if ((loc > 0) && (loc == n))
+
11644  loc--;
+
11645 
+
11646  population[idx[loc]].add_tool(
+
11647  tool,
+
11648  const_cast< Model<TSeq> * >(model)
+
11649  );
+
11650 
+
11651  std::swap(idx[loc], idx[n]);
+
11652 
+
11653  }
+
11654 
+
11655  };
+
11656 
+
11657 }
+
11658 #endif
+
11659 /*//////////////////////////////////////////////////////////////////////////////
+
11661 
+
11662  End of -include/epiworld/tool-distribute-meat.hpp-
+
11663 
+
11666 
+
11667 
+
11668 /*//////////////////////////////////////////////////////////////////////////////
+
11670 
+
11671  Start of -include/epiworld/tool-meat.hpp-
+
11672 
+
11675 
+
11676 
+
11677 
+
11678 #ifndef EPIWORLD_TOOLS_MEAT_HPP
+
11679 #define EPIWORLD_TOOLS_MEAT_HPP
11680 
-
11681  // Checking that there are variables in the model
-
11682  if (model != nullptr)
-
11683  {
-
11684 
-
11685  size_t K = model->get_agents_data_ncols();
-
11686  for (const auto & var: vars)
-
11687  {
-
11688  if ((var >= static_cast<int>(K)) | (var < 0))
-
11689  throw std::range_error(
-
11690  std::string("The variable ") +
-
11691  std::to_string(var) +
-
11692  std::string(" is out of range.") +
-
11693  std::string(" The agents only feature ") +
-
11694  std::to_string(K) +
-
11695  std::string("variables (features).")
-
11696  );
-
11697  }
-
11698 
-
11699  }
-
11700 
-
11701  std::vector< epiworld_double > coefs_f;
-
11702  for (auto c: coefs)
-
11703  coefs_f.push_back(static_cast<epiworld_double>(c));
-
11704 
-
11705  ToolFun<TSeq> fun_ = [coefs_f,vars](
-
11706  Tool<TSeq>& tool,
-
11707  Agent<TSeq> * agent,
-
11708  VirusPtr<TSeq> virus,
-
11709  Model<TSeq> * model
-
11710  ) -> epiworld_double {
-
11711 
-
11712  size_t K = coefs_f.size();
-
11713  epiworld_double res = 0.0;
+
11689 template<typename TSeq>
+
11690 inline ToolFun<TSeq> tool_fun_logit(
+
11691  std::vector< int > vars,
+
11692  std::vector< double > coefs,
+
11693  Model<TSeq> * model
+
11694 ) {
+
11695 
+
11696  // Checking that there are features
+
11697  if (coefs.size() == 0u)
+
11698  throw std::logic_error(
+
11699  "The -coefs- argument should feature at least one element."
+
11700  );
+
11701 
+
11702  if (coefs.size() != vars.size())
+
11703  throw std::length_error(
+
11704  std::string("The length of -coef- (") +
+
11705  std::to_string(coefs.size()) +
+
11706  std::string(") and -vars- (") +
+
11707  std::to_string(vars.size()) +
+
11708  std::string(") should match. ")
+
11709  );
+
11710 
+
11711  // Checking that there are variables in the model
+
11712  if (model != nullptr)
+
11713  {
11714 
-
11715  #if defined(__OPENMP) || defined(_OPENMP)
-
11716  #pragma omp simd reduction(+:res)
-
11717  #endif
-
11718  for (size_t i = 0u; i < K; ++i)
-
11719  res += agent->operator[](vars.at(i)) * coefs_f.at(i);
-
11720 
-
11721  return 1.0/(1.0 + std::exp(-res));
-
11722 
-
11723  };
-
11724 
-
11725  return fun_;
-
11726 
-
11727 }
-
11728 
-
11729 template<typename TSeq>
-
11730 inline Tool<TSeq>::Tool(std::string name)
-
11731 {
-
11732  set_name(name);
-
11733 }
+
11715  size_t K = model->get_agents_data_ncols();
+
11716  for (const auto & var: vars)
+
11717  {
+
11718  if ((var >= static_cast<int>(K)) | (var < 0))
+
11719  throw std::range_error(
+
11720  std::string("The variable ") +
+
11721  std::to_string(var) +
+
11722  std::string(" is out of range.") +
+
11723  std::string(" The agents only feature ") +
+
11724  std::to_string(K) +
+
11725  std::string("variables (features).")
+
11726  );
+
11727  }
+
11728 
+
11729  }
+
11730 
+
11731  std::vector< epiworld_double > coefs_f;
+
11732  for (auto c: coefs)
+
11733  coefs_f.push_back(static_cast<epiworld_double>(c));
11734 
-
11735 template<typename TSeq>
-
11736 inline Tool<TSeq>::Tool(
-
11737  std::string name,
-
11738  epiworld_double prevalence,
-
11739  bool as_proportion
-
11740  )
-
11741 {
-
11742  set_name(name);
-
11743 
-
11744  set_distribution(
-
11745  distribute_tool_randomly<TSeq>(prevalence, as_proportion)
-
11746  );
-
11747 }
-
11748 
-
11749 // template<typename TSeq>
-
11750 // inline Tool<TSeq>::Tool(TSeq d, std::string name) {
-
11751 // sequence = std::make_shared<TSeq>(d);
-
11752 // tool_name = std::make_shared<std::string>(name);
-
11753 // }
+
11735  ToolFun<TSeq> fun_ = [coefs_f,vars](
+
11736  Tool<TSeq>& tool,
+
11737  Agent<TSeq> * agent,
+
11738  VirusPtr<TSeq> virus,
+
11739  Model<TSeq> * model
+
11740  ) -> epiworld_double {
+
11741 
+
11742  size_t K = coefs_f.size();
+
11743  epiworld_double res = 0.0;
+
11744 
+
11745  #if defined(__OPENMP) || defined(_OPENMP)
+
11746  #pragma omp simd reduction(+:res)
+
11747  #endif
+
11748  for (size_t i = 0u; i < K; ++i)
+
11749  res += agent->operator[](vars.at(i)) * coefs_f.at(i);
+
11750 
+
11751  return 1.0/(1.0 + std::exp(-res));
+
11752 
+
11753  };
11754 
-
11755 template<typename TSeq>
-
11756 inline void Tool<TSeq>::set_sequence(TSeq d) {
-
11757  sequence = std::make_shared<TSeq>(d);
-
11758 }
-
11759 
-
11760 template<typename TSeq>
-
11761 inline void Tool<TSeq>::set_sequence(std::shared_ptr<TSeq> d) {
-
11762  sequence = d;
+
11755  return fun_;
+
11756 
+
11757 }
+
11758 
+
11759 template<typename TSeq>
+
11760 inline Tool<TSeq>::Tool(std::string name)
+
11761 {
+
11762  set_name(name);
11763 }
11764 
11765 template<typename TSeq>
-
11766 inline std::shared_ptr<TSeq> Tool<TSeq>::get_sequence() {
-
11767  return sequence;
-
11768 }
-
11769 
-
11770 template<typename TSeq>
-
11771 inline epiworld_double Tool<TSeq>::get_susceptibility_reduction(
-
11772  VirusPtr<TSeq> v,
-
11773  Model<TSeq> * model
-
11774 )
-
11775 {
-
11776 
-
11777  if (susceptibility_reduction_fun)
-
11778  return susceptibility_reduction_fun(*this, this->agent, v, model);
-
11779 
-
11780  return DEFAULT_TOOL_CONTAGION_REDUCTION;
-
11781 
-
11782 }
-
11783 
-
11784 template<typename TSeq>
-
11785 inline epiworld_double Tool<TSeq>::get_transmission_reduction(
-
11786  VirusPtr<TSeq> v,
-
11787  Model<TSeq> * model
-
11788 )
-
11789 {
-
11790 
-
11791  if (transmission_reduction_fun)
-
11792  return transmission_reduction_fun(*this, this->agent, v, model);
-
11793 
-
11794  return DEFAULT_TOOL_TRANSMISSION_REDUCTION;
-
11795 
-
11796 }
-
11797 
-
11798 template<typename TSeq>
-
11799 inline epiworld_double Tool<TSeq>::get_recovery_enhancer(
-
11800  VirusPtr<TSeq> v,
-
11801  Model<TSeq> * model
-
11802 )
-
11803 {
-
11804 
-
11805  if (recovery_enhancer_fun)
-
11806  return recovery_enhancer_fun(*this, this->agent, v, model);
-
11807 
-
11808  return DEFAULT_TOOL_RECOVERY_ENHANCER;
+
11766 inline Tool<TSeq>::Tool(
+
11767  std::string name,
+
11768  epiworld_double prevalence,
+
11769  bool as_proportion
+
11770  )
+
11771 {
+
11772  set_name(name);
+
11773 
+
11774  set_distribution(
+
11775  distribute_tool_randomly<TSeq>(prevalence, as_proportion)
+
11776  );
+
11777 }
+
11778 
+
11779 // template<typename TSeq>
+
11780 // inline Tool<TSeq>::Tool(TSeq d, std::string name) {
+
11781 // sequence = std::make_shared<TSeq>(d);
+
11782 // tool_name = std::make_shared<std::string>(name);
+
11783 // }
+
11784 
+
11785 template<typename TSeq>
+
11786 inline void Tool<TSeq>::set_sequence(TSeq d) {
+
11787  sequence = std::make_shared<TSeq>(d);
+
11788 }
+
11789 
+
11790 template<typename TSeq>
+
11791 inline void Tool<TSeq>::set_sequence(std::shared_ptr<TSeq> d) {
+
11792  sequence = d;
+
11793 }
+
11794 
+
11795 template<typename TSeq>
+
11796 inline std::shared_ptr<TSeq> Tool<TSeq>::get_sequence() {
+
11797  return sequence;
+
11798 }
+
11799 
+
11800 template<typename TSeq>
+
11801 inline epiworld_double Tool<TSeq>::get_susceptibility_reduction(
+
11802  VirusPtr<TSeq> v,
+
11803  Model<TSeq> * model
+
11804 )
+
11805 {
+
11806 
+
11807  if (susceptibility_reduction_fun)
+
11808  return susceptibility_reduction_fun(*this, this->agent, v, model);
11809 
-
11810 }
+
11810  return DEFAULT_TOOL_CONTAGION_REDUCTION;
11811 
-
11812 template<typename TSeq>
-
11813 inline epiworld_double Tool<TSeq>::get_death_reduction(
-
11814  VirusPtr<TSeq> v,
-
11815  Model<TSeq> * model
-
11816 )
-
11817 {
-
11818 
-
11819  if (death_reduction_fun)
-
11820  return death_reduction_fun(*this, this->agent, v, model);
-
11821 
-
11822  return DEFAULT_TOOL_DEATH_REDUCTION;
+
11812 }
+
11813 
+
11814 template<typename TSeq>
+
11815 inline epiworld_double Tool<TSeq>::get_transmission_reduction(
+
11816  VirusPtr<TSeq> v,
+
11817  Model<TSeq> * model
+
11818 )
+
11819 {
+
11820 
+
11821  if (transmission_reduction_fun)
+
11822  return transmission_reduction_fun(*this, this->agent, v, model);
11823 
-
11824 }
+
11824  return DEFAULT_TOOL_TRANSMISSION_REDUCTION;
11825 
-
11826 template<typename TSeq>
-
11827 inline void Tool<TSeq>::set_susceptibility_reduction_fun(
-
11828  ToolFun<TSeq> fun
-
11829 )
-
11830 {
-
11831  susceptibility_reduction_fun = fun;
-
11832 }
-
11833 
-
11834 template<typename TSeq>
-
11835 inline void Tool<TSeq>::set_transmission_reduction_fun(
-
11836  ToolFun<TSeq> fun
-
11837 )
-
11838 {
-
11839  transmission_reduction_fun = fun;
+
11826 }
+
11827 
+
11828 template<typename TSeq>
+
11829 inline epiworld_double Tool<TSeq>::get_recovery_enhancer(
+
11830  VirusPtr<TSeq> v,
+
11831  Model<TSeq> * model
+
11832 )
+
11833 {
+
11834 
+
11835  if (recovery_enhancer_fun)
+
11836  return recovery_enhancer_fun(*this, this->agent, v, model);
+
11837 
+
11838  return DEFAULT_TOOL_RECOVERY_ENHANCER;
+
11839 
11840 }
11841 
11842 template<typename TSeq>
-
11843 inline void Tool<TSeq>::set_recovery_enhancer_fun(
-
11844  ToolFun<TSeq> fun
-
11845 )
-
11846 {
-
11847  recovery_enhancer_fun = fun;
-
11848 }
-
11849 
-
11850 template<typename TSeq>
-
11851 inline void Tool<TSeq>::set_death_reduction_fun(
-
11852  ToolFun<TSeq> fun
-
11853 )
-
11854 {
-
11855  death_reduction_fun = fun;
-
11856 }
-
11857 
-
11858 template<typename TSeq>
-
11859 inline void Tool<TSeq>::set_susceptibility_reduction(epiworld_double * prob)
+
11843 inline epiworld_double Tool<TSeq>::get_death_reduction(
+
11844  VirusPtr<TSeq> v,
+
11845  Model<TSeq> * model
+
11846 )
+
11847 {
+
11848 
+
11849  if (death_reduction_fun)
+
11850  return death_reduction_fun(*this, this->agent, v, model);
+
11851 
+
11852  return DEFAULT_TOOL_DEATH_REDUCTION;
+
11853 
+
11854 }
+
11855 
+
11856 template<typename TSeq>
+
11857 inline void Tool<TSeq>::set_susceptibility_reduction_fun(
+
11858  ToolFun<TSeq> fun
+
11859 )
11860 {
-
11861 
-
11862  ToolFun<TSeq> tmpfun =
-
11863  [prob](Tool<TSeq> &, Agent<TSeq> *, VirusPtr<TSeq>, Model<TSeq> *)
-
11864  {
-
11865  return *prob;
-
11866  };
-
11867 
-
11868  susceptibility_reduction_fun = tmpfun;
-
11869 
+
11861  susceptibility_reduction_fun = fun;
+
11862 }
+
11863 
+
11864 template<typename TSeq>
+
11865 inline void Tool<TSeq>::set_transmission_reduction_fun(
+
11866  ToolFun<TSeq> fun
+
11867 )
+
11868 {
+
11869  transmission_reduction_fun = fun;
11870 }
11871 
-
11872 // EPIWORLD_SET_LAMBDA(susceptibility_reduction)
-
11873 template<typename TSeq>
-
11874 inline void Tool<TSeq>::set_transmission_reduction(epiworld_double * prob)
-
11875 {
-
11876 
-
11877  ToolFun<TSeq> tmpfun =
-
11878  [prob](Tool<TSeq> &, Agent<TSeq> *, VirusPtr<TSeq>, Model<TSeq> *)
-
11879  {
-
11880  return *prob;
-
11881  };
-
11882 
-
11883  transmission_reduction_fun = tmpfun;
-
11884 
-
11885 }
-
11886 
-
11887 // EPIWORLD_SET_LAMBDA(transmission_reduction)
+
11872 template<typename TSeq>
+
11873 inline void Tool<TSeq>::set_recovery_enhancer_fun(
+
11874  ToolFun<TSeq> fun
+
11875 )
+
11876 {
+
11877  recovery_enhancer_fun = fun;
+
11878 }
+
11879 
+
11880 template<typename TSeq>
+
11881 inline void Tool<TSeq>::set_death_reduction_fun(
+
11882  ToolFun<TSeq> fun
+
11883 )
+
11884 {
+
11885  death_reduction_fun = fun;
+
11886 }
+
11887 
11888 template<typename TSeq>
-
11889 inline void Tool<TSeq>::set_recovery_enhancer(epiworld_double * prob)
+
11889 inline void Tool<TSeq>::set_susceptibility_reduction(epiworld_double * prob)
11890 {
11891 
11892  ToolFun<TSeq> tmpfun =
@@ -10825,4146 +10825,4154 @@
11895  return *prob;
11896  };
11897 
-
11898  recovery_enhancer_fun = tmpfun;
+
11898  susceptibility_reduction_fun = tmpfun;
11899 
11900 }
11901 
-
11902 // EPIWORLD_SET_LAMBDA(recovery_enhancer)
+
11902 // EPIWORLD_SET_LAMBDA(susceptibility_reduction)
11903 template<typename TSeq>
-
11904 inline void Tool<TSeq>::set_death_reduction(epiworld_double * prob)
+
11904 inline void Tool<TSeq>::set_transmission_reduction(epiworld_double * prob)
11905 {
-
11906 
+
11906 
11907  ToolFun<TSeq> tmpfun =
11908  [prob](Tool<TSeq> &, Agent<TSeq> *, VirusPtr<TSeq>, Model<TSeq> *)
11909  {
11910  return *prob;
11911  };
11912 
-
11913  death_reduction_fun = tmpfun;
+
11913  transmission_reduction_fun = tmpfun;
11914 
11915 }
11916 
-
11917 // EPIWORLD_SET_LAMBDA(death_reduction)
-
11918 
-
11919 // #undef EPIWORLD_SET_LAMBDA
-
11920 template<typename TSeq>
-
11921 inline void Tool<TSeq>::set_susceptibility_reduction(
-
11922  epiworld_double prob
-
11923 )
-
11924 {
-
11925 
-
11926  ToolFun<TSeq> tmpfun =
-
11927  [prob](Tool<TSeq> &, Agent<TSeq> *, VirusPtr<TSeq>, Model<TSeq> *)
-
11928  {
-
11929  return prob;
-
11930  };
+
11917 // EPIWORLD_SET_LAMBDA(transmission_reduction)
+
11918 template<typename TSeq>
+
11919 inline void Tool<TSeq>::set_recovery_enhancer(epiworld_double * prob)
+
11920 {
+
11921 
+
11922  ToolFun<TSeq> tmpfun =
+
11923  [prob](Tool<TSeq> &, Agent<TSeq> *, VirusPtr<TSeq>, Model<TSeq> *)
+
11924  {
+
11925  return *prob;
+
11926  };
+
11927 
+
11928  recovery_enhancer_fun = tmpfun;
+
11929 
+
11930 }
11931 
-
11932  susceptibility_reduction_fun = tmpfun;
-
11933 
-
11934 }
-
11935 
-
11936 template<typename TSeq>
-
11937 inline void Tool<TSeq>::set_transmission_reduction(
-
11938  epiworld_double prob
-
11939 )
-
11940 {
-
11941 
-
11942  ToolFun<TSeq> tmpfun =
-
11943  [prob](Tool<TSeq> &, Agent<TSeq> *, VirusPtr<TSeq>, Model<TSeq> *)
-
11944  {
-
11945  return prob;
-
11946  };
-
11947 
-
11948  transmission_reduction_fun = tmpfun;
-
11949 
-
11950 }
-
11951 
-
11952 template<typename TSeq>
-
11953 inline void Tool<TSeq>::set_recovery_enhancer(
-
11954  epiworld_double prob
-
11955 )
-
11956 {
-
11957 
-
11958  ToolFun<TSeq> tmpfun =
-
11959  [prob](Tool<TSeq> &, Agent<TSeq> *, VirusPtr<TSeq>, Model<TSeq> *)
-
11960  {
-
11961  return prob;
-
11962  };
+
11932 // EPIWORLD_SET_LAMBDA(recovery_enhancer)
+
11933 template<typename TSeq>
+
11934 inline void Tool<TSeq>::set_death_reduction(epiworld_double * prob)
+
11935 {
+
11936 
+
11937  ToolFun<TSeq> tmpfun =
+
11938  [prob](Tool<TSeq> &, Agent<TSeq> *, VirusPtr<TSeq>, Model<TSeq> *)
+
11939  {
+
11940  return *prob;
+
11941  };
+
11942 
+
11943  death_reduction_fun = tmpfun;
+
11944 
+
11945 }
+
11946 
+
11947 // EPIWORLD_SET_LAMBDA(death_reduction)
+
11948 
+
11949 // #undef EPIWORLD_SET_LAMBDA
+
11950 template<typename TSeq>
+
11951 inline void Tool<TSeq>::set_susceptibility_reduction(
+
11952  epiworld_double prob
+
11953 )
+
11954 {
+
11955 
+
11956  ToolFun<TSeq> tmpfun =
+
11957  [prob](Tool<TSeq> &, Agent<TSeq> *, VirusPtr<TSeq>, Model<TSeq> *)
+
11958  {
+
11959  return prob;
+
11960  };
+
11961 
+
11962  susceptibility_reduction_fun = tmpfun;
11963 
-
11964  recovery_enhancer_fun = tmpfun;
+
11964 }
11965 
-
11966 }
-
11967 
-
11968 template<typename TSeq>
-
11969 inline void Tool<TSeq>::set_death_reduction(
-
11970  epiworld_double prob
-
11971 )
-
11972 {
-
11973 
-
11974  ToolFun<TSeq> tmpfun =
-
11975  [prob](Tool<TSeq> &, Agent<TSeq> *, VirusPtr<TSeq>, Model<TSeq> *)
-
11976  {
-
11977  return prob;
-
11978  };
+
11966 template<typename TSeq>
+
11967 inline void Tool<TSeq>::set_transmission_reduction(
+
11968  epiworld_double prob
+
11969 )
+
11970 {
+
11971 
+
11972  ToolFun<TSeq> tmpfun =
+
11973  [prob](Tool<TSeq> &, Agent<TSeq> *, VirusPtr<TSeq>, Model<TSeq> *)
+
11974  {
+
11975  return prob;
+
11976  };
+
11977 
+
11978  transmission_reduction_fun = tmpfun;
11979 
-
11980  death_reduction_fun = tmpfun;
+
11980 }
11981 
-
11982 }
-
11983 
-
11984 template<typename TSeq>
-
11985 inline void Tool<TSeq>::set_name(std::string name)
+
11982 template<typename TSeq>
+
11983 inline void Tool<TSeq>::set_recovery_enhancer(
+
11984  epiworld_double prob
+
11985 )
11986 {
-
11987  if (name != "")
-
11988  tool_name = std::make_shared<std::string>(name);
-
11989 }
-
11990 
-
11991 template<typename TSeq>
-
11992 inline std::string Tool<TSeq>::get_name() const {
+
11987 
+
11988  ToolFun<TSeq> tmpfun =
+
11989  [prob](Tool<TSeq> &, Agent<TSeq> *, VirusPtr<TSeq>, Model<TSeq> *)
+
11990  {
+
11991  return prob;
+
11992  };
11993 
-
11994  if (tool_name)
-
11995  return *tool_name;
-
11996 
-
11997  return "unknown tool";
-
11998 
-
11999 }
-
12000 
-
12001 template<typename TSeq>
-
12002 inline Agent<TSeq> * Tool<TSeq>::get_agent()
-
12003 {
-
12004  return this->agent;
-
12005 }
-
12006 
-
12007 template<typename TSeq>
-
12008 inline void Tool<TSeq>::set_agent(Agent<TSeq> * p, size_t idx)
-
12009 {
-
12010  agent = p;
-
12011  pos_in_agent = static_cast<int>(idx);
+
11994  recovery_enhancer_fun = tmpfun;
+
11995 
+
11996 }
+
11997 
+
11998 template<typename TSeq>
+
11999 inline void Tool<TSeq>::set_death_reduction(
+
12000  epiworld_double prob
+
12001 )
+
12002 {
+
12003 
+
12004  ToolFun<TSeq> tmpfun =
+
12005  [prob](Tool<TSeq> &, Agent<TSeq> *, VirusPtr<TSeq>, Model<TSeq> *)
+
12006  {
+
12007  return prob;
+
12008  };
+
12009 
+
12010  death_reduction_fun = tmpfun;
+
12011 
12012 }
12013 
12014 template<typename TSeq>
-
12015 inline int Tool<TSeq>::get_id() const {
-
12016  return id;
-
12017 }
-
12018 
-
12019 
-
12020 template<typename TSeq>
-
12021 inline void Tool<TSeq>::set_id(int id)
-
12022 {
-
12023  this->id = id;
-
12024 }
-
12025 
-
12026 template<typename TSeq>
-
12027 inline void Tool<TSeq>::set_date(int d)
-
12028 {
-
12029  this->date = d;
-
12030 }
-
12031 
-
12032 template<typename TSeq>
-
12033 inline int Tool<TSeq>::get_date() const
-
12034 {
-
12035  return date;
-
12036 }
-
12037 
-
12038 template<typename TSeq>
-
12039 inline void Tool<TSeq>::set_state(
-
12040  epiworld_fast_int init,
-
12041  epiworld_fast_int end
-
12042 )
-
12043 {
-
12044  state_init = init;
-
12045  state_post = end;
-
12046 }
-
12047 
-
12048 template<typename TSeq>
-
12049 inline void Tool<TSeq>::set_queue(
-
12050  epiworld_fast_int init,
-
12051  epiworld_fast_int end
-
12052 )
-
12053 {
-
12054  queue_init = init;
-
12055  queue_post = end;
-
12056 }
-
12057 
-
12058 template<typename TSeq>
-
12059 inline void Tool<TSeq>::get_state(
-
12060  epiworld_fast_int * init,
-
12061  epiworld_fast_int * post
-
12062 )
-
12063 {
-
12064  if (init != nullptr)
-
12065  *init = state_init;
-
12066 
-
12067  if (post != nullptr)
-
12068  *post = state_post;
-
12069 
-
12070 }
-
12071 
-
12072 template<typename TSeq>
-
12073 inline void Tool<TSeq>::get_queue(
-
12074  epiworld_fast_int * init,
-
12075  epiworld_fast_int * post
-
12076 )
-
12077 {
-
12078  if (init != nullptr)
-
12079  *init = queue_init;
-
12080 
-
12081  if (post != nullptr)
-
12082  *post = queue_post;
-
12083 
-
12084 }
-
12085 
-
12086 template<>
-
12087 inline bool Tool<std::vector<int>>::operator==(
-
12088  const Tool<std::vector<int>> & other
-
12089  ) const
-
12090 {
-
12091 
-
12092  if (sequence->size() != other.sequence->size())
-
12093  return false;
-
12094 
-
12095  for (size_t i = 0u; i < sequence->size(); ++i)
-
12096  {
-
12097  if (sequence->operator[](i) != other.sequence->operator[](i))
-
12098  return false;
-
12099  }
-
12100 
-
12101  if (tool_name != other.tool_name)
-
12102  return false;
-
12103 
-
12104  if (state_init != other.state_init)
-
12105  return false;
-
12106 
-
12107  if (state_post != other.state_post)
-
12108  return false;
-
12109 
-
12110  if (queue_init != other.queue_init)
-
12111  return false;
-
12112 
-
12113  if (queue_post != other.queue_post)
-
12114  return false;
+
12015 inline void Tool<TSeq>::set_name(std::string name)
+
12016 {
+
12017  if (name != "")
+
12018  tool_name = std::make_shared<std::string>(name);
+
12019 }
+
12020 
+
12021 template<typename TSeq>
+
12022 inline std::string Tool<TSeq>::get_name() const {
+
12023 
+
12024  if (tool_name)
+
12025  return *tool_name;
+
12026 
+
12027  return "unknown tool";
+
12028 
+
12029 }
+
12030 
+
12031 template<typename TSeq>
+
12032 inline Agent<TSeq> * Tool<TSeq>::get_agent()
+
12033 {
+
12034  return this->agent;
+
12035 }
+
12036 
+
12037 template<typename TSeq>
+
12038 inline void Tool<TSeq>::set_agent(Agent<TSeq> * p, size_t idx)
+
12039 {
+
12040  agent = p;
+
12041  pos_in_agent = static_cast<int>(idx);
+
12042 }
+
12043 
+
12044 template<typename TSeq>
+
12045 inline int Tool<TSeq>::get_id() const {
+
12046  return id;
+
12047 }
+
12048 
+
12049 
+
12050 template<typename TSeq>
+
12051 inline void Tool<TSeq>::set_id(int id)
+
12052 {
+
12053  this->id = id;
+
12054 }
+
12055 
+
12056 template<typename TSeq>
+
12057 inline void Tool<TSeq>::set_date(int d)
+
12058 {
+
12059  this->date = d;
+
12060 }
+
12061 
+
12062 template<typename TSeq>
+
12063 inline int Tool<TSeq>::get_date() const
+
12064 {
+
12065  return date;
+
12066 }
+
12067 
+
12068 template<typename TSeq>
+
12069 inline void Tool<TSeq>::set_state(
+
12070  epiworld_fast_int init,
+
12071  epiworld_fast_int end
+
12072 )
+
12073 {
+
12074  state_init = init;
+
12075  state_post = end;
+
12076 }
+
12077 
+
12078 template<typename TSeq>
+
12079 inline void Tool<TSeq>::set_queue(
+
12080  epiworld_fast_int init,
+
12081  epiworld_fast_int end
+
12082 )
+
12083 {
+
12084  queue_init = init;
+
12085  queue_post = end;
+
12086 }
+
12087 
+
12088 template<typename TSeq>
+
12089 inline void Tool<TSeq>::get_state(
+
12090  epiworld_fast_int * init,
+
12091  epiworld_fast_int * post
+
12092 )
+
12093 {
+
12094  if (init != nullptr)
+
12095  *init = state_init;
+
12096 
+
12097  if (post != nullptr)
+
12098  *post = state_post;
+
12099 
+
12100 }
+
12101 
+
12102 template<typename TSeq>
+
12103 inline void Tool<TSeq>::get_queue(
+
12104  epiworld_fast_int * init,
+
12105  epiworld_fast_int * post
+
12106 )
+
12107 {
+
12108  if (init != nullptr)
+
12109  *init = queue_init;
+
12110 
+
12111  if (post != nullptr)
+
12112  *post = queue_post;
+
12113 
+
12114 }
12115 
-
12116 
-
12117  return true;
-
12118 
-
12119 }
-
12120 
-
12121 template<typename TSeq>
-
12122 inline bool Tool<TSeq>::operator==(const Tool<TSeq> & other) const
-
12123 {
-
12124  if (*sequence != *other.sequence)
-
12125  return false;
-
12126 
-
12127  if (tool_name != other.tool_name)
-
12128  return false;
-
12129 
-
12130  if (state_init != other.state_init)
-
12131  return false;
-
12132 
-
12133  if (state_post != other.state_post)
-
12134  return false;
-
12135 
-
12136  if (queue_init != other.queue_init)
-
12137  return false;
-
12138 
-
12139  if (queue_post != other.queue_post)
-
12140  return false;
-
12141 
-
12142  return true;
-
12143 
-
12144 }
+
12116 template<>
+
12117 inline bool Tool<std::vector<int>>::operator==(
+
12118  const Tool<std::vector<int>> & other
+
12119  ) const
+
12120 {
+
12121 
+
12122  if (sequence->size() != other.sequence->size())
+
12123  return false;
+
12124 
+
12125  for (size_t i = 0u; i < sequence->size(); ++i)
+
12126  {
+
12127  if (sequence->operator[](i) != other.sequence->operator[](i))
+
12128  return false;
+
12129  }
+
12130 
+
12131  if (tool_name != other.tool_name)
+
12132  return false;
+
12133 
+
12134  if (state_init != other.state_init)
+
12135  return false;
+
12136 
+
12137  if (state_post != other.state_post)
+
12138  return false;
+
12139 
+
12140  if (queue_init != other.queue_init)
+
12141  return false;
+
12142 
+
12143  if (queue_post != other.queue_post)
+
12144  return false;
12145 
12146 
-
12147 template<typename TSeq>
-
12148 inline void Tool<TSeq>::print() const
-
12149 {
+
12147  return true;
+
12148 
+
12149 }
12150 
-
12151  printf_epiworld("Tool : %s\n", tool_name->c_str());
-
12152  printf_epiworld("Id : %s\n", (id < 0)? std::string("(empty)").c_str() : std::to_string(id).c_str());
-
12153  printf_epiworld("state_init : %i\n", static_cast<int>(state_init));
-
12154  printf_epiworld("state_post : %i\n", static_cast<int>(state_post));
-
12155  printf_epiworld("queue_init : %i\n", static_cast<int>(queue_init));
-
12156  printf_epiworld("queue_post : %i\n", static_cast<int>(queue_post));
-
12157 
-
12158 }
-
12159 
-
12160 template<typename TSeq>
-
12161 inline void Tool<TSeq>::distribute(Model<TSeq> * model)
-
12162 {
-
12163 
-
12164  if (dist_fun)
-
12165  {
-
12166 
-
12167  dist_fun(*this, model);
+
12151 template<typename TSeq>
+
12152 inline bool Tool<TSeq>::operator==(const Tool<TSeq> & other) const
+
12153 {
+
12154  if (*sequence != *other.sequence)
+
12155  return false;
+
12156 
+
12157  if (tool_name != other.tool_name)
+
12158  return false;
+
12159 
+
12160  if (state_init != other.state_init)
+
12161  return false;
+
12162 
+
12163  if (state_post != other.state_post)
+
12164  return false;
+
12165 
+
12166  if (queue_init != other.queue_init)
+
12167  return false;
12168 
-
12169  }
-
12170 
-
12171 }
-
12172 
-
12173 template<typename TSeq>
-
12174 inline void Tool<TSeq>::set_distribution(ToolToAgentFun<TSeq> fun)
-
12175 {
-
12176  dist_fun = fun;
-
12177 }
-
12178 
-
12179 #endif
-
12180 /*//////////////////////////////////////////////////////////////////////////////
-
12182 
-
12183  End of -include/epiworld/tool-meat.hpp-
-
12184 
+
12169  if (queue_post != other.queue_post)
+
12170  return false;
+
12171 
+
12172  return true;
+
12173 
+
12174 }
+
12175 
+
12176 
+
12177 template<typename TSeq>
+
12178 inline void Tool<TSeq>::print() const
+
12179 {
+
12180 
+
12181  printf_epiworld("Tool : %s\n", tool_name->c_str());
+
12182  printf_epiworld("Id : %s\n", (id < 0)? std::string("(empty)").c_str() : std::to_string(id).c_str());
+
12183  printf_epiworld("state_init : %i\n", static_cast<int>(state_init));
+
12184  printf_epiworld("state_post : %i\n", static_cast<int>(state_post));
+
12185  printf_epiworld("queue_init : %i\n", static_cast<int>(queue_init));
+
12186  printf_epiworld("queue_post : %i\n", static_cast<int>(queue_post));
12187 
-
12188 
+
12188 }
12189 
-
12190 /*//////////////////////////////////////////////////////////////////////////////
-
12192 
-
12193  Start of -include/epiworld/entity-bones.hpp-
-
12194 
-
12197 
+
12190 template<typename TSeq>
+
12191 inline void Tool<TSeq>::distribute(Model<TSeq> * model)
+
12192 {
+
12193 
+
12194  if (dist_fun)
+
12195  {
+
12196 
+
12197  dist_fun(*this, model);
12198 
-
12199 #ifndef EPIWORLD_ENTITY_BONES_HPP
-
12200 #define EPIWORLD_ENTITY_BONES_HPP
-
12201 
-
12202 template<typename TSeq>
-
12203 class Model;
-
12204 
-
12205 template<typename TSeq>
-
12206 class Agent;
-
12207 
-
12208 template<typename TSeq>
-
12209 class AgentsSample;
-
12210 
-
12211 template<typename TSeq>
-
12212 inline void default_add_entity(Event<TSeq> & a, Model<TSeq> * m);
-
12213 
-
12214 template<typename TSeq>
-
12215 inline void default_rm_entity(Event<TSeq> & a, Model<TSeq> * m);
-
12216 
-
12217 template<typename TSeq>
-
12218 class Entity {
-
12219  friend class Agent<TSeq>;
-
12220  friend class AgentsSample<TSeq>;
-
12221  friend class Model<TSeq>;
-
12222  friend void default_add_entity<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
12223  friend void default_rm_entity<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
12224 private:
-
12225 
-
12226  int id = -1;
-
12227  std::vector< size_t > agents; ///< Vector of agents
-
12228  std::vector< size_t > agents_location; ///< Location where the entity is stored in the agent
-
12229  size_t n_agents = 0u;
-
12230 
-
12240  std::vector< Agent<TSeq> * > sampled_agents;
-
12241  size_t sampled_agents_n = 0u;
-
12242  std::vector< size_t > sampled_agents_left;
-
12243  size_t sampled_agents_left_n = 0u;
-
12244  // int date_last_add_or_remove = -99; ///< Last time the entity added or removed an agent
+
12199  }
+
12200 
+
12201 }
+
12202 
+
12203 template<typename TSeq>
+
12204 inline void Tool<TSeq>::set_distribution(ToolToAgentFun<TSeq> fun)
+
12205 {
+
12206  dist_fun = fun;
+
12207 }
+
12208 
+
12209 #endif
+
12210 /*//////////////////////////////////////////////////////////////////////////////
+
12212 
+
12213  End of -include/epiworld/tool-meat.hpp-
+
12214 
+
12217 
+
12218 
+
12219 
+
12220 /*//////////////////////////////////////////////////////////////////////////////
+
12222 
+
12223  Start of -include/epiworld/entity-bones.hpp-
+
12224 
+
12227 
+
12228 
+
12229 #ifndef EPIWORLD_ENTITY_BONES_HPP
+
12230 #define EPIWORLD_ENTITY_BONES_HPP
+
12231 
+
12232 template<typename TSeq>
+
12233 class Model;
+
12234 
+
12235 template<typename TSeq>
+
12236 class Agent;
+
12237 
+
12238 template<typename TSeq>
+
12239 class AgentsSample;
+
12240 
+
12241 template<typename TSeq>
+
12242 inline void default_add_entity(Event<TSeq> & a, Model<TSeq> * m);
+
12243 
+
12244 template<typename TSeq>
+
12245 inline void default_rm_entity(Event<TSeq> & a, Model<TSeq> * m);
12246 
-
12247  int max_capacity = -1;
-
12248  std::string entity_name = "Unnamed entity";
-
12249 
-
12250  std::vector< epiworld_double > location = {0.0}; ///< An arbitrary vector for location
-
12251 
-
12252  epiworld_fast_int state_init = -99;
-
12253  epiworld_fast_int state_post = -99;
-
12254 
-
12255  epiworld_fast_int queue_init = 0; ///< Change of state when added to agent.
-
12256  epiworld_fast_int queue_post = 0; ///< Change of state when removed from agent.
-
12257 
-
12258  EntityToAgentFun<TSeq> dist_fun = nullptr;
-
12259 
-
12260 public:
-
12261 
-
12262 
-
12271  Entity(
-
12272  std::string name,
-
12273  EntityToAgentFun<TSeq> fun = nullptr
-
12274  ) :
-
12275  entity_name(name),
-
12276  dist_fun(fun)
-
12277  {};
-
12278 
-
12279  void add_agent(Agent<TSeq> & p, Model<TSeq> * model);
-
12280  void add_agent(Agent<TSeq> * p, Model<TSeq> * model);
-
12281  void rm_agent(size_t idx, Model<TSeq> * model);
-
12282  size_t size() const noexcept;
-
12283  void set_location(std::vector< epiworld_double > loc);
-
12284  std::vector< epiworld_double > & get_location();
-
12285 
-
12286  typename std::vector< Agent<TSeq> * >::iterator begin();
-
12287  typename std::vector< Agent<TSeq> * >::iterator end();
-
12288 
-
12289  typename std::vector< Agent<TSeq> * >::const_iterator begin() const;
-
12290  typename std::vector< Agent<TSeq> * >::const_iterator end() const;
+
12247 template<typename TSeq>
+
12248 class Entity {
+
12249  friend class Agent<TSeq>;
+
12250  friend class AgentsSample<TSeq>;
+
12251  friend class Model<TSeq>;
+
12252  friend void default_add_entity<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
12253  friend void default_rm_entity<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
12254 private:
+
12255 
+
12256  int id = -1;
+
12257  std::vector< size_t > agents; ///< Vector of agents
+
12258  std::vector< size_t > agents_location; ///< Location where the entity is stored in the agent
+
12259  size_t n_agents = 0u;
+
12260 
+
12270  std::vector< Agent<TSeq> * > sampled_agents;
+
12271  size_t sampled_agents_n = 0u;
+
12272  std::vector< size_t > sampled_agents_left;
+
12273  size_t sampled_agents_left_n = 0u;
+
12274  // int date_last_add_or_remove = -99; ///< Last time the entity added or removed an agent
+
12276 
+
12277  int max_capacity = -1;
+
12278  std::string entity_name = "Unnamed entity";
+
12279 
+
12280  std::vector< epiworld_double > location = {0.0}; ///< An arbitrary vector for location
+
12281 
+
12282  epiworld_fast_int state_init = -99;
+
12283  epiworld_fast_int state_post = -99;
+
12284 
+
12285  epiworld_fast_int queue_init = 0; ///< Change of state when added to agent.
+
12286  epiworld_fast_int queue_post = 0; ///< Change of state when removed from agent.
+
12287 
+
12288  EntityToAgentFun<TSeq> dist_fun = nullptr;
+
12289 
+
12290 public:
12291 
-
12292  size_t operator[](size_t i);
-
12293 
-
12294  int get_id() const noexcept;
-
12295  const std::string & get_name() const noexcept;
-
12296 
-
12297  void set_state(epiworld_fast_int init, epiworld_fast_int post);
-
12298  void set_queue(epiworld_fast_int init, epiworld_fast_int post);
-
12299  void get_state(epiworld_fast_int * init, epiworld_fast_int * post);
-
12300  void get_queue(epiworld_fast_int * init, epiworld_fast_int * post);
-
12301 
-
12302  void reset();
-
12303 
-
12304  bool operator==(const Entity<TSeq> & other) const;
-
12305  bool operator!=(const Entity<TSeq> & other) const {return !operator==(other);};
-
12306 
-
12314  void distribute(Model<TSeq> * model);
+
12292 
+
12301  Entity(
+
12302  std::string name,
+
12303  EntityToAgentFun<TSeq> fun = nullptr
+
12304  ) :
+
12305  entity_name(name),
+
12306  dist_fun(fun)
+
12307  {};
+
12308 
+
12309  void add_agent(Agent<TSeq> & p, Model<TSeq> * model);
+
12310  void add_agent(Agent<TSeq> * p, Model<TSeq> * model);
+
12311  void rm_agent(size_t idx, Model<TSeq> * model);
+
12312  size_t size() const noexcept;
+
12313  void set_location(std::vector< epiworld_double > loc);
+
12314  std::vector< epiworld_double > & get_location();
12315 
-
12316  std::vector< size_t > & get_agents();
-
12317 
-
12318  void print() const;
-
12319  void set_distribution(EntityToAgentFun<TSeq> fun);
-
12320 
-
12321 };
-
12322 
+
12316  typename std::vector< Agent<TSeq> * >::iterator begin();
+
12317  typename std::vector< Agent<TSeq> * >::iterator end();
+
12318 
+
12319  typename std::vector< Agent<TSeq> * >::const_iterator begin() const;
+
12320  typename std::vector< Agent<TSeq> * >::const_iterator end() const;
+
12321 
+
12322  size_t operator[](size_t i);
12323 
-
12324 #endif
-
12325 /*//////////////////////////////////////////////////////////////////////////////
-
12327 
-
12328  End of -include/epiworld/entity-bones.hpp-
-
12329 
-
12332 
+
12324  int get_id() const noexcept;
+
12325  const std::string & get_name() const noexcept;
+
12326 
+
12327  void set_state(epiworld_fast_int init, epiworld_fast_int post);
+
12328  void set_queue(epiworld_fast_int init, epiworld_fast_int post);
+
12329  void get_state(epiworld_fast_int * init, epiworld_fast_int * post);
+
12330  void get_queue(epiworld_fast_int * init, epiworld_fast_int * post);
+
12331 
+
12332  void reset();
12333 
-
12334 /*//////////////////////////////////////////////////////////////////////////////
+
12334  bool operator==(const Entity<TSeq> & other) const;
+
12335  bool operator!=(const Entity<TSeq> & other) const {return !operator==(other);};
12336 
-
12337  Start of -include/epiworld/entity-distribute-meat.hpp-
-
12338 
-
12341 
-
12342 
-
12343 #ifndef EPIWORLD_ENTITY_DISTRIBUTE_MEAT_HPP
-
12344 #define EPIWORLD_ENTITY_DISTRIBUTE_MEAT_HPP
+
12344  void distribute(Model<TSeq> * model);
12345 
-
12346 
-
12347 template <typename TSeq = EPI_DEFAULT_TSEQ>
-
12358 inline EntityToAgentFun<TSeq> distribute_entity_randomly(
-
12359  epiworld_double prevalence,
-
12360  bool as_proportion,
-
12361  bool to_unassigned
-
12362 )
-
12363 {
-
12364 
-
12365  return [prevalence, as_proportion, to_unassigned](
-
12366  Entity<TSeq> & e, Model<TSeq> * m
-
12367  ) -> void {
+
12346  std::vector< size_t > & get_agents();
+
12347 
+
12348  void print() const;
+
12349  void set_distribution(EntityToAgentFun<TSeq> fun);
+
12350 
+
12351 };
+
12352 
+
12353 
+
12354 #endif
+
12355 /*//////////////////////////////////////////////////////////////////////////////
+
12357 
+
12358  End of -include/epiworld/entity-bones.hpp-
+
12359 
+
12362 
+
12363 
+
12364 /*//////////////////////////////////////////////////////////////////////////////
+
12366 
+
12367  Start of -include/epiworld/entity-distribute-meat.hpp-
12368 
-
12369 
-
12370  // Preparing the sampling space
-
12371  std::vector< size_t > idx;
-
12372  if (to_unassigned)
-
12373  {
-
12374  for (const auto & a: m->get_agents())
-
12375  if (a.get_n_entities() == 0)
-
12376  idx.push_back(a.get_id());
-
12377  }
-
12378  else
-
12379  {
-
12380 
-
12381  for (const auto & a: m->get_agents())
-
12382  idx.push_back(a.get_id());
-
12383 
-
12384  }
-
12385 
-
12386  size_t n = idx.size();
-
12387 
-
12388  // Figuring out how many to sample
-
12389  int n_to_sample;
-
12390  if (as_proportion)
-
12391  {
-
12392  n_to_sample = static_cast<int>(std::floor(prevalence * n));
-
12393  if (n_to_sample > static_cast<int>(n))
-
12394  --n_to_sample;
-
12395 
-
12396  } else
-
12397  {
-
12398  n_to_sample = static_cast<int>(prevalence);
-
12399  if (n_to_sample > static_cast<int>(n))
-
12400  throw std::range_error("There are only " + std::to_string(n) +
-
12401  " individuals in the population. Cannot add the entity to " +
-
12402  std::to_string(n_to_sample));
-
12403  }
-
12404 
-
12405  int n_left = n;
-
12406  for (int i = 0; i < n_to_sample; ++i)
-
12407  {
-
12408  int loc = static_cast<epiworld_fast_uint>(
-
12409  floor(m->runif() * n_left--)
-
12410  );
-
12411 
-
12412  // Correcting for possible overflow
-
12413  if ((loc > 0) && (loc >= n_left))
-
12414  loc = n_left - 1;
-
12415 
-
12416  m->get_agent(idx[loc]).add_entity(e, m);
+
12371 
+
12372 
+
12373 #ifndef EPIWORLD_ENTITY_DISTRIBUTE_MEAT_HPP
+
12374 #define EPIWORLD_ENTITY_DISTRIBUTE_MEAT_HPP
+
12375 
+
12376 
+
12377 template <typename TSeq = EPI_DEFAULT_TSEQ>
+
12388 inline EntityToAgentFun<TSeq> distribute_entity_randomly(
+
12389  epiworld_double prevalence,
+
12390  bool as_proportion,
+
12391  bool to_unassigned
+
12392 )
+
12393 {
+
12394 
+
12395  return [prevalence, as_proportion, to_unassigned](
+
12396  Entity<TSeq> & e, Model<TSeq> * m
+
12397  ) -> void {
+
12398 
+
12399 
+
12400  // Preparing the sampling space
+
12401  std::vector< size_t > idx;
+
12402  if (to_unassigned)
+
12403  {
+
12404  for (const auto & a: m->get_agents())
+
12405  if (a.get_n_entities() == 0)
+
12406  idx.push_back(a.get_id());
+
12407  }
+
12408  else
+
12409  {
+
12410 
+
12411  for (const auto & a: m->get_agents())
+
12412  idx.push_back(a.get_id());
+
12413 
+
12414  }
+
12415 
+
12416  size_t n = idx.size();
12417 
-
12418  std::swap(idx[loc], idx[n_left]);
-
12419 
-
12420  }
-
12421 
-
12422  };
-
12423 
-
12424 }
+
12418  // Figuring out how many to sample
+
12419  int n_to_sample;
+
12420  if (as_proportion)
+
12421  {
+
12422  n_to_sample = static_cast<int>(std::floor(prevalence * n));
+
12423  if (n_to_sample > static_cast<int>(n))
+
12424  --n_to_sample;
12425 
-
12426 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
12437 inline EntityToAgentFun<TSeq> distribute_entity_to_range(
-
12438  int from,
-
12439  int to,
-
12440  bool to_unassigned = false
-
12441  ) {
-
12442 
-
12443  if (to_unassigned)
-
12444  {
+
12426  } else
+
12427  {
+
12428  n_to_sample = static_cast<int>(prevalence);
+
12429  if (n_to_sample > static_cast<int>(n))
+
12430  throw std::range_error("There are only " + std::to_string(n) +
+
12431  " individuals in the population. Cannot add the entity to " +
+
12432  std::to_string(n_to_sample));
+
12433  }
+
12434 
+
12435  int n_left = n;
+
12436  for (int i = 0; i < n_to_sample; ++i)
+
12437  {
+
12438  int loc = static_cast<epiworld_fast_uint>(
+
12439  floor(m->runif() * n_left--)
+
12440  );
+
12441 
+
12442  // Correcting for possible overflow
+
12443  if ((loc > 0) && (loc >= n_left))
+
12444  loc = n_left - 1;
12445 
-
12446  return [from, to](Entity<TSeq> & e, Model<TSeq> * m) -> void {
+
12446  m->get_agent(idx[loc]).add_entity(e, m);
12447 
-
12448  auto & agents = m->get_agents();
-
12449  for (size_t i = from; i < to; ++i)
-
12450  {
-
12451  if (agents[i].get_n_entities() == 0)
-
12452  e.add_agent(&agents[i], m);
-
12453  else
-
12454  throw std::logic_error(
-
12455  "Agent " + std::to_string(i) + " already has an entity."
-
12456  );
-
12457  }
-
12458 
-
12459  return;
-
12460 
-
12461  };
-
12462 
-
12463  }
-
12464  else
-
12465  {
-
12466 
-
12467  return [from, to](Entity<TSeq> & e, Model<TSeq> * m) -> void {
-
12468 
-
12469  auto & agents = m->get_agents();
-
12470  for (size_t i = from; i < to; ++i)
-
12471  {
-
12472  e.add_agent(&agents[i], m);
-
12473  }
-
12474 
-
12475  return;
-
12476 
-
12477  };
-
12478 
-
12479  }
-
12480 }
-
12481 
-
12482 
-
12483 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
12484 inline EntityToAgentFun<TSeq> distribute_entity_to_set(
-
12485  std::vector< size_t > & idx
-
12486  ) {
-
12487 
-
12488  return [idx](Entity<TSeq> & e, Model<TSeq> * m) -> void {
-
12489 
-
12490  for (const auto & i: idx)
-
12491  {
-
12492  e.add_agent(&m->get_agent(i), m);
-
12493  }
-
12494 
-
12495  };
+
12448  std::swap(idx[loc], idx[n_left]);
+
12449 
+
12450  }
+
12451 
+
12452  };
+
12453 
+
12454 }
+
12455 
+
12456 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
12467 inline EntityToAgentFun<TSeq> distribute_entity_to_range(
+
12468  int from,
+
12469  int to,
+
12470  bool to_unassigned = false
+
12471  ) {
+
12472 
+
12473  if (to_unassigned)
+
12474  {
+
12475 
+
12476  return [from, to](Entity<TSeq> & e, Model<TSeq> * m) -> void {
+
12477 
+
12478  auto & agents = m->get_agents();
+
12479  for (size_t i = from; i < to; ++i)
+
12480  {
+
12481  if (agents[i].get_n_entities() == 0)
+
12482  e.add_agent(&agents[i], m);
+
12483  else
+
12484  throw std::logic_error(
+
12485  "Agent " + std::to_string(i) + " already has an entity."
+
12486  );
+
12487  }
+
12488 
+
12489  return;
+
12490 
+
12491  };
+
12492 
+
12493  }
+
12494  else
+
12495  {
12496 
-
12497 }
+
12497  return [from, to](Entity<TSeq> & e, Model<TSeq> * m) -> void {
12498 
-
12499 #endif
-
12500 /*//////////////////////////////////////////////////////////////////////////////
-
12502 
-
12503  End of -include/epiworld/entity-distribute-meat.hpp-
-
12504 
-
12507 
+
12499  auto & agents = m->get_agents();
+
12500  for (size_t i = from; i < to; ++i)
+
12501  {
+
12502  e.add_agent(&agents[i], m);
+
12503  }
+
12504 
+
12505  return;
+
12506 
+
12507  };
12508 
-
12509 /*//////////////////////////////////////////////////////////////////////////////
+
12509  }
+
12510 }
12511 
-
12512  Start of -include/epiworld/entity-meat.hpp-
-
12513 
-
12516 
+
12512 
+
12513 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
12514 inline EntityToAgentFun<TSeq> distribute_entity_to_set(
+
12515  std::vector< size_t > & idx
+
12516  ) {
12517 
-
12518 #ifndef EPIWORLD_ENTITY_MEAT_HPP
-
12519 #define EPIWORLD_ENTITY_MEAT_HPP
-
12520 
-
12521 template<typename TSeq>
-
12522 inline void Entity<TSeq>::add_agent(
-
12523  Agent<TSeq> & p,
-
12524  Model<TSeq> * model
-
12525  )
-
12526 {
-
12527 
-
12528  // Need to add it to the events, through the individual
-
12529  p.add_entity(*this, model);
-
12530 
-
12531 }
+
12518  return [idx](Entity<TSeq> & e, Model<TSeq> * m) -> void {
+
12519 
+
12520  for (const auto & i: idx)
+
12521  {
+
12522  e.add_agent(&m->get_agent(i), m);
+
12523  }
+
12524 
+
12525  };
+
12526 
+
12527 }
+
12528 
+
12529 #endif
+
12530 /*//////////////////////////////////////////////////////////////////////////////
12532 
-
12533 template<typename TSeq>
-
12534 inline void Entity<TSeq>::add_agent(
-
12535  Agent<TSeq> * p,
-
12536  Model<TSeq> * model
-
12537  )
-
12538 {
-
12539  p->add_entity(*this, model);
-
12540 }
+
12533  End of -include/epiworld/entity-distribute-meat.hpp-
+
12534 
+
12537 
+
12538 
+
12539 /*//////////////////////////////////////////////////////////////////////////////
12541 
-
12542 template<typename TSeq>
-
12543 inline void Entity<TSeq>::rm_agent(size_t idx, Model<TSeq> * model)
-
12544 {
-
12545  if (idx >= n_agents)
-
12546  throw std::out_of_range(
-
12547  "Trying to remove agent "+ std::to_string(idx) +
-
12548  " out of " + std::to_string(n_agents)
-
12549  );
+
12542  Start of -include/epiworld/entity-meat.hpp-
+
12543 
+
12546 
+
12547 
+
12548 #ifndef EPIWORLD_ENTITY_MEAT_HPP
+
12549 #define EPIWORLD_ENTITY_MEAT_HPP
12550 
-
12551  model->get_agents()[agents[idx]].rm_entity(*this, model);
-
12552 
-
12553  return;
-
12554 }
-
12555 
-
12556 template<typename TSeq>
-
12557 inline size_t Entity<TSeq>::size() const noexcept
-
12558 {
-
12559  return n_agents;
-
12560 }
-
12561 
-
12562 template<typename TSeq>
-
12563 inline void Entity<TSeq>::set_location(std::vector< epiworld_double > loc)
-
12564 {
-
12565  location = loc;
-
12566 }
-
12567 
-
12568 template<typename TSeq>
-
12569 inline std::vector< epiworld_double > & Entity<TSeq>::get_location()
-
12570 {
-
12571  return location;
-
12572 }
-
12573 
-
12574 template<typename TSeq>
-
12575 inline typename std::vector< Agent<TSeq> * >::iterator Entity<TSeq>::begin()
-
12576 {
-
12577 
-
12578  if (n_agents == 0)
-
12579  return agents.end();
+
12551 template<typename TSeq>
+
12552 inline void Entity<TSeq>::add_agent(
+
12553  Agent<TSeq> & p,
+
12554  Model<TSeq> * model
+
12555  )
+
12556 {
+
12557 
+
12558  // Need to add it to the events, through the individual
+
12559  p.add_entity(*this, model);
+
12560 
+
12561 }
+
12562 
+
12563 template<typename TSeq>
+
12564 inline void Entity<TSeq>::add_agent(
+
12565  Agent<TSeq> * p,
+
12566  Model<TSeq> * model
+
12567  )
+
12568 {
+
12569  p->add_entity(*this, model);
+
12570 }
+
12571 
+
12572 template<typename TSeq>
+
12573 inline void Entity<TSeq>::rm_agent(size_t idx, Model<TSeq> * model)
+
12574 {
+
12575  if (idx >= n_agents)
+
12576  throw std::out_of_range(
+
12577  "Trying to remove agent "+ std::to_string(idx) +
+
12578  " out of " + std::to_string(n_agents)
+
12579  );
12580 
-
12581  return agents.begin();
+
12581  model->get_agents()[agents[idx]].rm_entity(*this, model);
12582 
-
12583 }
-
12584 
-
12585 template<typename TSeq>
-
12586 inline typename std::vector< Agent<TSeq> * >::iterator Entity<TSeq>::end()
-
12587 {
-
12588  return agents.begin() + n_agents;
-
12589 }
-
12590 
-
12591 template<typename TSeq>
-
12592 inline typename std::vector< Agent<TSeq> * >::const_iterator Entity<TSeq>::begin() const
-
12593 {
-
12594 
-
12595  if (n_agents == 0)
-
12596  return agents.end();
+
12583  return;
+
12584 }
+
12585 
+
12586 template<typename TSeq>
+
12587 inline size_t Entity<TSeq>::size() const noexcept
+
12588 {
+
12589  return n_agents;
+
12590 }
+
12591 
+
12592 template<typename TSeq>
+
12593 inline void Entity<TSeq>::set_location(std::vector< epiworld_double > loc)
+
12594 {
+
12595  location = loc;
+
12596 }
12597 
-
12598  return agents.begin();
-
12599 
-
12600 }
-
12601 
-
12602 template<typename TSeq>
-
12603 inline typename std::vector< Agent<TSeq> * >::const_iterator Entity<TSeq>::end() const
-
12604 {
-
12605  return agents.begin() + n_agents;
-
12606 }
+
12598 template<typename TSeq>
+
12599 inline std::vector< epiworld_double > & Entity<TSeq>::get_location()
+
12600 {
+
12601  return location;
+
12602 }
+
12603 
+
12604 template<typename TSeq>
+
12605 inline typename std::vector< Agent<TSeq> * >::iterator Entity<TSeq>::begin()
+
12606 {
12607 
-
12608 template<typename TSeq>
-
12609 size_t Entity<TSeq>::operator[](size_t i)
-
12610 {
-
12611  if (n_agents <= i)
-
12612  throw std::logic_error(
-
12613  "There are not that many agents in this entity. " +
-
12614  std::to_string(n_agents) + " <= " + std::to_string(i)
-
12615  );
-
12616 
-
12617  return i;
-
12618 }
-
12619 
-
12620 template<typename TSeq>
-
12621 inline int Entity<TSeq>::get_id() const noexcept
-
12622 {
-
12623  return id;
-
12624 }
-
12625 
-
12626 template<typename TSeq>
-
12627 inline const std::string & Entity<TSeq>::get_name() const noexcept
-
12628 {
-
12629  return entity_name;
+
12608  if (n_agents == 0)
+
12609  return agents.end();
+
12610 
+
12611  return agents.begin();
+
12612 
+
12613 }
+
12614 
+
12615 template<typename TSeq>
+
12616 inline typename std::vector< Agent<TSeq> * >::iterator Entity<TSeq>::end()
+
12617 {
+
12618  return agents.begin() + n_agents;
+
12619 }
+
12620 
+
12621 template<typename TSeq>
+
12622 inline typename std::vector< Agent<TSeq> * >::const_iterator Entity<TSeq>::begin() const
+
12623 {
+
12624 
+
12625  if (n_agents == 0)
+
12626  return agents.end();
+
12627 
+
12628  return agents.begin();
+
12629 
12630 }
12631 
12632 template<typename TSeq>
-
12633 inline void Entity<TSeq>::set_state(
-
12634  epiworld_fast_int init,
-
12635  epiworld_fast_int end
-
12636 )
-
12637 {
-
12638  state_init = init;
-
12639  state_post = end;
-
12640 }
-
12641 
-
12642 template<typename TSeq>
-
12643 inline void Entity<TSeq>::set_queue(
-
12644  epiworld_fast_int init,
-
12645  epiworld_fast_int end
-
12646 )
-
12647 {
-
12648  queue_init = init;
-
12649  queue_post = end;
-
12650 }
-
12651 
-
12652 template<typename TSeq>
-
12653 inline void Entity<TSeq>::get_state(
-
12654  epiworld_fast_int * init,
-
12655  epiworld_fast_int * post
-
12656 )
-
12657 {
-
12658  if (init != nullptr)
-
12659  *init = state_init;
-
12660 
-
12661  if (post != nullptr)
-
12662  *post = state_post;
-
12663 
-
12664 }
-
12665 
-
12666 template<typename TSeq>
-
12667 inline void Entity<TSeq>::get_queue(
-
12668  epiworld_fast_int * init,
-
12669  epiworld_fast_int * post
-
12670 )
-
12671 {
-
12672  if (init != nullptr)
-
12673  *init = queue_init;
-
12674 
-
12675  if (post != nullptr)
-
12676  *post = queue_post;
-
12677 
-
12678 }
-
12679 
-
12680 template<typename TSeq>
-
12681 inline void Entity<TSeq>::reset()
-
12682 {
-
12683  sampled_agents.clear();
-
12684  sampled_agents_n = 0u;
-
12685  sampled_agents_left.clear();
-
12686  sampled_agents_left_n = 0u;
-
12687 
-
12688  this->agents.clear();
-
12689  this->n_agents = 0u;
-
12690  this->agents_location.clear();
-
12691 
-
12692  return;
+
12633 inline typename std::vector< Agent<TSeq> * >::const_iterator Entity<TSeq>::end() const
+
12634 {
+
12635  return agents.begin() + n_agents;
+
12636 }
+
12637 
+
12638 template<typename TSeq>
+
12639 size_t Entity<TSeq>::operator[](size_t i)
+
12640 {
+
12641  if (n_agents <= i)
+
12642  throw std::logic_error(
+
12643  "There are not that many agents in this entity. " +
+
12644  std::to_string(n_agents) + " <= " + std::to_string(i)
+
12645  );
+
12646 
+
12647  return i;
+
12648 }
+
12649 
+
12650 template<typename TSeq>
+
12651 inline int Entity<TSeq>::get_id() const noexcept
+
12652 {
+
12653  return id;
+
12654 }
+
12655 
+
12656 template<typename TSeq>
+
12657 inline const std::string & Entity<TSeq>::get_name() const noexcept
+
12658 {
+
12659  return entity_name;
+
12660 }
+
12661 
+
12662 template<typename TSeq>
+
12663 inline void Entity<TSeq>::set_state(
+
12664  epiworld_fast_int init,
+
12665  epiworld_fast_int end
+
12666 )
+
12667 {
+
12668  state_init = init;
+
12669  state_post = end;
+
12670 }
+
12671 
+
12672 template<typename TSeq>
+
12673 inline void Entity<TSeq>::set_queue(
+
12674  epiworld_fast_int init,
+
12675  epiworld_fast_int end
+
12676 )
+
12677 {
+
12678  queue_init = init;
+
12679  queue_post = end;
+
12680 }
+
12681 
+
12682 template<typename TSeq>
+
12683 inline void Entity<TSeq>::get_state(
+
12684  epiworld_fast_int * init,
+
12685  epiworld_fast_int * post
+
12686 )
+
12687 {
+
12688  if (init != nullptr)
+
12689  *init = state_init;
+
12690 
+
12691  if (post != nullptr)
+
12692  *post = state_post;
12693 
12694 }
12695 
12696 template<typename TSeq>
-
12697 inline bool Entity<TSeq>::operator==(const Entity<TSeq> & other) const
-
12698 {
-
12699 
-
12700  if (id != other.id)
-
12701  return false;
-
12702 
-
12703  if (n_agents != other.n_agents)
-
12704  return false;
-
12705 
-
12706  for (size_t i = 0u; i < n_agents; ++i)
-
12707  {
-
12708  if (agents[i] != other.agents[i])
-
12709  return false;
-
12710  }
-
12711 
-
12712 
-
12713  if (max_capacity != other.max_capacity)
-
12714  return false;
-
12715 
-
12716  if (entity_name != other.entity_name)
-
12717  return false;
-
12718 
-
12719  if (location.size() != other.location.size())
-
12720  return false;
+
12697 inline void Entity<TSeq>::get_queue(
+
12698  epiworld_fast_int * init,
+
12699  epiworld_fast_int * post
+
12700 )
+
12701 {
+
12702  if (init != nullptr)
+
12703  *init = queue_init;
+
12704 
+
12705  if (post != nullptr)
+
12706  *post = queue_post;
+
12707 
+
12708 }
+
12709 
+
12710 template<typename TSeq>
+
12711 inline void Entity<TSeq>::reset()
+
12712 {
+
12713  sampled_agents.clear();
+
12714  sampled_agents_n = 0u;
+
12715  sampled_agents_left.clear();
+
12716  sampled_agents_left_n = 0u;
+
12717 
+
12718  this->agents.clear();
+
12719  this->n_agents = 0u;
+
12720  this->agents_location.clear();
12721 
-
12722  for (size_t i = 0u; i < location.size(); ++i)
-
12723  {
-
12724 
-
12725  if (location[i] != other.location[i])
-
12726  return false;
-
12727 
-
12728  }
+
12722  return;
+
12723 
+
12724 }
+
12725 
+
12726 template<typename TSeq>
+
12727 inline bool Entity<TSeq>::operator==(const Entity<TSeq> & other) const
+
12728 {
12729 
-
12730  if (state_init != other.state_init)
+
12730  if (id != other.id)
12731  return false;
12732 
-
12733  if (state_post != other.state_post)
+
12733  if (n_agents != other.n_agents)
12734  return false;
12735 
-
12736  if (queue_init != other.queue_init)
-
12737  return false;
-
12738 
-
12739  if (queue_post != other.queue_post)
-
12740  return false;
+
12736  for (size_t i = 0u; i < n_agents; ++i)
+
12737  {
+
12738  if (agents[i] != other.agents[i])
+
12739  return false;
+
12740  }
12741 
-
12742  return true;
-
12743 
-
12744 }
+
12742 
+
12743  if (max_capacity != other.max_capacity)
+
12744  return false;
12745 
-
12746 template<typename TSeq>
-
12747 inline void Entity<TSeq>::distribute(Model<TSeq> * model)
-
12748 {
-
12749 
-
12750  if (dist_fun)
-
12751  {
-
12752 
-
12753  dist_fun(*this, model);
+
12746  if (entity_name != other.entity_name)
+
12747  return false;
+
12748 
+
12749  if (location.size() != other.location.size())
+
12750  return false;
+
12751 
+
12752  for (size_t i = 0u; i < location.size(); ++i)
+
12753  {
12754 
-
12755  }
-
12756 
-
12757 }
-
12758 
-
12759 template<typename TSeq>
-
12760 inline std::vector< size_t > & Entity<TSeq>::get_agents()
-
12761 {
-
12762  return agents;
-
12763 }
-
12764 
-
12765 template<typename TSeq>
-
12766 inline void Entity<TSeq>::print() const
-
12767 {
+
12755  if (location[i] != other.location[i])
+
12756  return false;
+
12757 
+
12758  }
+
12759 
+
12760  if (state_init != other.state_init)
+
12761  return false;
+
12762 
+
12763  if (state_post != other.state_post)
+
12764  return false;
+
12765 
+
12766  if (queue_init != other.queue_init)
+
12767  return false;
12768 
-
12769  printf_epiworld(
-
12770  "Entity '%s' (id %i) with %i agents.\n",
-
12771  this->entity_name.c_str(),
-
12772  static_cast<int>(id),
-
12773  static_cast<int>(n_agents)
-
12774  );
-
12775 }
-
12776 
-
12777 template<typename TSeq>
-
12778 inline void Entity<TSeq>::set_distribution(EntityToAgentFun<TSeq> fun)
-
12779 {
-
12780  dist_fun = fun;
-
12781 }
+
12769  if (queue_post != other.queue_post)
+
12770  return false;
+
12771 
+
12772  return true;
+
12773 
+
12774 }
+
12775 
+
12776 template<typename TSeq>
+
12777 inline void Entity<TSeq>::distribute(Model<TSeq> * model)
+
12778 {
+
12779 
+
12780  if (dist_fun)
+
12781  {
12782 
-
12783 #endif
-
12784 /*//////////////////////////////////////////////////////////////////////////////
+
12783  dist_fun(*this, model);
+
12784 
+
12785  }
12786 
-
12787  End of -include/epiworld/entity-meat.hpp-
+
12787 }
12788 
-
12791 
-
12792 
-
12793 
-
12794 /*//////////////////////////////////////////////////////////////////////////////
-
12796 
-
12797  Start of -include/epiworld/entities-bones.hpp-
+
12789 template<typename TSeq>
+
12790 inline std::vector< size_t > & Entity<TSeq>::get_agents()
+
12791 {
+
12792  return agents;
+
12793 }
+
12794 
+
12795 template<typename TSeq>
+
12796 inline void Entity<TSeq>::print() const
+
12797 {
12798 
-
12801 
-
12802 
-
12803 #ifndef EPIWORLD_ENTITIES_BONES_HPP
-
12804 #define EPIWORLD_ENTITIES_BONES_HPP
-
12805 
-
12806 template<typename TSeq>
-
12807 class Virus;
-
12808 
-
12809 template<typename TSeq>
-
12810 class Agent;
-
12811 
+
12799  printf_epiworld(
+
12800  "Entity '%s' (id %i) with %i agents.\n",
+
12801  this->entity_name.c_str(),
+
12802  static_cast<int>(id),
+
12803  static_cast<int>(n_agents)
+
12804  );
+
12805 }
+
12806 
+
12807 template<typename TSeq>
+
12808 inline void Entity<TSeq>::set_distribution(EntityToAgentFun<TSeq> fun)
+
12809 {
+
12810  dist_fun = fun;
+
12811 }
12812 
-
12818 template<typename TSeq>
-
12819 class Entities {
-
12820  friend class Entity<TSeq>;
-
12821  friend class Agent<TSeq>;
-
12822 private:
-
12823  std::vector< Entity<TSeq> * > dat;
-
12824  const size_t n_entities;
-
12825 
-
12826 public:
-
12827 
-
12828  Entities() = delete;
-
12829  Entities(Agent<TSeq> & p);
-
12830 
-
12831  typename std::vector< Entity<TSeq> * >::iterator begin();
-
12832  typename std::vector< Entity<TSeq> * >::iterator end();
-
12833 
-
12834  Entity<TSeq> & operator()(size_t i);
-
12835  Entity<TSeq> & operator[](size_t i);
-
12836 
-
12837  size_t size() const noexcept;
+
12813 #endif
+
12814 /*//////////////////////////////////////////////////////////////////////////////
+
12816 
+
12817  End of -include/epiworld/entity-meat.hpp-
+
12818 
+
12821 
+
12822 
+
12823 
+
12824 /*//////////////////////////////////////////////////////////////////////////////
+
12826 
+
12827  Start of -include/epiworld/entities-bones.hpp-
+
12828 
+
12831 
+
12832 
+
12833 #ifndef EPIWORLD_ENTITIES_BONES_HPP
+
12834 #define EPIWORLD_ENTITIES_BONES_HPP
+
12835 
+
12836 template<typename TSeq>
+
12837 class Virus;
12838 
-
12839  bool operator==(const Entities<TSeq> & other) const;
-
12840 
-
12841 };
+
12839 template<typename TSeq>
+
12840 class Agent;
+
12841 
12842 
-
12843 template<typename TSeq>
-
12844 inline Entities<TSeq>::Entities(Agent<TSeq> & p) :
-
12845  n_entities(p.get_n_entities())
-
12846 {
-
12847 
-
12848  dat.reserve(n_entities);
-
12849  for (size_t i = 0u; i < n_entities; ++i)
-
12850  dat.push_back(&p.get_entity(i));
-
12851 
-
12852 }
-
12853 
-
12854 template<typename TSeq>
-
12855 inline typename std::vector< Entity<TSeq>* >::iterator Entities<TSeq>::begin()
-
12856 {
+
12848 template<typename TSeq>
+
12849 class Entities {
+
12850  friend class Entity<TSeq>;
+
12851  friend class Agent<TSeq>;
+
12852 private:
+
12853  std::vector< Entity<TSeq> * > dat;
+
12854  const size_t n_entities;
+
12855 
+
12856 public:
12857 
-
12858  if (n_entities == 0u)
-
12859  return dat.end();
-
12860 
-
12861  return dat.begin();
-
12862 }
+
12858  Entities() = delete;
+
12859  Entities(Agent<TSeq> & p);
+
12860 
+
12861  typename std::vector< Entity<TSeq> * >::iterator begin();
+
12862  typename std::vector< Entity<TSeq> * >::iterator end();
12863 
-
12864 template<typename TSeq>
-
12865 inline typename std::vector< Entity<TSeq>* >::iterator Entities<TSeq>::end()
-
12866 {
-
12867 
-
12868  return begin() + n_entities;
-
12869 }
+
12864  Entity<TSeq> & operator()(size_t i);
+
12865  Entity<TSeq> & operator[](size_t i);
+
12866 
+
12867  size_t size() const noexcept;
+
12868 
+
12869  bool operator==(const Entities<TSeq> & other) const;
12870 
-
12871 template<typename TSeq>
-
12872 inline Entity<TSeq> & Entities<TSeq>::operator()(size_t i)
-
12873 {
-
12874 
-
12875  if (i >= n_entities)
-
12876  throw std::range_error("Entity index out of range.");
+
12871 };
+
12872 
+
12873 template<typename TSeq>
+
12874 inline Entities<TSeq>::Entities(Agent<TSeq> & p) :
+
12875  n_entities(p.get_n_entities())
+
12876 {
12877 
-
12878  return *dat[i];
-
12879 
-
12880 }
+
12878  dat.reserve(n_entities);
+
12879  for (size_t i = 0u; i < n_entities; ++i)
+
12880  dat.push_back(&p.get_entity(i));
12881 
-
12882 template<typename TSeq>
-
12883 inline Entity<TSeq> & Entities<TSeq>::operator[](size_t i)
-
12884 {
-
12885 
-
12886  return *dat[i];
+
12882 }
+
12883 
+
12884 template<typename TSeq>
+
12885 inline typename std::vector< Entity<TSeq>* >::iterator Entities<TSeq>::begin()
+
12886 {
12887 
-
12888 }
-
12889 
-
12890 template<typename TSeq>
-
12891 inline size_t Entities<TSeq>::size() const noexcept
-
12892 {
-
12893  return n_entities;
-
12894 }
-
12895 
-
12896 template<typename TSeq>
-
12897 inline bool Entities<TSeq>::operator==(const Entities<TSeq> & other) const
-
12898 {
-
12899 
-
12900  if (n_entities != other.n_entities)
-
12901  return false;
-
12902 
-
12903  for (size_t i = 0u; i < dat.size(); ++i)
-
12904  {
-
12905  if (dat[i] != other.dat[i])
-
12906  return false;
-
12907  }
-
12908 
-
12909  return true;
+
12888  if (n_entities == 0u)
+
12889  return dat.end();
+
12890 
+
12891  return dat.begin();
+
12892 }
+
12893 
+
12894 template<typename TSeq>
+
12895 inline typename std::vector< Entity<TSeq>* >::iterator Entities<TSeq>::end()
+
12896 {
+
12897 
+
12898  return begin() + n_entities;
+
12899 }
+
12900 
+
12901 template<typename TSeq>
+
12902 inline Entity<TSeq> & Entities<TSeq>::operator()(size_t i)
+
12903 {
+
12904 
+
12905  if (i >= n_entities)
+
12906  throw std::range_error("Entity index out of range.");
+
12907 
+
12908  return *dat[i];
+
12909 
12910 }
12911 
-
12917 template<typename TSeq>
-
12918 class Entities_const {
-
12919  friend class Virus<TSeq>;
-
12920  friend class Agent<TSeq>;
-
12921 private:
-
12922  const std::vector< Entity<TSeq>* > dat;
-
12923  const size_t n_entities;
-
12924 
-
12925 public:
-
12926 
-
12927  Entities_const() = delete;
-
12928  Entities_const(const Agent<TSeq> & p);
+
12912 template<typename TSeq>
+
12913 inline Entity<TSeq> & Entities<TSeq>::operator[](size_t i)
+
12914 {
+
12915 
+
12916  return *dat[i];
+
12917 
+
12918 }
+
12919 
+
12920 template<typename TSeq>
+
12921 inline size_t Entities<TSeq>::size() const noexcept
+
12922 {
+
12923  return n_entities;
+
12924 }
+
12925 
+
12926 template<typename TSeq>
+
12927 inline bool Entities<TSeq>::operator==(const Entities<TSeq> & other) const
+
12928 {
12929 
-
12930  typename std::vector< Entity<TSeq>* >::const_iterator begin();
-
12931  typename std::vector< Entity<TSeq>* >::const_iterator end();
+
12930  if (n_entities != other.n_entities)
+
12931  return false;
12932 
-
12933  const Entity<TSeq> & operator()(size_t i);
-
12934  const Entity<TSeq> & operator[](size_t i);
-
12935 
-
12936  size_t size() const noexcept;
-
12937 
-
12938  bool operator==(const Entities_const<TSeq> & other) const;
-
12939 
-
12940 };
+
12933  for (size_t i = 0u; i < dat.size(); ++i)
+
12934  {
+
12935  if (dat[i] != other.dat[i])
+
12936  return false;
+
12937  }
+
12938 
+
12939  return true;
+
12940 }
12941 
-
12942 template<typename TSeq>
-
12943 inline Entities_const<TSeq>::Entities_const(const Agent<TSeq> & p) :
-
12944  n_entities(p.get_n_entities())
-
12945 {
-
12946 
-
12947  dat.reserve(n_entities);
-
12948  for (size_t i = 0u; i < n_entities; ++i)
-
12949  dat.push_back(&p.get_entity(i));
-
12950 
-
12951 }
-
12952 
-
12953 template<typename TSeq>
-
12954 inline typename std::vector< Entity<TSeq>* >::const_iterator Entities_const<TSeq>::begin() {
-
12955 
-
12956  if (n_entities == 0u)
-
12957  return dat.end();
-
12958 
-
12959  return dat.begin();
-
12960 }
-
12961 
-
12962 template<typename TSeq>
-
12963 inline typename std::vector< Entity<TSeq>* >::const_iterator Entities_const<TSeq>::end() {
-
12964 
-
12965  return begin() + n_entities;
-
12966 }
+
12947 template<typename TSeq>
+
12948 class Entities_const {
+
12949  friend class Virus<TSeq>;
+
12950  friend class Agent<TSeq>;
+
12951 private:
+
12952  const std::vector< Entity<TSeq>* > dat;
+
12953  const size_t n_entities;
+
12954 
+
12955 public:
+
12956 
+
12957  Entities_const() = delete;
+
12958  Entities_const(const Agent<TSeq> & p);
+
12959 
+
12960  typename std::vector< Entity<TSeq>* >::const_iterator begin();
+
12961  typename std::vector< Entity<TSeq>* >::const_iterator end();
+
12962 
+
12963  const Entity<TSeq> & operator()(size_t i);
+
12964  const Entity<TSeq> & operator[](size_t i);
+
12965 
+
12966  size_t size() const noexcept;
12967 
-
12968 template<typename TSeq>
-
12969 inline const Entity<TSeq> & Entities_const<TSeq>::operator()(size_t i)
-
12970 {
+
12968  bool operator==(const Entities_const<TSeq> & other) const;
+
12969 
+
12970 };
12971 
-
12972  if (i >= n_entities)
-
12973  throw std::range_error("Entity index out of range.");
-
12974 
-
12975  return *dat[i];
+
12972 template<typename TSeq>
+
12973 inline Entities_const<TSeq>::Entities_const(const Agent<TSeq> & p) :
+
12974  n_entities(p.get_n_entities())
+
12975 {
12976 
-
12977 }
-
12978 
-
12979 template<typename TSeq>
-
12980 inline const Entity<TSeq> & Entities_const<TSeq>::operator[](size_t i)
-
12981 {
+
12977  dat.reserve(n_entities);
+
12978  for (size_t i = 0u; i < n_entities; ++i)
+
12979  dat.push_back(&p.get_entity(i));
+
12980 
+
12981 }
12982 
-
12983  return *dat[i];
-
12984 
-
12985 }
-
12986 
-
12987 template<typename TSeq>
-
12988 inline size_t Entities_const<TSeq>::size() const noexcept
-
12989 {
-
12990  return n_entities;
-
12991 }
-
12992 
-
12993 template<typename TSeq>
-
12994 inline bool Entities_const<TSeq>::operator==(const Entities_const<TSeq> & other) const
-
12995 {
-
12996 
-
12997  if (n_entities != other.n_entities)
-
12998  return false;
-
12999 
-
13000  for (size_t i = 0u; i < dat.size(); ++i)
-
13001  {
-
13002  if (dat[i] != other.dat[i])
-
13003  return false;
-
13004  }
-
13005 
-
13006  return true;
+
12983 template<typename TSeq>
+
12984 inline typename std::vector< Entity<TSeq>* >::const_iterator Entities_const<TSeq>::begin() {
+
12985 
+
12986  if (n_entities == 0u)
+
12987  return dat.end();
+
12988 
+
12989  return dat.begin();
+
12990 }
+
12991 
+
12992 template<typename TSeq>
+
12993 inline typename std::vector< Entity<TSeq>* >::const_iterator Entities_const<TSeq>::end() {
+
12994 
+
12995  return begin() + n_entities;
+
12996 }
+
12997 
+
12998 template<typename TSeq>
+
12999 inline const Entity<TSeq> & Entities_const<TSeq>::operator()(size_t i)
+
13000 {
+
13001 
+
13002  if (i >= n_entities)
+
13003  throw std::range_error("Entity index out of range.");
+
13004 
+
13005  return *dat[i];
+
13006 
13007 }
13008 
-
13009 
-
13010 #endif
-
13011 /*//////////////////////////////////////////////////////////////////////////////
-
13013 
-
13014  End of -include/epiworld/entities-bones.hpp-
-
13015 
-
13018 
-
13019 
-
13020 
-
13021 /*//////////////////////////////////////////////////////////////////////////////
-
13023 
-
13024  Start of -include/epiworld/agent-meat-state.hpp-
-
13025 
-
13028 
+
13009 template<typename TSeq>
+
13010 inline const Entity<TSeq> & Entities_const<TSeq>::operator[](size_t i)
+
13011 {
+
13012 
+
13013  return *dat[i];
+
13014 
+
13015 }
+
13016 
+
13017 template<typename TSeq>
+
13018 inline size_t Entities_const<TSeq>::size() const noexcept
+
13019 {
+
13020  return n_entities;
+
13021 }
+
13022 
+
13023 template<typename TSeq>
+
13024 inline bool Entities_const<TSeq>::operator==(const Entities_const<TSeq> & other) const
+
13025 {
+
13026 
+
13027  if (n_entities != other.n_entities)
+
13028  return false;
13029 
-
13030 #ifndef EPIWORLD_PERSON_MEAT_STATE_HPP
-
13031 #define EPIWORLD_PERSON_MEAT_STATE_HPP
-
13032 
-
13033 // template<typename TSeq>
-
13034 // class Model;
+
13030  for (size_t i = 0u; i < dat.size(); ++i)
+
13031  {
+
13032  if (dat[i] != other.dat[i])
+
13033  return false;
+
13034  }
13035 
-
13036 // template<typename TSeq>
-
13037 // class Agent;
+
13036  return true;
+
13037 }
13038 
13039 
-
13050 /*//////////////////////////////////////////////////////////////////////////////
-
13052 
-
13053  Start of -include/epiworld//agent-meat-virus-sampling.hpp-
-
13054 
-
13057 
+
13040 #endif
+
13041 /*//////////////////////////////////////////////////////////////////////////////
+
13043 
+
13044  End of -include/epiworld/entities-bones.hpp-
+
13045 
+
13048 
+
13049 
+
13050 
+
13051 /*//////////////////////////////////////////////////////////////////////////////
+
13053 
+
13054  Start of -include/epiworld/agent-meat-state.hpp-
+
13055 
13058 
-
13059 #ifndef EPIWORLD_AGENT_MEAT_VIRUS_SAMPLING
-
13060 #define EPIWORLD_AGENT_MEAT_VIRUS_SAMPLING
-
13061 
-
13066 namespace sampler {
-
13067 
-
13081 template<typename TSeq>
-
13082 inline std::function<void(Agent<TSeq>*,Model<TSeq>*)> make_update_susceptible(
-
13083  std::vector< epiworld_fast_uint > exclude = {}
-
13084  )
-
13085 {
-
13086 
+
13059 
+
13060 #ifndef EPIWORLD_PERSON_MEAT_STATE_HPP
+
13061 #define EPIWORLD_PERSON_MEAT_STATE_HPP
+
13062 
+
13063 // template<typename TSeq>
+
13064 // class Model;
+
13065 
+
13066 // template<typename TSeq>
+
13067 // class Agent;
+
13068 
+
13069 
+
13080 /*//////////////////////////////////////////////////////////////////////////////
+
13082 
+
13083  Start of -include/epiworld//agent-meat-virus-sampling.hpp-
+
13084 
13087 
-
13088  if (exclude.size() == 0u)
-
13089  {
-
13090 
-
13091  std::function<void(Agent<TSeq>*,Model<TSeq>*)> sampler =
-
13092  [](Agent<TSeq> * p, Model<TSeq> * m) -> void
-
13093  {
-
13094 
-
13095  if (p->get_virus() != nullptr)
-
13096  throw std::logic_error(
-
13097  std::string("Using the -default_update_susceptible- on agents WITH viruses makes no sense! ") +
-
13098  std::string("Agent id ") + std::to_string(p->get_id()) +
-
13099  std::string(" has a virus.")
-
13100  );
-
13101 
-
13102  // This computes the prob of getting any neighbor variant
-
13103  size_t nviruses_tmp = 0u;
-
13104  for (auto & neighbor: p->get_neighbors())
-
13105  {
-
13106 
-
13107  auto & v = neighbor->get_virus();
-
13108  if (v == nullptr)
-
13109  continue;
-
13110 
-
13111  /* And it is a function of susceptibility_reduction as well */
-
13112  m->array_double_tmp[nviruses_tmp] =
-
13113  (1.0 - p->get_susceptibility_reduction(v, m)) *
-
13114  v->get_prob_infecting(m) *
-
13115  (1.0 - neighbor->get_transmission_reduction(v, m))
-
13116  ;
-
13117 
-
13118  m->array_virus_tmp[nviruses_tmp++] = &(*v);
-
13119 
-
13120  }
-
13121 
-
13122  // No virus to compute
-
13123  if (nviruses_tmp == 0u)
-
13124  return;
-
13125 
-
13126  // Running the roulette
-
13127  int which = roulette(nviruses_tmp, m);
-
13128 
-
13129  if (which < 0)
-
13130  return;
-
13131 
-
13132  p->set_virus(*m->array_virus_tmp[which], m);
-
13133 
-
13134  return;
-
13135  };
-
13136 
-
13137  return sampler;
-
13138 
-
13139  } else {
-
13140 
-
13141  // Making room for the query
-
13142  std::shared_ptr<std::vector<bool>> exclude_agent_bool =
-
13143  std::make_shared<std::vector<bool>>(0);
-
13144 
-
13145  std::shared_ptr<std::vector<epiworld_fast_uint>> exclude_agent_bool_idx =
-
13146  std::make_shared<std::vector<epiworld_fast_uint>>(exclude);
-
13147 
-
13148  std::function<void(Agent<TSeq>*,Model<TSeq>*)> sampler =
-
13149  [exclude_agent_bool,exclude_agent_bool_idx](Agent<TSeq> * p, Model<TSeq> * m) -> void
-
13150  {
+
13088 
+
13089 #ifndef EPIWORLD_AGENT_MEAT_VIRUS_SAMPLING
+
13090 #define EPIWORLD_AGENT_MEAT_VIRUS_SAMPLING
+
13091 
+
13096 namespace sampler {
+
13097 
+
13111 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
13112 inline std::function<void(Agent<TSeq>*,Model<TSeq>*)> make_update_susceptible(
+
13113  std::vector< epiworld_fast_uint > exclude = {}
+
13114  )
+
13115 {
+
13116 
+
13117 
+
13118  if (exclude.size() == 0u)
+
13119  {
+
13120 
+
13121  std::function<void(Agent<TSeq>*,Model<TSeq>*)> sampler =
+
13122  [](Agent<TSeq> * p, Model<TSeq> * m) -> void
+
13123  {
+
13124 
+
13125  if (p->get_virus() != nullptr)
+
13126  throw std::logic_error(
+
13127  std::string("Using the -default_update_susceptible- on agents WITH viruses makes no sense! ") +
+
13128  std::string("Agent id ") + std::to_string(p->get_id()) +
+
13129  std::string(" has a virus.")
+
13130  );
+
13131 
+
13132  // This computes the prob of getting any neighbor variant
+
13133  size_t nviruses_tmp = 0u;
+
13134  for (auto & neighbor: p->get_neighbors())
+
13135  {
+
13136 
+
13137  auto & v = neighbor->get_virus();
+
13138  if (v == nullptr)
+
13139  continue;
+
13140 
+
13141  /* And it is a function of susceptibility_reduction as well */
+
13142  m->array_double_tmp[nviruses_tmp] =
+
13143  (1.0 - p->get_susceptibility_reduction(v, m)) *
+
13144  v->get_prob_infecting(m) *
+
13145  (1.0 - neighbor->get_transmission_reduction(v, m))
+
13146  ;
+
13147 
+
13148  m->array_virus_tmp[nviruses_tmp++] = &(*v);
+
13149 
+
13150  }
13151 
-
13152  // The first time we call it, we need to initialize the vector
-
13153  if (exclude_agent_bool->size() == 0u)
-
13154  {
+
13152  // No virus to compute
+
13153  if (nviruses_tmp == 0u)
+
13154  return;
13155 
-
13156  exclude_agent_bool->resize(m->get_states().size(), false);
-
13157  for (auto s : *exclude_agent_bool_idx)
-
13158  {
-
13159  if (s >= exclude_agent_bool->size())
-
13160  throw std::logic_error(
-
13161  std::string("You are trying to exclude a state that is out of range: ") +
-
13162  std::to_string(s) + std::string(". There are only ") +
-
13163  std::to_string(exclude_agent_bool->size()) +
-
13164  std::string(" states in the model.")
-
13165  );
+
13156  // Running the roulette
+
13157  int which = roulette(nviruses_tmp, m);
+
13158 
+
13159  if (which < 0)
+
13160  return;
+
13161 
+
13162  p->set_virus(*m->array_virus_tmp[which], m);
+
13163 
+
13164  return;
+
13165  };
13166 
-
13167  exclude_agent_bool->operator[](s) = true;
+
13167  return sampler;
13168 
-
13169  }
+
13169  } else {
13170 
-
13171  }
-
13172 
-
13173  if (p->get_virus() != nullptr)
-
13174  throw std::logic_error(
-
13175  std::string("Using the -default_update_susceptible- on agents WITH viruses makes no sense! ") +
-
13176  std::string("Agent id ") + std::to_string(p->get_id()) +
-
13177  std::string(" has a virus.")
-
13178  );
-
13179 
-
13180  // This computes the prob of getting any neighbor variant
-
13181  size_t nviruses_tmp = 0u;
-
13182  for (auto & neighbor: p->get_neighbors())
-
13183  {
-
13184 
-
13185  // If the state is in the list, exclude it
-
13186  if (exclude_agent_bool->operator[](neighbor->get_state()))
-
13187  continue;
-
13188 
-
13189  auto & v = neighbor->get_virus();
-
13190  if (v == nullptr)
-
13191  continue;
-
13192 
-
13193 
-
13194  /* And it is a function of susceptibility_reduction as well */
-
13195  m->array_double_tmp[nviruses_tmp] =
-
13196  (1.0 - p->get_susceptibility_reduction(v, m)) *
-
13197  v->get_prob_infecting(m) *
-
13198  (1.0 - neighbor->get_transmission_reduction(v, m))
-
13199  ;
-
13200 
-
13201  m->array_virus_tmp[nviruses_tmp++] = &(*v);
-
13202 
-
13203  }
-
13204 
-
13205  // No virus to compute
-
13206  if (nviruses_tmp == 0u)
-
13207  return;
-
13208 
-
13209  // Running the roulette
-
13210  int which = roulette(nviruses_tmp, m);
-
13211 
-
13212  if (which < 0)
-
13213  return;
+
13171  // Making room for the query
+
13172  std::shared_ptr<std::vector<bool>> exclude_agent_bool =
+
13173  std::make_shared<std::vector<bool>>(0);
+
13174 
+
13175  std::shared_ptr<std::vector<epiworld_fast_uint>> exclude_agent_bool_idx =
+
13176  std::make_shared<std::vector<epiworld_fast_uint>>(exclude);
+
13177 
+
13178  std::function<void(Agent<TSeq>*,Model<TSeq>*)> sampler =
+
13179  [exclude_agent_bool,exclude_agent_bool_idx](Agent<TSeq> * p, Model<TSeq> * m) -> void
+
13180  {
+
13181 
+
13182  // The first time we call it, we need to initialize the vector
+
13183  if (exclude_agent_bool->size() == 0u)
+
13184  {
+
13185 
+
13186  exclude_agent_bool->resize(m->get_states().size(), false);
+
13187  for (auto s : *exclude_agent_bool_idx)
+
13188  {
+
13189  if (s >= exclude_agent_bool->size())
+
13190  throw std::logic_error(
+
13191  std::string("You are trying to exclude a state that is out of range: ") +
+
13192  std::to_string(s) + std::string(". There are only ") +
+
13193  std::to_string(exclude_agent_bool->size()) +
+
13194  std::string(" states in the model.")
+
13195  );
+
13196 
+
13197  exclude_agent_bool->operator[](s) = true;
+
13198 
+
13199  }
+
13200 
+
13201  }
+
13202 
+
13203  if (p->get_virus() != nullptr)
+
13204  throw std::logic_error(
+
13205  std::string("Using the -default_update_susceptible- on agents WITH viruses makes no sense! ") +
+
13206  std::string("Agent id ") + std::to_string(p->get_id()) +
+
13207  std::string(" has a virus.")
+
13208  );
+
13209 
+
13210  // This computes the prob of getting any neighbor variant
+
13211  size_t nviruses_tmp = 0u;
+
13212  for (auto & neighbor: p->get_neighbors())
+
13213  {
13214 
-
13215  p->set_virus(*m->array_virus_tmp[which], m);
-
13216 
-
13217  return;
+
13215  // If the state is in the list, exclude it
+
13216  if (exclude_agent_bool->operator[](neighbor->get_state()))
+
13217  continue;
13218 
-
13219  };
-
13220 
-
13221  return sampler;
-
13222 
-
13223  }
-
13224 
-
13225 }
-
13226 
-
13240 template<typename TSeq = int>
-
13241 inline std::function<Virus<TSeq>*(Agent<TSeq>*,Model<TSeq>*)> make_sample_virus_neighbors(
-
13242  std::vector< epiworld_fast_uint > exclude = {}
-
13243 )
-
13244 {
-
13245  if (exclude.size() == 0u)
-
13246  {
-
13247 
-
13248  std::function<Virus<TSeq>*(Agent<TSeq>*,Model<TSeq>*)> res =
-
13249  [](Agent<TSeq> * p, Model<TSeq> * m) -> Virus<TSeq>* {
+
13219  auto & v = neighbor->get_virus();
+
13220  if (v == nullptr)
+
13221  continue;
+
13222 
+
13223 
+
13224  /* And it is a function of susceptibility_reduction as well */
+
13225  m->array_double_tmp[nviruses_tmp] =
+
13226  (1.0 - p->get_susceptibility_reduction(v, m)) *
+
13227  v->get_prob_infecting(m) *
+
13228  (1.0 - neighbor->get_transmission_reduction(v, m))
+
13229  ;
+
13230 
+
13231  m->array_virus_tmp[nviruses_tmp++] = &(*v);
+
13232 
+
13233  }
+
13234 
+
13235  // No virus to compute
+
13236  if (nviruses_tmp == 0u)
+
13237  return;
+
13238 
+
13239  // Running the roulette
+
13240  int which = roulette(nviruses_tmp, m);
+
13241 
+
13242  if (which < 0)
+
13243  return;
+
13244 
+
13245  p->set_virus(*m->array_virus_tmp[which], m);
+
13246 
+
13247  return;
+
13248 
+
13249  };
13250 
-
13251  if (p->get_virus() != nullptr)
-
13252  throw std::logic_error(
-
13253  std::string("Using the -default_update_susceptible- on agents WITH viruses makes no sense! ") +
-
13254  std::string("Agent id ") + std::to_string(p->get_id()) +
-
13255  std::string(" has a virus.")
-
13256  );
-
13257 
-
13258  // This computes the prob of getting any neighbor variant
-
13259  size_t nviruses_tmp = 0u;
-
13260  for (auto & neighbor: p->get_neighbors())
-
13261  {
-
13262 
-
13263  if (neighbor->get_virus() == nullptr)
-
13264  continue;
-
13265 
-
13266  auto & v = neighbor->get_virus();
-
13267 
-
13268  #ifdef EPI_DEBUG
-
13269  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
-
13270  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
-
13271  #endif
-
13272 
-
13273  /* And it is a function of susceptibility_reduction as well */
-
13274  m->array_double_tmp[nviruses_tmp] =
-
13275  (1.0 - p->get_susceptibility_reduction(v, m)) *
-
13276  v->get_prob_infecting(m) *
-
13277  (1.0 - neighbor->get_transmission_reduction(v, m))
-
13278  ;
-
13279 
-
13280  m->array_virus_tmp[nviruses_tmp++] = &(*v);
-
13281 
-
13282  }
-
13283 
-
13284  // No virus to compute
-
13285  if (nviruses_tmp == 0u)
-
13286  return nullptr;
+
13251  return sampler;
+
13252 
+
13253  }
+
13254 
+
13255 }
+
13256 
+
13270 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
13271 inline std::function<Virus<TSeq>*(Agent<TSeq>*,Model<TSeq>*)> make_sample_virus_neighbors(
+
13272  std::vector< epiworld_fast_uint > exclude = {}
+
13273 )
+
13274 {
+
13275  if (exclude.size() == 0u)
+
13276  {
+
13277 
+
13278  std::function<Virus<TSeq>*(Agent<TSeq>*,Model<TSeq>*)> res =
+
13279  [](Agent<TSeq> * p, Model<TSeq> * m) -> Virus<TSeq>* {
+
13280 
+
13281  if (p->get_virus() != nullptr)
+
13282  throw std::logic_error(
+
13283  std::string("Using the -default_update_susceptible- on agents WITH viruses makes no sense! ") +
+
13284  std::string("Agent id ") + std::to_string(p->get_id()) +
+
13285  std::string(" has a virus.")
+
13286  );
13287 
-
13288  // Running the roulette
-
13289  int which = roulette(nviruses_tmp, m);
-
13290 
-
13291  if (which < 0)
-
13292  return nullptr;
-
13293 
-
13294  return m->array_virus_tmp[which];
+
13288  // This computes the prob of getting any neighbor variant
+
13289  size_t nviruses_tmp = 0u;
+
13290  for (auto & neighbor: p->get_neighbors())
+
13291  {
+
13292 
+
13293  if (neighbor->get_virus() == nullptr)
+
13294  continue;
13295 
-
13296  };
+
13296  auto & v = neighbor->get_virus();
13297 
-
13298  return res;
-
13299 
-
13300 
-
13301  } else {
-
13302 
-
13303  // Making room for the query
-
13304  std::shared_ptr<std::vector<bool>> exclude_agent_bool =
-
13305  std::make_shared<std::vector<bool>>(0);
-
13306 
-
13307  std::shared_ptr<std::vector<epiworld_fast_uint>> exclude_agent_bool_idx =
-
13308  std::make_shared<std::vector<epiworld_fast_uint>>(exclude);
-
13309 
-
13310 
-
13311  std::function<Virus<TSeq>*(Agent<TSeq>*,Model<TSeq>*)> res =
-
13312  [exclude_agent_bool,exclude_agent_bool_idx](Agent<TSeq> * p, Model<TSeq> * m) -> Virus<TSeq>* {
+
13298  #ifdef EPI_DEBUG
+
13299  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
+
13300  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
+
13301  #endif
+
13302 
+
13303  /* And it is a function of susceptibility_reduction as well */
+
13304  m->array_double_tmp[nviruses_tmp] =
+
13305  (1.0 - p->get_susceptibility_reduction(v, m)) *
+
13306  v->get_prob_infecting(m) *
+
13307  (1.0 - neighbor->get_transmission_reduction(v, m))
+
13308  ;
+
13309 
+
13310  m->array_virus_tmp[nviruses_tmp++] = &(*v);
+
13311 
+
13312  }
13313 
-
13314  // The first time we call it, we need to initialize the vector
-
13315  if (exclude_agent_bool->size() == 0u)
-
13316  {
+
13314  // No virus to compute
+
13315  if (nviruses_tmp == 0u)
+
13316  return nullptr;
13317 
-
13318  exclude_agent_bool->resize(m->get_states().size(), false);
-
13319  for (auto s : *exclude_agent_bool_idx)
-
13320  {
-
13321  if (s >= exclude_agent_bool->size())
-
13322  throw std::logic_error(
-
13323  std::string("You are trying to exclude a state that is out of range: ") +
-
13324  std::to_string(s) + std::string(". There are only ") +
-
13325  std::to_string(exclude_agent_bool->size()) +
-
13326  std::string(" states in the model.")
-
13327  );
-
13328 
-
13329  exclude_agent_bool->operator[](s) = true;
+
13318  // Running the roulette
+
13319  int which = roulette(nviruses_tmp, m);
+
13320 
+
13321  if (which < 0)
+
13322  return nullptr;
+
13323 
+
13324  return m->array_virus_tmp[which];
+
13325 
+
13326  };
+
13327 
+
13328  return res;
+
13329 
13330 
-
13331  }
+
13331  } else {
13332 
-
13333  }
-
13334 
-
13335  if (p->get_virus() != nullptr)
-
13336  throw std::logic_error(
-
13337  std::string("Using the -default_update_susceptible- on agents WITH viruses makes no sense! ") +
-
13338  std::string("Agent id ") + std::to_string(p->get_id()) +
-
13339  std::string(" has a virus.")
-
13340  );
-
13341 
-
13342  // This computes the prob of getting any neighbor variant
-
13343  size_t nviruses_tmp = 0u;
-
13344  for (auto & neighbor: p->get_neighbors())
-
13345  {
-
13346 
-
13347  // If the state is in the list, exclude it
-
13348  if (exclude_agent_bool->operator[](neighbor->get_state()))
-
13349  continue;
-
13350 
-
13351  if (neighbor->get_virus() == nullptr)
-
13352  continue;
-
13353 
-
13354  auto & v = neighbor->get_virus();
-
13355 
-
13356  #ifdef EPI_DEBUG
-
13357  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
-
13358  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
-
13359  #endif
-
13360 
-
13361  /* And it is a function of susceptibility_reduction as well */
-
13362  m->array_double_tmp[nviruses_tmp] =
-
13363  (1.0 - p->get_susceptibility_reduction(v, m)) *
-
13364  v->get_prob_infecting(m) *
-
13365  (1.0 - neighbor->get_transmission_reduction(v, m))
-
13366  ;
-
13367 
-
13368  m->array_virus_tmp[nviruses_tmp++] = &(*v);
-
13369 
-
13370  }
+
13333  // Making room for the query
+
13334  std::shared_ptr<std::vector<bool>> exclude_agent_bool =
+
13335  std::make_shared<std::vector<bool>>(0);
+
13336 
+
13337  std::shared_ptr<std::vector<epiworld_fast_uint>> exclude_agent_bool_idx =
+
13338  std::make_shared<std::vector<epiworld_fast_uint>>(exclude);
+
13339 
+
13340 
+
13341  std::function<Virus<TSeq>*(Agent<TSeq>*,Model<TSeq>*)> res =
+
13342  [exclude_agent_bool,exclude_agent_bool_idx](Agent<TSeq> * p, Model<TSeq> * m) -> Virus<TSeq>* {
+
13343 
+
13344  // The first time we call it, we need to initialize the vector
+
13345  if (exclude_agent_bool->size() == 0u)
+
13346  {
+
13347 
+
13348  exclude_agent_bool->resize(m->get_states().size(), false);
+
13349  for (auto s : *exclude_agent_bool_idx)
+
13350  {
+
13351  if (s >= exclude_agent_bool->size())
+
13352  throw std::logic_error(
+
13353  std::string("You are trying to exclude a state that is out of range: ") +
+
13354  std::to_string(s) + std::string(". There are only ") +
+
13355  std::to_string(exclude_agent_bool->size()) +
+
13356  std::string(" states in the model.")
+
13357  );
+
13358 
+
13359  exclude_agent_bool->operator[](s) = true;
+
13360 
+
13361  }
+
13362 
+
13363  }
+
13364 
+
13365  if (p->get_virus() != nullptr)
+
13366  throw std::logic_error(
+
13367  std::string("Using the -default_update_susceptible- on agents WITH viruses makes no sense! ") +
+
13368  std::string("Agent id ") + std::to_string(p->get_id()) +
+
13369  std::string(" has a virus.")
+
13370  );
13371 
-
13372  // No virus to compute
-
13373  if (nviruses_tmp == 0u)
-
13374  return nullptr;
-
13375 
-
13376  // Running the roulette
-
13377  int which = roulette(nviruses_tmp, m);
-
13378 
-
13379  if (which < 0)
-
13380  return nullptr;
-
13381 
-
13382  return m->array_virus_tmp[which];
+
13372  // This computes the prob of getting any neighbor variant
+
13373  size_t nviruses_tmp = 0u;
+
13374  for (auto & neighbor: p->get_neighbors())
+
13375  {
+
13376 
+
13377  // If the state is in the list, exclude it
+
13378  if (exclude_agent_bool->operator[](neighbor->get_state()))
+
13379  continue;
+
13380 
+
13381  if (neighbor->get_virus() == nullptr)
+
13382  continue;
13383 
-
13384  };
-
13385 
-
13386  return res;
-
13387 
-
13388  }
-
13389 
-
13390 }
-
13391 
-
13408 template<typename TSeq = int>
-
13409 inline Virus<TSeq> * sample_virus_single(Agent<TSeq> * p, Model<TSeq> * m)
-
13410 {
+
13384  auto & v = neighbor->get_virus();
+
13385 
+
13386  #ifdef EPI_DEBUG
+
13387  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
+
13388  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
+
13389  #endif
+
13390 
+
13391  /* And it is a function of susceptibility_reduction as well */
+
13392  m->array_double_tmp[nviruses_tmp] =
+
13393  (1.0 - p->get_susceptibility_reduction(v, m)) *
+
13394  v->get_prob_infecting(m) *
+
13395  (1.0 - neighbor->get_transmission_reduction(v, m))
+
13396  ;
+
13397 
+
13398  m->array_virus_tmp[nviruses_tmp++] = &(*v);
+
13399 
+
13400  }
+
13401 
+
13402  // No virus to compute
+
13403  if (nviruses_tmp == 0u)
+
13404  return nullptr;
+
13405 
+
13406  // Running the roulette
+
13407  int which = roulette(nviruses_tmp, m);
+
13408 
+
13409  if (which < 0)
+
13410  return nullptr;
13411 
-
13412  if (p->get_virus() != nullptr)
-
13413  throw std::logic_error(
-
13414  std::string("Using the -default_update_susceptible- on agents WITH viruses makes no sense!") +
-
13415  std::string("Agent id ") + std::to_string(p->get_id()) +
-
13416  std::string(" has a virus.")
-
13417  );
-
13418 
-
13419  // This computes the prob of getting any neighbor variant
-
13420  size_t nviruses_tmp = 0u;
-
13421  for (auto & neighbor: p->get_neighbors())
-
13422  {
-
13423  #ifdef EPI_DEBUG
-
13424  int _vcount_neigh = 0;
-
13425  #endif
-
13426 
-
13427  if (neighbor->get_virus() == nullptr)
-
13428  continue;
-
13429 
-
13430  auto & v = neighbor->get_virus();
-
13431 
-
13432  #ifdef EPI_DEBUG
-
13433  if (nviruses_tmp >= m->array_virus_tmp.size())
-
13434  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
-
13435  #endif
-
13436 
-
13437  /* And it is a function of susceptibility_reduction as well */
-
13438  m->array_double_tmp[nviruses_tmp] =
-
13439  (1.0 - p->get_susceptibility_reduction(v, m)) *
-
13440  v->get_prob_infecting(m) *
-
13441  (1.0 - neighbor->get_transmission_reduction(v, m))
-
13442  ;
-
13443 
-
13444  m->array_virus_tmp[nviruses_tmp++] = &(*v);
-
13445 
-
13446  #ifdef EPI_DEBUG
-
13447  if (
-
13448  (m->array_double_tmp[nviruses_tmp - 1] < 0.0) |
-
13449  (m->array_double_tmp[nviruses_tmp - 1] > 1.0)
-
13450  )
-
13451  {
-
13452  printf_epiworld(
-
13453  "[epi-debug] Agent %i's virus %i has transmission prob outside of [0, 1]: %.4f!\n",
-
13454  static_cast<int>(neighbor->get_id()),
-
13455  static_cast<int>(_vcount_neigh++),
-
13456  m->array_double_tmp[nviruses_tmp - 1]
-
13457  );
-
13458  }
-
13459  #endif
-
13460 
-
13461  }
-
13462 
-
13463 
-
13464  // No virus to compute
-
13465  if (nviruses_tmp == 0u)
-
13466  return nullptr;
-
13467 
-
13468  #ifdef EPI_DEBUG
-
13469  m->get_db().n_transmissions_potential++;
-
13470  #endif
-
13471 
-
13472  // Running the roulette
-
13473  int which = roulette(nviruses_tmp, m);
-
13474 
-
13475  if (which < 0)
-
13476  return nullptr;
-
13477 
-
13478  #ifdef EPI_DEBUG
-
13479  m->get_db().n_transmissions_today++;
-
13480  #endif
-
13481 
-
13482  return m->array_virus_tmp[which];
-
13483 
-
13484 }
-
13485 
-
13486 }
-
13487 
-
13488 #endif
-
13489 /*//////////////////////////////////////////////////////////////////////////////
-
13491 
-
13492  End of -include/epiworld//agent-meat-virus-sampling.hpp-
-
13493 
-
13496 
-
13497 
-
13498 
-
13499 
-
13500 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
13501 inline void default_update_susceptible(
-
13502  Agent<TSeq> * p,
-
13503  Model<TSeq> * m
-
13504  )
-
13505 {
-
13506 
-
13507  Virus<TSeq> * virus = sampler::sample_virus_single<TSeq>(p, m);
-
13508 
-
13509  if (virus == nullptr)
-
13510  return;
-
13511 
-
13512  p->set_virus(*virus, m);
-
13513 
-
13514  return;
-
13515 
-
13516 }
-
13517 
-
13518 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
13519 inline void default_update_exposed(Agent<TSeq> * p, Model<TSeq> * m) {
-
13520 
-
13521  if (p->get_virus() == nullptr)
-
13522  throw std::logic_error(
-
13523  std::string("Using the -default_update_exposed- on agents WITHOUT viruses makes no sense! ") +
-
13524  std::string("Agent id ") + std::to_string(p->get_id()) + std::string(" has no virus registered.")
-
13525  );
+
13412  return m->array_virus_tmp[which];
+
13413 
+
13414  };
+
13415 
+
13416  return res;
+
13417 
+
13418  }
+
13419 
+
13420 }
+
13421 
+
13438 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
13439 inline Virus<TSeq> * sample_virus_single(Agent<TSeq> * p, Model<TSeq> * m)
+
13440 {
+
13441 
+
13442  if (p->get_virus() != nullptr)
+
13443  throw std::logic_error(
+
13444  std::string("Using the -default_update_susceptible- on agents WITH viruses makes no sense!") +
+
13445  std::string("Agent id ") + std::to_string(p->get_id()) +
+
13446  std::string(" has a virus.")
+
13447  );
+
13448 
+
13449  // This computes the prob of getting any neighbor variant
+
13450  size_t nviruses_tmp = 0u;
+
13451  for (auto & neighbor: p->get_neighbors())
+
13452  {
+
13453  #ifdef EPI_DEBUG
+
13454  int _vcount_neigh = 0;
+
13455  #endif
+
13456 
+
13457  if (neighbor->get_virus() == nullptr)
+
13458  continue;
+
13459 
+
13460  auto & v = neighbor->get_virus();
+
13461 
+
13462  #ifdef EPI_DEBUG
+
13463  if (nviruses_tmp >= m->array_virus_tmp.size())
+
13464  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
+
13465  #endif
+
13466 
+
13467  /* And it is a function of susceptibility_reduction as well */
+
13468  m->array_double_tmp[nviruses_tmp] =
+
13469  (1.0 - p->get_susceptibility_reduction(v, m)) *
+
13470  v->get_prob_infecting(m) *
+
13471  (1.0 - neighbor->get_transmission_reduction(v, m))
+
13472  ;
+
13473 
+
13474  m->array_virus_tmp[nviruses_tmp++] = &(*v);
+
13475 
+
13476  #ifdef EPI_DEBUG
+
13477  if (
+
13478  (m->array_double_tmp[nviruses_tmp - 1] < 0.0) |
+
13479  (m->array_double_tmp[nviruses_tmp - 1] > 1.0)
+
13480  )
+
13481  {
+
13482  printf_epiworld(
+
13483  "[epi-debug] Agent %i's virus %i has transmission prob outside of [0, 1]: %.4f!\n",
+
13484  static_cast<int>(neighbor->get_id()),
+
13485  static_cast<int>(_vcount_neigh++),
+
13486  m->array_double_tmp[nviruses_tmp - 1]
+
13487  );
+
13488  }
+
13489  #endif
+
13490 
+
13491  }
+
13492 
+
13493 
+
13494  // No virus to compute
+
13495  if (nviruses_tmp == 0u)
+
13496  return nullptr;
+
13497 
+
13498  #ifdef EPI_DEBUG
+
13499  m->get_db().n_transmissions_potential++;
+
13500  #endif
+
13501 
+
13502  // Running the roulette
+
13503  int which = roulette(nviruses_tmp, m);
+
13504 
+
13505  if (which < 0)
+
13506  return nullptr;
+
13507 
+
13508  #ifdef EPI_DEBUG
+
13509  m->get_db().n_transmissions_today++;
+
13510  #endif
+
13511 
+
13512  return m->array_virus_tmp[which];
+
13513 
+
13514 }
+
13515 
+
13516 }
+
13517 
+
13518 #endif
+
13519 /*//////////////////////////////////////////////////////////////////////////////
+
13521 
+
13522  End of -include/epiworld//agent-meat-virus-sampling.hpp-
+
13523 
13526 
-
13527  // Die
-
13528  auto & virus = p->get_virus();
-
13529  m->array_double_tmp[0u] =
-
13530  virus->get_prob_death(m) * (1.0 - p->get_death_reduction(virus, m));
-
13531 
-
13532  // Recover
-
13533  m->array_double_tmp[1u] =
-
13534  1.0 - (1.0 - virus->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(virus, m));
-
13535 
+
13527 
+
13528 
+
13529 
+
13530 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
13531 inline void default_update_susceptible(
+
13532  Agent<TSeq> * p,
+
13533  Model<TSeq> * m
+
13534  )
+
13535 {
13536 
-
13537  // Running the roulette
-
13538  int which = roulette(2u, m);
-
13539 
-
13540  if (which < 0)
-
13541  return;
-
13542 
-
13543  // Which roulette happen?
-
13544  if (which == 0u) // If odd
-
13545  {
-
13546 
-
13547  p->rm_agent_by_virus(m);
-
13548 
-
13549  } else {
+
13537  Virus<TSeq> * virus = sampler::sample_virus_single<TSeq>(p, m);
+
13538 
+
13539  if (virus == nullptr)
+
13540  return;
+
13541 
+
13542  p->set_virus(*virus, m);
+
13543 
+
13544  return;
+
13545 
+
13546 }
+
13547 
+
13548 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
13549 inline void default_update_exposed(Agent<TSeq> * p, Model<TSeq> * m) {
13550 
-
13551  p->rm_virus(m);
-
13552 
-
13553  }
-
13554 
-
13555  return ;
+
13551  if (p->get_virus() == nullptr)
+
13552  throw std::logic_error(
+
13553  std::string("Using the -default_update_exposed- on agents WITHOUT viruses makes no sense! ") +
+
13554  std::string("Agent id ") + std::to_string(p->get_id()) + std::string(" has no virus registered.")
+
13555  );
13556 
-
13557 }
-
13558 
-
13559 #endif
-
13560 /*//////////////////////////////////////////////////////////////////////////////
-
13562 
-
13563  End of -include/epiworld/agent-meat-state.hpp-
-
13564 
-
13567 
-
13568 
-
13569 /*//////////////////////////////////////////////////////////////////////////////
-
13571 
-
13572  Start of -include/epiworld/agent-bones.hpp-
-
13573 
+
13557  // Die
+
13558  auto & virus = p->get_virus();
+
13559  m->array_double_tmp[0u] =
+
13560  virus->get_prob_death(m) * (1.0 - p->get_death_reduction(virus, m));
+
13561 
+
13562  // Recover
+
13563  m->array_double_tmp[1u] =
+
13564  1.0 - (1.0 - virus->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(virus, m));
+
13565 
+
13566 
+
13567  // Running the roulette
+
13568  int which = roulette(2u, m);
+
13569 
+
13570  if (which < 0)
+
13571  return;
+
13572 
+
13573  // Which roulette happen?
+
13574  if (which == 0u) // If odd
+
13575  {
13576 
-
13577 
-
13578 #ifndef EPIWORLD_PERSON_BONES_HPP
-
13579 #define EPIWORLD_PERSON_BONES_HPP
+
13577  p->rm_agent_by_virus(m);
+
13578 
+
13579  } else {
13580 
-
13581 template<typename TSeq>
-
13582 class Model;
-
13583 
-
13584 template<typename TSeq>
-
13585 class Virus;
+
13581  p->rm_virus(m);
+
13582 
+
13583  }
+
13584 
+
13585  return ;
13586 
-
13587 template<typename TSeq>
-
13588 class Viruses;
-
13589 
-
13590 template<typename TSeq>
-
13591 class Viruses_const;
+
13587 }
+
13588 
+
13589 #endif
+
13590 /*//////////////////////////////////////////////////////////////////////////////
13592 
-
13593 template<typename TSeq>
-
13594 class Tool;
-
13595 
-
13596 template<typename TSeq>
-
13597 class Tools;
+
13593  End of -include/epiworld/agent-meat-state.hpp-
+
13594 
+
13597 
13598 
-
13599 template<typename TSeq>
-
13600 class Tools_const;
+
13599 /*//////////////////////////////////////////////////////////////////////////////
13601 
-
13602 template<typename TSeq>
-
13603 class Queue;
-
13604 
-
13605 template<typename TSeq>
-
13606 struct Event;
+
13602  Start of -include/epiworld/agent-bones.hpp-
+
13603 
+
13606 
13607 
-
13608 template<typename TSeq>
-
13609 class Entity;
+
13608 #ifndef EPIWORLD_PERSON_BONES_HPP
+
13609 #define EPIWORLD_PERSON_BONES_HPP
13610 
13611 template<typename TSeq>
-
13612 class Entities;
+
13612 class Model;
13613 
13614 template<typename TSeq>
-
13615 inline void default_add_virus(Event<TSeq> & a, Model<TSeq> * m);
+
13615 class Virus;
13616 
13617 template<typename TSeq>
-
13618 inline void default_add_tool(Event<TSeq> & a, Model<TSeq> * m);
+
13618 class Viruses;
13619 
13620 template<typename TSeq>
-
13621 inline void default_add_entity(Event<TSeq> & a, Model<TSeq> * m);
+
13621 class Viruses_const;
13622 
13623 template<typename TSeq>
-
13624 inline void default_rm_virus(Event<TSeq> & a, Model<TSeq> * m);
+
13624 class Tool;
13625 
13626 template<typename TSeq>
-
13627 inline void default_rm_tool(Event<TSeq> & a, Model<TSeq> * m);
+
13627 class Tools;
13628 
13629 template<typename TSeq>
-
13630 inline void default_rm_entity(Event<TSeq> & a, Model<TSeq> * m);
+
13630 class Tools_const;
13631 
13632 template<typename TSeq>
-
13633 inline void default_change_state(Event<TSeq> & a, Model<TSeq> * m);
+
13633 class Queue;
13634 
-
13635 
-
13636 
-
13642 template<typename TSeq>
-
13643 class Agent {
-
13644  friend class Model<TSeq>;
-
13645  friend class Virus<TSeq>;
-
13646  friend class Tool<TSeq>;
-
13647  friend class Tools<TSeq>;
-
13648  friend class Tools_const<TSeq>;
-
13649  friend class Queue<TSeq>;
-
13650  friend class Entities<TSeq>;
-
13651  friend class AgentsSample<TSeq>;
-
13652  friend void default_add_virus<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
13653  friend void default_add_tool<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
13654  friend void default_add_entity<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
13655  friend void default_rm_virus<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
13656  friend void default_rm_tool<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
13657  friend void default_rm_entity<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
13658  friend void default_change_state<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
-
13659 private:
-
13660 
-
13661  Model<TSeq> * model;
-
13662 
-
13663  std::vector< size_t > neighbors;
-
13664  std::vector< size_t > neighbors_locations;
-
13665  size_t n_neighbors = 0u;
+
13635 template<typename TSeq>
+
13636 struct Event;
+
13637 
+
13638 template<typename TSeq>
+
13639 class Entity;
+
13640 
+
13641 template<typename TSeq>
+
13642 class Entities;
+
13643 
+
13644 template<typename TSeq>
+
13645 inline void default_add_virus(Event<TSeq> & a, Model<TSeq> * m);
+
13646 
+
13647 template<typename TSeq>
+
13648 inline void default_add_tool(Event<TSeq> & a, Model<TSeq> * m);
+
13649 
+
13650 template<typename TSeq>
+
13651 inline void default_add_entity(Event<TSeq> & a, Model<TSeq> * m);
+
13652 
+
13653 template<typename TSeq>
+
13654 inline void default_rm_virus(Event<TSeq> & a, Model<TSeq> * m);
+
13655 
+
13656 template<typename TSeq>
+
13657 inline void default_rm_tool(Event<TSeq> & a, Model<TSeq> * m);
+
13658 
+
13659 template<typename TSeq>
+
13660 inline void default_rm_entity(Event<TSeq> & a, Model<TSeq> * m);
+
13661 
+
13662 template<typename TSeq>
+
13663 inline void default_change_state(Event<TSeq> & a, Model<TSeq> * m);
+
13664 
+
13665 
13666 
-
13667  std::vector< size_t > entities;
-
13668  std::vector< size_t > entities_locations;
-
13669  size_t n_entities = 0u;
-
13670 
-
13671  epiworld_fast_uint state = 0u;
-
13672  epiworld_fast_uint state_prev = 0u; ///< For accounting, if need to undo a change.
-
13673 
-
13674  int state_last_changed = -1; ///< Last time the agent was updated.
-
13675  int id = -1;
-
13676 
-
13677  VirusPtr<TSeq> virus = nullptr;
-
13678 
-
13679  std::vector< ToolPtr<TSeq> > tools;
-
13680  epiworld_fast_uint n_tools = 0u;
-
13681 
-
13682  std::vector< Agent<TSeq> * > sampled_agents = {};
-
13683  size_t sampled_agents_n = 0u;
-
13684  std::vector< size_t > sampled_agents_left = {};
-
13685  size_t sampled_agents_left_n = 0u;
-
13686  int date_last_build_sample = -99;
-
13687 
-
13688 public:
-
13689 
-
13690  Agent();
-
13691  Agent(Agent<TSeq> && p);
-
13692  Agent(const Agent<TSeq> & p);
-
13693  Agent<TSeq> & operator=(const Agent<TSeq> & other_agent);
-
13694 
-
13706  void add_tool(
-
13707  ToolPtr<TSeq> tool,
-
13708  Model<TSeq> * model,
-
13709  epiworld_fast_int state_new = -99,
-
13710  epiworld_fast_int queue = -99
-
13711  );
-
13712 
-
13713  void add_tool(
-
13714  Tool<TSeq> tool,
-
13715  Model<TSeq> * model,
-
13716  epiworld_fast_int state_new = -99,
-
13717  epiworld_fast_int queue = -99
-
13718  );
+
13672 template<typename TSeq>
+
13673 class Agent {
+
13674  friend class Model<TSeq>;
+
13675  friend class Virus<TSeq>;
+
13676  friend class Tool<TSeq>;
+
13677  friend class Tools<TSeq>;
+
13678  friend class Tools_const<TSeq>;
+
13679  friend class Queue<TSeq>;
+
13680  friend class Entities<TSeq>;
+
13681  friend class AgentsSample<TSeq>;
+
13682  friend void default_add_virus<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
13683  friend void default_add_tool<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
13684  friend void default_add_entity<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
13685  friend void default_rm_virus<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
13686  friend void default_rm_tool<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
13687  friend void default_rm_entity<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
13688  friend void default_change_state<TSeq>(Event<TSeq> & a, Model<TSeq> * m);
+
13689 private:
+
13690 
+
13691  Model<TSeq> * model;
+
13692 
+
13693  std::vector< size_t > neighbors;
+
13694  std::vector< size_t > neighbors_locations;
+
13695  size_t n_neighbors = 0u;
+
13696 
+
13697  std::vector< size_t > entities;
+
13698  std::vector< size_t > entities_locations;
+
13699  size_t n_entities = 0u;
+
13700 
+
13701  epiworld_fast_uint state = 0u;
+
13702  epiworld_fast_uint state_prev = 0u; ///< For accounting, if need to undo a change.
+
13703 
+
13704  int state_last_changed = -1; ///< Last time the agent was updated.
+
13705  int id = -1;
+
13706 
+
13707  VirusPtr<TSeq> virus = nullptr;
+
13708 
+
13709  std::vector< ToolPtr<TSeq> > tools;
+
13710  epiworld_fast_uint n_tools = 0u;
+
13711 
+
13712  std::vector< Agent<TSeq> * > sampled_agents = {};
+
13713  size_t sampled_agents_n = 0u;
+
13714  std::vector< size_t > sampled_agents_left = {};
+
13715  size_t sampled_agents_left_n = 0u;
+
13716  int date_last_build_sample = -99;
+
13717 
+
13718 public:
13719 
-
13720  void set_virus(
-
13721  VirusPtr<TSeq> virus,
-
13722  Model<TSeq> * model,
-
13723  epiworld_fast_int state_new = -99,
-
13724  epiworld_fast_int queue = -99
-
13725  );
-
13726 
-
13727  void set_virus(
-
13728  Virus<TSeq> virus,
-
13729  Model<TSeq> * model,
-
13730  epiworld_fast_int state_new = -99,
-
13731  epiworld_fast_int queue = -99
-
13732  );
-
13733 
-
13734  void add_entity(
-
13735  Entity<TSeq> & entity,
-
13736  Model<TSeq> * model,
-
13737  epiworld_fast_int state_new = -99,
-
13738  epiworld_fast_int queue = -99
-
13739  );
-
13740 
-
13741  void rm_tool(
-
13742  epiworld_fast_uint tool_idx,
-
13743  Model<TSeq> * model,
-
13744  epiworld_fast_int state_new = -99,
-
13745  epiworld_fast_int queue = -99
-
13746  );
-
13747 
-
13748  void rm_tool(
-
13749  ToolPtr<TSeq> & tool,
-
13750  Model<TSeq> * model,
-
13751  epiworld_fast_int state_new = -99,
-
13752  epiworld_fast_int queue = -99
-
13753  );
-
13754 
-
13755  void rm_virus(
-
13756  Model<TSeq> * model,
-
13757  epiworld_fast_int state_new = -99,
-
13758  epiworld_fast_int queue = -99
-
13759  );
-
13760 
-
13761  void rm_entity(
-
13762  epiworld_fast_uint entity_idx,
-
13763  Model<TSeq> * model,
-
13764  epiworld_fast_int state_new = -99,
-
13765  epiworld_fast_int queue = -99
-
13766  );
-
13767 
-
13768  void rm_entity(
-
13769  Entity<TSeq> & entity,
-
13770  Model<TSeq> * model,
-
13771  epiworld_fast_int state_new = -99,
-
13772  epiworld_fast_int queue = -99
-
13773  );
-
13774 
-
13775  void rm_agent_by_virus(
-
13776  Model<TSeq> * model,
-
13777  epiworld_fast_int state_new = -99,
-
13778  epiworld_fast_int queue = -99
-
13779  ); ///< Agent removed by virus
-
13781 
-
13789  epiworld_double get_susceptibility_reduction(VirusPtr<TSeq> v, Model<TSeq> * model);
-
13790  epiworld_double get_transmission_reduction(VirusPtr<TSeq> v, Model<TSeq> * model);
-
13791  epiworld_double get_recovery_enhancer(VirusPtr<TSeq> v, Model<TSeq> * model);
-
13792  epiworld_double get_death_reduction(VirusPtr<TSeq> v, Model<TSeq> * model);
-
13794 
-
13795  int get_id() const; ///< Id of the individual
-
13796 
-
13797  VirusPtr<TSeq> & get_virus();
-
13798  const VirusPtr<TSeq> & get_virus() const;
-
13799 
-
13800  ToolPtr<TSeq> & get_tool(int i);
-
13801  Tools<TSeq> get_tools();
-
13802  const Tools_const<TSeq> get_tools() const;
-
13803  size_t get_n_tools() const noexcept;
+
13720  Agent();
+
13721  Agent(Agent<TSeq> && p);
+
13722  Agent(const Agent<TSeq> & p);
+
13723  Agent<TSeq> & operator=(const Agent<TSeq> & other_agent);
+
13724 
+
13736  void add_tool(
+
13737  ToolPtr<TSeq> tool,
+
13738  Model<TSeq> * model,
+
13739  epiworld_fast_int state_new = -99,
+
13740  epiworld_fast_int queue = -99
+
13741  );
+
13742 
+
13743  void add_tool(
+
13744  Tool<TSeq> tool,
+
13745  Model<TSeq> * model,
+
13746  epiworld_fast_int state_new = -99,
+
13747  epiworld_fast_int queue = -99
+
13748  );
+
13749 
+
13750  void set_virus(
+
13751  VirusPtr<TSeq> virus,
+
13752  Model<TSeq> * model,
+
13753  epiworld_fast_int state_new = -99,
+
13754  epiworld_fast_int queue = -99
+
13755  );
+
13756 
+
13757  void set_virus(
+
13758  Virus<TSeq> virus,
+
13759  Model<TSeq> * model,
+
13760  epiworld_fast_int state_new = -99,
+
13761  epiworld_fast_int queue = -99
+
13762  );
+
13763 
+
13764  void add_entity(
+
13765  Entity<TSeq> & entity,
+
13766  Model<TSeq> * model,
+
13767  epiworld_fast_int state_new = -99,
+
13768  epiworld_fast_int queue = -99
+
13769  );
+
13770 
+
13771  void rm_tool(
+
13772  epiworld_fast_uint tool_idx,
+
13773  Model<TSeq> * model,
+
13774  epiworld_fast_int state_new = -99,
+
13775  epiworld_fast_int queue = -99
+
13776  );
+
13777 
+
13778  void rm_tool(
+
13779  ToolPtr<TSeq> & tool,
+
13780  Model<TSeq> * model,
+
13781  epiworld_fast_int state_new = -99,
+
13782  epiworld_fast_int queue = -99
+
13783  );
+
13784 
+
13785  void rm_virus(
+
13786  Model<TSeq> * model,
+
13787  epiworld_fast_int state_new = -99,
+
13788  epiworld_fast_int queue = -99
+
13789  );
+
13790 
+
13791  void rm_entity(
+
13792  epiworld_fast_uint entity_idx,
+
13793  Model<TSeq> * model,
+
13794  epiworld_fast_int state_new = -99,
+
13795  epiworld_fast_int queue = -99
+
13796  );
+
13797 
+
13798  void rm_entity(
+
13799  Entity<TSeq> & entity,
+
13800  Model<TSeq> * model,
+
13801  epiworld_fast_int state_new = -99,
+
13802  epiworld_fast_int queue = -99
+
13803  );
13804 
-
13805  void mutate_virus();
-
13806  void add_neighbor(
-
13807  Agent<TSeq> & p,
-
13808  bool check_source = true,
-
13809  bool check_target = true
-
13810  );
-
13811 
-
13819  void swap_neighbors(
-
13820  Agent<TSeq> & other,
-
13821  size_t n_this,
-
13822  size_t n_other
-
13823  );
+
13805  void rm_agent_by_virus(
+
13806  Model<TSeq> * model,
+
13807  epiworld_fast_int state_new = -99,
+
13808  epiworld_fast_int queue = -99
+
13809  ); ///< Agent removed by virus
+
13811 
+
13819  epiworld_double get_susceptibility_reduction(VirusPtr<TSeq> v, Model<TSeq> * model);
+
13820  epiworld_double get_transmission_reduction(VirusPtr<TSeq> v, Model<TSeq> * model);
+
13821  epiworld_double get_recovery_enhancer(VirusPtr<TSeq> v, Model<TSeq> * model);
+
13822  epiworld_double get_death_reduction(VirusPtr<TSeq> v, Model<TSeq> * model);
13824 
-
13825  std::vector< Agent<TSeq> * > get_neighbors();
-
13826  size_t get_n_neighbors() const;
-
13827 
-
13828  void change_state(
-
13829  Model<TSeq> * model,
-
13830  epiworld_fast_uint new_state,
-
13831  epiworld_fast_int queue = 0
-
13832  );
-
13833 
-
13834  const epiworld_fast_uint & get_state() const;
-
13835 
-
13836  void reset();
-
13837 
-
13838  bool has_tool(epiworld_fast_uint t) const;
-
13839  bool has_tool(std::string name) const;
-
13840  bool has_tool(const Tool<TSeq> & t) const;
-
13841  bool has_virus(epiworld_fast_uint t) const;
-
13842  bool has_virus(std::string name) const;
-
13843  bool has_virus(const Virus<TSeq> & v) const;
-
13844  bool has_entity(epiworld_fast_uint t) const;
-
13845  bool has_entity(std::string name) const;
-
13846 
-
13847  void print(Model<TSeq> * model, bool compressed = false) const;
-
13848 
-
13865  double & operator()(size_t j);
-
13866  double & operator[](size_t j);
-
13867  double operator()(size_t j) const;
-
13868  double operator[](size_t j) const;
-
13870 
-
13871  Entities<TSeq> get_entities();
-
13872  const Entities_const<TSeq> get_entities() const;
-
13873  const Entity<TSeq> & get_entity(size_t i) const;
-
13874  Entity<TSeq> & get_entity(size_t i);
-
13875  size_t get_n_entities() const;
+
13825  int get_id() const; ///< Id of the individual
+
13826 
+
13827  VirusPtr<TSeq> & get_virus();
+
13828  const VirusPtr<TSeq> & get_virus() const;
+
13829 
+
13830  ToolPtr<TSeq> & get_tool(int i);
+
13831  Tools<TSeq> get_tools();
+
13832  const Tools_const<TSeq> get_tools() const;
+
13833  size_t get_n_tools() const noexcept;
+
13834 
+
13835  void mutate_virus();
+
13836  void add_neighbor(
+
13837  Agent<TSeq> & p,
+
13838  bool check_source = true,
+
13839  bool check_target = true
+
13840  );
+
13841 
+
13849  void swap_neighbors(
+
13850  Agent<TSeq> & other,
+
13851  size_t n_this,
+
13852  size_t n_other
+
13853  );
+
13854 
+
13855  std::vector< Agent<TSeq> * > get_neighbors();
+
13856  size_t get_n_neighbors() const;
+
13857 
+
13858  void change_state(
+
13859  Model<TSeq> * model,
+
13860  epiworld_fast_uint new_state,
+
13861  epiworld_fast_int queue = 0
+
13862  );
+
13863 
+
13864  const epiworld_fast_uint & get_state() const;
+
13865 
+
13866  void reset();
+
13867 
+
13868  bool has_tool(epiworld_fast_uint t) const;
+
13869  bool has_tool(std::string name) const;
+
13870  bool has_tool(const Tool<TSeq> & t) const;
+
13871  bool has_virus(epiworld_fast_uint t) const;
+
13872  bool has_virus(std::string name) const;
+
13873  bool has_virus(const Virus<TSeq> & v) const;
+
13874  bool has_entity(epiworld_fast_uint t) const;
+
13875  bool has_entity(std::string name) const;
13876 
-
13877  bool operator==(const Agent<TSeq> & other) const;
-
13878  bool operator!=(const Agent<TSeq> & other) const {return !operator==(other);};
-
13879 
-
13880 };
-
13881 
-
13882 
-
13883 
-
13884 #endif
-
13885 /*//////////////////////////////////////////////////////////////////////////////
-
13887 
-
13888  End of -include/epiworld/agent-bones.hpp-
-
13889 
-
13892 
-
13893 
-
13894 /*//////////////////////////////////////////////////////////////////////////////
-
13896 
-
13897  Start of -include/epiworld/agent-meat.hpp-
-
13898 
-
13901 
-
13902 
-
13903 #ifndef EPIWORLD_PERSON_MEAT_HPP
-
13904 #define EPIWORLD_PERSON_MEAT_HPP
-
13905 
-
13906 #define CHECK_COALESCE_(proposed_, virus_tool_, alt_) \
-
13907  if (static_cast<int>(proposed_) == -99) {\
-
13908  if (static_cast<int>(virus_tool_) == -99) \
-
13909  (proposed_) = (alt_);\
-
13910  else (proposed_) = (virus_tool_);}
+
13877  void print(Model<TSeq> * model, bool compressed = false) const;
+
13878 
+
13895  double & operator()(size_t j);
+
13896  double & operator[](size_t j);
+
13897  double operator()(size_t j) const;
+
13898  double operator[](size_t j) const;
+
13900 
+
13901  Entities<TSeq> get_entities();
+
13902  const Entities_const<TSeq> get_entities() const;
+
13903  const Entity<TSeq> & get_entity(size_t i) const;
+
13904  Entity<TSeq> & get_entity(size_t i);
+
13905  size_t get_n_entities() const;
+
13906 
+
13907  bool operator==(const Agent<TSeq> & other) const;
+
13908  bool operator!=(const Agent<TSeq> & other) const {return !operator==(other);};
+
13909 
+
13910 };
13911 
-
13912 // To large to add directly here
-
13913 /*//////////////////////////////////////////////////////////////////////////////
-
13915 
-
13916  Start of -include/epiworld//agent-events-meat.hpp-
+
13912 
+
13913 
+
13914 #endif
+
13915 /*//////////////////////////////////////////////////////////////////////////////
13917 
-
13920 
-
13921 
-
13922 #ifndef EPIWORLD_AGENT_EVENTS_MEAT_HPP
-
13923 #define EPIWORLD_AGENT_EVENTS_MEAT_HPP
-
13924 
-
13925 template<typename TSeq>
-
13926 inline void default_add_virus(Event<TSeq> & a, Model<TSeq> * m)
-
13927 {
+
13918  End of -include/epiworld/agent-bones.hpp-
+
13919 
+
13922 
+
13923 
+
13924 /*//////////////////////////////////////////////////////////////////////////////
+
13926 
+
13927  Start of -include/epiworld/agent-meat.hpp-
13928 
-
13929  Agent<TSeq> * p = a.agent;
-
13930  VirusPtr<TSeq> v = a.virus;
13931 
-
13932  // Has a agent? If so, we need to register the transmission
-
13933  if (v->get_agent())
-
13934  {
+
13932 
+
13933 #ifndef EPIWORLD_PERSON_MEAT_HPP
+
13934 #define EPIWORLD_PERSON_MEAT_HPP
13935 
-
13936  // ... only if not the same agent
-
13937  if (v->get_agent()->get_id() != p->get_id())
-
13938  m->get_db().record_transmission(
-
13939  v->get_agent()->get_id(),
-
13940  p->get_id(),
-
13941  v->get_id(),
-
13942  v->get_date()
-
13943  );
-
13944 
-
13945  }
-
13946 
-
13947  p->virus = std::make_shared< Virus<TSeq> >(*v);
-
13948  p->virus->set_date(m->today());
-
13949  p->virus->set_agent(p);
+
13936 #define CHECK_COALESCE_(proposed_, virus_tool_, alt_) \
+
13937  if (static_cast<int>(proposed_) == -99) {\
+
13938  if (static_cast<int>(virus_tool_) == -99) \
+
13939  (proposed_) = (alt_);\
+
13940  else (proposed_) = (virus_tool_);}
+
13941 
+
13942 // To large to add directly here
+
13943 /*//////////////////////////////////////////////////////////////////////////////
+
13945 
+
13946  Start of -include/epiworld//agent-events-meat.hpp-
+
13947 
13950 
-
13951  // Change of state needs to be recorded and updated on the
-
13952  // tools.
-
13953  if (p->state_prev != p->state)
-
13954  {
-
13955  auto & db = m->get_db();
-
13956  db.update_state(p->state_prev, p->state);
-
13957 
-
13958  for (size_t i = 0u; i < p->n_tools; ++i)
-
13959  db.update_tool(p->tools[i]->get_id(), p->state_prev, p->state);
-
13960  }
+
13951 
+
13952 #ifndef EPIWORLD_AGENT_EVENTS_MEAT_HPP
+
13953 #define EPIWORLD_AGENT_EVENTS_MEAT_HPP
+
13954 
+
13955 template<typename TSeq>
+
13956 inline void default_add_virus(Event<TSeq> & a, Model<TSeq> * m)
+
13957 {
+
13958 
+
13959  Agent<TSeq> * p = a.agent;
+
13960  VirusPtr<TSeq> v = a.virus;
13961 
-
13962  // Lastly, we increase the daily count of the virus
-
13963  #ifdef EPI_DEBUG
-
13964  m->get_db().today_virus.at(v->get_id()).at(p->state)++;
-
13965  #else
-
13966  m->get_db().today_virus[v->get_id()][p->state]++;
-
13967  #endif
-
13968 
-
13969 }
-
13970 
-
13971 template<typename TSeq>
-
13972 inline void default_add_tool(Event<TSeq> & a, Model<TSeq> * m)
-
13973 {
+
13962  // Has a agent? If so, we need to register the transmission
+
13963  if (v->get_agent())
+
13964  {
+
13965 
+
13966  // ... only if not the same agent
+
13967  if (v->get_agent()->get_id() != p->get_id())
+
13968  m->get_db().record_transmission(
+
13969  v->get_agent()->get_id(),
+
13970  p->get_id(),
+
13971  v->get_id(),
+
13972  v->get_date()
+
13973  );
13974 
-
13975  Agent<TSeq> * p = a.agent;
-
13976  ToolPtr<TSeq> t = a.tool;
-
13977 
-
13978  // Update tool accounting
-
13979  p->n_tools++;
-
13980  size_t n_tools = p->n_tools;
-
13981 
-
13982  if (n_tools <= p->tools.size())
-
13983  p->tools[n_tools - 1] = std::make_shared< Tool<TSeq> >(*t);
-
13984  else
-
13985  p->tools.push_back(std::make_shared< Tool<TSeq> >(*t));
-
13986 
-
13987  n_tools--;
-
13988 
-
13989  p->tools[n_tools]->set_date(m->today());
-
13990  p->tools[n_tools]->set_agent(p, n_tools);
+
13975  }
+
13976 
+
13977  p->virus = std::make_shared< Virus<TSeq> >(*v);
+
13978  p->virus->set_date(m->today());
+
13979  p->virus->set_agent(p);
+
13980 
+
13981  // Change of state needs to be recorded and updated on the
+
13982  // tools.
+
13983  if (p->state_prev != p->state)
+
13984  {
+
13985  auto & db = m->get_db();
+
13986  db.update_state(p->state_prev, p->state);
+
13987 
+
13988  for (size_t i = 0u; i < p->n_tools; ++i)
+
13989  db.update_tool(p->tools[i]->get_id(), p->state_prev, p->state);
+
13990  }
13991 
-
13992  // Change of state needs to be recorded and updated on the
-
13993  // tools.
-
13994  if (p->state_prev != p->state)
-
13995  {
-
13996  auto & db = m->get_db();
-
13997  db.update_state(p->state_prev, p->state);
+
13992  // Lastly, we increase the daily count of the virus
+
13993  #ifdef EPI_DEBUG
+
13994  m->get_db().today_virus.at(v->get_id()).at(p->state)++;
+
13995  #else
+
13996  m->get_db().today_virus[v->get_id()][p->state]++;
+
13997  #endif
13998 
-
13999  if (p->virus)
-
14000  db.update_virus(p->virus->get_id(), p->state_prev, p->state);
-
14001  }
-
14002 
-
14003  m->get_db().today_tool[t->get_id()][p->state]++;
+
13999 }
+
14000 
+
14001 template<typename TSeq>
+
14002 inline void default_add_tool(Event<TSeq> & a, Model<TSeq> * m)
+
14003 {
14004 
-
14005 
-
14006 }
-
14007 
-
14008 template<typename TSeq>
-
14009 inline void default_rm_virus(Event<TSeq> & a, Model<TSeq> * model)
-
14010 {
+
14005  Agent<TSeq> * p = a.agent;
+
14006  ToolPtr<TSeq> t = a.tool;
+
14007 
+
14008  // Update tool accounting
+
14009  p->n_tools++;
+
14010  size_t n_tools = p->n_tools;
14011 
-
14012  Agent<TSeq> * p = a.agent;
-
14013  VirusPtr<TSeq> & v = a.virus;
-
14014 
-
14015  // Calling the virus action over the removed virus
-
14016  v->post_recovery(model);
-
14017 
-
14018  p->virus = nullptr;
-
14019 
-
14020  // Change of state needs to be recorded and updated on the
-
14021  // tools.
-
14022  if (p->state_prev != p->state)
-
14023  {
-
14024  auto & db = model->get_db();
-
14025  db.update_state(p->state_prev, p->state);
-
14026 
-
14027  for (size_t i = 0u; i < p->n_tools; ++i)
-
14028  db.update_tool(p->tools[i]->get_id(), p->state_prev, p->state);
-
14029  }
-
14030 
-
14031  // The counters of the virus only needs to decrease
-
14032  #ifdef EPI_DEBUG
-
14033  model->get_db().today_virus.at(v->get_id()).at(p->state_prev)--;
-
14034  #else
-
14035  model->get_db().today_virus[v->get_id()][p->state_prev]--;
-
14036  #endif
+
14012  if (n_tools <= p->tools.size())
+
14013  p->tools[n_tools - 1] = std::make_shared< Tool<TSeq> >(*t);
+
14014  else
+
14015  p->tools.push_back(std::make_shared< Tool<TSeq> >(*t));
+
14016 
+
14017  n_tools--;
+
14018 
+
14019  p->tools[n_tools]->set_date(m->today());
+
14020  p->tools[n_tools]->set_agent(p, n_tools);
+
14021 
+
14022  // Change of state needs to be recorded and updated on the
+
14023  // tools.
+
14024  if (p->state_prev != p->state)
+
14025  {
+
14026  auto & db = m->get_db();
+
14027  db.update_state(p->state_prev, p->state);
+
14028 
+
14029  if (p->virus)
+
14030  db.update_virus(p->virus->get_id(), p->state_prev, p->state);
+
14031  }
+
14032 
+
14033  m->get_db().today_tool[t->get_id()][p->state]++;
+
14034 
+
14035 
+
14036 }
14037 
-
14038 
-
14039  return;
-
14040 
-
14041 }
-
14042 
-
14043 template<typename TSeq>
-
14044 inline void default_rm_tool(Event<TSeq> & a, Model<TSeq> * m)
-
14045 {
-
14046 
-
14047  Agent<TSeq> * p = a.agent;
-
14048  ToolPtr<TSeq> & t = a.agent->tools[a.tool->pos_in_agent];
+
14038 template<typename TSeq>
+
14039 inline void default_rm_virus(Event<TSeq> & a, Model<TSeq> * model)
+
14040 {
+
14041 
+
14042  Agent<TSeq> * p = a.agent;
+
14043  VirusPtr<TSeq> & v = a.virus;
+
14044 
+
14045  // Calling the virus action over the removed virus
+
14046  v->post_recovery(model);
+
14047 
+
14048  p->virus = nullptr;
14049 
-
14050  if (--p->n_tools > 0)
-
14051  {
-
14052  p->tools[p->n_tools]->pos_in_agent = t->pos_in_agent;
-
14053  std::swap(
-
14054  p->tools[t->pos_in_agent],
-
14055  p->tools[p->n_tools]
-
14056  );
-
14057  }
-
14058 
-
14059  // Change of state needs to be recorded and updated on the
-
14060  // tools.
-
14061  if (p->state_prev != p->state)
-
14062  {
-
14063  auto & db = m->get_db();
-
14064  db.update_state(p->state_prev, p->state);
-
14065 
-
14066  if (p->virus)
-
14067  db.update_virus(p->virus->get_id(), p->state_prev, p->state);
-
14068  }
-
14069 
-
14070  // Lastly, we increase the daily count of the tool
-
14071  #ifdef EPI_DEBUG
-
14072  m->get_db().today_tool.at(t->get_id()).at(p->state_prev)--;
-
14073  #else
-
14074  m->get_db().today_tool[t->get_id()][p->state_prev]--;
-
14075  #endif
+
14050  // Change of state needs to be recorded and updated on the
+
14051  // tools.
+
14052  if (p->state_prev != p->state)
+
14053  {
+
14054  auto & db = model->get_db();
+
14055  db.update_state(p->state_prev, p->state);
+
14056 
+
14057  for (size_t i = 0u; i < p->n_tools; ++i)
+
14058  db.update_tool(p->tools[i]->get_id(), p->state_prev, p->state);
+
14059  }
+
14060 
+
14061  // The counters of the virus only needs to decrease
+
14062  #ifdef EPI_DEBUG
+
14063  model->get_db().today_virus.at(v->get_id()).at(p->state_prev)--;
+
14064  #else
+
14065  model->get_db().today_virus[v->get_id()][p->state_prev]--;
+
14066  #endif
+
14067 
+
14068 
+
14069  return;
+
14070 
+
14071 }
+
14072 
+
14073 template<typename TSeq>
+
14074 inline void default_rm_tool(Event<TSeq> & a, Model<TSeq> * m)
+
14075 {
14076 
-
14077  return;
-
14078 
-
14079 }
-
14080 
-
14081 template<typename TSeq>
-
14082 inline void default_change_state(Event<TSeq> & a, Model<TSeq> * m)
-
14083 {
-
14084 
-
14085  Agent<TSeq> * p = a.agent;
-
14086 
-
14087  if (p->state_prev != p->state)
-
14088  {
-
14089  auto & db = m->get_db();
-
14090  db.update_state(p->state_prev, p->state);
-
14091 
-
14092  if (p->virus)
-
14093  db.update_virus(p->virus->get_id(), p->state_prev, p->state);
-
14094 
-
14095  for (size_t i = 0u; i < p->n_tools; ++i)
-
14096  db.update_tool(p->tools[i]->get_id(), p->state_prev, p->state);
-
14097 
+
14077  Agent<TSeq> * p = a.agent;
+
14078  ToolPtr<TSeq> & t = a.agent->tools[a.tool->pos_in_agent];
+
14079 
+
14080  if (--p->n_tools > 0)
+
14081  {
+
14082  p->tools[p->n_tools]->pos_in_agent = t->pos_in_agent;
+
14083  std::swap(
+
14084  p->tools[t->pos_in_agent],
+
14085  p->tools[p->n_tools]
+
14086  );
+
14087  }
+
14088 
+
14089  // Change of state needs to be recorded and updated on the
+
14090  // tools.
+
14091  if (p->state_prev != p->state)
+
14092  {
+
14093  auto & db = m->get_db();
+
14094  db.update_state(p->state_prev, p->state);
+
14095 
+
14096  if (p->virus)
+
14097  db.update_virus(p->virus->get_id(), p->state_prev, p->state);
14098  }
14099 
-
14100 }
-
14101 
-
14102 template<typename TSeq>
-
14103 inline void default_add_entity(Event<TSeq> & a, Model<TSeq> *)
-
14104 {
-
14105 
-
14106  Agent<TSeq> * p = a.agent;
-
14107  Entity<TSeq> * e = a.entity;
+
14100  // Lastly, we increase the daily count of the tool
+
14101  #ifdef EPI_DEBUG
+
14102  m->get_db().today_tool.at(t->get_id()).at(p->state_prev)--;
+
14103  #else
+
14104  m->get_db().today_tool[t->get_id()][p->state_prev]--;
+
14105  #endif
+
14106 
+
14107  return;
14108 
-
14109  // Checking the agent and the entity are not linked
-
14110  if ((p->get_n_entities() > 0) && (e->size() > 0))
-
14111  {
-
14112 
-
14113  if (p->get_n_entities() > e->size()) // Slower search through the agent
-
14114  {
-
14115  for (size_t i = 0u; i < e->size(); ++i)
-
14116  if(static_cast<int>(e->operator[](i)) == p->get_id())
-
14117  throw std::logic_error("An entity cannot be reassigned to an agent.");
-
14118  }
-
14119  else // Slower search through the entity
-
14120  {
-
14121  for (size_t i = 0u; i < p->get_n_entities(); ++i)
-
14122  if(p->get_entity(i).get_id() == e->get_id())
-
14123  throw std::logic_error("An entity cannot be reassigned to an agent.");
-
14124  }
-
14125 
-
14126  // It means that agent and entity were not associated.
-
14127  }
-
14128 
-
14129  // Adding the entity to the agent
-
14130  if (++p->n_entities <= p->entities.size())
-
14131  {
-
14132 
-
14133  p->entities[p->n_entities - 1] = e->get_id();
-
14134  p->entities_locations[p->n_entities - 1] = e->n_agents;
+
14109 }
+
14110 
+
14111 template<typename TSeq>
+
14112 inline void default_change_state(Event<TSeq> & a, Model<TSeq> * m)
+
14113 {
+
14114 
+
14115  Agent<TSeq> * p = a.agent;
+
14116 
+
14117  if (p->state_prev != p->state)
+
14118  {
+
14119  auto & db = m->get_db();
+
14120  db.update_state(p->state_prev, p->state);
+
14121 
+
14122  if (p->virus)
+
14123  db.update_virus(p->virus->get_id(), p->state_prev, p->state);
+
14124 
+
14125  for (size_t i = 0u; i < p->n_tools; ++i)
+
14126  db.update_tool(p->tools[i]->get_id(), p->state_prev, p->state);
+
14127 
+
14128  }
+
14129 
+
14130 }
+
14131 
+
14132 template<typename TSeq>
+
14133 inline void default_add_entity(Event<TSeq> & a, Model<TSeq> *)
+
14134 {
14135 
-
14136  } else
-
14137  {
-
14138  p->entities.push_back(e->get_id());
-
14139  p->entities_locations.push_back(e->n_agents);
-
14140  }
-
14141 
-
14142  // Adding the agent to the entity
-
14143  // Adding the entity to the agent
-
14144  if (++e->n_agents <= e->agents.size())
-
14145  {
-
14146 
-
14147  e->agents[e->n_agents - 1] = p->get_id();
-
14148  // Adjusted by '-1' since the list of entities in the agent just grew.
-
14149  e->agents_location[e->n_agents - 1] = p->n_entities - 1;
-
14150 
-
14151  } else
-
14152  {
-
14153  e->agents.push_back(p->get_id());
-
14154  e->agents_location.push_back(p->n_entities - 1);
-
14155  }
-
14156 
-
14157  // Today was the last modification
-
14158  // e->date_last_add_or_remove = m->today();
-
14159 
-
14160 }
-
14161 
-
14162 template<typename TSeq>
-
14163 inline void default_rm_entity(Event<TSeq> & a, Model<TSeq> * m)
-
14164 {
-
14165 
-
14166  Agent<TSeq> * p = a.agent;
-
14167  Entity<TSeq> * e = a.entity;
-
14168  size_t idx_agent_in_entity = a.idx_agent;
-
14169  size_t idx_entity_in_agent = a.idx_object;
-
14170 
-
14171  if (--p->n_entities > 0)
-
14172  {
-
14173 
-
14174  // When we move the end entity to the new location, the
-
14175  // moved entity needs to reflect the change, i.e., where the
-
14176  // entity will now be located in the agent
-
14177  size_t agent_location_in_last_entity =
-
14178  p->entities_locations[p->n_entities];
-
14179 
-
14180  Entity<TSeq> * last_entity =
-
14181  &m->get_entity(p->entities[p->n_entities]); ///< Last entity of the agent
-
14182 
-
14183  // The end entity will be located where the removed was
-
14184  last_entity->agents_location[agent_location_in_last_entity] =
-
14185  idx_entity_in_agent;
+
14136  Agent<TSeq> * p = a.agent;
+
14137  Entity<TSeq> * e = a.entity;
+
14138 
+
14139  // Checking the agent and the entity are not linked
+
14140  if ((p->get_n_entities() > 0) && (e->size() > 0))
+
14141  {
+
14142 
+
14143  if (p->get_n_entities() > e->size()) // Slower search through the agent
+
14144  {
+
14145  for (size_t i = 0u; i < e->size(); ++i)
+
14146  if(static_cast<int>(e->operator[](i)) == p->get_id())
+
14147  throw std::logic_error("An entity cannot be reassigned to an agent.");
+
14148  }
+
14149  else // Slower search through the entity
+
14150  {
+
14151  for (size_t i = 0u; i < p->get_n_entities(); ++i)
+
14152  if(p->get_entity(i).get_id() == e->get_id())
+
14153  throw std::logic_error("An entity cannot be reassigned to an agent.");
+
14154  }
+
14155 
+
14156  // It means that agent and entity were not associated.
+
14157  }
+
14158 
+
14159  // Adding the entity to the agent
+
14160  if (++p->n_entities <= p->entities.size())
+
14161  {
+
14162 
+
14163  p->entities[p->n_entities - 1] = e->get_id();
+
14164  p->entities_locations[p->n_entities - 1] = e->n_agents;
+
14165 
+
14166  } else
+
14167  {
+
14168  p->entities.push_back(e->get_id());
+
14169  p->entities_locations.push_back(e->n_agents);
+
14170  }
+
14171 
+
14172  // Adding the agent to the entity
+
14173  // Adding the entity to the agent
+
14174  if (++e->n_agents <= e->agents.size())
+
14175  {
+
14176 
+
14177  e->agents[e->n_agents - 1] = p->get_id();
+
14178  // Adjusted by '-1' since the list of entities in the agent just grew.
+
14179  e->agents_location[e->n_agents - 1] = p->n_entities - 1;
+
14180 
+
14181  } else
+
14182  {
+
14183  e->agents.push_back(p->get_id());
+
14184  e->agents_location.push_back(p->n_entities - 1);
+
14185  }
14186 
-
14187  // We now make the swap
-
14188  std::swap(
-
14189  p->entities[p->n_entities],
-
14190  p->entities[idx_entity_in_agent]
-
14191  );
-
14192 
-
14193  }
-
14194 
-
14195  if (--e->n_agents > 0)
-
14196  {
-
14197 
-
14198  // When we move the end agent to the new location, the
-
14199  // moved agent needs to reflect the change, i.e., where the
-
14200  // agent will now be located in the entity
-
14201  size_t entity_location_in_last_agent = e->agents_location[e->n_agents];
-
14202 
-
14203  Agent<TSeq> * last_agent =
-
14204  &m->get_agents()[e->agents[e->n_agents]]; ///< Last agent of the entity
-
14205 
-
14206  // The end entity will be located where the removed was
-
14207  last_agent->entities_locations[entity_location_in_last_agent] =
-
14208  idx_agent_in_entity;
+
14187  // Today was the last modification
+
14188  // e->date_last_add_or_remove = m->today();
+
14189 
+
14190 }
+
14191 
+
14192 template<typename TSeq>
+
14193 inline void default_rm_entity(Event<TSeq> & a, Model<TSeq> * m)
+
14194 {
+
14195 
+
14196  Agent<TSeq> * p = a.agent;
+
14197  Entity<TSeq> * e = a.entity;
+
14198  size_t idx_agent_in_entity = a.idx_agent;
+
14199  size_t idx_entity_in_agent = a.idx_object;
+
14200 
+
14201  if (--p->n_entities > 0)
+
14202  {
+
14203 
+
14204  // When we move the end entity to the new location, the
+
14205  // moved entity needs to reflect the change, i.e., where the
+
14206  // entity will now be located in the agent
+
14207  size_t agent_location_in_last_entity =
+
14208  p->entities_locations[p->n_entities];
14209 
-
14210  // We now make the swap
-
14211  std::swap(
-
14212  e->agents[e->n_agents],
-
14213  e->agents[idx_agent_in_entity]
-
14214  );
-
14215 
-
14216  }
-
14217 
-
14218  // Setting the date of the last removal
-
14219  // e->date_last_add_or_remove = m->today();
-
14220 
-
14221  return;
+
14210  Entity<TSeq> * last_entity =
+
14211  &m->get_entity(p->entities[p->n_entities]); ///< Last entity of the agent
+
14212 
+
14213  // The end entity will be located where the removed was
+
14214  last_entity->agents_location[agent_location_in_last_entity] =
+
14215  idx_entity_in_agent;
+
14216 
+
14217  // We now make the swap
+
14218  std::swap(
+
14219  p->entities[p->n_entities],
+
14220  p->entities[idx_entity_in_agent]
+
14221  );
14222 
-
14223 }
-
14224 #endif
-
14225 /*//////////////////////////////////////////////////////////////////////////////
+
14223  }
+
14224 
+
14225  if (--e->n_agents > 0)
+
14226  {
14227 
-
14228  End of -include/epiworld//agent-events-meat.hpp-
-
14229 
-
14232 
-
14233 
-
14234 
-
14235 template<typename TSeq>
-
14236 inline Agent<TSeq>::Agent() {}
-
14237 
-
14238 template<typename TSeq>
-
14239 inline Agent<TSeq>::Agent(Agent<TSeq> && p) :
-
14240  model(p.model),
-
14241  neighbors(std::move(p.neighbors)),
-
14242  neighbors_locations(std::move(p.neighbors_locations)),
-
14243  n_neighbors(p.n_neighbors),
-
14244  entities(std::move(p.entities)),
-
14245  entities_locations(std::move(p.entities_locations)),
-
14246  n_entities(p.n_entities),
-
14247  state(p.state),
-
14248  state_prev(p.state_prev),
-
14249  state_last_changed(p.state_last_changed),
-
14250  id(p.id),
-
14251  tools(std::move(p.tools)), /// Needs to be adjusted
-
14252  n_tools(p.n_tools)
-
14253 {
-
14254 
-
14255  state = p.state;
-
14256  id = p.id;
-
14257 
-
14258  // Dealing with the virus
-
14259  if (p.virus != nullptr)
-
14260  {
-
14261  virus = std::move(p.virus);
-
14262  virus->set_agent(this);
-
14263  }
+
14228  // When we move the end agent to the new location, the
+
14229  // moved agent needs to reflect the change, i.e., where the
+
14230  // agent will now be located in the entity
+
14231  size_t entity_location_in_last_agent = e->agents_location[e->n_agents];
+
14232 
+
14233  Agent<TSeq> * last_agent =
+
14234  &m->get_agents()[e->agents[e->n_agents]]; ///< Last agent of the entity
+
14235 
+
14236  // The end entity will be located where the removed was
+
14237  last_agent->entities_locations[entity_location_in_last_agent] =
+
14238  idx_agent_in_entity;
+
14239 
+
14240  // We now make the swap
+
14241  std::swap(
+
14242  e->agents[e->n_agents],
+
14243  e->agents[idx_agent_in_entity]
+
14244  );
+
14245 
+
14246  }
+
14247 
+
14248  // Setting the date of the last removal
+
14249  // e->date_last_add_or_remove = m->today();
+
14250 
+
14251  return;
+
14252 
+
14253 }
+
14254 #endif
+
14255 /*//////////////////////////////////////////////////////////////////////////////
+
14257 
+
14258  End of -include/epiworld//agent-events-meat.hpp-
+
14259 
+
14262 
+
14263 
14264 
-
14265  int loc = 0;
-
14266  for (auto & t : tools)
-
14267  {
-
14268 
-
14269  // Will create a copy of the virus, with the exeption of
-
14270  // the virus code
-
14271  t->agent = this;
-
14272  t->pos_in_agent = loc++;
-
14273 
-
14274  }
-
14275 
-
14276 }
-
14277 
-
14278 template<typename TSeq>
-
14279 inline Agent<TSeq>::Agent(const Agent<TSeq> & p) :
-
14280  model(p.model),
-
14281  neighbors(p.neighbors),
-
14282  neighbors_locations(p.neighbors_locations),
-
14283  n_neighbors(p.n_neighbors),
-
14284  entities(p.entities),
-
14285  entities_locations(p.entities_locations),
-
14286  n_entities(p.n_entities),
-
14287  sampled_agents(0u),
-
14288  sampled_agents_n(0u),
-
14289  sampled_agents_left_n(0u),
-
14290  date_last_build_sample(-99)
-
14291 {
-
14292 
-
14293  state = p.state;
-
14294  id = p.id;
-
14295 
-
14296  // Dealing with the virus
-
14297  if (p.virus != nullptr)
-
14298  {
-
14299  virus = std::make_shared<Virus<TSeq>>(*p.virus);
-
14300  virus->set_agent(this);
-
14301  }
-
14302 
+
14265 template<typename TSeq>
+
14266 inline Agent<TSeq>::Agent() {}
+
14267 
+
14268 template<typename TSeq>
+
14269 inline Agent<TSeq>::Agent(Agent<TSeq> && p) :
+
14270  model(p.model),
+
14271  neighbors(std::move(p.neighbors)),
+
14272  neighbors_locations(std::move(p.neighbors_locations)),
+
14273  n_neighbors(p.n_neighbors),
+
14274  entities(std::move(p.entities)),
+
14275  entities_locations(std::move(p.entities_locations)),
+
14276  n_entities(p.n_entities),
+
14277  state(p.state),
+
14278  state_prev(p.state_prev),
+
14279  state_last_changed(p.state_last_changed),
+
14280  id(p.id),
+
14281  tools(std::move(p.tools)), /// Needs to be adjusted
+
14282  n_tools(p.n_tools)
+
14283 {
+
14284 
+
14285  state = p.state;
+
14286  id = p.id;
+
14287 
+
14288  // Dealing with the virus
+
14289  if (p.virus != nullptr)
+
14290  {
+
14291  virus = std::move(p.virus);
+
14292  virus->set_agent(this);
+
14293  }
+
14294 
+
14295  int loc = 0;
+
14296  for (auto & t : tools)
+
14297  {
+
14298 
+
14299  // Will create a copy of the virus, with the exeption of
+
14300  // the virus code
+
14301  t->agent = this;
+
14302  t->pos_in_agent = loc++;
14303 
-
14304  tools.reserve(p.get_n_tools());
-
14305  n_tools = tools.size();
-
14306  for (size_t i = 0u; i < n_tools; ++i)
-
14307  {
-
14308 
-
14309  // Will create a copy of the virus, with the exeption of
-
14310  // the virus code
-
14311  tools.emplace_back(std::make_shared<Tool<TSeq>>(*p.tools[i]));
-
14312  tools.back()->set_agent(this, i);
-
14313 
-
14314  }
-
14315 
-
14316 }
-
14317 
-
14318 template<typename TSeq>
-
14319 inline Agent<TSeq> & Agent<TSeq>::operator=(
-
14320  const Agent<TSeq> & other_agent
-
14321 )
-
14322 {
-
14323 
-
14324  model = other_agent.model;
-
14325 
-
14326  neighbors = other_agent.neighbors;
-
14327  neighbors_locations = other_agent.neighbors_locations;
-
14328  n_neighbors = other_agent.n_neighbors;
-
14329 
-
14330  entities = other_agent.entities;
-
14331  entities_locations = other_agent.entities_locations;
-
14332  n_entities = other_agent.n_entities;
+
14304  }
+
14305 
+
14306 }
+
14307 
+
14308 template<typename TSeq>
+
14309 inline Agent<TSeq>::Agent(const Agent<TSeq> & p) :
+
14310  model(p.model),
+
14311  neighbors(p.neighbors),
+
14312  neighbors_locations(p.neighbors_locations),
+
14313  n_neighbors(p.n_neighbors),
+
14314  entities(p.entities),
+
14315  entities_locations(p.entities_locations),
+
14316  n_entities(p.n_entities),
+
14317  sampled_agents(0u),
+
14318  sampled_agents_n(0u),
+
14319  sampled_agents_left_n(0u),
+
14320  date_last_build_sample(-99)
+
14321 {
+
14322 
+
14323  state = p.state;
+
14324  id = p.id;
+
14325 
+
14326  // Dealing with the virus
+
14327  if (p.virus != nullptr)
+
14328  {
+
14329  virus = std::make_shared<Virus<TSeq>>(*p.virus);
+
14330  virus->set_agent(this);
+
14331  }
+
14332 
14333 
-
14334  sampled_agents.clear();
-
14335  sampled_agents_n = 0;
-
14336  sampled_agents_left_n = 0;
-
14337  date_last_build_sample = -99;
-
14338 
-
14339  // neighbors = other_agent.neighbors;
-
14340  // entities = other_agent.entities;
-
14341  // entities_locations = other_agent.entities_locations;
-
14342  // n_entities = other_agent.n_entities;
-
14343  state = other_agent.state;
-
14344  state_prev = other_agent.state_prev;
-
14345  state_last_changed = other_agent.state_last_changed;
-
14346  id = other_agent.id;
-
14347 
-
14348  if (other_agent.virus != nullptr)
-
14349  {
-
14350  virus = std::make_shared<Virus<TSeq>>(*other_agent.virus);
-
14351  virus->set_agent(this);
-
14352  } else
-
14353  virus = nullptr;
-
14354 
-
14355  // tools = other_agent.tools;
-
14356  n_tools = other_agent.n_tools;
-
14357  for (size_t i = 0u; i < n_tools; ++i)
-
14358  {
-
14359  tools[i] = std::make_shared<Tool<TSeq>>(*other_agent.tools[i]);
-
14360  tools[i]->set_agent(this, i);
-
14361  }
-
14362 
-
14363  return *this;
-
14364 
-
14365 }
-
14366 
-
14367 template<typename TSeq>
-
14368 inline void Agent<TSeq>::add_tool(
-
14369  ToolPtr<TSeq> tool,
-
14370  Model<TSeq> * model,
-
14371  epiworld_fast_int state_new,
-
14372  epiworld_fast_int queue
-
14373 ) {
-
14374 
-
14375  // Checking the virus exists
-
14376  if (tool->get_id() >= static_cast<int>(model->get_db().get_n_tools()))
-
14377  throw std::range_error("The tool with id: " + std::to_string(tool->get_id()) +
-
14378  " has not been registered. There are only " + std::to_string(model->get_n_tools()) +
-
14379  " included in the model.");
-
14380 
-
14381  CHECK_COALESCE_(state_new, tool->state_init, state);
-
14382  CHECK_COALESCE_(queue, tool->queue_init, Queue<TSeq>::NoOne);
-
14383 
-
14384  model->events_add(
-
14385  this, nullptr, tool, nullptr, state_new, queue, default_add_tool<TSeq>, -1, -1
-
14386  );
-
14387 
-
14388 }
-
14389 
-
14390 template<typename TSeq>
-
14391 inline void Agent<TSeq>::add_tool(
-
14392  Tool<TSeq> tool,
-
14393  Model<TSeq> * model,
-
14394  epiworld_fast_int state_new,
-
14395  epiworld_fast_int queue
-
14396 )
-
14397 {
-
14398  ToolPtr<TSeq> tool_ptr = std::make_shared< Tool<TSeq> >(tool);
-
14399  add_tool(tool_ptr, model, state_new, queue);
-
14400 }
-
14401 
-
14402 template<typename TSeq>
-
14403 inline void Agent<TSeq>::set_virus(
-
14404  VirusPtr<TSeq> virus,
-
14405  Model<TSeq> * model,
-
14406  epiworld_fast_int state_new,
-
14407  epiworld_fast_int queue
-
14408 )
-
14409 {
+
14334  tools.reserve(p.get_n_tools());
+
14335  n_tools = tools.size();
+
14336  for (size_t i = 0u; i < n_tools; ++i)
+
14337  {
+
14338 
+
14339  // Will create a copy of the virus, with the exeption of
+
14340  // the virus code
+
14341  tools.emplace_back(std::make_shared<Tool<TSeq>>(*p.tools[i]));
+
14342  tools.back()->set_agent(this, i);
+
14343 
+
14344  }
+
14345 
+
14346 }
+
14347 
+
14348 template<typename TSeq>
+
14349 inline Agent<TSeq> & Agent<TSeq>::operator=(
+
14350  const Agent<TSeq> & other_agent
+
14351 )
+
14352 {
+
14353 
+
14354  model = other_agent.model;
+
14355 
+
14356  neighbors = other_agent.neighbors;
+
14357  neighbors_locations = other_agent.neighbors_locations;
+
14358  n_neighbors = other_agent.n_neighbors;
+
14359 
+
14360  entities = other_agent.entities;
+
14361  entities_locations = other_agent.entities_locations;
+
14362  n_entities = other_agent.n_entities;
+
14363 
+
14364  sampled_agents.clear();
+
14365  sampled_agents_n = 0;
+
14366  sampled_agents_left_n = 0;
+
14367  date_last_build_sample = -99;
+
14368 
+
14369  // neighbors = other_agent.neighbors;
+
14370  // entities = other_agent.entities;
+
14371  // entities_locations = other_agent.entities_locations;
+
14372  // n_entities = other_agent.n_entities;
+
14373  state = other_agent.state;
+
14374  state_prev = other_agent.state_prev;
+
14375  state_last_changed = other_agent.state_last_changed;
+
14376  id = other_agent.id;
+
14377 
+
14378  if (other_agent.virus != nullptr)
+
14379  {
+
14380  virus = std::make_shared<Virus<TSeq>>(*other_agent.virus);
+
14381  virus->set_agent(this);
+
14382  } else
+
14383  virus = nullptr;
+
14384 
+
14385  // tools = other_agent.tools;
+
14386  n_tools = other_agent.n_tools;
+
14387  for (size_t i = 0u; i < n_tools; ++i)
+
14388  {
+
14389  tools[i] = std::make_shared<Tool<TSeq>>(*other_agent.tools[i]);
+
14390  tools[i]->set_agent(this, i);
+
14391  }
+
14392 
+
14393  return *this;
+
14394 
+
14395 }
+
14396 
+
14397 template<typename TSeq>
+
14398 inline void Agent<TSeq>::add_tool(
+
14399  ToolPtr<TSeq> tool,
+
14400  Model<TSeq> * model,
+
14401  epiworld_fast_int state_new,
+
14402  epiworld_fast_int queue
+
14403 ) {
+
14404 
+
14405  // Checking the virus exists
+
14406  if (tool->get_id() >= static_cast<int>(model->get_db().get_n_tools()))
+
14407  throw std::range_error("The tool with id: " + std::to_string(tool->get_id()) +
+
14408  " has not been registered. There are only " + std::to_string(model->get_n_tools()) +
+
14409  " included in the model.");
14410 
-
14411  // Checking the virus exists
-
14412  if (virus->get_id() >= static_cast<int>(model->get_db().get_n_viruses()))
-
14413  throw std::range_error("The virus with id: " + std::to_string(virus->get_id()) +
-
14414  " has not been registered. There are only " + std::to_string(model->get_n_viruses()) +
-
14415  " included in the model.");
-
14416 
-
14417  CHECK_COALESCE_(state_new, virus->state_init, state);
-
14418  CHECK_COALESCE_(queue, virus->queue_init, Queue<TSeq>::NoOne);
+
14411  CHECK_COALESCE_(state_new, tool->state_init, state);
+
14412  CHECK_COALESCE_(queue, tool->queue_init, Queue<TSeq>::NoOne);
+
14413 
+
14414  model->events_add(
+
14415  this, nullptr, tool, nullptr, state_new, queue, default_add_tool<TSeq>, -1, -1
+
14416  );
+
14417 
+
14418 }
14419 
-
14420  model->events_add(
-
14421  this, virus, nullptr, nullptr, state_new, queue, default_add_virus<TSeq>, -1, -1
-
14422  );
-
14423 
-
14424 }
-
14425 
-
14426 template<typename TSeq>
-
14427 inline void Agent<TSeq>::set_virus(
-
14428  Virus<TSeq> virus,
-
14429  Model<TSeq> * model,
-
14430  epiworld_fast_int state_new,
-
14431  epiworld_fast_int queue
-
14432 )
-
14433 {
-
14434  VirusPtr<TSeq> virus_ptr = std::make_shared< Virus<TSeq> >(virus);
-
14435  set_virus(virus_ptr, model, state_new, queue);
-
14436 }
-
14437 
-
14438 template<typename TSeq>
-
14439 inline void Agent<TSeq>::add_entity(
-
14440  Entity<TSeq> & entity,
-
14441  Model<TSeq> * model,
-
14442  epiworld_fast_int state_new,
-
14443  epiworld_fast_int queue
-
14444 )
-
14445 {
+
14420 template<typename TSeq>
+
14421 inline void Agent<TSeq>::add_tool(
+
14422  Tool<TSeq> tool,
+
14423  Model<TSeq> * model,
+
14424  epiworld_fast_int state_new,
+
14425  epiworld_fast_int queue
+
14426 )
+
14427 {
+
14428  ToolPtr<TSeq> tool_ptr = std::make_shared< Tool<TSeq> >(tool);
+
14429  add_tool(tool_ptr, model, state_new, queue);
+
14430 }
+
14431 
+
14432 template<typename TSeq>
+
14433 inline void Agent<TSeq>::set_virus(
+
14434  VirusPtr<TSeq> virus,
+
14435  Model<TSeq> * model,
+
14436  epiworld_fast_int state_new,
+
14437  epiworld_fast_int queue
+
14438 )
+
14439 {
+
14440 
+
14441  // Checking the virus exists
+
14442  if (virus->get_id() >= static_cast<int>(model->get_db().get_n_viruses()))
+
14443  throw std::range_error("The virus with id: " + std::to_string(virus->get_id()) +
+
14444  " has not been registered. There are only " + std::to_string(model->get_n_viruses()) +
+
14445  " included in the model.");
14446 
-
14447  CHECK_COALESCE_(state_new, entity.state_init, state);
-
14448  CHECK_COALESCE_(queue, entity.queue_init, Queue<TSeq>::NoOne);
+
14447  CHECK_COALESCE_(state_new, virus->state_init, state);
+
14448  CHECK_COALESCE_(queue, virus->queue_init, Queue<TSeq>::NoOne);
14449 
-
14450  if (model != nullptr)
-
14451  {
-
14452 
-
14453  model->events_add(
-
14454  this, nullptr, nullptr, &entity, state_new, queue, default_add_entity<TSeq>, -1, -1
-
14455  );
-
14456 
-
14457  }
-
14458  else // If no model is passed, then we assume that we only need to add the
-
14459  // model entity
-
14460  {
-
14461 
-
14462  Event<TSeq> a(
-
14463  this, nullptr, nullptr, &entity, state_new, queue, default_add_entity<TSeq>,
-
14464  -1, -1
-
14465  );
-
14466 
-
14467  default_add_entity(a, model); /* passing model makes nothing */
-
14468 
-
14469  }
-
14470 
-
14471 }
-
14472 
-
14473 template<typename TSeq>
-
14474 inline void Agent<TSeq>::rm_tool(
-
14475  epiworld_fast_uint tool_idx,
-
14476  Model<TSeq> * model,
-
14477  epiworld_fast_int state_new,
-
14478  epiworld_fast_int queue
-
14479 )
-
14480 {
-
14481 
-
14482  CHECK_COALESCE_(state_new, tools[tool_idx]->state_post, state);
-
14483  CHECK_COALESCE_(queue, tools[tool_idx]->queue_post, Queue<TSeq>::NoOne);
-
14484 
-
14485  if (tool_idx >= n_tools)
-
14486  throw std::range_error(
-
14487  "The Tool you want to remove is out of range. This Agent only has " +
-
14488  std::to_string(n_tools) + " tools."
-
14489  );
-
14490 
-
14491  model->events_add(
-
14492  this, nullptr, tools[tool_idx], nullptr, state_new, queue, default_rm_tool<TSeq>, -1, -1
-
14493  );
-
14494 
-
14495 }
-
14496 
-
14497 template<typename TSeq>
-
14498 inline void Agent<TSeq>::rm_tool(
-
14499  ToolPtr<TSeq> & tool,
-
14500  Model<TSeq> * model,
-
14501  epiworld_fast_int state_new,
-
14502  epiworld_fast_int queue
-
14503 )
-
14504 {
-
14505 
-
14506  if (tool->agent != this)
-
14507  throw std::logic_error("Cannot remove a virus from another agent!");
-
14508 
-
14509  model->events_add(
-
14510  this, nullptr, tool, nullptr, state_new, queue, default_rm_tool<TSeq>, -1, -1
-
14511  );
-
14512 
-
14513 }
+
14450  model->events_add(
+
14451  this, virus, nullptr, nullptr, state_new, queue, default_add_virus<TSeq>, -1, -1
+
14452  );
+
14453 
+
14454 }
+
14455 
+
14456 template<typename TSeq>
+
14457 inline void Agent<TSeq>::set_virus(
+
14458  Virus<TSeq> virus,
+
14459  Model<TSeq> * model,
+
14460  epiworld_fast_int state_new,
+
14461  epiworld_fast_int queue
+
14462 )
+
14463 {
+
14464  VirusPtr<TSeq> virus_ptr = std::make_shared< Virus<TSeq> >(virus);
+
14465  set_virus(virus_ptr, model, state_new, queue);
+
14466 }
+
14467 
+
14468 template<typename TSeq>
+
14469 inline void Agent<TSeq>::add_entity(
+
14470  Entity<TSeq> & entity,
+
14471  Model<TSeq> * model,
+
14472  epiworld_fast_int state_new,
+
14473  epiworld_fast_int queue
+
14474 )
+
14475 {
+
14476 
+
14477  CHECK_COALESCE_(state_new, entity.state_init, state);
+
14478  CHECK_COALESCE_(queue, entity.queue_init, Queue<TSeq>::NoOne);
+
14479 
+
14480  if (model != nullptr)
+
14481  {
+
14482 
+
14483  model->events_add(
+
14484  this, nullptr, nullptr, &entity, state_new, queue, default_add_entity<TSeq>, -1, -1
+
14485  );
+
14486 
+
14487  }
+
14488  else // If no model is passed, then we assume that we only need to add the
+
14489  // model entity
+
14490  {
+
14491 
+
14492  Event<TSeq> a(
+
14493  this, nullptr, nullptr, &entity, state_new, queue, default_add_entity<TSeq>,
+
14494  -1, -1
+
14495  );
+
14496 
+
14497  default_add_entity(a, model); /* passing model makes nothing */
+
14498 
+
14499  }
+
14500 
+
14501 }
+
14502 
+
14503 template<typename TSeq>
+
14504 inline void Agent<TSeq>::rm_tool(
+
14505  epiworld_fast_uint tool_idx,
+
14506  Model<TSeq> * model,
+
14507  epiworld_fast_int state_new,
+
14508  epiworld_fast_int queue
+
14509 )
+
14510 {
+
14511 
+
14512  CHECK_COALESCE_(state_new, tools[tool_idx]->state_post, state);
+
14513  CHECK_COALESCE_(queue, tools[tool_idx]->queue_post, Queue<TSeq>::NoOne);
14514 
-
14515 template<typename TSeq>
-
14516 inline void Agent<TSeq>::rm_virus(
-
14517  Model<TSeq> * model,
-
14518  epiworld_fast_int state_new,
-
14519  epiworld_fast_int queue
-
14520 )
-
14521 {
-
14522 
-
14523  if (virus == nullptr)
-
14524  throw std::logic_error(
-
14525  "There is no virus to remove here!"
-
14526  );
-
14527 
-
14528  CHECK_COALESCE_(state_new, virus->state_post, state);
-
14529  CHECK_COALESCE_(queue, virus->queue_post, Queue<TSeq>::Everyone);
-
14530 
-
14531  model->events_add(
-
14532  this, virus, nullptr, nullptr, state_new, queue,
-
14533  default_rm_virus<TSeq>, -1, -1
-
14534  );
-
14535 
-
14536 }
-
14537 
-
14538 template<typename TSeq>
-
14539 inline void Agent<TSeq>::rm_entity(
-
14540  epiworld_fast_uint entity_idx,
-
14541  Model<TSeq> * model,
-
14542  epiworld_fast_int state_new,
-
14543  epiworld_fast_int queue
-
14544 )
-
14545 {
-
14546 
-
14547  if (entity_idx >= n_entities)
-
14548  throw std::range_error(
-
14549  "The Entity you want to remove is out of range. This Agent only has " +
-
14550  std::to_string(n_entities) + " entitites."
-
14551  );
-
14552  else if (n_entities == 0u)
-
14553  throw std::logic_error(
-
14554  "There is entity to remove here!"
-
14555  );
-
14556 
-
14557  CHECK_COALESCE_(state_new, model->get_entity(entity_idx).state_post, state);
-
14558  CHECK_COALESCE_(queue, model->get_entity(entity_idx).queue_post, Queue<TSeq>::NoOne);
-
14559 
-
14560  model->events_add(
-
14561  this,
-
14562  nullptr,
-
14563  nullptr,
-
14564  &model->get_entity(entity_idx),
-
14565  state_new,
-
14566  queue,
-
14567  default_rm_entity<TSeq>,
-
14568  entities_locations[entity_idx],
-
14569  entity_idx
-
14570  );
-
14571 }
-
14572 
-
14573 template<typename TSeq>
-
14574 inline void Agent<TSeq>::rm_entity(
-
14575  Entity<TSeq> & entity,
-
14576  Model<TSeq> * model,
-
14577  epiworld_fast_int state_new,
-
14578  epiworld_fast_int queue
-
14579 )
-
14580 {
-
14581 
-
14582  // Looking for entity location in the agent
-
14583  int entity_idx = -1;
-
14584  for (size_t i = 0u; i < n_entities; ++i)
-
14585  {
-
14586  if (static_cast<int>(entities[i]) == entity.get_id())
-
14587  {
-
14588  entity_idx = i;
-
14589  break;
-
14590  }
-
14591  }
-
14592 
-
14593  if (entity_idx == -1)
-
14594  throw std::logic_error(
-
14595  std::string("The agent ") +
-
14596  std::to_string(id) +
-
14597  std::string(" is not associated with entity \"") +
-
14598  entity.get_name() +
-
14599  std::string("\".")
-
14600  );
-
14601 
-
14602  CHECK_COALESCE_(state_new, entity.state_post, state);
-
14603  CHECK_COALESCE_(queue, entity.queue_post, Queue<TSeq>::NoOne);
-
14604 
-
14605  model->events_add(
-
14606  this,
-
14607  nullptr,
-
14608  nullptr,
-
14609  &model->entities[entity.get_id()],
-
14610  state_new,
-
14611  queue,
-
14612  default_rm_entity<TSeq>,
-
14613  entities_locations[entity_idx],
-
14614  entity_idx
-
14615  );
-
14616 }
-
14617 
-
14618 template<typename TSeq>
-
14619 inline void Agent<TSeq>::rm_agent_by_virus(
-
14620  Model<TSeq> * model,
-
14621  epiworld_fast_int state_new,
-
14622  epiworld_fast_int queue
-
14623 )
-
14624 {
-
14625 
-
14626  CHECK_COALESCE_(state_new, virus->state_removed, state);
-
14627  CHECK_COALESCE_(queue, virus->queue_removed, Queue<TSeq>::Everyone);
-
14628 
-
14629  model->events_add(
-
14630  this, virus, nullptr, nullptr, state_new, queue,
-
14631  default_rm_virus<TSeq>, -1, -1
-
14632  );
-
14633 
-
14634 }
-
14635 
-
14636 template<typename TSeq>
-
14637 inline epiworld_double Agent<TSeq>::get_susceptibility_reduction(
-
14638  VirusPtr<TSeq> v,
-
14639  Model<TSeq> * model
-
14640 ) {
-
14641 
-
14642  return model->susceptibility_reduction_mixer(this, v, model);
-
14643 }
-
14644 
-
14645 template<typename TSeq>
-
14646 inline epiworld_double Agent<TSeq>::get_transmission_reduction(
-
14647  VirusPtr<TSeq> v,
-
14648  Model<TSeq> * model
-
14649 ) {
-
14650  return model->transmission_reduction_mixer(this, v, model);
-
14651 }
-
14652 
-
14653 template<typename TSeq>
-
14654 inline epiworld_double Agent<TSeq>::get_recovery_enhancer(
-
14655  VirusPtr<TSeq> v,
-
14656  Model<TSeq> * model
-
14657 ) {
-
14658  return model->recovery_enhancer_mixer(this, v, model);
-
14659 }
-
14660 
-
14661 template<typename TSeq>
-
14662 inline epiworld_double Agent<TSeq>::get_death_reduction(
-
14663  VirusPtr<TSeq> v,
-
14664  Model<TSeq> * model
-
14665 ) {
-
14666  return model->death_reduction_mixer(this, v, model);
-
14667 }
-
14668 
-
14669 template<typename TSeq>
-
14670 inline int Agent<TSeq>::get_id() const
-
14671 {
-
14672  return id;
+
14515  if (tool_idx >= n_tools)
+
14516  throw std::range_error(
+
14517  "The Tool you want to remove is out of range. This Agent only has " +
+
14518  std::to_string(n_tools) + " tools."
+
14519  );
+
14520 
+
14521  model->events_add(
+
14522  this, nullptr, tools[tool_idx], nullptr, state_new, queue, default_rm_tool<TSeq>, -1, -1
+
14523  );
+
14524 
+
14525 }
+
14526 
+
14527 template<typename TSeq>
+
14528 inline void Agent<TSeq>::rm_tool(
+
14529  ToolPtr<TSeq> & tool,
+
14530  Model<TSeq> * model,
+
14531  epiworld_fast_int state_new,
+
14532  epiworld_fast_int queue
+
14533 )
+
14534 {
+
14535 
+
14536  if (tool->agent != this)
+
14537  throw std::logic_error("Cannot remove a virus from another agent!");
+
14538 
+
14539  model->events_add(
+
14540  this, nullptr, tool, nullptr, state_new, queue, default_rm_tool<TSeq>, -1, -1
+
14541  );
+
14542 
+
14543 }
+
14544 
+
14545 template<typename TSeq>
+
14546 inline void Agent<TSeq>::rm_virus(
+
14547  Model<TSeq> * model,
+
14548  epiworld_fast_int state_new,
+
14549  epiworld_fast_int queue
+
14550 )
+
14551 {
+
14552 
+
14553  if (virus == nullptr)
+
14554  throw std::logic_error(
+
14555  "There is no virus to remove here!"
+
14556  );
+
14557 
+
14558  CHECK_COALESCE_(state_new, virus->state_post, state);
+
14559  CHECK_COALESCE_(queue, virus->queue_post, Queue<TSeq>::Everyone);
+
14560 
+
14561  model->events_add(
+
14562  this, virus, nullptr, nullptr, state_new, queue,
+
14563  default_rm_virus<TSeq>, -1, -1
+
14564  );
+
14565 
+
14566 }
+
14567 
+
14568 template<typename TSeq>
+
14569 inline void Agent<TSeq>::rm_entity(
+
14570  epiworld_fast_uint entity_idx,
+
14571  Model<TSeq> * model,
+
14572  epiworld_fast_int state_new,
+
14573  epiworld_fast_int queue
+
14574 )
+
14575 {
+
14576 
+
14577  if (entity_idx >= n_entities)
+
14578  throw std::range_error(
+
14579  "The Entity you want to remove is out of range. This Agent only has " +
+
14580  std::to_string(n_entities) + " entitites."
+
14581  );
+
14582  else if (n_entities == 0u)
+
14583  throw std::logic_error(
+
14584  "There is entity to remove here!"
+
14585  );
+
14586 
+
14587  CHECK_COALESCE_(state_new, model->get_entity(entity_idx).state_post, state);
+
14588  CHECK_COALESCE_(queue, model->get_entity(entity_idx).queue_post, Queue<TSeq>::NoOne);
+
14589 
+
14590  model->events_add(
+
14591  this,
+
14592  nullptr,
+
14593  nullptr,
+
14594  &model->get_entity(entity_idx),
+
14595  state_new,
+
14596  queue,
+
14597  default_rm_entity<TSeq>,
+
14598  entities_locations[entity_idx],
+
14599  entity_idx
+
14600  );
+
14601 }
+
14602 
+
14603 template<typename TSeq>
+
14604 inline void Agent<TSeq>::rm_entity(
+
14605  Entity<TSeq> & entity,
+
14606  Model<TSeq> * model,
+
14607  epiworld_fast_int state_new,
+
14608  epiworld_fast_int queue
+
14609 )
+
14610 {
+
14611 
+
14612  // Looking for entity location in the agent
+
14613  int entity_idx = -1;
+
14614  for (size_t i = 0u; i < n_entities; ++i)
+
14615  {
+
14616  if (static_cast<int>(entities[i]) == entity.get_id())
+
14617  {
+
14618  entity_idx = i;
+
14619  break;
+
14620  }
+
14621  }
+
14622 
+
14623  if (entity_idx == -1)
+
14624  throw std::logic_error(
+
14625  std::string("The agent ") +
+
14626  std::to_string(id) +
+
14627  std::string(" is not associated with entity \"") +
+
14628  entity.get_name() +
+
14629  std::string("\".")
+
14630  );
+
14631 
+
14632  CHECK_COALESCE_(state_new, entity.state_post, state);
+
14633  CHECK_COALESCE_(queue, entity.queue_post, Queue<TSeq>::NoOne);
+
14634 
+
14635  model->events_add(
+
14636  this,
+
14637  nullptr,
+
14638  nullptr,
+
14639  &model->entities[entity.get_id()],
+
14640  state_new,
+
14641  queue,
+
14642  default_rm_entity<TSeq>,
+
14643  entities_locations[entity_idx],
+
14644  entity_idx
+
14645  );
+
14646 }
+
14647 
+
14648 template<typename TSeq>
+
14649 inline void Agent<TSeq>::rm_agent_by_virus(
+
14650  Model<TSeq> * model,
+
14651  epiworld_fast_int state_new,
+
14652  epiworld_fast_int queue
+
14653 )
+
14654 {
+
14655 
+
14656  CHECK_COALESCE_(state_new, virus->state_removed, state);
+
14657  CHECK_COALESCE_(queue, virus->queue_removed, Queue<TSeq>::Everyone);
+
14658 
+
14659  model->events_add(
+
14660  this, virus, nullptr, nullptr, state_new, queue,
+
14661  default_rm_virus<TSeq>, -1, -1
+
14662  );
+
14663 
+
14664 }
+
14665 
+
14666 template<typename TSeq>
+
14667 inline epiworld_double Agent<TSeq>::get_susceptibility_reduction(
+
14668  VirusPtr<TSeq> v,
+
14669  Model<TSeq> * model
+
14670 ) {
+
14671 
+
14672  return model->susceptibility_reduction_mixer(this, v, model);
14673 }
14674 
14675 template<typename TSeq>
-
14676 inline VirusPtr<TSeq> & Agent<TSeq>::get_virus() {
-
14677  return virus;
-
14678 }
-
14679 
-
14680 template<typename TSeq>
-
14681 inline const VirusPtr<TSeq> & Agent<TSeq>::get_virus() const {
-
14682  return virus;
-
14683 }
-
14684 
-
14685 
-
14686 template<typename TSeq>
-
14687 inline Tools<TSeq> Agent<TSeq>::get_tools() {
-
14688  return Tools<TSeq>(*this);
+
14676 inline epiworld_double Agent<TSeq>::get_transmission_reduction(
+
14677  VirusPtr<TSeq> v,
+
14678  Model<TSeq> * model
+
14679 ) {
+
14680  return model->transmission_reduction_mixer(this, v, model);
+
14681 }
+
14682 
+
14683 template<typename TSeq>
+
14684 inline epiworld_double Agent<TSeq>::get_recovery_enhancer(
+
14685  VirusPtr<TSeq> v,
+
14686  Model<TSeq> * model
+
14687 ) {
+
14688  return model->recovery_enhancer_mixer(this, v, model);
14689 }
14690 
14691 template<typename TSeq>
-
14692 inline const Tools_const<TSeq> Agent<TSeq>::get_tools() const {
-
14693  return Tools_const<TSeq>(*this);
-
14694 }
-
14695 
-
14696 template<typename TSeq>
-
14697 inline ToolPtr<TSeq> & Agent<TSeq>::get_tool(int i)
-
14698 {
-
14699  return tools.at(i);
-
14700 }
-
14701 
-
14702 template<typename TSeq>
-
14703 inline size_t Agent<TSeq>::get_n_tools() const noexcept
-
14704 {
-
14705  return n_tools;
-
14706 }
-
14707 
-
14708 template<typename TSeq>
-
14709 inline void Agent<TSeq>::mutate_virus()
-
14710 {
-
14711 
-
14712  virus->mutate();
-
14713 
-
14714 }
+
14692 inline epiworld_double Agent<TSeq>::get_death_reduction(
+
14693  VirusPtr<TSeq> v,
+
14694  Model<TSeq> * model
+
14695 ) {
+
14696  return model->death_reduction_mixer(this, v, model);
+
14697 }
+
14698 
+
14699 template<typename TSeq>
+
14700 inline int Agent<TSeq>::get_id() const
+
14701 {
+
14702  return id;
+
14703 }
+
14704 
+
14705 template<typename TSeq>
+
14706 inline VirusPtr<TSeq> & Agent<TSeq>::get_virus() {
+
14707  return virus;
+
14708 }
+
14709 
+
14710 template<typename TSeq>
+
14711 inline const VirusPtr<TSeq> & Agent<TSeq>::get_virus() const {
+
14712  return virus;
+
14713 }
+
14714 
14715 
14716 template<typename TSeq>
-
14717 inline void Agent<TSeq>::add_neighbor(
-
14718  Agent<TSeq> & p,
-
14719  bool check_source,
-
14720  bool check_target
-
14721 ) {
-
14722  // Can we find the neighbor?
-
14723  bool found = false;
-
14724  if (check_source)
-
14725  {
-
14726 
-
14727  for (auto & n: neighbors)
-
14728  if (static_cast<int>(n) == p.get_id())
-
14729  {
-
14730  found = true;
-
14731  break;
-
14732  }
-
14733 
-
14734  }
-
14735 
-
14736  // Three things going on here:
-
14737  // - Where in the neighbor will this be
-
14738  // - What is the neighbor's id
-
14739  // - Increasing the number of neighbors
-
14740  if (!found)
-
14741  {
-
14742 
-
14743  neighbors_locations.push_back(p.get_n_neighbors());
-
14744  neighbors.push_back(p.get_id());
-
14745  n_neighbors++;
-
14746 
-
14747  }
-
14748 
-
14749 
-
14750  found = false;
-
14751  if (check_target)
-
14752  {
-
14753 
-
14754  for (auto & n: p.neighbors)
-
14755  if (static_cast<int>(n) == id)
-
14756  {
-
14757  found = true;
-
14758  break;
-
14759  }
-
14760 
-
14761  }
-
14762 
-
14763  if (!found)
-
14764  {
+
14717 inline Tools<TSeq> Agent<TSeq>::get_tools() {
+
14718  return Tools<TSeq>(*this);
+
14719 }
+
14720 
+
14721 template<typename TSeq>
+
14722 inline const Tools_const<TSeq> Agent<TSeq>::get_tools() const {
+
14723  return Tools_const<TSeq>(*this);
+
14724 }
+
14725 
+
14726 template<typename TSeq>
+
14727 inline ToolPtr<TSeq> & Agent<TSeq>::get_tool(int i)
+
14728 {
+
14729  return tools.at(i);
+
14730 }
+
14731 
+
14732 template<typename TSeq>
+
14733 inline size_t Agent<TSeq>::get_n_tools() const noexcept
+
14734 {
+
14735  return n_tools;
+
14736 }
+
14737 
+
14738 template<typename TSeq>
+
14739 inline void Agent<TSeq>::mutate_virus()
+
14740 {
+
14741 
+
14742  virus->mutate();
+
14743 
+
14744 }
+
14745 
+
14746 template<typename TSeq>
+
14747 inline void Agent<TSeq>::add_neighbor(
+
14748  Agent<TSeq> & p,
+
14749  bool check_source,
+
14750  bool check_target
+
14751 ) {
+
14752  // Can we find the neighbor?
+
14753  bool found = false;
+
14754  if (check_source)
+
14755  {
+
14756 
+
14757  for (auto & n: neighbors)
+
14758  if (static_cast<int>(n) == p.get_id())
+
14759  {
+
14760  found = true;
+
14761  break;
+
14762  }
+
14763 
+
14764  }
14765 
-
14766  p.neighbors_locations.push_back(n_neighbors - 1);
-
14767  p.neighbors.push_back(id);
-
14768  p.n_neighbors++;
-
14769 
-
14770  }
-
14771 
+
14766  // Three things going on here:
+
14767  // - Where in the neighbor will this be
+
14768  // - What is the neighbor's id
+
14769  // - Increasing the number of neighbors
+
14770  if (!found)
+
14771  {
14772 
-
14773 }
-
14774 
-
14775 template<typename TSeq>
-
14776 inline void Agent<TSeq>::swap_neighbors(
-
14777  Agent<TSeq> & other,
-
14778  size_t n_this,
-
14779  size_t n_other
-
14780 )
-
14781 {
-
14782 
-
14783  // Getting the agents
-
14784  auto & pop = model->population;
-
14785  auto & neigh_this = pop[neighbors[n_this]];
-
14786  auto & neigh_other = pop[other.neighbors[n_other]];
-
14787 
-
14788  // Getting the locations in the neighbors
-
14789  size_t loc_this_in_neigh = neighbors_locations[n_this];
-
14790  size_t loc_other_in_neigh = other.neighbors_locations[n_other];
-
14791 
-
14792  // Changing ids
-
14793  std::swap(neighbors[n_this], other.neighbors[n_other]);
-
14794 
-
14795  if (!model->directed)
-
14796  {
-
14797  std::swap(
-
14798  neigh_this.neighbors[loc_this_in_neigh],
-
14799  neigh_other.neighbors[loc_other_in_neigh]
-
14800  );
-
14801 
-
14802  // Changing the locations
-
14803  std::swap(neighbors_locations[n_this], other.neighbors_locations[n_other]);
-
14804 
-
14805  std::swap(
-
14806  neigh_this.neighbors_locations[loc_this_in_neigh],
-
14807  neigh_other.neighbors_locations[loc_other_in_neigh]
-
14808  );
-
14809  }
-
14810 
-
14811 }
+
14773  neighbors_locations.push_back(p.get_n_neighbors());
+
14774  neighbors.push_back(p.get_id());
+
14775  n_neighbors++;
+
14776 
+
14777  }
+
14778 
+
14779 
+
14780  found = false;
+
14781  if (check_target)
+
14782  {
+
14783 
+
14784  for (auto & n: p.neighbors)
+
14785  if (static_cast<int>(n) == id)
+
14786  {
+
14787  found = true;
+
14788  break;
+
14789  }
+
14790 
+
14791  }
+
14792 
+
14793  if (!found)
+
14794  {
+
14795 
+
14796  p.neighbors_locations.push_back(n_neighbors - 1);
+
14797  p.neighbors.push_back(id);
+
14798  p.n_neighbors++;
+
14799 
+
14800  }
+
14801 
+
14802 
+
14803 }
+
14804 
+
14805 template<typename TSeq>
+
14806 inline void Agent<TSeq>::swap_neighbors(
+
14807  Agent<TSeq> & other,
+
14808  size_t n_this,
+
14809  size_t n_other
+
14810 )
+
14811 {
14812 
-
14813 template<typename TSeq>
-
14814 inline std::vector< Agent<TSeq> *> Agent<TSeq>::get_neighbors()
-
14815 {
-
14816  std::vector< Agent<TSeq> * > res(n_neighbors, nullptr);
-
14817  for (size_t i = 0u; i < n_neighbors; ++i)
-
14818  res[i] = &model->population[neighbors[i]];
-
14819 
-
14820  return res;
-
14821 }
-
14822 
-
14823 template<typename TSeq>
-
14824 inline size_t Agent<TSeq>::get_n_neighbors() const
-
14825 {
-
14826  return n_neighbors;
-
14827 }
-
14828 
-
14829 template<typename TSeq>
-
14830 inline void Agent<TSeq>::change_state(
-
14831  Model<TSeq> * model,
-
14832  epiworld_fast_uint new_state,
-
14833  epiworld_fast_int queue
-
14834  )
-
14835 {
-
14836 
-
14837  model->events_add(
-
14838  this, nullptr, nullptr, nullptr, new_state, queue,
-
14839  default_change_state<TSeq>, -1, -1
-
14840  );
-
14841 
-
14842  return;
-
14843 
-
14844 }
-
14845 
-
14846 template<typename TSeq>
-
14847 inline const epiworld_fast_uint & Agent<TSeq>::get_state() const {
-
14848  return state;
-
14849 }
-
14850 
-
14851 template<typename TSeq>
-
14852 inline void Agent<TSeq>::reset()
-
14853 {
-
14854 
-
14855  this->virus = nullptr;
-
14856 
-
14857  this->tools.clear();
-
14858  n_tools = 0u;
-
14859 
-
14860  this->entities.clear();
-
14861  this->entities_locations.clear();
-
14862  this->n_entities = 0u;
-
14863 
-
14864  this->state = 0u;
-
14865  this->state_prev = 0u;
+
14813  // Getting the agents
+
14814  auto & pop = model->population;
+
14815  auto & neigh_this = pop[neighbors[n_this]];
+
14816  auto & neigh_other = pop[other.neighbors[n_other]];
+
14817 
+
14818  // Getting the locations in the neighbors
+
14819  size_t loc_this_in_neigh = neighbors_locations[n_this];
+
14820  size_t loc_other_in_neigh = other.neighbors_locations[n_other];
+
14821 
+
14822  // Changing ids
+
14823  std::swap(neighbors[n_this], other.neighbors[n_other]);
+
14824 
+
14825  if (!model->directed)
+
14826  {
+
14827  std::swap(
+
14828  neigh_this.neighbors[loc_this_in_neigh],
+
14829  neigh_other.neighbors[loc_other_in_neigh]
+
14830  );
+
14831 
+
14832  // Changing the locations
+
14833  std::swap(neighbors_locations[n_this], other.neighbors_locations[n_other]);
+
14834 
+
14835  std::swap(
+
14836  neigh_this.neighbors_locations[loc_this_in_neigh],
+
14837  neigh_other.neighbors_locations[loc_other_in_neigh]
+
14838  );
+
14839  }
+
14840 
+
14841 }
+
14842 
+
14843 template<typename TSeq>
+
14844 inline std::vector< Agent<TSeq> *> Agent<TSeq>::get_neighbors()
+
14845 {
+
14846  std::vector< Agent<TSeq> * > res(n_neighbors, nullptr);
+
14847  for (size_t i = 0u; i < n_neighbors; ++i)
+
14848  res[i] = &model->population[neighbors[i]];
+
14849 
+
14850  return res;
+
14851 }
+
14852 
+
14853 template<typename TSeq>
+
14854 inline size_t Agent<TSeq>::get_n_neighbors() const
+
14855 {
+
14856  return n_neighbors;
+
14857 }
+
14858 
+
14859 template<typename TSeq>
+
14860 inline void Agent<TSeq>::change_state(
+
14861  Model<TSeq> * model,
+
14862  epiworld_fast_uint new_state,
+
14863  epiworld_fast_int queue
+
14864  )
+
14865 {
14866 
-
14867  this->state_last_changed = -1;
-
14868 
-
14869 }
-
14870 
-
14871 template<typename TSeq>
-
14872 inline bool Agent<TSeq>::has_tool(epiworld_fast_uint t) const
-
14873 {
-
14874 
-
14875  for (auto & tool : tools)
-
14876  if (tool->get_id() == static_cast<int>(t))
-
14877  return true;
-
14878 
-
14879  return false;
+
14867  model->events_add(
+
14868  this, nullptr, nullptr, nullptr, new_state, queue,
+
14869  default_change_state<TSeq>, -1, -1
+
14870  );
+
14871 
+
14872  return;
+
14873 
+
14874 }
+
14875 
+
14876 template<typename TSeq>
+
14877 inline const epiworld_fast_uint & Agent<TSeq>::get_state() const {
+
14878  return state;
+
14879 }
14880 
-
14881 }
-
14882 
-
14883 template<typename TSeq>
-
14884 inline bool Agent<TSeq>::has_tool(std::string name) const
-
14885 {
+
14881 template<typename TSeq>
+
14882 inline void Agent<TSeq>::reset()
+
14883 {
+
14884 
+
14885  this->virus = nullptr;
14886 
-
14887  for (auto & tool : tools)
-
14888  if (tool->get_name() == name)
-
14889  return true;
-
14890 
-
14891  return false;
-
14892 
-
14893 }
-
14894 
-
14895 template<typename TSeq>
-
14896 inline bool Agent<TSeq>::has_tool(const Tool<TSeq> & tool) const
-
14897 {
-
14898 
-
14899  return has_tool(tool.get_id());
+
14887  this->tools.clear();
+
14888  n_tools = 0u;
+
14889 
+
14890  this->entities.clear();
+
14891  this->entities_locations.clear();
+
14892  this->n_entities = 0u;
+
14893 
+
14894  this->state = 0u;
+
14895  this->state_prev = 0u;
+
14896 
+
14897  this->state_last_changed = -1;
+
14898 
+
14899 }
14900 
-
14901 }
-
14902 
-
14903 template<typename TSeq>
-
14904 inline bool Agent<TSeq>::has_virus(epiworld_fast_uint t) const
-
14905 {
-
14906  if (virus->get_id() == static_cast<int>(t))
-
14907  return true;
+
14901 template<typename TSeq>
+
14902 inline bool Agent<TSeq>::has_tool(epiworld_fast_uint t) const
+
14903 {
+
14904 
+
14905  for (auto & tool : tools)
+
14906  if (tool->get_id() == static_cast<int>(t))
+
14907  return true;
14908 
14909  return false;
-
14910 }
-
14911 
-
14912 template<typename TSeq>
-
14913 inline bool Agent<TSeq>::has_virus(std::string name) const
-
14914 {
-
14915 
-
14916  if (virus->get_name() == name)
-
14917  return true;
-
14918 
-
14919  return false;
+
14910 
+
14911 }
+
14912 
+
14913 template<typename TSeq>
+
14914 inline bool Agent<TSeq>::has_tool(std::string name) const
+
14915 {
+
14916 
+
14917  for (auto & tool : tools)
+
14918  if (tool->get_name() == name)
+
14919  return true;
14920 
-
14921 }
+
14921  return false;
14922 
-
14923 template<typename TSeq>
-
14924 inline bool Agent<TSeq>::has_virus(const Virus<TSeq> & virus) const
-
14925 {
-
14926 
-
14927  return has_virus(virus.get_id());
+
14923 }
+
14924 
+
14925 template<typename TSeq>
+
14926 inline bool Agent<TSeq>::has_tool(const Tool<TSeq> & tool) const
+
14927 {
14928 
-
14929 }
+
14929  return has_tool(tool.get_id());
14930 
-
14931 template<typename TSeq>
-
14932 inline bool Agent<TSeq>::has_entity(epiworld_fast_uint t) const
-
14933 {
-
14934 
-
14935  for (auto & entity : entities)
-
14936  if (entity == t)
-
14937  return true;
+
14931 }
+
14932 
+
14933 template<typename TSeq>
+
14934 inline bool Agent<TSeq>::has_virus(epiworld_fast_uint t) const
+
14935 {
+
14936  if (virus->get_id() == static_cast<int>(t))
+
14937  return true;
14938 
14939  return false;
-
14940 
-
14941 }
-
14942 
-
14943 template<typename TSeq>
-
14944 inline bool Agent<TSeq>::has_entity(std::string name) const
-
14945 {
-
14946 
-
14947  for (auto & entity : entities)
-
14948  if (model->get_entity(entity).get_name() == name)
-
14949  return true;
+
14940 }
+
14941 
+
14942 template<typename TSeq>
+
14943 inline bool Agent<TSeq>::has_virus(std::string name) const
+
14944 {
+
14945 
+
14946  if (virus->get_name() == name)
+
14947  return true;
+
14948 
+
14949  return false;
14950 
-
14951  return false;
+
14951 }
14952 
-
14953 }
-
14954 
-
14955 template<typename TSeq>
-
14956 inline void Agent<TSeq>::print(
-
14957  Model<TSeq> * model,
-
14958  bool compressed
-
14959  ) const
-
14960 {
-
14961 
-
14962  if (compressed)
-
14963  {
-
14964  printf_epiworld(
-
14965  "Agent: %i, state: %s (%i), Has virus: %s, NTools: %ii NNeigh: %i\n",
-
14966  static_cast<int>(id),
-
14967  model->states_labels[state].c_str(),
-
14968  static_cast<int>(state),
-
14969  virus == nullptr ? std::string("no").c_str() : std::string("yes").c_str(),
-
14970  static_cast<int>(n_tools),
-
14971  static_cast<int>(neighbors.size())
-
14972  );
-
14973  }
-
14974  else {
-
14975 
-
14976  printf_epiworld("Information about agent id %i\n",
-
14977  static_cast<int>(this->id));
-
14978  printf_epiworld(" State : %s (%i)\n",
-
14979  model->states_labels[state].c_str(), static_cast<int>(state));
-
14980  printf_epiworld(" Has virus : %s\n", virus == nullptr ?
-
14981  std::string("no").c_str() : std::string("yes").c_str());
-
14982  printf_epiworld(" Tool count : %i\n", static_cast<int>(n_tools));
-
14983  printf_epiworld(" Neigh. count : %i\n", static_cast<int>(neighbors.size()));
+
14953 template<typename TSeq>
+
14954 inline bool Agent<TSeq>::has_virus(const Virus<TSeq> & virus) const
+
14955 {
+
14956 
+
14957  return has_virus(virus.get_id());
+
14958 
+
14959 }
+
14960 
+
14961 template<typename TSeq>
+
14962 inline bool Agent<TSeq>::has_entity(epiworld_fast_uint t) const
+
14963 {
+
14964 
+
14965  for (auto & entity : entities)
+
14966  if (entity == t)
+
14967  return true;
+
14968 
+
14969  return false;
+
14970 
+
14971 }
+
14972 
+
14973 template<typename TSeq>
+
14974 inline bool Agent<TSeq>::has_entity(std::string name) const
+
14975 {
+
14976 
+
14977  for (auto & entity : entities)
+
14978  if (model->get_entity(entity).get_name() == name)
+
14979  return true;
+
14980 
+
14981  return false;
+
14982 
+
14983 }
14984 
-
14985  size_t nfeats = model->get_agents_data_ncols();
-
14986  if (nfeats > 0)
-
14987  {
-
14988 
-
14989  printf_epiworld(
-
14990  "This model includes features (%i): [ ",
-
14991  static_cast<int>(nfeats)
-
14992  );
-
14993 
-
14994  int max_to_show = static_cast<int>((nfeats > 10)? 10 : nfeats);
-
14995 
-
14996  for (int k = 0; k < max_to_show; ++k)
-
14997  {
-
14998  printf_epiworld("%.2f", this->operator[](k));
-
14999 
-
15000  if (k != (max_to_show - 1))
-
15001  {
-
15002  printf_epiworld(", ");
-
15003  } else {
-
15004  printf_epiworld(" ]\n");
-
15005  }
-
15006 
-
15007  }
-
15008 
-
15009  }
-
15010 
-
15011  }
-
15012 
-
15013  return;
+
14985 template<typename TSeq>
+
14986 inline void Agent<TSeq>::print(
+
14987  Model<TSeq> * model,
+
14988  bool compressed
+
14989  ) const
+
14990 {
+
14991 
+
14992  if (compressed)
+
14993  {
+
14994  printf_epiworld(
+
14995  "Agent: %i, state: %s (%i), Has virus: %s, NTools: %ii NNeigh: %i\n",
+
14996  static_cast<int>(id),
+
14997  model->states_labels[state].c_str(),
+
14998  static_cast<int>(state),
+
14999  virus == nullptr ? std::string("no").c_str() : std::string("yes").c_str(),
+
15000  static_cast<int>(n_tools),
+
15001  static_cast<int>(neighbors.size())
+
15002  );
+
15003  }
+
15004  else {
+
15005 
+
15006  printf_epiworld("Information about agent id %i\n",
+
15007  static_cast<int>(this->id));
+
15008  printf_epiworld(" State : %s (%i)\n",
+
15009  model->states_labels[state].c_str(), static_cast<int>(state));
+
15010  printf_epiworld(" Has virus : %s\n", virus == nullptr ?
+
15011  std::string("no").c_str() : std::string("yes").c_str());
+
15012  printf_epiworld(" Tool count : %i\n", static_cast<int>(n_tools));
+
15013  printf_epiworld(" Neigh. count : %i\n", static_cast<int>(neighbors.size()));
15014 
-
15015 }
-
15016 
-
15017 template<typename TSeq>
-
15018 inline double & Agent<TSeq>::operator()(size_t j)
-
15019 {
-
15020 
-
15021  if (model->agents_data_ncols <= j)
-
15022  throw std::logic_error("The requested feature of the agent is out of range.");
+
15015  size_t nfeats = model->get_agents_data_ncols();
+
15016  if (nfeats > 0)
+
15017  {
+
15018 
+
15019  printf_epiworld(
+
15020  "This model includes features (%i): [ ",
+
15021  static_cast<int>(nfeats)
+
15022  );
15023 
-
15024  return *(model->agents_data + j * model->size() + id);
+
15024  int max_to_show = static_cast<int>((nfeats > 10)? 10 : nfeats);
15025 
-
15026 }
-
15027 
-
15028 template<typename TSeq>
-
15029 inline double & Agent<TSeq>::operator[](size_t j)
-
15030 {
-
15031  return *(model->agents_data + j * model->size() + id);
-
15032 }
-
15033 
-
15034 template<typename TSeq>
-
15035 inline double Agent<TSeq>::operator()(size_t j) const
-
15036 {
-
15037 
-
15038  if (model->agents_data_ncols <= j)
-
15039  throw std::logic_error("The requested feature of the agent is out of range.");
+
15026  for (int k = 0; k < max_to_show; ++k)
+
15027  {
+
15028  printf_epiworld("%.2f", this->operator[](k));
+
15029 
+
15030  if (k != (max_to_show - 1))
+
15031  {
+
15032  printf_epiworld(", ");
+
15033  } else {
+
15034  printf_epiworld(" ]\n");
+
15035  }
+
15036 
+
15037  }
+
15038 
+
15039  }
15040 
-
15041  return *(model->agents_data + j * model->size() + id);
+
15041  }
15042 
-
15043 }
+
15043  return;
15044 
-
15045 template<typename TSeq>
-
15046 inline double Agent<TSeq>::operator[](size_t j) const
-
15047 {
-
15048  return *(model->agents_data + j * model->size() + id);
-
15049 }
+
15045 }
+
15046 
+
15047 template<typename TSeq>
+
15048 inline double & Agent<TSeq>::operator()(size_t j)
+
15049 {
15050 
-
15051 template<typename TSeq>
-
15052 inline Entities<TSeq> Agent<TSeq>::get_entities()
-
15053 {
-
15054  return Entities<TSeq>(*this);
-
15055 }
-
15056 
-
15057 template<typename TSeq>
-
15058 inline const Entities_const<TSeq> Agent<TSeq>::get_entities() const
-
15059 {
-
15060  return Entities_const<TSeq>(*this);
-
15061 }
-
15062 
-
15063 template<typename TSeq>
-
15064 inline const Entity<TSeq> & Agent<TSeq>::get_entity(size_t i) const
-
15065 {
-
15066  if (n_entities == 0)
-
15067  throw std::range_error("Agent id " + std::to_string(id) + " has no entities.");
-
15068 
-
15069  if (i >= n_entities)
-
15070  throw std::range_error("Trying to get to an agent's entity outside of the range.");
-
15071 
-
15072  return model->get_entity(entities[i]);
+
15051  if (model->agents_data_ncols <= j)
+
15052  throw std::logic_error("The requested feature of the agent is out of range.");
+
15053 
+
15054  return *(model->agents_data + j * model->size() + id);
+
15055 
+
15056 }
+
15057 
+
15058 template<typename TSeq>
+
15059 inline double & Agent<TSeq>::operator[](size_t j)
+
15060 {
+
15061  return *(model->agents_data + j * model->size() + id);
+
15062 }
+
15063 
+
15064 template<typename TSeq>
+
15065 inline double Agent<TSeq>::operator()(size_t j) const
+
15066 {
+
15067 
+
15068  if (model->agents_data_ncols <= j)
+
15069  throw std::logic_error("The requested feature of the agent is out of range.");
+
15070 
+
15071  return *(model->agents_data + j * model->size() + id);
+
15072 
15073 }
15074 
15075 template<typename TSeq>
-
15076 inline Entity<TSeq> & Agent<TSeq>::get_entity(size_t i)
-
15077 {
-
15078  if (n_entities == 0)
-
15079  throw std::range_error("Agent id " + std::to_string(id) + " has no entities.");
+
15076 inline double Agent<TSeq>::operator[](size_t j) const
+
15077 {
+
15078  return *(model->agents_data + j * model->size() + id);
+
15079 }
15080 
-
15081  if (i >= n_entities)
-
15082  throw std::range_error("Trying to get to an agent's entity outside of the range.");
-
15083 
-
15084  return model->get_entity(entities[i]);
+
15081 template<typename TSeq>
+
15082 inline Entities<TSeq> Agent<TSeq>::get_entities()
+
15083 {
+
15084  return Entities<TSeq>(*this);
15085 }
15086 
15087 template<typename TSeq>
-
15088 inline size_t Agent<TSeq>::get_n_entities() const
+
15088 inline const Entities_const<TSeq> Agent<TSeq>::get_entities() const
15089 {
-
15090  return n_entities;
+
15090  return Entities_const<TSeq>(*this);
15091 }
15092 
15093 template<typename TSeq>
-
15094 inline bool Agent<TSeq>::operator==(const Agent<TSeq> & other) const
+
15094 inline const Entity<TSeq> & Agent<TSeq>::get_entity(size_t i) const
15095 {
-
15096 
-
15097  EPI_DEBUG_FAIL_AT_TRUE(
-
15098  n_neighbors != other.n_neighbors,
-
15099  "Agent:: n_eighbors don't match"
-
15100  )
+
15096  if (n_entities == 0)
+
15097  throw std::range_error("Agent id " + std::to_string(id) + " has no entities.");
+
15098 
+
15099  if (i >= n_entities)
+
15100  throw std::range_error("Trying to get to an agent's entity outside of the range.");
15101 
-
15102 
-
15103  for (size_t i = 0u; i < n_neighbors; ++i)
-
15104  {
-
15105  EPI_DEBUG_FAIL_AT_TRUE(
-
15106  neighbors[i] != other.neighbors[i],
-
15107  "Agent:: neighbor[i] don't match"
-
15108  )
-
15109  }
-
15110 
-
15111  EPI_DEBUG_FAIL_AT_TRUE(
-
15112  n_entities != other.n_entities,
-
15113  "Agent:: n_entities don't match"
-
15114  )
-
15115 
-
15116 
-
15117  for (size_t i = 0u; i < n_entities; ++i)
-
15118  {
-
15119  EPI_DEBUG_FAIL_AT_TRUE(
-
15120  entities[i] != other.entities[i],
-
15121  "Agent:: entities[i] don't match"
-
15122  )
-
15123  }
-
15124 
-
15125  EPI_DEBUG_FAIL_AT_TRUE(
-
15126  state != other.state,
-
15127  "Agent:: state don't match"
-
15128  )
-
15129 
-
15130 
-
15131  EPI_DEBUG_FAIL_AT_TRUE(
-
15132  state_prev != other.state_prev,
-
15133  "Agent:: state_prev don't match"
-
15134  )
-
15135 
-
15136 
-
15137  // EPI_DEBUG_FAIL_AT_TRUE(
-
15138  // state_last_changed != other.state_last_changed,
-
15139  // "Agent:: state_last_changed don't match"
-
15140  // ) ///< Last time the agent was updated.
-
15141 
-
15142  EPI_DEBUG_FAIL_AT_TRUE(
-
15143  ((virus == nullptr) && (other.virus != nullptr)) ||
-
15144  ((virus != nullptr) && (other.virus == nullptr)),
-
15145  "Agent:: virus don't match"
-
15146  )
-
15147 
-
15148  if ((virus != nullptr) && (other.virus != nullptr))
-
15149  {
-
15150  EPI_DEBUG_FAIL_AT_TRUE(
-
15151  *virus != *other.virus,
-
15152  "Agent:: virus doesn't match"
-
15153  )
-
15154  }
-
15155 
-
15156  EPI_DEBUG_FAIL_AT_TRUE(n_tools != other.n_tools, "Agent:: n_tools don't match")
-
15157 
-
15158  for (size_t i = 0u; i < n_tools; ++i)
-
15159  {
-
15160 
-
15161  EPI_DEBUG_FAIL_AT_TRUE(
-
15162  tools[i] != other.tools[i],
-
15163  "Agent:: tools[i] don't match"
+
15102  return model->get_entity(entities[i]);
+
15103 }
+
15104 
+
15105 template<typename TSeq>
+
15106 inline Entity<TSeq> & Agent<TSeq>::get_entity(size_t i)
+
15107 {
+
15108  if (n_entities == 0)
+
15109  throw std::range_error("Agent id " + std::to_string(id) + " has no entities.");
+
15110 
+
15111  if (i >= n_entities)
+
15112  throw std::range_error("Trying to get to an agent's entity outside of the range.");
+
15113 
+
15114  return model->get_entity(entities[i]);
+
15115 }
+
15116 
+
15117 template<typename TSeq>
+
15118 inline size_t Agent<TSeq>::get_n_entities() const
+
15119 {
+
15120  return n_entities;
+
15121 }
+
15122 
+
15123 template<typename TSeq>
+
15124 inline bool Agent<TSeq>::operator==(const Agent<TSeq> & other) const
+
15125 {
+
15126 
+
15127  EPI_DEBUG_FAIL_AT_TRUE(
+
15128  n_neighbors != other.n_neighbors,
+
15129  "Agent:: n_eighbors don't match"
+
15130  )
+
15131 
+
15132 
+
15133  for (size_t i = 0u; i < n_neighbors; ++i)
+
15134  {
+
15135  EPI_DEBUG_FAIL_AT_TRUE(
+
15136  neighbors[i] != other.neighbors[i],
+
15137  "Agent:: neighbor[i] don't match"
+
15138  )
+
15139  }
+
15140 
+
15141  EPI_DEBUG_FAIL_AT_TRUE(
+
15142  n_entities != other.n_entities,
+
15143  "Agent:: n_entities don't match"
+
15144  )
+
15145 
+
15146 
+
15147  for (size_t i = 0u; i < n_entities; ++i)
+
15148  {
+
15149  EPI_DEBUG_FAIL_AT_TRUE(
+
15150  entities[i] != other.entities[i],
+
15151  "Agent:: entities[i] don't match"
+
15152  )
+
15153  }
+
15154 
+
15155  EPI_DEBUG_FAIL_AT_TRUE(
+
15156  state != other.state,
+
15157  "Agent:: state don't match"
+
15158  )
+
15159 
+
15160 
+
15161  EPI_DEBUG_FAIL_AT_TRUE(
+
15162  state_prev != other.state_prev,
+
15163  "Agent:: state_prev don't match"
15164  )
-
15165 
-
15166  }
-
15167 
-
15168  return true;
-
15169 
-
15170 }
+
15165 
+
15166 
+
15167  // EPI_DEBUG_FAIL_AT_TRUE(
+
15168  // state_last_changed != other.state_last_changed,
+
15169  // "Agent:: state_last_changed don't match"
+
15170  // ) ///< Last time the agent was updated.
15171 
-
15172 #undef CHECK_COALESCE_
-
15173 
-
15174 #endif
-
15175 /*//////////////////////////////////////////////////////////////////////////////
-
15177 
-
15178  End of -include/epiworld/agent-meat.hpp-
-
15179 
-
15182 
-
15183 
-
15184 
-
15185 /*//////////////////////////////////////////////////////////////////////////////
-
15187 
-
15188  Start of -include/epiworld/agentssample-bones.hpp-
-
15189 
-
15192 
-
15193 
-
15194 #ifndef EPIWORLD_AGENTS_BONES_HPP
-
15195 #define EPIWORLD_AGENTS_BONES_HPP
-
15196 
-
15197 class SAMPLETYPE {
-
15198 public:
-
15199  static const int MODEL = 0;
-
15200  static const int ENTITY = 1;
-
15201  static const int AGENT = 2;
-
15202 };
-
15203 
-
15204 // template<typename TSeq>
-
15205 // class Agent;
-
15206 
-
15207 // template<typename TSeq>
-
15208 // class Model;
+
15172  EPI_DEBUG_FAIL_AT_TRUE(
+
15173  ((virus == nullptr) && (other.virus != nullptr)) ||
+
15174  ((virus != nullptr) && (other.virus == nullptr)),
+
15175  "Agent:: virus don't match"
+
15176  )
+
15177 
+
15178  if ((virus != nullptr) && (other.virus != nullptr))
+
15179  {
+
15180  EPI_DEBUG_FAIL_AT_TRUE(
+
15181  *virus != *other.virus,
+
15182  "Agent:: virus doesn't match"
+
15183  )
+
15184  }
+
15185 
+
15186  EPI_DEBUG_FAIL_AT_TRUE(n_tools != other.n_tools, "Agent:: n_tools don't match")
+
15187 
+
15188  for (size_t i = 0u; i < n_tools; ++i)
+
15189  {
+
15190 
+
15191  EPI_DEBUG_FAIL_AT_TRUE(
+
15192  tools[i] != other.tools[i],
+
15193  "Agent:: tools[i] don't match"
+
15194  )
+
15195 
+
15196  }
+
15197 
+
15198  return true;
+
15199 
+
15200 }
+
15201 
+
15202 #undef CHECK_COALESCE_
+
15203 
+
15204 #endif
+
15205 /*//////////////////////////////////////////////////////////////////////////////
+
15207 
+
15208  End of -include/epiworld/agent-meat.hpp-
15209 
-
15210 // template<typename TSeq>
-
15211 // class Entity;
15212 
-
15220 template<typename TSeq>
-
15221 class AgentsSample {
-
15222 private:
+
15213 
+
15214 
+
15215 /*//////////////////////////////////////////////////////////////////////////////
+
15217 
+
15218  Start of -include/epiworld/agentssample-bones.hpp-
+
15219 
+
15222 
15223 
-
15224  size_t sample_size = 0u;
-
15225 
-
15226  std::vector< Agent<TSeq>* >* agents = nullptr; ///< Pointer to sample of agents
-
15227  size_t * agents_n = nullptr; ///< Size of sample of agents
-
15228 
-
15229  std::vector< size_t >* agents_left = nullptr; ///< Pointer to agents left (iota)
-
15230  size_t * agents_left_n = nullptr; ///< Size of agents left
-
15231 
-
15232  Model<TSeq> * model = nullptr; ///< Extracts runif() and (if the case) population.
-
15233  Entity<TSeq> * entity = nullptr; ///
-
15234  Agent<TSeq> * agent = nullptr;
-
15235 
-
15236  int sample_type = SAMPLETYPE::AGENT;
-
15237  std::vector< size_t > states = {};
-
15238 
-
15239  void sample_n(size_t n); ///< Backbone function for sampling
-
15240 
-
15241 
-
15242 public:
-
15243 
-
15244  // Not available (for now)
-
15245  AgentsSample() = delete; ///< Default constructor
-
15246  AgentsSample(const AgentsSample<TSeq> & a) = delete; ///< Copy constructor
-
15247  AgentsSample(AgentsSample<TSeq> && a) = delete; ///< Move constructor
-
15248 
-
15249  AgentsSample(
-
15250  Model<TSeq> & model_, size_t n,
-
15251  std::vector< size_t > states_ = {},
-
15252  bool truncate = false
-
15253  );
-
15254 
-
15255  AgentsSample(
-
15256  Model<TSeq> * model,
-
15257  Entity<TSeq> & entity_,
-
15258  size_t n,
-
15259  std::vector< size_t > states_ = {},
-
15260  bool truncate = false
-
15261  );
-
15262 
-
15263  AgentsSample(
-
15264  Model<TSeq> * model,
-
15265  Agent<TSeq> & agent_,
-
15266  size_t n,
-
15267  std::vector< size_t > states_ = {},
-
15268  bool truncate = false
-
15269  );
+
15224 #ifndef EPIWORLD_AGENTS_BONES_HPP
+
15225 #define EPIWORLD_AGENTS_BONES_HPP
+
15226 
+
15227 class SAMPLETYPE {
+
15228 public:
+
15229  static const int MODEL = 0;
+
15230  static const int ENTITY = 1;
+
15231  static const int AGENT = 2;
+
15232 };
+
15233 
+
15234 // template<typename TSeq>
+
15235 // class Agent;
+
15236 
+
15237 // template<typename TSeq>
+
15238 // class Model;
+
15239 
+
15240 // template<typename TSeq>
+
15241 // class Entity;
+
15242 
+
15250 template<typename TSeq>
+
15251 class AgentsSample {
+
15252 private:
+
15253 
+
15254  size_t sample_size = 0u;
+
15255 
+
15256  std::vector< Agent<TSeq>* >* agents = nullptr; ///< Pointer to sample of agents
+
15257  size_t * agents_n = nullptr; ///< Size of sample of agents
+
15258 
+
15259  std::vector< size_t >* agents_left = nullptr; ///< Pointer to agents left (iota)
+
15260  size_t * agents_left_n = nullptr; ///< Size of agents left
+
15261 
+
15262  Model<TSeq> * model = nullptr; ///< Extracts runif() and (if the case) population.
+
15263  Entity<TSeq> * entity = nullptr; ///
+
15264  Agent<TSeq> * agent = nullptr;
+
15265 
+
15266  int sample_type = SAMPLETYPE::AGENT;
+
15267  std::vector< size_t > states = {};
+
15268 
+
15269  void sample_n(size_t n); ///< Backbone function for sampling
15270 
-
15271  ~AgentsSample();
-
15272 
-
15273  typename std::vector< Agent<TSeq> * >::iterator begin();
-
15274  typename std::vector< Agent<TSeq> * >::iterator end();
-
15275 
-
15276  Agent<TSeq> * operator[](size_t n);
-
15277  Agent<TSeq> * operator()(size_t n);
-
15278  size_t size() const noexcept;
-
15279 
-
15280 };
-
15281 
-
15282 template<typename TSeq>
-
15283 inline AgentsSample<TSeq>::AgentsSample(
-
15284  Model<TSeq> & model_,
-
15285  size_t n,
-
15286  std::vector< size_t > states_,
-
15287  bool truncate
-
15288  ) {
-
15289 
-
15290  states = states_;
-
15291 
-
15292  if (truncate)
-
15293  {
-
15294 
-
15295  if (n > model_.size())
-
15296  n = model_.size();
-
15297 
-
15298  } else if (n > model_.size())
-
15299  throw std::logic_error(
-
15300  "There are only " + std::to_string(model_.size()) + " agents. You cannot " +
-
15301  "sample " + std::to_string(n));
+
15271 
+
15272 public:
+
15273 
+
15274  // Not available (for now)
+
15275  AgentsSample() = delete; ///< Default constructor
+
15276  AgentsSample(const AgentsSample<TSeq> & a) = delete; ///< Copy constructor
+
15277  AgentsSample(AgentsSample<TSeq> && a) = delete; ///< Move constructor
+
15278 
+
15279  AgentsSample(
+
15280  Model<TSeq> & model_, size_t n,
+
15281  std::vector< size_t > states_ = {},
+
15282  bool truncate = false
+
15283  );
+
15284 
+
15285  AgentsSample(
+
15286  Model<TSeq> * model,
+
15287  Entity<TSeq> & entity_,
+
15288  size_t n,
+
15289  std::vector< size_t > states_ = {},
+
15290  bool truncate = false
+
15291  );
+
15292 
+
15293  AgentsSample(
+
15294  Model<TSeq> * model,
+
15295  Agent<TSeq> & agent_,
+
15296  size_t n,
+
15297  std::vector< size_t > states_ = {},
+
15298  bool truncate = false
+
15299  );
+
15300 
+
15301  ~AgentsSample();
15302 
-
15303  sample_size = n;
-
15304  model = &model_;
-
15305  sample_type = SAMPLETYPE::MODEL;
-
15306 
-
15307  agents = &model_.sampled_population;
-
15308  agents_n = &model_.sampled_population_n;
+
15303  typename std::vector< Agent<TSeq> * >::iterator begin();
+
15304  typename std::vector< Agent<TSeq> * >::iterator end();
+
15305 
+
15306  Agent<TSeq> * operator[](size_t n);
+
15307  Agent<TSeq> * operator()(size_t n);
+
15308  size_t size() const noexcept;
15309 
-
15310  agents_left = &model_.population_left;
-
15311  agents_left_n = &model_.population_left_n;
-
15312 
-
15313  sample_n(n);
-
15314 
-
15315  return;
-
15316 
-
15317 }
-
15318 
-
15319 template<typename TSeq>
-
15320 inline AgentsSample<TSeq>::AgentsSample(
-
15321  Model<TSeq> * model,
-
15322  Entity<TSeq> & entity_,
-
15323  size_t n,
-
15324  std::vector< size_t > states_,
-
15325  bool truncate
-
15326  ) {
+
15310 };
+
15311 
+
15312 template<typename TSeq>
+
15313 inline AgentsSample<TSeq>::AgentsSample(
+
15314  Model<TSeq> & model_,
+
15315  size_t n,
+
15316  std::vector< size_t > states_,
+
15317  bool truncate
+
15318  ) {
+
15319 
+
15320  states = states_;
+
15321 
+
15322  if (truncate)
+
15323  {
+
15324 
+
15325  if (n > model_.size())
+
15326  n = model_.size();
15327 
-
15328  states = states_;
-
15329 
-
15330  if (truncate)
-
15331  {
+
15328  } else if (n > model_.size())
+
15329  throw std::logic_error(
+
15330  "There are only " + std::to_string(model_.size()) + " agents. You cannot " +
+
15331  "sample " + std::to_string(n));
15332 
-
15333  if (n > entity_.size())
-
15334  n = entity_.size();
-
15335 
-
15336  } else if (n > entity_.size())
-
15337  throw std::logic_error(
-
15338  "There are only " + std::to_string(entity_.size()) + " agents. You cannot " +
-
15339  "sample " + std::to_string(n));
-
15340 
-
15341  sample_size = n;
-
15342  model = &entity_.model;
-
15343  sample_type = SAMPLETYPE::ENTITY;
-
15344 
-
15345  agents = &entity_.sampled_agents;
-
15346  agents_n = &entity_.sampled_agents_n;
-
15347 
-
15348  agents_left = &entity_.sampled_agents_left;
-
15349  agents_left_n = &entity_.sampled_agents_left_n;
-
15350 
-
15351  sample_n(n);
-
15352 
-
15353  return;
-
15354 
-
15355 }
-
15356 
-
15369 template<typename TSeq>
-
15370 inline AgentsSample<TSeq>::AgentsSample(
-
15371  Model<TSeq> * model,
-
15372  Agent<TSeq> & agent_,
-
15373  size_t n,
-
15374  std::vector< size_t > states_,
-
15375  bool truncate
-
15376  )
-
15377 {
-
15378 
-
15379  states = states_;
-
15380  sample_type = SAMPLETYPE::AGENT;
-
15381 
-
15382  agent = &agent_;
-
15383 
-
15384  agents = &agent_.sampled_agents;
-
15385  agents_n = &agent_.sampled_agents_n;
+
15333  sample_size = n;
+
15334  model = &model_;
+
15335  sample_type = SAMPLETYPE::MODEL;
+
15336 
+
15337  agents = &model_.sampled_population;
+
15338  agents_n = &model_.sampled_population_n;
+
15339 
+
15340  agents_left = &model_.population_left;
+
15341  agents_left_n = &model_.population_left_n;
+
15342 
+
15343  sample_n(n);
+
15344 
+
15345  return;
+
15346 
+
15347 }
+
15348 
+
15349 template<typename TSeq>
+
15350 inline AgentsSample<TSeq>::AgentsSample(
+
15351  Model<TSeq> * model,
+
15352  Entity<TSeq> & entity_,
+
15353  size_t n,
+
15354  std::vector< size_t > states_,
+
15355  bool truncate
+
15356  ) {
+
15357 
+
15358  states = states_;
+
15359 
+
15360  if (truncate)
+
15361  {
+
15362 
+
15363  if (n > entity_.size())
+
15364  n = entity_.size();
+
15365 
+
15366  } else if (n > entity_.size())
+
15367  throw std::logic_error(
+
15368  "There are only " + std::to_string(entity_.size()) + " agents. You cannot " +
+
15369  "sample " + std::to_string(n));
+
15370 
+
15371  sample_size = n;
+
15372  model = &entity_.model;
+
15373  sample_type = SAMPLETYPE::ENTITY;
+
15374 
+
15375  agents = &entity_.sampled_agents;
+
15376  agents_n = &entity_.sampled_agents_n;
+
15377 
+
15378  agents_left = &entity_.sampled_agents_left;
+
15379  agents_left_n = &entity_.sampled_agents_left_n;
+
15380 
+
15381  sample_n(n);
+
15382 
+
15383  return;
+
15384 
+
15385 }
15386 
-
15387  // Computing the cumulative sum of counts across entities
-
15388  size_t agents_in_entities = 0;
-
15389  Entities<TSeq> entities_a = agent->get_entities();
-
15390 
-
15391  std::vector< size_t > cum_agents_count(entities_a.size(), 0);
-
15392  int idx = -1;
-
15393  for (auto & e : entities_a)
-
15394  {
-
15395  if (++idx == 0)
-
15396  cum_agents_count[idx] = (e->size() - 1u);
-
15397  else
-
15398  cum_agents_count[idx] = (
-
15399  (e->size() - 1u) +
-
15400  cum_agents_count[idx - 1]
-
15401  );
-
15402 
-
15403  agents_in_entities += (e->size() - 1u);
-
15404  }
-
15405 
-
15406  if (truncate)
-
15407  {
-
15408 
-
15409  if (n > agents_in_entities)
-
15410  n = agents_in_entities;
-
15411 
-
15412  } else if (n > agents_in_entities)
-
15413  throw std::logic_error(
-
15414  "There are only " + std::to_string(agents_in_entities) +
-
15415  " agents. You cannot " +
-
15416  "sample " + std::to_string(n)
-
15417  );
-
15418 
-
15419  sample_size = n;
+
15399 template<typename TSeq>
+
15400 inline AgentsSample<TSeq>::AgentsSample(
+
15401  Model<TSeq> * model,
+
15402  Agent<TSeq> & agent_,
+
15403  size_t n,
+
15404  std::vector< size_t > states_,
+
15405  bool truncate
+
15406  )
+
15407 {
+
15408 
+
15409  states = states_;
+
15410  sample_type = SAMPLETYPE::AGENT;
+
15411 
+
15412  agent = &agent_;
+
15413 
+
15414  agents = &agent_.sampled_agents;
+
15415  agents_n = &agent_.sampled_agents_n;
+
15416 
+
15417  // Computing the cumulative sum of counts across entities
+
15418  size_t agents_in_entities = 0;
+
15419  Entities<TSeq> entities_a = agent->get_entities();
15420 
-
15421  if (agents->size() < n)
-
15422  agents->resize(n);
-
15423 
-
15424  size_t i_obs = 0u;
-
15425  for (size_t i = 0u; i < sample_size; ++i)
-
15426  {
-
15427 
-
15428  // Sampling a single agent from the set of entities
-
15429  int jth = std::floor(model->runif() * agents_in_entities);
-
15430  for (size_t e = 0u; e < cum_agents_count.size(); ++e)
-
15431  {
-
15432 
-
15433  // Are we in the limit?
-
15434  if (jth <= cum_agents_count[e])
-
15435  {
-
15436  size_t agent_idx = 0u;
-
15437  if (e == 0) // From the first group
-
15438  agent_idx = entities_a[e][jth]->get_id();
-
15439  else
-
15440  agent_idx = entities_a[e][jth - cum_agents_count[e - 1]]->get_id();
+
15421  std::vector< size_t > cum_agents_count(entities_a.size(), 0);
+
15422  int idx = -1;
+
15423  for (auto & e : entities_a)
+
15424  {
+
15425  if (++idx == 0)
+
15426  cum_agents_count[idx] = (e->size() - 1u);
+
15427  else
+
15428  cum_agents_count[idx] = (
+
15429  (e->size() - 1u) +
+
15430  cum_agents_count[idx - 1]
+
15431  );
+
15432 
+
15433  agents_in_entities += (e->size() - 1u);
+
15434  }
+
15435 
+
15436  if (truncate)
+
15437  {
+
15438 
+
15439  if (n > agents_in_entities)
+
15440  n = agents_in_entities;
15441 
-
15442 
-
15443  // Checking if states was specified
-
15444  if (states.size())
-
15445  {
-
15446 
-
15447  // Getting the state
-
15448  size_t state = model->population[agent_idx].get_state();
-
15449 
-
15450  if (std::find(states.begin(), states.end(), state) != states.end())
-
15451  continue;
-
15452 
-
15453  }
-
15454 
-
15455  agents->operator[](i_obs++) = &(model->population[agent_idx]);
-
15456 
-
15457  break;
-
15458  }
-
15459 
-
15460  }
-
15461  }
-
15462 
-
15463  return;
-
15464 
-
15465 }
-
15466 
-
15467 template<typename TSeq>
-
15468 inline AgentsSample<TSeq>::~AgentsSample() {}
-
15469 
-
15470 template<typename TSeq>
-
15471 inline size_t AgentsSample<TSeq>::size() const noexcept
-
15472 {
-
15473  return this->sample_size;
-
15474 }
-
15475 
-
15476 template<typename TSeq>
-
15477 inline Agent<TSeq> * AgentsSample<TSeq>::operator[](size_t i)
-
15478 {
+
15442  } else if (n > agents_in_entities)
+
15443  throw std::logic_error(
+
15444  "There are only " + std::to_string(agents_in_entities) +
+
15445  " agents. You cannot " +
+
15446  "sample " + std::to_string(n)
+
15447  );
+
15448 
+
15449  sample_size = n;
+
15450 
+
15451  if (agents->size() < n)
+
15452  agents->resize(n);
+
15453 
+
15454  size_t i_obs = 0u;
+
15455  for (size_t i = 0u; i < sample_size; ++i)
+
15456  {
+
15457 
+
15458  // Sampling a single agent from the set of entities
+
15459  int jth = std::floor(model->runif() * agents_in_entities);
+
15460  for (size_t e = 0u; e < cum_agents_count.size(); ++e)
+
15461  {
+
15462 
+
15463  // Are we in the limit?
+
15464  if (jth <= cum_agents_count[e])
+
15465  {
+
15466  size_t agent_idx = 0u;
+
15467  if (e == 0) // From the first group
+
15468  agent_idx = entities_a[e][jth]->get_id();
+
15469  else
+
15470  agent_idx = entities_a[e][jth - cum_agents_count[e - 1]]->get_id();
+
15471 
+
15472 
+
15473  // Checking if states was specified
+
15474  if (states.size())
+
15475  {
+
15476 
+
15477  // Getting the state
+
15478  size_t state = model->population[agent_idx].get_state();
15479 
-
15480  return agents->operator[](i);
-
15481 
-
15482 }
-
15483 
-
15484 template<typename TSeq>
-
15485 inline Agent<TSeq> * AgentsSample<TSeq>::operator()(size_t i)
-
15486 {
-
15487 
-
15488  if (i >= this->sample_size)
-
15489  throw std::range_error("The requested agent is out of range.");
-
15490 
-
15491  return agents->operator[](i);
+
15480  if (std::find(states.begin(), states.end(), state) != states.end())
+
15481  continue;
+
15482 
+
15483  }
+
15484 
+
15485  agents->operator[](i_obs++) = &(model->population[agent_idx]);
+
15486 
+
15487  break;
+
15488  }
+
15489 
+
15490  }
+
15491  }
15492 
-
15493 }
+
15493  return;
15494 
-
15495 template<typename TSeq>
-
15496 inline typename std::vector< Agent<TSeq> * >::iterator AgentsSample<TSeq>::begin()
-
15497 {
-
15498 
-
15499  if (sample_size > 0u)
-
15500  return agents->begin();
-
15501  else
-
15502  return agents->end();
-
15503 
+
15495 }
+
15496 
+
15497 template<typename TSeq>
+
15498 inline AgentsSample<TSeq>::~AgentsSample() {}
+
15499 
+
15500 template<typename TSeq>
+
15501 inline size_t AgentsSample<TSeq>::size() const noexcept
+
15502 {
+
15503  return this->sample_size;
15504 }
15505 
15506 template<typename TSeq>
-
15507 inline typename std::vector< Agent<TSeq> * >::iterator AgentsSample<TSeq>::end()
+
15507 inline Agent<TSeq> * AgentsSample<TSeq>::operator[](size_t i)
15508 {
15509 
-
15510  return agents->begin() + sample_size;
+
15510  return agents->operator[](i);
15511 
15512 }
15513 
15514 template<typename TSeq>
-
15515 inline void AgentsSample<TSeq>::sample_n(size_t n)
+
15515 inline Agent<TSeq> * AgentsSample<TSeq>::operator()(size_t i)
15516 {
15517 
-
15518  // Reducing size
-
15519  if (states.size())
-
15520  {
-
15521 
-
15522  // Getting the number of agents left
-
15523  agents_left->clear();
+
15518  if (i >= this->sample_size)
+
15519  throw std::range_error("The requested agent is out of range.");
+
15520 
+
15521  return agents->operator[](i);
+
15522 
+
15523 }
15524 
-
15525  if (sample_type == SAMPLETYPE::MODEL)
-
15526  {
-
15527 
-
15528  // Making some room
-
15529  agents_left->reserve(model->size());
-
15530 
-
15531  // Iterating through the agents in the population
-
15532  for (size_t a_i = 0u; a_i < model->population.size(); ++a_i)
-
15533  {
-
15534 
-
15535  // If the agent is within the selected set of states,
-
15536  // then we add it to the list of agents left
-
15537  size_t s = model->population[a_i].get_state();
-
15538  if (std::find(states.begin(), states.end(), s) != states.end())
-
15539  agents_left->push_back(a_i);
-
15540 
-
15541  }
-
15542 
-
15543  }
-
15544  else if (sample_type == SAMPLETYPE::ENTITY)
-
15545  {
-
15546 
-
15547  // Making room
-
15548  agents_left->reserve(entity->size());
-
15549 
-
15550  // Iterating through the agents in the entity
-
15551  for (size_t a_i = 0u; a_i < entity->size(); ++a_i)
-
15552  {
-
15553  size_t s = model->population[entity->agents[a_i]].get_state();
-
15554  if (std::find(states.begin(), states.end(), s) != states.end())
-
15555  agents_left->push_back(a_i);
-
15556 
-
15557  }
-
15558 
-
15559  }
+
15525 template<typename TSeq>
+
15526 inline typename std::vector< Agent<TSeq> * >::iterator AgentsSample<TSeq>::begin()
+
15527 {
+
15528 
+
15529  if (sample_size > 0u)
+
15530  return agents->begin();
+
15531  else
+
15532  return agents->end();
+
15533 
+
15534 }
+
15535 
+
15536 template<typename TSeq>
+
15537 inline typename std::vector< Agent<TSeq> * >::iterator AgentsSample<TSeq>::end()
+
15538 {
+
15539 
+
15540  return agents->begin() + sample_size;
+
15541 
+
15542 }
+
15543 
+
15544 template<typename TSeq>
+
15545 inline void AgentsSample<TSeq>::sample_n(size_t n)
+
15546 {
+
15547 
+
15548  // Reducing size
+
15549  if (states.size())
+
15550  {
+
15551 
+
15552  // Getting the number of agents left
+
15553  agents_left->clear();
+
15554 
+
15555  if (sample_type == SAMPLETYPE::MODEL)
+
15556  {
+
15557 
+
15558  // Making some room
+
15559  agents_left->reserve(model->size());
15560 
-
15561  } else {
-
15562 
-
15563  // Checking if the size of the entity has changed (or hasn't been initialized)
-
15564  if (sample_type == SAMPLETYPE::MODEL)
-
15565  {
-
15566 
-
15567  if (model->size() != agents_left->size())
-
15568  {
-
15569  agents_left->resize(model->size(), 0u);
-
15570  std::iota(agents_left->begin(), agents_left->end(), 0u);
+
15561  // Iterating through the agents in the population
+
15562  for (size_t a_i = 0u; a_i < model->population.size(); ++a_i)
+
15563  {
+
15564 
+
15565  // If the agent is within the selected set of states,
+
15566  // then we add it to the list of agents left
+
15567  size_t s = model->population[a_i].get_state();
+
15568  if (std::find(states.begin(), states.end(), s) != states.end())
+
15569  agents_left->push_back(a_i);
+
15570 
15571  }
15572 
-
15573  } else if (sample_type == SAMPLETYPE::ENTITY) {
-
15574 
-
15575  if (entity->size() != agents_left->size())
-
15576  {
-
15577 
-
15578  agents_left->resize(entity->size(), 0u);
-
15579  std::iota(agents_left->begin(), agents_left->end(), 0u);
-
15580 
-
15581  }
-
15582 
-
15583  }
-
15584 
-
15585  }
+
15573  }
+
15574  else if (sample_type == SAMPLETYPE::ENTITY)
+
15575  {
+
15576 
+
15577  // Making room
+
15578  agents_left->reserve(entity->size());
+
15579 
+
15580  // Iterating through the agents in the entity
+
15581  for (size_t a_i = 0u; a_i < entity->size(); ++a_i)
+
15582  {
+
15583  size_t s = model->population[entity->agents[a_i]].get_state();
+
15584  if (std::find(states.begin(), states.end(), s) != states.end())
+
15585  agents_left->push_back(a_i);
15586 
-
15587  // Restart the counter of agents left
-
15588  *agents_left_n = agents_left->size();
-
15589 
-
15590  // Making sure we have enough room for the sample of agents
-
15591  if (agents->size() < sample_size)
-
15592  agents->resize(sample_size, nullptr);
-
15593 
-
15594  if (sample_type == SAMPLETYPE::MODEL)
-
15595  {
+
15587  }
+
15588 
+
15589  }
+
15590 
+
15591  } else {
+
15592 
+
15593  // Checking if the size of the entity has changed (or hasn't been initialized)
+
15594  if (sample_type == SAMPLETYPE::MODEL)
+
15595  {
15596 
-
15597  #ifdef EPI_DEBUG
-
15598  std::vector< bool > __sampled(model->size(), true);
-
15599  for (auto & a_i: *agents_left)
-
15600  __sampled[a_i] = false;
-
15601  #endif
+
15597  if (model->size() != agents_left->size())
+
15598  {
+
15599  agents_left->resize(model->size(), 0u);
+
15600  std::iota(agents_left->begin(), agents_left->end(), 0u);
+
15601  }
15602 
-
15603  for (size_t i = 0u; i < n; ++i)
-
15604  {
-
15605 
-
15606  // Sampling from 0 to (agents_left_n - 1)
-
15607  size_t ith_ = static_cast<size_t>(model->runif() * ((*agents_left_n)--));
-
15608 
-
15609  // Getting the id of the agent and adding it to the list of agents
-
15610  size_t ith = agents_left->operator[](ith_);
-
15611  agents->operator[](i) = &model->population[ith];
+
15603  } else if (sample_type == SAMPLETYPE::ENTITY) {
+
15604 
+
15605  if (entity->size() != agents_left->size())
+
15606  {
+
15607 
+
15608  agents_left->resize(entity->size(), 0u);
+
15609  std::iota(agents_left->begin(), agents_left->end(), 0u);
+
15610 
+
15611  }
15612 
-
15613  #ifdef EPI_DEBUG
-
15614  if (__sampled[ith])
-
15615  throw std::logic_error("The same agent was sampled twice.");
-
15616  else
-
15617  __sampled[ith] = true;
-
15618  #endif
+
15613  }
+
15614 
+
15615  }
+
15616 
+
15617  // Restart the counter of agents left
+
15618  *agents_left_n = agents_left->size();
15619 
-
15620  // Updating list
-
15621  std::swap(
-
15622  agents_left->operator[](ith_),
-
15623  agents_left->operator[](*agents_left_n)
-
15624  );
-
15625 
-
15626  }
-
15627 
-
15628 
-
15629  }
-
15630  else if (sample_type == SAMPLETYPE::ENTITY)
-
15631  {
+
15620  // Making sure we have enough room for the sample of agents
+
15621  if (agents->size() < sample_size)
+
15622  agents->resize(sample_size, nullptr);
+
15623 
+
15624  if (sample_type == SAMPLETYPE::MODEL)
+
15625  {
+
15626 
+
15627  #ifdef EPI_DEBUG
+
15628  std::vector< bool > __sampled(model->size(), true);
+
15629  for (auto & a_i: *agents_left)
+
15630  __sampled[a_i] = false;
+
15631  #endif
15632 
-
15633  #ifdef EPI_DEBUG
-
15634  std::vector< bool > __sampled(entity->size(), true);
-
15635  for (auto & a_i: *agents_left)
-
15636  __sampled[a_i] = false;
-
15637  #endif
-
15638 
-
15639  for (size_t i = 0u; i < n; ++i)
-
15640  {
-
15641 
-
15642  size_t ith_ = static_cast<size_t>(model->runif() * ((*agents_left_n)--));
-
15643  size_t ith = agents_left->operator[](ith_);
-
15644  agents->operator[](i) = &model->population[entity->agents[ith]];
-
15645 
-
15646  #ifdef EPI_DEBUG
-
15647  if (__sampled[ith])
-
15648  throw std::logic_error("The same agent was sampled twice.");
-
15649  else
-
15650  __sampled[ith] = true;
-
15651  #endif
-
15652 
-
15653  // Updating list
-
15654  std::swap(agents_left->operator[](ith_), agents_left->operator[](*agents_left_n));
+
15633  for (size_t i = 0u; i < n; ++i)
+
15634  {
+
15635 
+
15636  // Sampling from 0 to (agents_left_n - 1)
+
15637  size_t ith_ = static_cast<size_t>(model->runif() * ((*agents_left_n)--));
+
15638 
+
15639  // Getting the id of the agent and adding it to the list of agents
+
15640  size_t ith = agents_left->operator[](ith_);
+
15641  agents->operator[](i) = &model->population[ith];
+
15642 
+
15643  #ifdef EPI_DEBUG
+
15644  if (__sampled[ith])
+
15645  throw std::logic_error("The same agent was sampled twice.");
+
15646  else
+
15647  __sampled[ith] = true;
+
15648  #endif
+
15649 
+
15650  // Updating list
+
15651  std::swap(
+
15652  agents_left->operator[](ith_),
+
15653  agents_left->operator[](*agents_left_n)
+
15654  );
15655 
15656  }
15657 
-
15658  }
-
15659 
-
15660  return;
-
15661 
-
15662 }
-
15663 
-
15664 #endif
-
15665 /*//////////////////////////////////////////////////////////////////////////////
-
15667 
-
15668  End of -include/epiworld/agentssample-bones.hpp-
-
15669 
-
15672 
-
15673 
-
15674 
-
15675 /*//////////////////////////////////////////////////////////////////////////////
-
15677 
-
15678  Start of -include/epiworld/groupsampler-bones.hpp-
-
15679 
+
15658 
+
15659  }
+
15660  else if (sample_type == SAMPLETYPE::ENTITY)
+
15661  {
+
15662 
+
15663  #ifdef EPI_DEBUG
+
15664  std::vector< bool > __sampled(entity->size(), true);
+
15665  for (auto & a_i: *agents_left)
+
15666  __sampled[a_i] = false;
+
15667  #endif
+
15668 
+
15669  for (size_t i = 0u; i < n; ++i)
+
15670  {
+
15671 
+
15672  size_t ith_ = static_cast<size_t>(model->runif() * ((*agents_left_n)--));
+
15673  size_t ith = agents_left->operator[](ith_);
+
15674  agents->operator[](i) = &model->population[entity->agents[ith]];
+
15675 
+
15676  #ifdef EPI_DEBUG
+
15677  if (__sampled[ith])
+
15678  throw std::logic_error("The same agent was sampled twice.");
+
15679  else
+
15680  __sampled[ith] = true;
+
15681  #endif
15682 
-
15683 
-
15684 #ifndef GROUPSAMPLER_BONES_HPP
-
15685 #define GROUPSAMPLER_BONES_HPP
-
15686 
-
15690 template<typename TSeq>
-
15691 class GroupSampler {
-
15692 
-
15693 private:
-
15694 
-
15695  std::vector< double > contact_matrix; ///< Contact matrix between groups
-
15696  std::vector< size_t > group_sizes; ///< Sizes of the groups
-
15697  std::vector< double > cumulate; ///< Cumulative sum of the contact matrix (row-major for faster access)
-
15698 
-
15708  inline int idx(const int i, const int j, bool rowmajor = false) const
-
15709  {
-
15710 
-
15711  if (rowmajor)
-
15712  return i * group_sizes.size() + j;
-
15713 
-
15714  return j * group_sizes.size() + i;
-
15715 
-
15716  }
-
15717 
-
15718 public:
-
15719 
-
15720  GroupSampler() {};
-
15721 
-
15722  GroupSampler(
-
15723  const std::vector< double > & contact_matrix_,
-
15724  const std::vector< size_t > & group_sizes_,
-
15725  bool normalize = true
-
15726  );
-
15727 
-
15728  int sample_1(
-
15729  Model<TSeq> * model,
-
15730  const int origin_group
-
15731  );
-
15732 
-
15733  void sample_n(
-
15734  Model<TSeq> * model,
-
15735  std::vector< int > & sample,
-
15736  const int origin_group,
-
15737  const int nsamples
-
15738  );
-
15739 
-
15740 };
-
15741 
-
15742 #endif
-
15743 /*//////////////////////////////////////////////////////////////////////////////
+
15683  // Updating list
+
15684  std::swap(agents_left->operator[](ith_), agents_left->operator[](*agents_left_n));
+
15685 
+
15686  }
+
15687 
+
15688  }
+
15689 
+
15690  return;
+
15691 
+
15692 }
+
15693 
+
15694 #endif
+
15695 /*//////////////////////////////////////////////////////////////////////////////
+
15697 
+
15698  End of -include/epiworld/agentssample-bones.hpp-
+
15699 
+
15702 
+
15703 
+
15704 
+
15705 /*//////////////////////////////////////////////////////////////////////////////
+
15707 
+
15708  Start of -include/epiworld/groupsampler-bones.hpp-
+
15709 
+
15712 
+
15713 
+
15714 #ifndef GROUPSAMPLER_BONES_HPP
+
15715 #define GROUPSAMPLER_BONES_HPP
+
15716 
+
15720 template<typename TSeq>
+
15721 class GroupSampler {
+
15722 
+
15723 private:
+
15724 
+
15725  std::vector< double > contact_matrix; ///< Contact matrix between groups
+
15726  std::vector< size_t > group_sizes; ///< Sizes of the groups
+
15727  std::vector< double > cumulate; ///< Cumulative sum of the contact matrix (row-major for faster access)
+
15728 
+
15738  inline int idx(const int i, const int j, bool rowmajor = false) const
+
15739  {
+
15740 
+
15741  if (rowmajor)
+
15742  return i * group_sizes.size() + j;
+
15743 
+
15744  return j * group_sizes.size() + i;
15745 
-
15746  End of -include/epiworld/groupsampler-bones.hpp-
+
15746  }
15747 
-
15750 
+
15748 public:
+
15749 
+
15750  GroupSampler() {};
15751 
-
15752 /*//////////////////////////////////////////////////////////////////////////////
-
15754 
-
15755  Start of -include/epiworld/groupsampler-meat.hpp-
-
15756 
-
15759 
-
15760 
-
15761 #ifndef GROUPSAMPLER_MEAT_HPP
-
15762 #define GROUPSAMPLER_MEAT_HPP
-
15763 
-
15764 template<typename TSeq>
-
15765 inline GroupSampler<TSeq>::GroupSampler(
-
15766  const std::vector< double > & contact_matrix_,
-
15767  const std::vector< size_t > & group_sizes_,
-
15768  bool normalize
-
15769  ): contact_matrix(contact_matrix_), group_sizes(group_sizes_) {
-
15770 
+
15752  GroupSampler(
+
15753  const std::vector< double > & contact_matrix_,
+
15754  const std::vector< size_t > & group_sizes_,
+
15755  bool normalize = true
+
15756  );
+
15757 
+
15758  int sample_1(
+
15759  Model<TSeq> * model,
+
15760  const int origin_group
+
15761  );
+
15762 
+
15763  void sample_n(
+
15764  Model<TSeq> * model,
+
15765  std::vector< int > & sample,
+
15766  const int origin_group,
+
15767  const int nsamples
+
15768  );
+
15769 
+
15770 };
15771 
-
15772  this->cumulate.resize(contact_matrix.size());
-
15773  std::fill(cumulate.begin(), cumulate.end(), 0.0);
-
15774 
-
15775  // Cumulative sum
-
15776  for (size_t j = 0; j < group_sizes.size(); ++j)
-
15777  {
-
15778  for (size_t i = 0; i < group_sizes.size(); ++i)
-
15779  cumulate[idx(i, j, true)] +=
-
15780  cumulate[idx(i, j - 1, true)] +
-
15781  contact_matrix[idx(i, j)];
-
15782  }
-
15783 
-
15784  if (normalize)
-
15785  {
-
15786  for (size_t i = 0; i < group_sizes.size(); ++i)
-
15787  {
-
15788  double sum = 0.0;
-
15789  for (size_t j = 0; j < group_sizes.size(); ++j)
-
15790  sum += contact_matrix[idx(i, j, true)];
-
15791  for (size_t j = 0; j < group_sizes.size(); ++j)
-
15792  contact_matrix[idx(i, j, true)] /= sum;
-
15793  }
-
15794  }
-
15795 
-
15796  };
-
15797 
-
15798 template<typename TSeq>
-
15799 int GroupSampler<TSeq>::sample_1(
-
15800  Model<TSeq> * model,
-
15801  const int origin_group
-
15802  )
-
15803 {
+
15772 #endif
+
15773 /*//////////////////////////////////////////////////////////////////////////////
+
15775 
+
15776  End of -include/epiworld/groupsampler-bones.hpp-
+
15777 
+
15780 
+
15781 
+
15782 /*//////////////////////////////////////////////////////////////////////////////
+
15784 
+
15785  Start of -include/epiworld/groupsampler-meat.hpp-
+
15786 
+
15789 
+
15790 
+
15791 #ifndef GROUPSAMPLER_MEAT_HPP
+
15792 #define GROUPSAMPLER_MEAT_HPP
+
15793 
+
15794 template<typename TSeq>
+
15795 inline GroupSampler<TSeq>::GroupSampler(
+
15796  const std::vector< double > & contact_matrix_,
+
15797  const std::vector< size_t > & group_sizes_,
+
15798  bool normalize
+
15799  ): contact_matrix(contact_matrix_), group_sizes(group_sizes_) {
+
15800 
+
15801 
+
15802  this->cumulate.resize(contact_matrix.size());
+
15803  std::fill(cumulate.begin(), cumulate.end(), 0.0);
15804 
-
15805  // Random number
-
15806  double r = model->runif();
-
15807 
-
15808  // Finding the group
-
15809  size_t j = 0;
-
15810  while (r > cumulate[idx(origin_group, j, true)])
-
15811  ++j;
-
15812 
-
15813  // Adjusting the prob
-
15814  r = r - (j == 0 ? 0.0 : cumulate[idx(origin_group, j - 1, true)]);
-
15815 
-
15816  int res = static_cast<int>(
-
15817  std::floor(r * group_sizes[j])
-
15818  );
-
15819 
-
15820  // Making sure we are not picking outside of the group
-
15821  if (res >= static_cast<int>(group_sizes[j]))
-
15822  res = static_cast<int>(group_sizes[j]) - 1;
-
15823 
-
15824  return model->get_entities()[j][res]->get_id();
+
15805  // Cumulative sum
+
15806  for (size_t j = 0; j < group_sizes.size(); ++j)
+
15807  {
+
15808  for (size_t i = 0; i < group_sizes.size(); ++i)
+
15809  cumulate[idx(i, j, true)] +=
+
15810  cumulate[idx(i, j - 1, true)] +
+
15811  contact_matrix[idx(i, j)];
+
15812  }
+
15813 
+
15814  if (normalize)
+
15815  {
+
15816  for (size_t i = 0; i < group_sizes.size(); ++i)
+
15817  {
+
15818  double sum = 0.0;
+
15819  for (size_t j = 0; j < group_sizes.size(); ++j)
+
15820  sum += contact_matrix[idx(i, j, true)];
+
15821  for (size_t j = 0; j < group_sizes.size(); ++j)
+
15822  contact_matrix[idx(i, j, true)] /= sum;
+
15823  }
+
15824  }
15825 
-
15826 }
+
15826  };
15827 
15828 template<typename TSeq>
-
15829 void GroupSampler<TSeq>::sample_n(
+
15829 int GroupSampler<TSeq>::sample_1(
15830  Model<TSeq> * model,
-
15831  std::vector< int > & sample,
-
15832  const int origin_group,
-
15833  const int nsamples
-
15834 )
-
15835 {
-
15836 
-
15837  for (int i = 0; i < nsamples; ++i)
-
15838  sample[i] = sample_1(model, origin_group);
-
15839 
-
15840  return;
-
15841 
-
15842 }
-
15843 
-
15844 #endif
-
15845 /*//////////////////////////////////////////////////////////////////////////////
-
15847 
-
15848  End of -include/epiworld/groupsampler-meat.hpp-
+
15831  const int origin_group
+
15832  )
+
15833 {
+
15834 
+
15835  // Random number
+
15836  double r = model->runif();
+
15837 
+
15838  // Finding the group
+
15839  size_t j = 0;
+
15840  while (r > cumulate[idx(origin_group, j, true)])
+
15841  ++j;
+
15842 
+
15843  // Adjusting the prob
+
15844  r = r - (j == 0 ? 0.0 : cumulate[idx(origin_group, j - 1, true)]);
+
15845 
+
15846  int res = static_cast<int>(
+
15847  std::floor(r * group_sizes[j])
+
15848  );
15849 
-
15852 
+
15850  // Making sure we are not picking outside of the group
+
15851  if (res >= static_cast<int>(group_sizes[j]))
+
15852  res = static_cast<int>(group_sizes[j]) - 1;
15853 
-
15854 
-
15855 /*//////////////////////////////////////////////////////////////////////////////
+
15854  return model->get_entities()[j][res]->get_id();
+
15855 
+
15856 }
15857 
-
15858  Start of -include/epiworld/models/models.hpp-
-
15859 
-
15862 
-
15863 
-
15864 #ifndef EPIWORLD_MODELS_HPP
-
15865 #define EPIWORLD_MODELS_HPP
+
15858 template<typename TSeq>
+
15859 void GroupSampler<TSeq>::sample_n(
+
15860  Model<TSeq> * model,
+
15861  std::vector< int > & sample,
+
15862  const int origin_group,
+
15863  const int nsamples
+
15864 )
+
15865 {
15866 
-
15867 namespace epimodels {
-
15868 
-
15869 /*//////////////////////////////////////////////////////////////////////////////
+
15867  for (int i = 0; i < nsamples; ++i)
+
15868  sample[i] = sample_1(model, origin_group);
+
15869 
+
15870  return;
15871 
-
15872  Start of -include/epiworld//models/init-functions.hpp-
+
15872 }
15873 
-
15876 
+
15874 #endif
+
15875 /*//////////////////////////////////////////////////////////////////////////////
15877 
-
15878 #ifndef EPIWORLD_MODELS_INIT_FUNCTIONS_HPP
-
15879 #define EPIWORLD_MODELS_INIT_FUNCTIONS_HPP
-
15880 
-
15885 template<typename TSeq>
-
15886 inline std::function<void(epiworld::Model<TSeq>*)> create_init_function_sir(
-
15887  std::vector< double > proportions_
-
15888 ) {
+
15878  End of -include/epiworld/groupsampler-meat.hpp-
+
15879 
+
15882 
+
15883 
+
15884 
+
15885 /*//////////////////////////////////////////////////////////////////////////////
+
15887 
+
15888  Start of -include/epiworld/models/models.hpp-
15889 
-
15890  // Checking widths
-
15891  if (proportions_.size() != 1u)
-
15892  throw std::invalid_argument(
-
15893  "The vector of proportions must have a single element."
-
15894  );
-
15895 
-
15896  // Proportion should be within [0, 1]
-
15897  if ((proportions_[0] < 0.0) || (proportions_[0] > 1.0))
-
15898  throw std::invalid_argument(
-
15899  "The proportion must be within (0, 1)."
-
15900  );
+
15892 
+
15893 
+
15894 #ifndef EPIWORLD_MODELS_HPP
+
15895 #define EPIWORLD_MODELS_HPP
+
15896 
+
15897 namespace epimodels {
+
15898 
+
15899 /*//////////////////////////////////////////////////////////////////////////////
15901 
-
15902  double prop = proportions_[0u];
+
15902  Start of -include/epiworld//models/init-functions.hpp-
15903 
-
15904  std::function<void(epiworld::Model<TSeq>*)> fun =
-
15905  [prop] (epiworld::Model<TSeq> * model) -> void {
15906 
-
15907  // Figuring out information about the viruses
-
15908  double tot = 0.0;
-
15909  double n = static_cast<double>(model->size());
-
15910  for (const auto & agent: model->get_agents())
-
15911  {
-
15912  if (agent.get_virus() != nullptr)
-
15913  tot += 1.0;
-
15914  }
-
15915  tot /= n;
-
15916 
-
15917  // Putting the total into context
-
15918  double tot_left = 1.0 - tot;
+
15907 
+
15908 #ifndef EPIWORLD_MODELS_INIT_FUNCTIONS_HPP
+
15909 #define EPIWORLD_MODELS_INIT_FUNCTIONS_HPP
+
15910 
+
15915 template<typename TSeq>
+
15916 inline std::function<void(epiworld::Model<TSeq>*)> create_init_function_sir(
+
15917  std::vector< double > proportions_
+
15918 ) {
15919 
-
15920  // Since susceptible and infected are "fixed,"
-
15921  // we only need to change recovered
-
15922  size_t nrecovered = prop * tot_left * n;
-
15923 
-
15924  epiworld::AgentsSample<TSeq> sample(
-
15925  *model,
-
15926  nrecovered,
-
15927  {0u},
-
15928  true
-
15929  );
-
15930 
-
15931  // Setting up the initial states
-
15932  for (auto & agent : sample)
-
15933  agent->change_state(model, 2, Queue<TSeq>::NoOne);
-
15934 
-
15935  // Running the events
-
15936  model->events_run();
-
15937 
-
15938  return;
-
15939 
-
15940  };
-
15941 
-
15942  return fun;
-
15943 
-
15944 }
-
15945 
-
15950 template<typename TSeq>
-
15951 inline std::function<void(epiworld::Model<TSeq>*)> create_init_function_sird(
-
15952  std::vector< double > prop
-
15953 ) {
-
15954 
-
15955  // Check length of prop equals two
-
15956  if (prop.size() != 2u)
-
15957  throw std::invalid_argument(
-
15958  "The vector of proportions must have two elements."
+
15920  // Checking widths
+
15921  if (proportions_.size() != 1u)
+
15922  throw std::invalid_argument(
+
15923  "The vector of proportions must have a single element."
+
15924  );
+
15925 
+
15926  // Proportion should be within [0, 1]
+
15927  if ((proportions_[0] < 0.0) || (proportions_[0] > 1.0))
+
15928  throw std::invalid_argument(
+
15929  "The proportion must be within (0, 1)."
+
15930  );
+
15931 
+
15932  double prop = proportions_[0u];
+
15933 
+
15934  std::function<void(epiworld::Model<TSeq>*)> fun =
+
15935  [prop] (epiworld::Model<TSeq> * model) -> void {
+
15936 
+
15937  // Figuring out information about the viruses
+
15938  double tot = 0.0;
+
15939  double n = static_cast<double>(model->size());
+
15940  for (const auto & agent: model->get_agents())
+
15941  {
+
15942  if (agent.get_virus() != nullptr)
+
15943  tot += 1.0;
+
15944  }
+
15945  tot /= n;
+
15946 
+
15947  // Putting the total into context
+
15948  double tot_left = 1.0 - tot;
+
15949 
+
15950  // Since susceptible and infected are "fixed,"
+
15951  // we only need to change recovered
+
15952  size_t nrecovered = prop * tot_left * n;
+
15953 
+
15954  epiworld::AgentsSample<TSeq> sample(
+
15955  *model,
+
15956  nrecovered,
+
15957  {0u},
+
15958  true
15959  );
15960 
-
15961  // Check elements in prop are within [0, 1] and sum up to 1
-
15962  double tot = 0.0;
-
15963  for (auto & v : prop)
-
15964  {
-
15965  if ((v < 0.0) || (v > 1.0))
-
15966  throw std::invalid_argument(
-
15967  "The proportion must be within (0, 1)."
-
15968  );
-
15969  tot += v;
-
15970  }
+
15961  // Setting up the initial states
+
15962  for (auto & agent : sample)
+
15963  agent->change_state(model, 2, Queue<TSeq>::NoOne);
+
15964 
+
15965  // Running the events
+
15966  model->events_run();
+
15967 
+
15968  return;
+
15969 
+
15970  };
15971 
-
15972  if (tot >= 1.0)
-
15973  throw std::invalid_argument(
-
15974  "The proportions must sum up to 1."
-
15975  );
-
15976 
-
15977  std::function<void(epiworld::Model<TSeq>*)> fun =
-
15978  [prop] (epiworld::Model<TSeq> * model) -> void {
-
15979 
-
15980  // Figuring out information about the viruses
-
15981  double tot = 0.0;
-
15982  double n = static_cast<double>(model->size());
-
15983  for (const auto & agent: model->get_agents())
-
15984  {
-
15985  if (agent.get_virus() != nullptr)
-
15986  tot += 1.0;
-
15987  }
-
15988  tot /= n;
-
15989 
-
15990  // Putting the total into context
-
15991  double tot_left = 1.0 - tot;
-
15992 
-
15993  // Since susceptible and infected are "fixed,"
-
15994  // we only need to change recovered
-
15995  size_t nrecovered = prop[0u] * tot_left * n;
-
15996  size_t ndeceased = prop[01] * tot_left * n;
-
15997 
-
15998  epiworld::AgentsSample<TSeq> sample_recover(
-
15999  *model,
-
16000  nrecovered,
-
16001  {0u},
-
16002  true
-
16003  );
-
16004 
-
16005  // Setting up the initial states
-
16006  for (auto & agent : sample_recover)
-
16007  agent->change_state(model, 2, Queue<TSeq>::NoOne);
-
16008 
-
16009  epiworld::AgentsSample<TSeq> sample_deceased(
-
16010  *model,
-
16011  ndeceased,
-
16012  {0u},
-
16013  true
-
16014  );
-
16015 
-
16016  // Setting up the initial states
-
16017  for (auto & agent : sample_deceased)
-
16018  agent->change_state(model, 3, Queue<TSeq>::NoOne);
-
16019 
-
16020  // Running the events
-
16021  model->events_run();
+
15972  return fun;
+
15973 
+
15974 }
+
15975 
+
15980 template<typename TSeq>
+
15981 inline std::function<void(epiworld::Model<TSeq>*)> create_init_function_sird(
+
15982  std::vector< double > prop
+
15983 ) {
+
15984 
+
15985  // Check length of prop equals two
+
15986  if (prop.size() != 2u)
+
15987  throw std::invalid_argument(
+
15988  "The vector of proportions must have two elements."
+
15989  );
+
15990 
+
15991  // Check elements in prop are within [0, 1] and sum up to 1
+
15992  double tot = 0.0;
+
15993  for (auto & v : prop)
+
15994  {
+
15995  if ((v < 0.0) || (v > 1.0))
+
15996  throw std::invalid_argument(
+
15997  "The proportion must be within (0, 1)."
+
15998  );
+
15999  tot += v;
+
16000  }
+
16001 
+
16002  if (tot >= 1.0)
+
16003  throw std::invalid_argument(
+
16004  "The proportions must sum up to 1."
+
16005  );
+
16006 
+
16007  std::function<void(epiworld::Model<TSeq>*)> fun =
+
16008  [prop] (epiworld::Model<TSeq> * model) -> void {
+
16009 
+
16010  // Figuring out information about the viruses
+
16011  double tot = 0.0;
+
16012  double n = static_cast<double>(model->size());
+
16013  for (const auto & agent: model->get_agents())
+
16014  {
+
16015  if (agent.get_virus() != nullptr)
+
16016  tot += 1.0;
+
16017  }
+
16018  tot /= n;
+
16019 
+
16020  // Putting the total into context
+
16021  double tot_left = 1.0 - tot;
16022 
-
16023  return;
-
16024 
-
16025  };
-
16026 
-
16027  return fun;
-
16028 
-
16029 }
-
16030 
-
16031 
-
16036 template<typename TSeq>
-
16037 inline std::function<void(epiworld::Model<TSeq>*)> create_init_function_seir(
-
16038  std::vector< double > proportions_
-
16039 ) {
-
16040 
-
16041  // Checking widths
-
16042  if (proportions_.size() != 2u) {
-
16043  throw std::invalid_argument("-proportions_- must have two entries.");
-
16044  }
+
16023  // Since susceptible and infected are "fixed,"
+
16024  // we only need to change recovered
+
16025  size_t nrecovered = prop[0u] * tot_left * n;
+
16026  size_t ndeceased = prop[01] * tot_left * n;
+
16027 
+
16028  epiworld::AgentsSample<TSeq> sample_recover(
+
16029  *model,
+
16030  nrecovered,
+
16031  {0u},
+
16032  true
+
16033  );
+
16034 
+
16035  // Setting up the initial states
+
16036  for (auto & agent : sample_recover)
+
16037  agent->change_state(model, 2, Queue<TSeq>::NoOne);
+
16038 
+
16039  epiworld::AgentsSample<TSeq> sample_deceased(
+
16040  *model,
+
16041  ndeceased,
+
16042  {0u},
+
16043  true
+
16044  );
16045 
-
16046  // proportions_ are values between 0 and 1, otherwise error
-
16047  for (auto & v : proportions_)
-
16048  if ((v < 0.0) || (v > 1.0))
-
16049  throw std::invalid_argument(
-
16050  "-proportions_- must have values between 0 and 1."
-
16051  );
+
16046  // Setting up the initial states
+
16047  for (auto & agent : sample_deceased)
+
16048  agent->change_state(model, 3, Queue<TSeq>::NoOne);
+
16049 
+
16050  // Running the events
+
16051  model->events_run();
16052 
-
16053 
-
16054  std::function<void(epiworld::Model<TSeq>*)> fun =
-
16055  [proportions_] (epiworld::Model<TSeq> * model) -> void {
+
16053  return;
+
16054 
+
16055  };
16056 
-
16057  // Figuring out information about the viruses
-
16058  double tot = 0.0;
-
16059  double n = static_cast<double>(model->size());
-
16060  for (const auto & agent: model->get_agents())
-
16061  {
-
16062  if (agent.get_virus() != nullptr)
-
16063  tot += 1.0;
-
16064  }
-
16065  tot /= n;
-
16066 
-
16067  // Putting the total into context
-
16068  double tot_left = 1.0 - tot;
-
16069 
-
16070  // Since susceptible and infected are "fixed,"
-
16071  // we only need to change recovered
-
16072  size_t nexposed = proportions_[0u] * tot * n;
-
16073  size_t nrecovered = proportions_[1u] * tot_left * n;
-
16074 
-
16075  epiworld::AgentsSample<TSeq> sample_suscept(
-
16076  *model,
-
16077  nrecovered,
-
16078  {0u},
-
16079  true
-
16080  );
-
16081 
-
16082  // Setting up the initial states
-
16083  for (auto & agent : sample_suscept)
-
16084  agent->change_state(model, 3, Queue<TSeq>::NoOne);
-
16085 
-
16086  epiworld::AgentsSample<TSeq> sample_exposed(
-
16087  *model,
-
16088  nexposed,
-
16089  {1u},
-
16090  true
-
16091  );
-
16092 
-
16093  // Setting up the initial states
-
16094  for (auto & agent : sample_exposed)
-
16095  agent->change_state(model, 2, Queue<TSeq>::NoOne);
-
16096 
-
16097  // Running the events
-
16098  model->events_run();
+
16057  return fun;
+
16058 
+
16059 }
+
16060 
+
16061 
+
16066 template<typename TSeq>
+
16067 inline std::function<void(epiworld::Model<TSeq>*)> create_init_function_seir(
+
16068  std::vector< double > proportions_
+
16069 ) {
+
16070 
+
16071  // Checking widths
+
16072  if (proportions_.size() != 2u) {
+
16073  throw std::invalid_argument("-proportions_- must have two entries.");
+
16074  }
+
16075 
+
16076  // proportions_ are values between 0 and 1, otherwise error
+
16077  for (auto & v : proportions_)
+
16078  if ((v < 0.0) || (v > 1.0))
+
16079  throw std::invalid_argument(
+
16080  "-proportions_- must have values between 0 and 1."
+
16081  );
+
16082 
+
16083 
+
16084  std::function<void(epiworld::Model<TSeq>*)> fun =
+
16085  [proportions_] (epiworld::Model<TSeq> * model) -> void {
+
16086 
+
16087  // Figuring out information about the viruses
+
16088  double tot = 0.0;
+
16089  double n = static_cast<double>(model->size());
+
16090  for (const auto & agent: model->get_agents())
+
16091  {
+
16092  if (agent.get_virus() != nullptr)
+
16093  tot += 1.0;
+
16094  }
+
16095  tot /= n;
+
16096 
+
16097  // Putting the total into context
+
16098  double tot_left = 1.0 - tot;
16099 
-
16100  return;
-
16101 
-
16102  };
-
16103 
-
16104  return fun;
-
16105 
-
16106 }
-
16107 
-
16112 template<typename TSeq>
-
16113 inline std::function<void(epiworld::Model<TSeq>*)> create_init_function_seird(
-
16114  std::vector< double > proportions_
-
16115 ) {
-
16116 
-
16117  // Checking widths
-
16118  if (proportions_.size() != 3u) {
-
16119  throw std::invalid_argument("-proportions_- must have three entries.");
-
16120  }
-
16121 
-
16122  // proportions_ are values between 0 and 1, otherwise error
-
16123  for (auto & v : proportions_)
-
16124  if ((v < 0.0) || (v > 1.0))
-
16125  throw std::invalid_argument(
-
16126  "-proportions_- must have values between 0 and 1."
-
16127  );
-
16128 
-
16129  // Last first two terms shouldn't add up to more than 1
-
16130  if ((proportions_[1u] + proportions_[2u]) > 1.0)
-
16131  throw std::invalid_argument(
-
16132  "The last two terms of -proportions_- must add up to less than 1."
-
16133  );
-
16134 
-
16135  std::function<void(epiworld::Model<TSeq>*)> fun =
-
16136  [proportions_] (epiworld::Model<TSeq> * model) -> void {
+
16100  // Since susceptible and infected are "fixed,"
+
16101  // we only need to change recovered
+
16102  size_t nexposed = proportions_[0u] * tot * n;
+
16103  size_t nrecovered = proportions_[1u] * tot_left * n;
+
16104 
+
16105  epiworld::AgentsSample<TSeq> sample_suscept(
+
16106  *model,
+
16107  nrecovered,
+
16108  {0u},
+
16109  true
+
16110  );
+
16111 
+
16112  // Setting up the initial states
+
16113  for (auto & agent : sample_suscept)
+
16114  agent->change_state(model, 3, Queue<TSeq>::NoOne);
+
16115 
+
16116  epiworld::AgentsSample<TSeq> sample_exposed(
+
16117  *model,
+
16118  nexposed,
+
16119  {1u},
+
16120  true
+
16121  );
+
16122 
+
16123  // Setting up the initial states
+
16124  for (auto & agent : sample_exposed)
+
16125  agent->change_state(model, 2, Queue<TSeq>::NoOne);
+
16126 
+
16127  // Running the events
+
16128  model->events_run();
+
16129 
+
16130  return;
+
16131 
+
16132  };
+
16133 
+
16134  return fun;
+
16135 
+
16136 }
16137 
-
16138  // Figuring out information about the viruses
-
16139  double tot = 0.0;
-
16140  double n = static_cast<double>(model->size());
-
16141 
-
16142  for (const auto & agent: model->get_agents())
-
16143  {
-
16144  if (agent.get_virus() != nullptr)
-
16145  tot += 1.0;
-
16146  }
-
16147  tot /= n;
-
16148 
-
16149  // Putting the total into context
-
16150  double tot_left = 1.0 - tot;
+
16142 template<typename TSeq>
+
16143 inline std::function<void(epiworld::Model<TSeq>*)> create_init_function_seird(
+
16144  std::vector< double > proportions_
+
16145 ) {
+
16146 
+
16147  // Checking widths
+
16148  if (proportions_.size() != 3u) {
+
16149  throw std::invalid_argument("-proportions_- must have three entries.");
+
16150  }
16151 
-
16152  // Since susceptible and infected are "fixed,"
-
16153  // we only need to change recovered
-
16154  size_t nexposed = proportions_[0u] * tot * n;
-
16155  size_t nrecovered = proportions_[1u] * tot_left * n;
-
16156  size_t ndeceased = proportions_[2u] * tot_left * n;
-
16157 
-
16158  epiworld::AgentsSample<TSeq> sample_suscept(
-
16159  *model,
-
16160  nrecovered,
-
16161  {0u},
-
16162  true
+
16152  // proportions_ are values between 0 and 1, otherwise error
+
16153  for (auto & v : proportions_)
+
16154  if ((v < 0.0) || (v > 1.0))
+
16155  throw std::invalid_argument(
+
16156  "-proportions_- must have values between 0 and 1."
+
16157  );
+
16158 
+
16159  // Last first two terms shouldn't add up to more than 1
+
16160  if ((proportions_[1u] + proportions_[2u]) > 1.0)
+
16161  throw std::invalid_argument(
+
16162  "The last two terms of -proportions_- must add up to less than 1."
16163  );
16164 
-
16165  // Setting up the initial states
-
16166  for (auto & agent : sample_suscept)
-
16167  agent->change_state(model, 3, Queue<TSeq>::NoOne);
-
16168 
-
16169  epiworld::AgentsSample<TSeq> sample_exposed(
-
16170  *model,
-
16171  nexposed,
-
16172  {1u},
-
16173  true
-
16174  );
-
16175 
-
16176  // Setting up the initial states
-
16177  for (auto & agent : sample_exposed)
-
16178  agent->change_state(model, 2, Queue<TSeq>::NoOne);
-
16179 
-
16180  // Running the events
-
16181  model->events_run();
-
16182 
-
16183  // Setting the initial states for the deceased
-
16184  epiworld::AgentsSample<TSeq> sample_deceased(
-
16185  *model,
-
16186  ndeceased,
-
16187  {0u},
-
16188  true
-
16189  );
-
16190 
-
16191  // Setting up the initial states
-
16192  for (auto & agent : sample_deceased)
-
16193  agent->change_state(model, 4, Queue<TSeq>::NoOne);
-
16194 
-
16195  // Running the events
-
16196  model->events_run();
-
16197 
-
16198  return;
-
16199 
-
16200  };
-
16201 
-
16202  return fun;
-
16203 
-
16204 }
+
16165  std::function<void(epiworld::Model<TSeq>*)> fun =
+
16166  [proportions_] (epiworld::Model<TSeq> * model) -> void {
+
16167 
+
16168  // Figuring out information about the viruses
+
16169  double tot = 0.0;
+
16170  double n = static_cast<double>(model->size());
+
16171 
+
16172  for (const auto & agent: model->get_agents())
+
16173  {
+
16174  if (agent.get_virus() != nullptr)
+
16175  tot += 1.0;
+
16176  }
+
16177  tot /= n;
+
16178 
+
16179  // Putting the total into context
+
16180  double tot_left = 1.0 - tot;
+
16181 
+
16182  // Since susceptible and infected are "fixed,"
+
16183  // we only need to change recovered
+
16184  size_t nexposed = proportions_[0u] * tot * n;
+
16185  size_t nrecovered = proportions_[1u] * tot_left * n;
+
16186  size_t ndeceased = proportions_[2u] * tot_left * n;
+
16187 
+
16188  epiworld::AgentsSample<TSeq> sample_suscept(
+
16189  *model,
+
16190  nrecovered,
+
16191  {0u},
+
16192  true
+
16193  );
+
16194 
+
16195  // Setting up the initial states
+
16196  for (auto & agent : sample_suscept)
+
16197  agent->change_state(model, 3, Queue<TSeq>::NoOne);
+
16198 
+
16199  epiworld::AgentsSample<TSeq> sample_exposed(
+
16200  *model,
+
16201  nexposed,
+
16202  {1u},
+
16203  true
+
16204  );
16205 
-
16206 
-
16207 #endif
-
16208 /*//////////////////////////////////////////////////////////////////////////////
-
16210 
-
16211  End of -include/epiworld//models/init-functions.hpp-
+
16206  // Setting up the initial states
+
16207  for (auto & agent : sample_exposed)
+
16208  agent->change_state(model, 2, Queue<TSeq>::NoOne);
+
16209 
+
16210  // Running the events
+
16211  model->events_run();
16212 
-
16215 
-
16216 
-
16217 
-
16218 /*//////////////////////////////////////////////////////////////////////////////
-
16220 
-
16221  Start of -include/epiworld//models/globalevents.hpp-
-
16222 
-
16225 
-
16226 
-
16227 #ifndef EPIWORLD_GLOBALEVENTS_HPP
-
16228 #define EPIWORLD_GLOBALEVENTS_HPP
+
16213  // Setting the initial states for the deceased
+
16214  epiworld::AgentsSample<TSeq> sample_deceased(
+
16215  *model,
+
16216  ndeceased,
+
16217  {0u},
+
16218  true
+
16219  );
+
16220 
+
16221  // Setting up the initial states
+
16222  for (auto & agent : sample_deceased)
+
16223  agent->change_state(model, 4, Queue<TSeq>::NoOne);
+
16224 
+
16225  // Running the events
+
16226  model->events_run();
+
16227 
+
16228  return;
16229 
-
16230 // This function creates a global action that distributes a tool
-
16231 // to agents with probability p.
-
16240 template<typename TSeq>
-
16241 inline std::function<void(Model<TSeq>*)> globalevent_tool(
-
16242  Tool<TSeq> & tool,
-
16243  double p
-
16244 ) {
+
16230  };
+
16231 
+
16232  return fun;
+
16233 
+
16234 }
+
16235 
+
16236 
+
16237 #endif
+
16238 /*//////////////////////////////////////////////////////////////////////////////
+
16240 
+
16241  End of -include/epiworld//models/init-functions.hpp-
+
16242 
16245 
-
16246  std::function<void(Model<TSeq>*)> fun = [p,&tool](
-
16247  Model<TSeq> * model
-
16248  ) -> void {
-
16249 
-
16250  for (auto & agent : model->get_agents())
-
16251  {
+
16246 
+
16247 
+
16248 /*//////////////////////////////////////////////////////////////////////////////
+
16250 
+
16251  Start of -include/epiworld//models/globalevents.hpp-
16252 
-
16253  // Check if the agent has the tool
-
16254  if (agent.has_tool(tool))
-
16255  continue;
+
16255 
16256 
-
16257  // Adding the tool
-
16258  if (model->runif() < p)
-
16259  agent.add_tool(tool, model);
-
16260 
-
16261 
-
16262  }
-
16263 
-
16264  #ifdef EPIWORLD_DEBUG
-
16265  tool.print();
-
16266  #endif
-
16267 
-
16268  return;
-
16269 
-
16270 
-
16271  };
-
16272 
-
16273  return fun;
-
16274 
-
16275 }
-
16276 
-
16277 // Same function as above, but p is now a function of a vector of coefficients
-
16278 // and a vector of variables.
-
16289 template<typename TSeq>
-
16290 inline std::function<void(Model<TSeq>*)> globalevent_tool_logit(
-
16291  Tool<TSeq> & tool,
-
16292  std::vector< size_t > vars,
-
16293  std::vector< double > coefs
-
16294 ) {
-
16295 
-
16296  std::function<void(Model<TSeq>*)> fun = [coefs,vars,&tool](
-
16297  Model<TSeq> * model
-
16298  ) -> void {
-
16299 
-
16300  for (auto & agent : model->get_agents())
-
16301  {
+
16257 #ifndef EPIWORLD_GLOBALEVENTS_HPP
+
16258 #define EPIWORLD_GLOBALEVENTS_HPP
+
16259 
+
16260 // This function creates a global action that distributes a tool
+
16261 // to agents with probability p.
+
16270 template<typename TSeq>
+
16271 inline std::function<void(Model<TSeq>*)> globalevent_tool(
+
16272  Tool<TSeq> & tool,
+
16273  double p
+
16274 ) {
+
16275 
+
16276  std::function<void(Model<TSeq>*)> fun = [p,&tool](
+
16277  Model<TSeq> * model
+
16278  ) -> void {
+
16279 
+
16280  for (auto & agent : model->get_agents())
+
16281  {
+
16282 
+
16283  // Check if the agent has the tool
+
16284  if (agent.has_tool(tool))
+
16285  continue;
+
16286 
+
16287  // Adding the tool
+
16288  if (model->runif() < p)
+
16289  agent.add_tool(tool, model);
+
16290 
+
16291 
+
16292  }
+
16293 
+
16294  #ifdef EPIWORLD_DEBUG
+
16295  tool.print();
+
16296  #endif
+
16297 
+
16298  return;
+
16299 
+
16300 
+
16301  };
16302 
-
16303  // Check if the agent has the tool
-
16304  if (agent.has_tool(tool))
-
16305  continue;
+
16303  return fun;
+
16304 
+
16305 }
16306 
-
16307  // Computing the probability using a logit. Uses OpenMP reduction
-
16308  // to sum the coefficients.
-
16309  double p = 0.0;
-
16310  #if defined(__OPENMP) || defined(_OPENMP)
-
16311  #pragma omp parallel for reduction(+:p)
-
16312  #endif
-
16313  for (size_t i = 0u; i < coefs.size(); ++i)
-
16314  p += coefs.at(i) * agent(vars[i]);
-
16315 
-
16316  p = 1.0 / (1.0 + std::exp(-p));
-
16317 
-
16318  // Adding the tool
-
16319  if (model->runif() < p)
-
16320  agent.add_tool(tool, model);
-
16321 
-
16322 
-
16323  }
-
16324 
-
16325  #ifdef EPIWORLD_DEBUG
-
16326  tool.print();
-
16327  #endif
-
16328 
-
16329  return;
-
16330 
-
16331 
-
16332  };
-
16333 
-
16334  return fun;
-
16335 
-
16336 }
-
16337 
-
16338 // A global action that updates a parameter in the model.
-
16347 template<typename TSeq>
-
16348 inline std::function<void(Model<TSeq>*)> globalevent_set_param(
-
16349  std::string param,
-
16350  double value
-
16351 ) {
-
16352 
-
16353  std::function<void(Model<TSeq>*)> fun = [value,param](
-
16354  Model<TSeq> * model
-
16355  ) -> void {
-
16356 
-
16357  model->set_param(param, value);
+
16307 // Same function as above, but p is now a function of a vector of coefficients
+
16308 // and a vector of variables.
+
16319 template<typename TSeq>
+
16320 inline std::function<void(Model<TSeq>*)> globalevent_tool_logit(
+
16321  Tool<TSeq> & tool,
+
16322  std::vector< size_t > vars,
+
16323  std::vector< double > coefs
+
16324 ) {
+
16325 
+
16326  std::function<void(Model<TSeq>*)> fun = [coefs,vars,&tool](
+
16327  Model<TSeq> * model
+
16328  ) -> void {
+
16329 
+
16330  for (auto & agent : model->get_agents())
+
16331  {
+
16332 
+
16333  // Check if the agent has the tool
+
16334  if (agent.has_tool(tool))
+
16335  continue;
+
16336 
+
16337  // Computing the probability using a logit. Uses OpenMP reduction
+
16338  // to sum the coefficients.
+
16339  double p = 0.0;
+
16340  #if defined(__OPENMP) || defined(_OPENMP)
+
16341  #pragma omp parallel for reduction(+:p)
+
16342  #endif
+
16343  for (size_t i = 0u; i < coefs.size(); ++i)
+
16344  p += coefs.at(i) * agent(vars[i]);
+
16345 
+
16346  p = 1.0 / (1.0 + std::exp(-p));
+
16347 
+
16348  // Adding the tool
+
16349  if (model->runif() < p)
+
16350  agent.add_tool(tool, model);
+
16351 
+
16352 
+
16353  }
+
16354 
+
16355  #ifdef EPIWORLD_DEBUG
+
16356  tool.print();
+
16357  #endif
16358 
16359  return;
16360 
@@ -14974,4307 +14982,4329 @@
16364  return fun;
16365 
16366 }
-
16367 #endif
-
16368 /*//////////////////////////////////////////////////////////////////////////////
-
16370 
-
16371  End of -include/epiworld//models/globalevents.hpp-
-
16372 
-
16375 
-
16376 
-
16377 /*//////////////////////////////////////////////////////////////////////////////
-
16379 
-
16380  Start of -include/epiworld//models/sis.hpp-
-
16381 
-
16384 
-
16385 
-
16386 #ifndef EPIWORLD_MODELS_SIS_HPP
-
16387 #define EPIWORLD_MODELS_SIS_HPP
+
16367 
+
16368 // A global action that updates a parameter in the model.
+
16377 template<typename TSeq>
+
16378 inline std::function<void(Model<TSeq>*)> globalevent_set_param(
+
16379  std::string param,
+
16380  double value
+
16381 ) {
+
16382 
+
16383  std::function<void(Model<TSeq>*)> fun = [value,param](
+
16384  Model<TSeq> * model
+
16385  ) -> void {
+
16386 
+
16387  model->set_param(param, value);
16388 
-
16397 template<typename TSeq = int>
-
16398 class ModelSIS : public epiworld::Model<TSeq>
-
16399 {
+
16389  return;
+
16390 
+
16391 
+
16392  };
+
16393 
+
16394  return fun;
+
16395 
+
16396 }
+
16397 #endif
+
16398 /*//////////////////////////////////////////////////////////////////////////////
16400 
-
16401 public:
+
16401  End of -include/epiworld//models/globalevents.hpp-
16402 
-
16403  static const int SUSCEPTIBLE = 0;
-
16404  static const int INFECTED = 1;
16405 
-
16406  ModelSIS() {};
-
16407 
-
16408  ModelSIS(
-
16409  ModelSIS<TSeq> & model,
-
16410  const std::string & vname,
-
16411  epiworld_double prevalence,
-
16412  epiworld_double transmission_rate,
-
16413  epiworld_double recovery_rate
-
16414  );
+
16406 
+
16407 /*//////////////////////////////////////////////////////////////////////////////
+
16409 
+
16410  Start of -include/epiworld//models/sis.hpp-
+
16411 
+
16414 
16415 
-
16416  ModelSIS(
-
16417  const std::string & vname,
-
16418  epiworld_double prevalence,
-
16419  epiworld_double transmission_rate,
-
16420  epiworld_double recovery_rate
-
16421  );
-
16422 
-
16423 };
-
16424 
-
16425 template<typename TSeq>
-
16426 inline ModelSIS<TSeq>::ModelSIS(
-
16427  ModelSIS<TSeq> & model,
-
16428  const std::string & vname,
-
16429  epiworld_double prevalence,
-
16430  epiworld_double transmission_rate,
-
16431  epiworld_double recovery_rate
-
16432  )
-
16433 {
-
16434 
-
16435  model.set_name("Susceptible-Infected-Susceptible (SIS)");
-
16436 
-
16437  // Adding statuses
-
16438  model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
-
16439  model.add_state("Infected", epiworld::default_update_exposed<TSeq>);
-
16440 
-
16441  // Setting up parameters
-
16442  model.add_param(transmission_rate, "Transmission rate");
-
16443  model.add_param(recovery_rate, "Recovery rate");
-
16444 
-
16445  // Preparing the virus -------------------------------------------
-
16446  epiworld::Virus<TSeq> virus(vname, prevalence, true);
-
16447  virus.set_state(ModelSIS<TSeq>::INFECTED, ModelSIS<TSeq>::SUSCEPTIBLE, ModelSIS<TSeq>::SUSCEPTIBLE);
-
16448 
-
16449  virus.set_prob_infecting(&model("Transmission rate"));
-
16450  virus.set_prob_recovery(&model("Recovery rate"));
-
16451  virus.set_prob_death(0.0);
-
16452 
-
16453  model.add_virus(virus);
+
16416 #ifndef EPIWORLD_MODELS_SIS_HPP
+
16417 #define EPIWORLD_MODELS_SIS_HPP
+
16418 
+
16427 template<typename TSeq = int>
+
16428 class ModelSIS : public epiworld::Model<TSeq>
+
16429 {
+
16430 
+
16431 public:
+
16432 
+
16433  static const int SUSCEPTIBLE = 0;
+
16434  static const int INFECTED = 1;
+
16435 
+
16436  ModelSIS() {};
+
16437 
+
16438  ModelSIS(
+
16439  ModelSIS<TSeq> & model,
+
16440  const std::string & vname,
+
16441  epiworld_double prevalence,
+
16442  epiworld_double transmission_rate,
+
16443  epiworld_double recovery_rate
+
16444  );
+
16445 
+
16446  ModelSIS(
+
16447  const std::string & vname,
+
16448  epiworld_double prevalence,
+
16449  epiworld_double transmission_rate,
+
16450  epiworld_double recovery_rate
+
16451  );
+
16452 
+
16453 };
16454 
-
16455  return;
-
16456 
-
16457 }
-
16458 
-
16459 template<typename TSeq>
-
16460 inline ModelSIS<TSeq>::ModelSIS(
-
16461  const std::string & vname,
-
16462  epiworld_double prevalence,
-
16463  epiworld_double transmission_rate,
-
16464  epiworld_double recovery_rate
-
16465  )
-
16466 {
-
16467 
-
16468  ModelSIS<TSeq>(
-
16469  *this,
-
16470  vname,
-
16471  prevalence,
-
16472  transmission_rate,
-
16473  recovery_rate
-
16474  );
-
16475 
-
16476  return;
-
16477 
-
16478 }
-
16479 
-
16480 #endif
-
16481 /*//////////////////////////////////////////////////////////////////////////////
-
16483 
-
16484  End of -include/epiworld//models/sis.hpp-
-
16485 
+
16455 template<typename TSeq>
+
16456 inline ModelSIS<TSeq>::ModelSIS(
+
16457  ModelSIS<TSeq> & model,
+
16458  const std::string & vname,
+
16459  epiworld_double prevalence,
+
16460  epiworld_double transmission_rate,
+
16461  epiworld_double recovery_rate
+
16462  )
+
16463 {
+
16464 
+
16465  model.set_name("Susceptible-Infected-Susceptible (SIS)");
+
16466 
+
16467  // Adding statuses
+
16468  model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
+
16469  model.add_state("Infected", epiworld::default_update_exposed<TSeq>);
+
16470 
+
16471  // Setting up parameters
+
16472  model.add_param(transmission_rate, "Transmission rate");
+
16473  model.add_param(recovery_rate, "Recovery rate");
+
16474 
+
16475  // Preparing the virus -------------------------------------------
+
16476  epiworld::Virus<TSeq> virus(vname, prevalence, true);
+
16477  virus.set_state(ModelSIS<TSeq>::INFECTED, ModelSIS<TSeq>::SUSCEPTIBLE, ModelSIS<TSeq>::SUSCEPTIBLE);
+
16478 
+
16479  virus.set_prob_infecting(&model("Transmission rate"));
+
16480  virus.set_prob_recovery(&model("Recovery rate"));
+
16481  virus.set_prob_death(0.0);
+
16482 
+
16483  model.add_virus(virus);
+
16484 
+
16485  return;
+
16486 
+
16487 }
16488 
-
16489 
-
16490 /*//////////////////////////////////////////////////////////////////////////////
-
16492 
-
16493  Start of -include/epiworld//models/sir.hpp-
-
16494 
+
16489 template<typename TSeq>
+
16490 inline ModelSIS<TSeq>::ModelSIS(
+
16491  const std::string & vname,
+
16492  epiworld_double prevalence,
+
16493  epiworld_double transmission_rate,
+
16494  epiworld_double recovery_rate
+
16495  )
+
16496 {
16497 
-
16498 
-
16499 #ifndef EPIWORLD_SIR_H
-
16500 #define EPIWORLD_SIR_H
-
16501 
-
16511 template<typename TSeq = int>
-
16512 class ModelSIR : public epiworld::Model<TSeq>
-
16513 {
-
16514 public:
+
16498  ModelSIS<TSeq>(
+
16499  *this,
+
16500  vname,
+
16501  prevalence,
+
16502  transmission_rate,
+
16503  recovery_rate
+
16504  );
+
16505 
+
16506  return;
+
16507 
+
16508 }
+
16509 
+
16510 #endif
+
16511 /*//////////////////////////////////////////////////////////////////////////////
+
16513 
+
16514  End of -include/epiworld//models/sis.hpp-
16515 
-
16516  ModelSIR() {};
-
16517 
-
16518  ModelSIR(
-
16519  ModelSIR<TSeq> & model,
-
16520  const std::string & vname,
-
16521  epiworld_double prevalence,
-
16522  epiworld_double transmission_rate,
-
16523  epiworld_double recovery_rate
-
16524  );
-
16525 
-
16526  ModelSIR(
-
16527  const std::string & vname,
-
16528  epiworld_double prevalence,
-
16529  epiworld_double transmission_rate,
-
16530  epiworld_double recovery_rate
-
16531  );
-
16532 
-
16538  ModelSIR<TSeq> & initial_states(
-
16539  std::vector< double > proportions_,
-
16540  std::vector< int > queue_ = {}
-
16541  );
-
16542 
-
16543 };
-
16544 
-
16545 template<typename TSeq>
-
16546 inline ModelSIR<TSeq>::ModelSIR(
-
16547  ModelSIR<TSeq> & model,
-
16548  const std::string & vname,
-
16549  epiworld_double prevalence,
-
16550  epiworld_double transmission_rate,
-
16551  epiworld_double recovery_rate
-
16552  )
-
16553 {
-
16554 
-
16555  // Adding statuses
-
16556  model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
-
16557  model.add_state("Infected", epiworld::default_update_exposed<TSeq>);
-
16558  model.add_state("Recovered");
-
16559 
-
16560  // Setting up parameters
-
16561  model.add_param(recovery_rate, "Recovery rate");
-
16562  model.add_param(transmission_rate, "Transmission rate");
-
16563 
-
16564  // Preparing the virus -------------------------------------------
-
16565  epiworld::Virus<TSeq> virus(vname, prevalence, true);
-
16566  virus.set_state(1,2,2);
-
16567 
-
16568  virus.set_prob_recovery(&model("Recovery rate"));
-
16569  virus.set_prob_infecting(&model("Transmission rate"));
-
16570 
-
16571  model.add_virus(virus);
-
16572 
-
16573  model.set_name("Susceptible-Infected-Recovered (SIR)");
+
16518 
+
16519 
+
16520 /*//////////////////////////////////////////////////////////////////////////////
+
16522 
+
16523  Start of -include/epiworld//models/sir.hpp-
+
16524 
+
16527 
+
16528 
+
16529 #ifndef EPIWORLD_SIR_H
+
16530 #define EPIWORLD_SIR_H
+
16531 
+
16541 template<typename TSeq = int>
+
16542 class ModelSIR : public epiworld::Model<TSeq>
+
16543 {
+
16544 public:
+
16545 
+
16546  ModelSIR() {};
+
16547 
+
16548  ModelSIR(
+
16549  ModelSIR<TSeq> & model,
+
16550  const std::string & vname,
+
16551  epiworld_double prevalence,
+
16552  epiworld_double transmission_rate,
+
16553  epiworld_double recovery_rate
+
16554  );
+
16555 
+
16556  ModelSIR(
+
16557  const std::string & vname,
+
16558  epiworld_double prevalence,
+
16559  epiworld_double transmission_rate,
+
16560  epiworld_double recovery_rate
+
16561  );
+
16562 
+
16568  ModelSIR<TSeq> & initial_states(
+
16569  std::vector< double > proportions_,
+
16570  std::vector< int > queue_ = {}
+
16571  );
+
16572 
+
16573 };
16574 
-
16575  return;
-
16576 
-
16577 }
-
16578 
-
16579 template<typename TSeq>
-
16580 inline ModelSIR<TSeq>::ModelSIR(
-
16581  const std::string & vname,
-
16582  epiworld_double prevalence,
-
16583  epiworld_double transmission_rate,
-
16584  epiworld_double recovery_rate
-
16585  )
-
16586 {
-
16587 
-
16588  ModelSIR<TSeq>(
-
16589  *this,
-
16590  vname,
-
16591  prevalence,
-
16592  transmission_rate,
-
16593  recovery_rate
-
16594  );
-
16595 
-
16596  return;
-
16597 
-
16598 }
-
16599 
-
16600 template<typename TSeq>
-
16601 inline ModelSIR<TSeq> & ModelSIR<TSeq>::initial_states(
-
16602  std::vector< double > proportions_,
-
16603  std::vector< int > /* queue_ */
-
16604 ) {
-
16605 
-
16606  Model<TSeq>::initial_states_fun =
-
16607  create_init_function_sir<TSeq>(proportions_)
-
16608  ;
-
16609 
-
16610  return *this;
-
16611 
-
16612 }
-
16613 
-
16614 #endif
-
16615 /*//////////////////////////////////////////////////////////////////////////////
+
16575 template<typename TSeq>
+
16576 inline ModelSIR<TSeq>::ModelSIR(
+
16577  ModelSIR<TSeq> & model,
+
16578  const std::string & vname,
+
16579  epiworld_double prevalence,
+
16580  epiworld_double transmission_rate,
+
16581  epiworld_double recovery_rate
+
16582  )
+
16583 {
+
16584 
+
16585  // Adding statuses
+
16586  model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
+
16587  model.add_state("Infected", epiworld::default_update_exposed<TSeq>);
+
16588  model.add_state("Recovered");
+
16589 
+
16590  // Setting up parameters
+
16591  model.add_param(recovery_rate, "Recovery rate");
+
16592  model.add_param(transmission_rate, "Transmission rate");
+
16593 
+
16594  // Preparing the virus -------------------------------------------
+
16595  epiworld::Virus<TSeq> virus(vname, prevalence, true);
+
16596  virus.set_state(1,2,2);
+
16597 
+
16598  virus.set_prob_recovery(&model("Recovery rate"));
+
16599  virus.set_prob_infecting(&model("Transmission rate"));
+
16600 
+
16601  model.add_virus(virus);
+
16602 
+
16603  model.set_name("Susceptible-Infected-Recovered (SIR)");
+
16604 
+
16605  return;
+
16606 
+
16607 }
+
16608 
+
16609 template<typename TSeq>
+
16610 inline ModelSIR<TSeq>::ModelSIR(
+
16611  const std::string & vname,
+
16612  epiworld_double prevalence,
+
16613  epiworld_double transmission_rate,
+
16614  epiworld_double recovery_rate
+
16615  )
+
16616 {
16617 
-
16618  End of -include/epiworld//models/sir.hpp-
-
16619 
-
16622 
-
16623 
-
16624 /*//////////////////////////////////////////////////////////////////////////////
-
16626 
-
16627  Start of -include/epiworld//models/seir.hpp-
-
16628 
-
16631 
-
16632 
-
16633 #ifndef EPIWORLD_MODELS_SEIR_HPP
-
16634 #define EPIWORLD_MODELS_SEIR_HPP
-
16635 
-
16646 template<typename TSeq = int>
-
16647 class ModelSEIR : public epiworld::Model<TSeq>
-
16648 {
+
16618  ModelSIR<TSeq>(
+
16619  *this,
+
16620  vname,
+
16621  prevalence,
+
16622  transmission_rate,
+
16623  recovery_rate
+
16624  );
+
16625 
+
16626  return;
+
16627 
+
16628 }
+
16629 
+
16630 template<typename TSeq>
+
16631 inline ModelSIR<TSeq> & ModelSIR<TSeq>::initial_states(
+
16632  std::vector< double > proportions_,
+
16633  std::vector< int > /* queue_ */
+
16634 ) {
+
16635 
+
16636  Model<TSeq>::initial_states_fun =
+
16637  create_init_function_sir<TSeq>(proportions_)
+
16638  ;
+
16639 
+
16640  return *this;
+
16641 
+
16642 }
+
16643 
+
16644 #endif
+
16645 /*//////////////////////////////////////////////////////////////////////////////
+
16647 
+
16648  End of -include/epiworld//models/sir.hpp-
16649 
-
16650 public:
-
16651  static const int SUSCEPTIBLE = 0;
-
16652  static const int EXPOSED = 1;
-
16653  static const int INFECTED = 2;
-
16654  static const int REMOVED = 3;
-
16655 
-
16656  ModelSEIR() {};
-
16657 
-
16658  ModelSEIR(
-
16659  ModelSEIR<TSeq> & model,
-
16660  const std::string & vname,
-
16661  epiworld_double prevalence,
-
16662  epiworld_double transmission_rate,
-
16663  epiworld_double avg_incubation_days,
-
16664  epiworld_double recovery_rate
-
16665  );
-
16666 
-
16667  ModelSEIR(
-
16668  const std::string & vname,
-
16669  epiworld_double prevalence,
-
16670  epiworld_double transmission_rate,
-
16671  epiworld_double avg_incubation_days,
-
16672  epiworld_double recovery_rate
-
16673  );
-
16674 
-
16675  epiworld::UpdateFun<TSeq> update_exposed_seir = [](
-
16676  epiworld::Agent<TSeq> * p,
-
16677  epiworld::Model<TSeq> * m
-
16678  ) -> void {
+
16652 
+
16653 
+
16654 /*//////////////////////////////////////////////////////////////////////////////
+
16656 
+
16657  Start of -include/epiworld//models/seir.hpp-
+
16658 
+
16661 
+
16662 
+
16663 #ifndef EPIWORLD_MODELS_SEIR_HPP
+
16664 #define EPIWORLD_MODELS_SEIR_HPP
+
16665 
+
16676 template<typename TSeq = int>
+
16677 class ModelSEIR : public epiworld::Model<TSeq>
+
16678 {
16679 
-
16680  // Getting the virus
-
16681  auto v = p->get_virus();
-
16682 
-
16683  // Does the agent become infected?
-
16684  if (m->runif() < 1.0/(v->get_incubation(m)))
-
16685  p->change_state(m, ModelSEIR<TSeq>::INFECTED);
-
16686 
-
16687  return;
-
16688  };
-
16689 
-
16690 
-
16691  epiworld::UpdateFun<TSeq> update_infected_seir = [](
-
16692  epiworld::Agent<TSeq> * p,
-
16693  epiworld::Model<TSeq> * m
-
16694  ) -> void {
-
16695  // Does the agent recover?
-
16696  if (m->runif() < (m->par("Recovery rate")))
-
16697  p->rm_virus(m);
-
16698 
-
16699  return;
-
16700  };
-
16701 
-
16708  ModelSEIR<TSeq> & initial_states(
-
16709  std::vector< double > proportions_,
-
16710  std::vector< int > queue_ = {}
-
16711  );
+
16680 public:
+
16681  static const int SUSCEPTIBLE = 0;
+
16682  static const int EXPOSED = 1;
+
16683  static const int INFECTED = 2;
+
16684  static const int REMOVED = 3;
+
16685 
+
16686  ModelSEIR() {};
+
16687 
+
16688  ModelSEIR(
+
16689  ModelSEIR<TSeq> & model,
+
16690  const std::string & vname,
+
16691  epiworld_double prevalence,
+
16692  epiworld_double transmission_rate,
+
16693  epiworld_double avg_incubation_days,
+
16694  epiworld_double recovery_rate
+
16695  );
+
16696 
+
16697  ModelSEIR(
+
16698  const std::string & vname,
+
16699  epiworld_double prevalence,
+
16700  epiworld_double transmission_rate,
+
16701  epiworld_double avg_incubation_days,
+
16702  epiworld_double recovery_rate
+
16703  );
+
16704 
+
16705  epiworld::UpdateFun<TSeq> update_exposed_seir = [](
+
16706  epiworld::Agent<TSeq> * p,
+
16707  epiworld::Model<TSeq> * m
+
16708  ) -> void {
+
16709 
+
16710  // Getting the virus
+
16711  auto v = p->get_virus();
16712 
-
16713 };
-
16714 
-
16715 
-
16716 template<typename TSeq>
-
16717 inline ModelSEIR<TSeq>::ModelSEIR(
-
16718  ModelSEIR<TSeq> & model,
-
16719  const std::string & vname,
-
16720  epiworld_double prevalence,
-
16721  epiworld_double transmission_rate,
-
16722  epiworld_double avg_incubation_days,
-
16723  epiworld_double recovery_rate
-
16724  )
-
16725 {
-
16726 
-
16727  // Adding statuses
-
16728  model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
-
16729  model.add_state("Exposed", model.update_exposed_seir);
-
16730  model.add_state("Infected", model.update_infected_seir);
-
16731  model.add_state("Removed");
-
16732 
-
16733  // Setting up parameters
-
16734  model.add_param(transmission_rate, "Transmission rate");
-
16735  model.add_param(avg_incubation_days, "Incubation days");
-
16736  model.add_param(recovery_rate, "Recovery rate");
-
16737 
-
16738  // Preparing the virus -------------------------------------------
-
16739  epiworld::Virus<TSeq> virus(vname, prevalence, true);
-
16740  virus.set_state(ModelSEIR<TSeq>::EXPOSED, ModelSEIR<TSeq>::REMOVED, ModelSEIR<TSeq>::REMOVED);
-
16741 
-
16742  virus.set_prob_infecting(&model("Transmission rate"));
-
16743  virus.set_incubation(&model("Incubation days"));
-
16744  virus.set_prob_recovery(&model("Recovery rate"));
-
16745 
-
16746  // Adding the tool and the virus
-
16747  model.add_virus(virus);
-
16748 
-
16749  model.set_name("Susceptible-Exposed-Infected-Removed (SEIR)");
-
16750 
-
16751  return;
-
16752 
-
16753 }
-
16754 
-
16755 template<typename TSeq>
-
16756 inline ModelSEIR<TSeq>::ModelSEIR(
-
16757  const std::string & vname,
-
16758  epiworld_double prevalence,
-
16759  epiworld_double transmission_rate,
-
16760  epiworld_double avg_incubation_days,
-
16761  epiworld_double recovery_rate
-
16762  )
-
16763 {
-
16764 
-
16765  ModelSEIR<TSeq>(
-
16766  *this,
-
16767  vname,
-
16768  prevalence,
-
16769  transmission_rate,
-
16770  avg_incubation_days,
-
16771  recovery_rate
-
16772  );
-
16773 
-
16774  return;
-
16775 
-
16776 }
-
16777 
-
16778 template<typename TSeq>
-
16779 inline ModelSEIR<TSeq> & ModelSEIR<TSeq>::initial_states(
-
16780  std::vector< double > proportions_,
-
16781  std::vector< int > /**/
-
16782 ) {
-
16783 
-
16784  Model<TSeq>::initial_states_fun =
-
16785  create_init_function_seir<TSeq>(proportions_)
-
16786  ;
-
16787 
-
16788  return *this;
-
16789 
-
16790 }
-
16791 
-
16792 #endif
-
16793 /*//////////////////////////////////////////////////////////////////////////////
-
16795 
-
16796  End of -include/epiworld//models/seir.hpp-
-
16797 
-
16800 
-
16801 
-
16802 /*//////////////////////////////////////////////////////////////////////////////
-
16804 
-
16805  Start of -include/epiworld//models/surveillance.hpp-
-
16806 
-
16809 
-
16810 
-
16811 #ifndef EPIWORLD_MODELS_SURVEILLANCE_HPP
-
16812 #define EPIWORLD_MODELS_SURVEILLANCE_HPP
-
16813 
-
16814 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
16815 class ModelSURV : public epiworld::Model<TSeq> {
-
16816 
-
16817 private:
-
16818  // state
-
16819  static const int SUSCEPTIBLE = 0;
-
16820  static const int LATENT = 1;
-
16821  static const int SYMPTOMATIC = 2;
-
16822  static const int SYMPTOMATIC_ISOLATED = 3; // sampled and discovered
-
16823  static const int ASYMPTOMATIC = 4;
-
16824  static const int ASYMPTOMATIC_ISOLATED = 5;
-
16825  static const int RECOVERED = 6;
-
16826  static const int REMOVED = 7;
+
16713  // Does the agent become infected?
+
16714  if (m->runif() < 1.0/(v->get_incubation(m)))
+
16715  p->change_state(m, ModelSEIR<TSeq>::INFECTED);
+
16716 
+
16717  return;
+
16718  };
+
16719 
+
16720 
+
16721  epiworld::UpdateFun<TSeq> update_infected_seir = [](
+
16722  epiworld::Agent<TSeq> * p,
+
16723  epiworld::Model<TSeq> * m
+
16724  ) -> void {
+
16725  // Does the agent recover?
+
16726  if (m->runif() < (m->par("Recovery rate")))
+
16727  p->rm_virus(m);
+
16728 
+
16729  return;
+
16730  };
+
16731 
+
16738  ModelSEIR<TSeq> & initial_states(
+
16739  std::vector< double > proportions_,
+
16740  std::vector< int > queue_ = {}
+
16741  );
+
16742 
+
16743 };
+
16744 
+
16745 
+
16746 template<typename TSeq>
+
16747 inline ModelSEIR<TSeq>::ModelSEIR(
+
16748  ModelSEIR<TSeq> & model,
+
16749  const std::string & vname,
+
16750  epiworld_double prevalence,
+
16751  epiworld_double transmission_rate,
+
16752  epiworld_double avg_incubation_days,
+
16753  epiworld_double recovery_rate
+
16754  )
+
16755 {
+
16756 
+
16757  // Adding statuses
+
16758  model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
+
16759  model.add_state("Exposed", model.update_exposed_seir);
+
16760  model.add_state("Infected", model.update_infected_seir);
+
16761  model.add_state("Removed");
+
16762 
+
16763  // Setting up parameters
+
16764  model.add_param(transmission_rate, "Transmission rate");
+
16765  model.add_param(avg_incubation_days, "Incubation days");
+
16766  model.add_param(recovery_rate, "Recovery rate");
+
16767 
+
16768  // Preparing the virus -------------------------------------------
+
16769  epiworld::Virus<TSeq> virus(vname, prevalence, true);
+
16770  virus.set_state(ModelSEIR<TSeq>::EXPOSED, ModelSEIR<TSeq>::REMOVED, ModelSEIR<TSeq>::REMOVED);
+
16771 
+
16772  virus.set_prob_infecting(&model("Transmission rate"));
+
16773  virus.set_incubation(&model("Incubation days"));
+
16774  virus.set_prob_recovery(&model("Recovery rate"));
+
16775 
+
16776  // Adding the tool and the virus
+
16777  model.add_virus(virus);
+
16778 
+
16779  model.set_name("Susceptible-Exposed-Infected-Removed (SEIR)");
+
16780 
+
16781  return;
+
16782 
+
16783 }
+
16784 
+
16785 template<typename TSeq>
+
16786 inline ModelSEIR<TSeq>::ModelSEIR(
+
16787  const std::string & vname,
+
16788  epiworld_double prevalence,
+
16789  epiworld_double transmission_rate,
+
16790  epiworld_double avg_incubation_days,
+
16791  epiworld_double recovery_rate
+
16792  )
+
16793 {
+
16794 
+
16795  ModelSEIR<TSeq>(
+
16796  *this,
+
16797  vname,
+
16798  prevalence,
+
16799  transmission_rate,
+
16800  avg_incubation_days,
+
16801  recovery_rate
+
16802  );
+
16803 
+
16804  return;
+
16805 
+
16806 }
+
16807 
+
16808 template<typename TSeq>
+
16809 inline ModelSEIR<TSeq> & ModelSEIR<TSeq>::initial_states(
+
16810  std::vector< double > proportions_,
+
16811  std::vector< int > /**/
+
16812 ) {
+
16813 
+
16814  Model<TSeq>::initial_states_fun =
+
16815  create_init_function_seir<TSeq>(proportions_)
+
16816  ;
+
16817 
+
16818  return *this;
+
16819 
+
16820 }
+
16821 
+
16822 #endif
+
16823 /*//////////////////////////////////////////////////////////////////////////////
+
16825 
+
16826  End of -include/epiworld//models/seir.hpp-
16827 
-
16828 public:
-
16829 
-
16871  ModelSURV() {};
-
16872 
-
16873  ModelSURV(
-
16874  ModelSURV<TSeq> & model,
-
16875  const std::string & vname,
-
16876  epiworld_fast_uint prevalence = 50,
-
16877  epiworld_double efficacy_vax = 0.9,
-
16878  epiworld_double latent_period = 3u,
-
16879  epiworld_double infect_period = 6u,
-
16880  epiworld_double prob_symptoms = 0.6,
-
16881  epiworld_double prop_vaccinated = 0.25,
-
16882  epiworld_double prop_vax_redux_transm = 0.5,
-
16883  epiworld_double prop_vax_redux_infect = 0.5,
-
16884  epiworld_double surveillance_prob = 0.001,
-
16885  epiworld_double prob_transmission = 1.0,
-
16886  epiworld_double prob_death = 0.001,
-
16887  epiworld_double prob_noreinfect = 0.9
-
16888  );
-
16889 
-
16890  ModelSURV(
-
16891  const std::string & vname,
-
16892  epiworld_fast_uint prevalence = 50,
-
16893  epiworld_double efficacy_vax = 0.9,
-
16894  epiworld_double latent_period = 3u,
-
16895  epiworld_double infect_period = 6u,
-
16896  epiworld_double prob_symptoms = 0.6,
-
16897  epiworld_double prop_vaccinated = 0.25,
-
16898  epiworld_double prop_vax_redux_transm = 0.5,
-
16899  epiworld_double prop_vax_redux_infect = 0.5,
-
16900  epiworld_double surveillance_prob = 0.001,
-
16901  epiworld_double prob_transmission = 1.0,
-
16902  epiworld_double prob_death = 0.001,
-
16903  epiworld_double prob_noreinfect = 0.9
-
16904  );
-
16906 
-
16907 };
-
16908 
-
16909 template<typename TSeq>
-
16910 inline ModelSURV<TSeq>::ModelSURV(
-
16911  ModelSURV<TSeq> & model,
-
16912  const std::string & vname,
-
16913  epiworld_fast_uint prevalence,
-
16914  epiworld_double efficacy_vax,
-
16915  epiworld_double latent_period,
-
16916  epiworld_double infect_period,
-
16917  epiworld_double prob_symptoms,
-
16918  epiworld_double prop_vaccinated,
-
16919  epiworld_double prop_vax_redux_transm,
-
16920  epiworld_double prop_vax_redux_infect,
-
16921  epiworld_double surveillance_prob,
-
16922  epiworld_double prob_transmission,
-
16923  epiworld_double prob_death,
-
16924  epiworld_double prob_noreinfect
-
16925  )
-
16926 {
-
16927 
-
16928  EPI_NEW_UPDATEFUN_LAMBDA(surveillance_update_susceptible, TSeq) {
-
16929 
-
16930  // This computes the prob of getting any neighbor variant
-
16931  epiworld_fast_uint nviruses_tmp = 0u;
-
16932  for (auto & neighbor: p->get_neighbors())
-
16933  {
-
16934 
-
16935  auto & v = neighbor->get_virus();
+
16830 
+
16831 
+
16832 /*//////////////////////////////////////////////////////////////////////////////
+
16834 
+
16835  Start of -include/epiworld//models/surveillance.hpp-
+
16836 
+
16839 
+
16840 
+
16841 #ifndef EPIWORLD_MODELS_SURVEILLANCE_HPP
+
16842 #define EPIWORLD_MODELS_SURVEILLANCE_HPP
+
16843 
+
16844 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
16845 class ModelSURV : public epiworld::Model<TSeq> {
+
16846 
+
16847 private:
+
16848  // state
+
16849  static const int SUSCEPTIBLE = 0;
+
16850  static const int LATENT = 1;
+
16851  static const int SYMPTOMATIC = 2;
+
16852  static const int SYMPTOMATIC_ISOLATED = 3; // sampled and discovered
+
16853  static const int ASYMPTOMATIC = 4;
+
16854  static const int ASYMPTOMATIC_ISOLATED = 5;
+
16855  static const int RECOVERED = 6;
+
16856  static const int REMOVED = 7;
+
16857 
+
16858 public:
+
16859 
+
16901  ModelSURV() {};
+
16902 
+
16903  ModelSURV(
+
16904  ModelSURV<TSeq> & model,
+
16905  const std::string & vname,
+
16906  epiworld_fast_uint prevalence = 50,
+
16907  epiworld_double efficacy_vax = 0.9,
+
16908  epiworld_double latent_period = 3u,
+
16909  epiworld_double infect_period = 6u,
+
16910  epiworld_double prob_symptoms = 0.6,
+
16911  epiworld_double prop_vaccinated = 0.25,
+
16912  epiworld_double prop_vax_redux_transm = 0.5,
+
16913  epiworld_double prop_vax_redux_infect = 0.5,
+
16914  epiworld_double surveillance_prob = 0.001,
+
16915  epiworld_double prob_transmission = 1.0,
+
16916  epiworld_double prob_death = 0.001,
+
16917  epiworld_double prob_noreinfect = 0.9
+
16918  );
+
16919 
+
16920  ModelSURV(
+
16921  const std::string & vname,
+
16922  epiworld_fast_uint prevalence = 50,
+
16923  epiworld_double efficacy_vax = 0.9,
+
16924  epiworld_double latent_period = 3u,
+
16925  epiworld_double infect_period = 6u,
+
16926  epiworld_double prob_symptoms = 0.6,
+
16927  epiworld_double prop_vaccinated = 0.25,
+
16928  epiworld_double prop_vax_redux_transm = 0.5,
+
16929  epiworld_double prop_vax_redux_infect = 0.5,
+
16930  epiworld_double surveillance_prob = 0.001,
+
16931  epiworld_double prob_transmission = 1.0,
+
16932  epiworld_double prob_death = 0.001,
+
16933  epiworld_double prob_noreinfect = 0.9
+
16934  );
16936 
-
16937  if (v == nullptr)
-
16938  continue;
-
16939 
-
16940  /* And it is a function of susceptibility_reduction as well */
-
16941  epiworld_double tmp_transmission =
-
16942  (1.0 - p->get_susceptibility_reduction(v, m)) *
-
16943  v->get_prob_infecting(m) *
-
16944  (1.0 - neighbor->get_transmission_reduction(v, m))
-
16945  ;
-
16946 
-
16947  m->array_double_tmp[nviruses_tmp] = tmp_transmission;
-
16948  m->array_virus_tmp[nviruses_tmp++] = &(*v);
-
16949  }
-
16950 
-
16951  // No virus to compute on
-
16952  if (nviruses_tmp == 0)
-
16953  return;
-
16954 
-
16955  // Running the roulette
-
16956  int which = roulette(nviruses_tmp, m);
-
16957 
-
16958  if (which < 0)
-
16959  return;
-
16960 
-
16961  p->set_virus(*m->array_virus_tmp[which], m);
-
16962  return;
-
16963 
-
16964  };
-
16965 
-
16966 
-
16967  epiworld::UpdateFun<TSeq> surveillance_update_exposed =
-
16968  [](epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m) -> void
-
16969  {
-
16970 
-
16971  epiworld::VirusPtr<TSeq> & v = p->get_virus();
-
16972  epiworld_double p_die = v->get_prob_death(m) * (1.0 - p->get_death_reduction(v, m));
-
16973 
-
16974  epiworld_fast_uint days_since_exposed = m->today() - v->get_date();
-
16975  epiworld_fast_uint state = p->get_state();
-
16976 
-
16977  // Figuring out latent period
-
16978  if (v->get_data().size() == 0u)
-
16979  {
-
16980  epiworld_double latent_days = m->rgamma(m->par("Latent period"), 1.0);
-
16981  v->get_data().push_back(latent_days);
-
16982 
-
16983  v->get_data().push_back(
-
16984  m->rgamma(m->par("Infect period"), 1.0) + latent_days
-
16985  );
-
16986  }
-
16987 
-
16988  // If still latent, nothing happens
-
16989  if (days_since_exposed <= v->get_data()[0u])
-
16990  return;
-
16991 
-
16992  // If past days infected + latent, then bye.
-
16993  if (days_since_exposed >= v->get_data()[1u])
-
16994  {
-
16995  p->rm_virus(m);
-
16996  return;
-
16997  }
-
16998 
-
16999  // If it is infected, then it can be asymptomatic or symptomatic
-
17000  if (state == ModelSURV<TSeq>::LATENT)
-
17001  {
-
17002 
-
17003  // Will be symptomatic?
-
17004  if (EPI_RUNIF() < m->par("Prob of symptoms"))
-
17005  p->change_state(m, ModelSURV<TSeq>::SYMPTOMATIC);
-
17006  else
-
17007  p->change_state(m, ModelSURV<TSeq>::ASYMPTOMATIC);
-
17008 
-
17009  return;
-
17010 
-
17011  }
-
17012 
-
17013  // Otherwise, it can be removed
-
17014  if (EPI_RUNIF() < p_die)
-
17015  {
-
17016  p->change_state(m, ModelSURV<TSeq>::REMOVED, -1);
-
17017  return;
-
17018  }
-
17019 
-
17020  return;
+
16937 };
+
16938 
+
16939 template<typename TSeq>
+
16940 inline ModelSURV<TSeq>::ModelSURV(
+
16941  ModelSURV<TSeq> & model,
+
16942  const std::string & vname,
+
16943  epiworld_fast_uint prevalence,
+
16944  epiworld_double efficacy_vax,
+
16945  epiworld_double latent_period,
+
16946  epiworld_double infect_period,
+
16947  epiworld_double prob_symptoms,
+
16948  epiworld_double prop_vaccinated,
+
16949  epiworld_double prop_vax_redux_transm,
+
16950  epiworld_double prop_vax_redux_infect,
+
16951  epiworld_double surveillance_prob,
+
16952  epiworld_double prob_transmission,
+
16953  epiworld_double prob_death,
+
16954  epiworld_double prob_noreinfect
+
16955  )
+
16956 {
+
16957 
+
16958  EPI_NEW_UPDATEFUN_LAMBDA(surveillance_update_susceptible, TSeq) {
+
16959 
+
16960  // This computes the prob of getting any neighbor variant
+
16961  epiworld_fast_uint nviruses_tmp = 0u;
+
16962  for (auto & neighbor: p->get_neighbors())
+
16963  {
+
16964 
+
16965  auto & v = neighbor->get_virus();
+
16966 
+
16967  if (v == nullptr)
+
16968  continue;
+
16969 
+
16970  /* And it is a function of susceptibility_reduction as well */
+
16971  epiworld_double tmp_transmission =
+
16972  (1.0 - p->get_susceptibility_reduction(v, m)) *
+
16973  v->get_prob_infecting(m) *
+
16974  (1.0 - neighbor->get_transmission_reduction(v, m))
+
16975  ;
+
16976 
+
16977  m->array_double_tmp[nviruses_tmp] = tmp_transmission;
+
16978  m->array_virus_tmp[nviruses_tmp++] = &(*v);
+
16979  }
+
16980 
+
16981  // No virus to compute on
+
16982  if (nviruses_tmp == 0)
+
16983  return;
+
16984 
+
16985  // Running the roulette
+
16986  int which = roulette(nviruses_tmp, m);
+
16987 
+
16988  if (which < 0)
+
16989  return;
+
16990 
+
16991  p->set_virus(*m->array_virus_tmp[which], m);
+
16992  return;
+
16993 
+
16994  };
+
16995 
+
16996 
+
16997  epiworld::UpdateFun<TSeq> surveillance_update_exposed =
+
16998  [](epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m) -> void
+
16999  {
+
17000 
+
17001  epiworld::VirusPtr<TSeq> & v = p->get_virus();
+
17002  epiworld_double p_die = v->get_prob_death(m) * (1.0 - p->get_death_reduction(v, m));
+
17003 
+
17004  epiworld_fast_uint days_since_exposed = m->today() - v->get_date();
+
17005  epiworld_fast_uint state = p->get_state();
+
17006 
+
17007  // Figuring out latent period
+
17008  if (v->get_data().size() == 0u)
+
17009  {
+
17010  epiworld_double latent_days = m->rgamma(m->par("Latent period"), 1.0);
+
17011  v->get_data().push_back(latent_days);
+
17012 
+
17013  v->get_data().push_back(
+
17014  m->rgamma(m->par("Infect period"), 1.0) + latent_days
+
17015  );
+
17016  }
+
17017 
+
17018  // If still latent, nothing happens
+
17019  if (days_since_exposed <= v->get_data()[0u])
+
17020  return;
17021 
-
17022  };
-
17023 
-
17024  std::vector< epiworld_fast_uint > exposed_state = {
-
17025  SYMPTOMATIC,
-
17026  SYMPTOMATIC_ISOLATED,
-
17027  ASYMPTOMATIC,
-
17028  ASYMPTOMATIC_ISOLATED,
-
17029  LATENT
-
17030  };
-
17031 
-
17032  epiworld::GlobalFun<TSeq> surveillance_program =
-
17033  [exposed_state](
-
17034  epiworld::Model<TSeq>* m
-
17035  ) -> void
-
17036  {
-
17037 
-
17038  // How many will we find
-
17039  std::binomial_distribution<> bdist(m->size(), m->par("Surveilance prob."));
-
17040  int nsampled = bdist(*m->get_rand_endgine());
-
17041 
-
17042  int to_go = nsampled + 1;
-
17043 
-
17044  epiworld_double ndetected = 0.0;
-
17045  epiworld_double ndetected_asympt = 0.0;
-
17046 
-
17047  auto & pop = m->get_agents();
-
17048  std::vector< bool > sampled(m->size(), false);
+
17022  // If past days infected + latent, then bye.
+
17023  if (days_since_exposed >= v->get_data()[1u])
+
17024  {
+
17025  p->rm_virus(m);
+
17026  return;
+
17027  }
+
17028 
+
17029  // If it is infected, then it can be asymptomatic or symptomatic
+
17030  if (state == ModelSURV<TSeq>::LATENT)
+
17031  {
+
17032 
+
17033  // Will be symptomatic?
+
17034  if (EPI_RUNIF() < m->par("Prob of symptoms"))
+
17035  p->change_state(m, ModelSURV<TSeq>::SYMPTOMATIC);
+
17036  else
+
17037  p->change_state(m, ModelSURV<TSeq>::ASYMPTOMATIC);
+
17038 
+
17039  return;
+
17040 
+
17041  }
+
17042 
+
17043  // Otherwise, it can be removed
+
17044  if (EPI_RUNIF() < p_die)
+
17045  {
+
17046  p->change_state(m, ModelSURV<TSeq>::REMOVED, -1);
+
17047  return;
+
17048  }
17049 
-
17050  while (to_go-- > 0)
-
17051  {
-
17052 
-
17053  // Who is the lucky one
-
17054  epiworld_fast_uint i = static_cast<epiworld_fast_uint>(std::floor(EPI_RUNIF() * m->size()));
-
17055 
-
17056  if (sampled[i])
-
17057  continue;
-
17058 
-
17059  sampled[i] = true;
-
17060  epiworld::Agent<TSeq> * p = &pop[i];
-
17061 
-
17062  // If still exposed for the next term
-
17063  if (epiworld::IN(p->get_state(), exposed_state ))
-
17064  {
-
17065 
-
17066  ndetected += 1.0;
-
17067  if (p->get_state() == ModelSURV<TSeq>::ASYMPTOMATIC)
-
17068  {
-
17069  ndetected_asympt += 1.0;
-
17070  p->change_state(m, ModelSURV<TSeq>::ASYMPTOMATIC_ISOLATED);
-
17071  }
-
17072  else
-
17073  {
-
17074  p->change_state(m, ModelSURV<TSeq>::SYMPTOMATIC_ISOLATED);
-
17075  }
-
17076 
-
17077  }
-
17078 
-
17079  }
-
17080 
-
17081  // Writing the user data
-
17082  std::vector< int > totals;
-
17083  m->get_db().get_today_total(nullptr,&totals);
-
17084  m->add_user_data(
-
17085  {
-
17086  static_cast<epiworld_double>(nsampled),
-
17087  ndetected,
-
17088  ndetected_asympt,
-
17089  static_cast<epiworld_double>(totals[ModelSURV<TSeq>::ASYMPTOMATIC])
-
17090  }
-
17091  );
-
17092 
-
17093 
-
17094  };
+
17050  return;
+
17051 
+
17052  };
+
17053 
+
17054  std::vector< epiworld_fast_uint > exposed_state = {
+
17055  SYMPTOMATIC,
+
17056  SYMPTOMATIC_ISOLATED,
+
17057  ASYMPTOMATIC,
+
17058  ASYMPTOMATIC_ISOLATED,
+
17059  LATENT
+
17060  };
+
17061 
+
17062  epiworld::GlobalFun<TSeq> surveillance_program =
+
17063  [exposed_state](
+
17064  epiworld::Model<TSeq>* m
+
17065  ) -> void
+
17066  {
+
17067 
+
17068  // How many will we find
+
17069  std::binomial_distribution<> bdist(m->size(), m->par("Surveilance prob."));
+
17070  int nsampled = bdist(*m->get_rand_endgine());
+
17071 
+
17072  int to_go = nsampled + 1;
+
17073 
+
17074  epiworld_double ndetected = 0.0;
+
17075  epiworld_double ndetected_asympt = 0.0;
+
17076 
+
17077  auto & pop = m->get_agents();
+
17078  std::vector< bool > sampled(m->size(), false);
+
17079 
+
17080  while (to_go-- > 0)
+
17081  {
+
17082 
+
17083  // Who is the lucky one
+
17084  epiworld_fast_uint i = static_cast<epiworld_fast_uint>(std::floor(EPI_RUNIF() * m->size()));
+
17085 
+
17086  if (sampled[i])
+
17087  continue;
+
17088 
+
17089  sampled[i] = true;
+
17090  epiworld::Agent<TSeq> * p = &pop[i];
+
17091 
+
17092  // If still exposed for the next term
+
17093  if (epiworld::IN(p->get_state(), exposed_state ))
+
17094  {
17095 
-
17096  model.add_state("Susceptible", surveillance_update_susceptible);
-
17097  model.add_state("Latent", surveillance_update_exposed);
-
17098  model.add_state("Symptomatic", surveillance_update_exposed);
-
17099  model.add_state("Symptomatic isolated", surveillance_update_exposed);
-
17100  model.add_state("Asymptomatic", surveillance_update_exposed);
-
17101  model.add_state("Asymptomatic isolated", surveillance_update_exposed);
-
17102  model.add_state("Recovered");
-
17103  model.add_state("Removed");
-
17104 
-
17105  // General model parameters
-
17106  model.add_param(latent_period, "Latent period");
-
17107  model.add_param(infect_period, "Infect period");
-
17108  model.add_param(prob_symptoms, "Prob of symptoms");
-
17109  model.add_param(surveillance_prob, "Surveilance prob.");
-
17110  model.add_param(efficacy_vax, "Vax efficacy");
-
17111  model.add_param(prop_vax_redux_transm, "Vax redux transmission");
-
17112  model.add_param(prob_transmission, "Prob of transmission");
-
17113  model.add_param(prob_death, "Prob. death");
-
17114  model.add_param(prob_noreinfect, "Prob. no reinfect");
-
17115 
-
17116  // Virus ------------------------------------------------------------------
-
17117  epiworld::Virus<TSeq> covid("Covid19", prevalence, false);
-
17118  covid.set_state(LATENT, RECOVERED, REMOVED);
-
17119  covid.set_post_immunity(&model("Prob. no reinfect"));
-
17120  covid.set_prob_death(&model("Prob. death"));
-
17121 
-
17122  epiworld::VirusFun<TSeq> ptransmitfun = [](
-
17123  epiworld::Agent<TSeq> * p,
-
17124  epiworld::Virus<TSeq> &,
-
17125  epiworld::Model<TSeq> * m
-
17126  ) -> epiworld_double
-
17127  {
-
17128  // No chance of infecting
-
17129  epiworld_fast_uint s = p->get_state();
-
17130  if (s == ModelSURV<TSeq>::LATENT)
-
17131  return static_cast<epiworld_double>(0.0);
-
17132  else if (s == ModelSURV<TSeq>::SYMPTOMATIC_ISOLATED)
-
17133  return static_cast<epiworld_double>(0.0);
-
17134  else if (s == ModelSURV<TSeq>::ASYMPTOMATIC_ISOLATED)
-
17135  return static_cast<epiworld_double>(0.0);
-
17136 
-
17137  // Otherwise
-
17138  return m->par("Prob of transmission");
-
17139  };
-
17140 
-
17141  covid.set_prob_infecting_fun(ptransmitfun);
-
17142 
-
17143  model.add_virus(covid);
-
17144 
-
17145  model.set_user_data({"nsampled", "ndetected", "ndetected_asympt", "nasymptomatic"});
-
17146  model.add_globalevent(surveillance_program, "Surveilance program", -1);
-
17147 
-
17148  // Vaccine tool -----------------------------------------------------------
-
17149  epiworld::Tool<TSeq> vax("Vaccine", prop_vaccinated, true);
-
17150  vax.set_susceptibility_reduction(&model("Vax efficacy"));
-
17151  vax.set_transmission_reduction(&model("Vax redux transmission"));
-
17152 
-
17153  model.add_tool(vax);
-
17154 
-
17155  model.set_name("Surveillance");
-
17156 
-
17157  return;
-
17158 
-
17159 }
-
17160 
-
17161 template<typename TSeq>
-
17162 inline ModelSURV<TSeq>::ModelSURV(
-
17163  const std::string & vname,
-
17164  epiworld_fast_uint prevalence,
-
17165  epiworld_double efficacy_vax,
-
17166  epiworld_double latent_period,
-
17167  epiworld_double infect_period,
-
17168  epiworld_double prob_symptoms,
-
17169  epiworld_double prop_vaccinated,
-
17170  epiworld_double prop_vax_redux_transm,
-
17171  epiworld_double prop_vax_redux_infect,
-
17172  epiworld_double surveillance_prob,
-
17173  epiworld_double prob_transmission,
-
17174  epiworld_double prob_death,
-
17175  epiworld_double prob_noreinfect
-
17176  )
-
17177 {
-
17178 
-
17179  ModelSURV(
-
17180  *this,
-
17181  vname,
-
17182  prevalence,
-
17183  efficacy_vax,
-
17184  latent_period,
-
17185  infect_period,
-
17186  prob_symptoms,
-
17187  prop_vaccinated,
-
17188  prop_vax_redux_transm,
-
17189  prop_vax_redux_infect,
-
17190  surveillance_prob,
-
17191  prob_transmission,
-
17192  prob_death,
-
17193  prob_noreinfect
-
17194  );
-
17195 
-
17196  return;
-
17197 
-
17198 }
-
17199 
-
17200 #endif
-
17201 /*//////////////////////////////////////////////////////////////////////////////
-
17203 
-
17204  End of -include/epiworld//models/surveillance.hpp-
-
17205 
-
17208 
-
17209 
-
17210 /*//////////////////////////////////////////////////////////////////////////////
-
17212 
-
17213  Start of -include/epiworld//models/sirconnected.hpp-
-
17214 
-
17217 
-
17218 
-
17219 #ifndef EPIWORLD_MODELS_SIRCONNECTED_HPP
-
17220 #define EPIWORLD_MODELS_SIRCONNECTED_HPP
-
17221 
-
17222 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
17223 class ModelSIRCONN : public epiworld::Model<TSeq>
-
17224 {
-
17225 
-
17226 private:
-
17227 
-
17228  std::vector< epiworld::Agent<TSeq> * > infected;
-
17229  void update_infected();
-
17230 
-
17231 public:
-
17232 
-
17233  static const int SUSCEPTIBLE = 0;
-
17234  static const int INFECTED = 1;
-
17235  static const int RECOVERED = 2;
-
17236 
-
17237 
-
17238  ModelSIRCONN() {};
+
17096  ndetected += 1.0;
+
17097  if (p->get_state() == ModelSURV<TSeq>::ASYMPTOMATIC)
+
17098  {
+
17099  ndetected_asympt += 1.0;
+
17100  p->change_state(m, ModelSURV<TSeq>::ASYMPTOMATIC_ISOLATED);
+
17101  }
+
17102  else
+
17103  {
+
17104  p->change_state(m, ModelSURV<TSeq>::SYMPTOMATIC_ISOLATED);
+
17105  }
+
17106 
+
17107  }
+
17108 
+
17109  }
+
17110 
+
17111  // Writing the user data
+
17112  std::vector< int > totals;
+
17113  m->get_db().get_today_total(nullptr,&totals);
+
17114  m->add_user_data(
+
17115  {
+
17116  static_cast<epiworld_double>(nsampled),
+
17117  ndetected,
+
17118  ndetected_asympt,
+
17119  static_cast<epiworld_double>(totals[ModelSURV<TSeq>::ASYMPTOMATIC])
+
17120  }
+
17121  );
+
17122 
+
17123 
+
17124  };
+
17125 
+
17126  model.add_state("Susceptible", surveillance_update_susceptible);
+
17127  model.add_state("Latent", surveillance_update_exposed);
+
17128  model.add_state("Symptomatic", surveillance_update_exposed);
+
17129  model.add_state("Symptomatic isolated", surveillance_update_exposed);
+
17130  model.add_state("Asymptomatic", surveillance_update_exposed);
+
17131  model.add_state("Asymptomatic isolated", surveillance_update_exposed);
+
17132  model.add_state("Recovered");
+
17133  model.add_state("Removed");
+
17134 
+
17135  // General model parameters
+
17136  model.add_param(latent_period, "Latent period");
+
17137  model.add_param(infect_period, "Infect period");
+
17138  model.add_param(prob_symptoms, "Prob of symptoms");
+
17139  model.add_param(surveillance_prob, "Surveilance prob.");
+
17140  model.add_param(efficacy_vax, "Vax efficacy");
+
17141  model.add_param(prop_vax_redux_transm, "Vax redux transmission");
+
17142  model.add_param(prob_transmission, "Prob of transmission");
+
17143  model.add_param(prob_death, "Prob. death");
+
17144  model.add_param(prob_noreinfect, "Prob. no reinfect");
+
17145 
+
17146  // Virus ------------------------------------------------------------------
+
17147  epiworld::Virus<TSeq> covid("Covid19", prevalence, false);
+
17148  covid.set_state(LATENT, RECOVERED, REMOVED);
+
17149  covid.set_post_immunity(&model("Prob. no reinfect"));
+
17150  covid.set_prob_death(&model("Prob. death"));
+
17151 
+
17152  epiworld::VirusFun<TSeq> ptransmitfun = [](
+
17153  epiworld::Agent<TSeq> * p,
+
17154  epiworld::Virus<TSeq> &,
+
17155  epiworld::Model<TSeq> * m
+
17156  ) -> epiworld_double
+
17157  {
+
17158  // No chance of infecting
+
17159  epiworld_fast_uint s = p->get_state();
+
17160  if (s == ModelSURV<TSeq>::LATENT)
+
17161  return static_cast<epiworld_double>(0.0);
+
17162  else if (s == ModelSURV<TSeq>::SYMPTOMATIC_ISOLATED)
+
17163  return static_cast<epiworld_double>(0.0);
+
17164  else if (s == ModelSURV<TSeq>::ASYMPTOMATIC_ISOLATED)
+
17165  return static_cast<epiworld_double>(0.0);
+
17166 
+
17167  // Otherwise
+
17168  return m->par("Prob of transmission");
+
17169  };
+
17170 
+
17171  covid.set_prob_infecting_fun(ptransmitfun);
+
17172 
+
17173  model.add_virus(covid);
+
17174 
+
17175  model.set_user_data({"nsampled", "ndetected", "ndetected_asympt", "nasymptomatic"});
+
17176  model.add_globalevent(surveillance_program, "Surveilance program", -1);
+
17177 
+
17178  // Vaccine tool -----------------------------------------------------------
+
17179  epiworld::Tool<TSeq> vax("Vaccine", prop_vaccinated, true);
+
17180  vax.set_susceptibility_reduction(&model("Vax efficacy"));
+
17181  vax.set_transmission_reduction(&model("Vax redux transmission"));
+
17182 
+
17183  model.add_tool(vax);
+
17184 
+
17185  model.set_name("Surveillance");
+
17186 
+
17187  return;
+
17188 
+
17189 }
+
17190 
+
17191 template<typename TSeq>
+
17192 inline ModelSURV<TSeq>::ModelSURV(
+
17193  const std::string & vname,
+
17194  epiworld_fast_uint prevalence,
+
17195  epiworld_double efficacy_vax,
+
17196  epiworld_double latent_period,
+
17197  epiworld_double infect_period,
+
17198  epiworld_double prob_symptoms,
+
17199  epiworld_double prop_vaccinated,
+
17200  epiworld_double prop_vax_redux_transm,
+
17201  epiworld_double prop_vax_redux_infect,
+
17202  epiworld_double surveillance_prob,
+
17203  epiworld_double prob_transmission,
+
17204  epiworld_double prob_death,
+
17205  epiworld_double prob_noreinfect
+
17206  )
+
17207 {
+
17208 
+
17209  ModelSURV(
+
17210  *this,
+
17211  vname,
+
17212  prevalence,
+
17213  efficacy_vax,
+
17214  latent_period,
+
17215  infect_period,
+
17216  prob_symptoms,
+
17217  prop_vaccinated,
+
17218  prop_vax_redux_transm,
+
17219  prop_vax_redux_infect,
+
17220  surveillance_prob,
+
17221  prob_transmission,
+
17222  prob_death,
+
17223  prob_noreinfect
+
17224  );
+
17225 
+
17226  return;
+
17227 
+
17228 }
+
17229 
+
17230 #endif
+
17231 /*//////////////////////////////////////////////////////////////////////////////
+
17233 
+
17234  End of -include/epiworld//models/surveillance.hpp-
+
17235 
+
17238 
17239 
-
17240  ModelSIRCONN(
-
17241  ModelSIRCONN<TSeq> & model,
-
17242  const std::string & vname,
-
17243  epiworld_fast_uint n,
-
17244  epiworld_double prevalence,
-
17245  epiworld_double contact_rate,
-
17246  epiworld_double transmission_rate,
-
17247  epiworld_double recovery_rate
-
17248  );
-
17249 
-
17250  ModelSIRCONN(
-
17251  const std::string & vname,
-
17252  epiworld_fast_uint n,
-
17253  epiworld_double prevalence,
-
17254  epiworld_double contact_rate,
-
17255  epiworld_double transmission_rate,
-
17256  epiworld_double recovery_rate
-
17257  );
-
17258 
-
17259  ModelSIRCONN<TSeq> & run(
-
17260  epiworld_fast_uint ndays,
-
17261  int seed = -1
-
17262  );
-
17263 
-
17264  void reset();
-
17265 
-
17266  Model<TSeq> * clone_ptr();
-
17267 
-
17273  ModelSIRCONN<TSeq> & initial_states(
-
17274  std::vector< double > proportions_,
-
17275  std::vector< int > queue_ = {}
-
17276  );
-
17277 
-
17282  size_t get_n_infected() const
-
17283  {
-
17284  return infected.size();
-
17285  }
-
17286 
-
17287  /***
-
17288  * @brief Compute expected generation time
-
17289  * @param max_days Maximum number of days.
-
17290  * @param max_contacts Maximum number of contacts.
-
17291  */
-
17292  std::vector< double > generation_time_expected(
-
17293  int max_days = 200,
-
17294  int max_contacts = 200
-
17295  ) const;
-
17296 
-
17297 };
-
17298 
-
17299 template<typename TSeq>
-
17300 inline void ModelSIRCONN<TSeq>::update_infected()
-
17301 {
-
17302 
-
17303  infected.clear();
-
17304  infected.reserve(this->size());
-
17305 
-
17306  for (auto & p : this->get_agents())
-
17307  {
-
17308  if (p.get_state() == ModelSIRCONN<TSeq>::INFECTED)
-
17309  {
-
17310  infected.push_back(&p);
-
17311  }
-
17312  }
-
17313 
-
17314  Model<TSeq>::set_rand_binom(
-
17315  this->get_n_infected(),
-
17316  static_cast<double>(Model<TSeq>::par("Contact rate"))/
-
17317  static_cast<double>(Model<TSeq>::size())
-
17318  );
-
17319 
-
17320  return;
-
17321 
-
17322 }
-
17323 
-
17324 template<typename TSeq>
-
17325 inline ModelSIRCONN<TSeq> & ModelSIRCONN<TSeq>::run(
-
17326  epiworld_fast_uint ndays,
-
17327  int seed
-
17328 )
-
17329 {
-
17330 
-
17331  Model<TSeq>::run(ndays, seed);
-
17332  return *this;
-
17333 
-
17334 }
+
17240 /*//////////////////////////////////////////////////////////////////////////////
+
17242 
+
17243  Start of -include/epiworld//models/sirconnected.hpp-
+
17244 
+
17247 
+
17248 
+
17249 #ifndef EPIWORLD_MODELS_SIRCONNECTED_HPP
+
17250 #define EPIWORLD_MODELS_SIRCONNECTED_HPP
+
17251 
+
17252 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
17253 class ModelSIRCONN : public epiworld::Model<TSeq>
+
17254 {
+
17255 
+
17256 private:
+
17257 
+
17258  std::vector< epiworld::Agent<TSeq> * > infected;
+
17259  void update_infected();
+
17260 
+
17261 public:
+
17262 
+
17263  static const int SUSCEPTIBLE = 0;
+
17264  static const int INFECTED = 1;
+
17265  static const int RECOVERED = 2;
+
17266 
+
17267 
+
17268  ModelSIRCONN() {};
+
17269 
+
17270  ModelSIRCONN(
+
17271  ModelSIRCONN<TSeq> & model,
+
17272  const std::string & vname,
+
17273  epiworld_fast_uint n,
+
17274  epiworld_double prevalence,
+
17275  epiworld_double contact_rate,
+
17276  epiworld_double transmission_rate,
+
17277  epiworld_double recovery_rate
+
17278  );
+
17279 
+
17280  ModelSIRCONN(
+
17281  const std::string & vname,
+
17282  epiworld_fast_uint n,
+
17283  epiworld_double prevalence,
+
17284  epiworld_double contact_rate,
+
17285  epiworld_double transmission_rate,
+
17286  epiworld_double recovery_rate
+
17287  );
+
17288 
+
17289  ModelSIRCONN<TSeq> & run(
+
17290  epiworld_fast_uint ndays,
+
17291  int seed = -1
+
17292  );
+
17293 
+
17294  void reset();
+
17295 
+
17296  Model<TSeq> * clone_ptr();
+
17297 
+
17303  ModelSIRCONN<TSeq> & initial_states(
+
17304  std::vector< double > proportions_,
+
17305  std::vector< int > queue_ = {}
+
17306  );
+
17307 
+
17312  size_t get_n_infected() const
+
17313  {
+
17314  return infected.size();
+
17315  }
+
17316 
+
17317  /***
+
17318  * @brief Compute expected generation time
+
17319  * @param max_days Maximum number of days.
+
17320  * @param max_contacts Maximum number of contacts.
+
17321  */
+
17322  std::vector< double > generation_time_expected(
+
17323  int max_days = 200,
+
17324  int max_contacts = 200
+
17325  ) const;
+
17326 
+
17327 };
+
17328 
+
17329 template<typename TSeq>
+
17330 inline void ModelSIRCONN<TSeq>::update_infected()
+
17331 {
+
17332 
+
17333  infected.clear();
+
17334  infected.reserve(this->size());
17335 
-
17336 template<typename TSeq>
-
17337 inline void ModelSIRCONN<TSeq>::reset()
-
17338 {
-
17339 
-
17340  Model<TSeq>::reset();
-
17341 
-
17342  this->update_infected();
+
17336  for (auto & p : this->get_agents())
+
17337  {
+
17338  if (p.get_state() == ModelSIRCONN<TSeq>::INFECTED)
+
17339  {
+
17340  infected.push_back(&p);
+
17341  }
+
17342  }
17343 
-
17344  return;
-
17345 
-
17346 }
-
17347 
-
17348 template<typename TSeq>
-
17349 inline Model<TSeq> * ModelSIRCONN<TSeq>::clone_ptr()
-
17350 {
-
17351 
-
17352  ModelSIRCONN<TSeq> * ptr = new ModelSIRCONN<TSeq>(
-
17353  *dynamic_cast<const ModelSIRCONN<TSeq>*>(this)
-
17354  );
-
17355 
-
17356  return dynamic_cast< Model<TSeq> *>(ptr);
-
17357 
-
17358 }
-
17359 
-
17370 template<typename TSeq>
-
17371 inline ModelSIRCONN<TSeq>::ModelSIRCONN(
-
17372  ModelSIRCONN<TSeq> & model,
-
17373  const std::string & vname,
-
17374  epiworld_fast_uint n,
-
17375  epiworld_double prevalence,
-
17376  epiworld_double contact_rate,
-
17377  epiworld_double transmission_rate,
-
17378  epiworld_double recovery_rate
-
17379  // epiworld_double prob_reinfection
-
17380  )
-
17381 {
-
17382 
-
17383  epiworld::UpdateFun<TSeq> update_susceptible = [](
-
17384  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
17385  ) -> void
-
17386  {
+
17344  Model<TSeq>::set_rand_binom(
+
17345  this->get_n_infected(),
+
17346  static_cast<double>(Model<TSeq>::par("Contact rate"))/
+
17347  static_cast<double>(Model<TSeq>::size())
+
17348  );
+
17349 
+
17350  return;
+
17351 
+
17352 }
+
17353 
+
17354 template<typename TSeq>
+
17355 inline ModelSIRCONN<TSeq> & ModelSIRCONN<TSeq>::run(
+
17356  epiworld_fast_uint ndays,
+
17357  int seed
+
17358 )
+
17359 {
+
17360 
+
17361  Model<TSeq>::run(ndays, seed);
+
17362  return *this;
+
17363 
+
17364 }
+
17365 
+
17366 template<typename TSeq>
+
17367 inline void ModelSIRCONN<TSeq>::reset()
+
17368 {
+
17369 
+
17370  Model<TSeq>::reset();
+
17371 
+
17372  this->update_infected();
+
17373 
+
17374  return;
+
17375 
+
17376 }
+
17377 
+
17378 template<typename TSeq>
+
17379 inline Model<TSeq> * ModelSIRCONN<TSeq>::clone_ptr()
+
17380 {
+
17381 
+
17382  ModelSIRCONN<TSeq> * ptr = new ModelSIRCONN<TSeq>(
+
17383  *dynamic_cast<const ModelSIRCONN<TSeq>*>(this)
+
17384  );
+
17385 
+
17386  return dynamic_cast< Model<TSeq> *>(ptr);
17387 
-
17388  int ndraw = m->rbinom();
+
17388 }
17389 
-
17390  if (ndraw == 0)
-
17391  return;
-
17392 
-
17393  ModelSIRCONN<TSeq> * model = dynamic_cast<ModelSIRCONN<TSeq> *>(m);
-
17394  size_t ninfected = model->get_n_infected();
-
17395 
-
17396  // Drawing from the set
-
17397  int nviruses_tmp = 0;
-
17398  for (int i = 0; i < ndraw; ++i)
-
17399  {
-
17400  // Now selecting who is transmitting the disease
-
17401  int which = static_cast<int>(
-
17402  std::floor(ninfected * m->runif())
-
17403  );
-
17404 
-
17405  /* There is a bug in which runif() returns 1.0. It is rare, but
-
17406  * we saw it here. See the Notes section in the C++ manual
-
17407  * https://en.cppreference.com/mwiki/index.php?title=cpp/numeric/random/uniform_real_distribution&oldid=133329
-
17408  * And the reported bug in GCC:
-
17409  * https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63176
-
17410  *
-
17411  */
-
17412  if (which == static_cast<int>(ninfected))
-
17413  --which;
-
17414 
-
17415  epiworld::Agent<TSeq> & neighbor = *model->infected[which];
-
17416 
-
17417  // Can't sample itself
-
17418  if (neighbor.get_id() == p->get_id())
-
17419  continue;
-
17420 
-
17421  // The neighbor is infected because it is on the list!
-
17422  if (neighbor.get_virus() == nullptr)
-
17423  continue;
-
17424 
-
17425  auto & v = neighbor.get_virus();
-
17426 
-
17427  #ifdef EPI_DEBUG
-
17428  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
-
17429  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
-
17430  #endif
-
17431 
-
17432  /* And it is a function of susceptibility_reduction as well */
-
17433  m->array_double_tmp[nviruses_tmp] =
-
17434  (1.0 - p->get_susceptibility_reduction(v, m)) *
-
17435  v->get_prob_infecting(m) *
-
17436  (1.0 - neighbor.get_transmission_reduction(v, m))
-
17437  ;
-
17438 
-
17439  m->array_virus_tmp[nviruses_tmp++] = &(*v);
-
17440 
-
17441  }
-
17442 
-
17443  // No virus to compute
-
17444  if (nviruses_tmp == 0u)
-
17445  return;
+
17400 template<typename TSeq>
+
17401 inline ModelSIRCONN<TSeq>::ModelSIRCONN(
+
17402  ModelSIRCONN<TSeq> & model,
+
17403  const std::string & vname,
+
17404  epiworld_fast_uint n,
+
17405  epiworld_double prevalence,
+
17406  epiworld_double contact_rate,
+
17407  epiworld_double transmission_rate,
+
17408  epiworld_double recovery_rate
+
17409  // epiworld_double prob_reinfection
+
17410  )
+
17411 {
+
17412 
+
17413  epiworld::UpdateFun<TSeq> update_susceptible = [](
+
17414  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
17415  ) -> void
+
17416  {
+
17417 
+
17418  int ndraw = m->rbinom();
+
17419 
+
17420  if (ndraw == 0)
+
17421  return;
+
17422 
+
17423  ModelSIRCONN<TSeq> * model = dynamic_cast<ModelSIRCONN<TSeq> *>(m);
+
17424  size_t ninfected = model->get_n_infected();
+
17425 
+
17426  // Drawing from the set
+
17427  int nviruses_tmp = 0;
+
17428  for (int i = 0; i < ndraw; ++i)
+
17429  {
+
17430  // Now selecting who is transmitting the disease
+
17431  int which = static_cast<int>(
+
17432  std::floor(ninfected * m->runif())
+
17433  );
+
17434 
+
17435  /* There is a bug in which runif() returns 1.0. It is rare, but
+
17436  * we saw it here. See the Notes section in the C++ manual
+
17437  * https://en.cppreference.com/mwiki/index.php?title=cpp/numeric/random/uniform_real_distribution&oldid=133329
+
17438  * And the reported bug in GCC:
+
17439  * https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63176
+
17440  *
+
17441  */
+
17442  if (which == static_cast<int>(ninfected))
+
17443  --which;
+
17444 
+
17445  epiworld::Agent<TSeq> & neighbor = *model->infected[which];
17446 
-
17447  // Running the roulette
-
17448  int which = roulette(nviruses_tmp, m);
-
17449 
-
17450  if (which < 0)
-
17451  return;
-
17452 
-
17453  p->set_virus(*m->array_virus_tmp[which], m);
+
17447  // Can't sample itself
+
17448  if (neighbor.get_id() == p->get_id())
+
17449  continue;
+
17450 
+
17451  // The neighbor is infected because it is on the list!
+
17452  if (neighbor.get_virus() == nullptr)
+
17453  continue;
17454 
-
17455  return;
+
17455  auto & v = neighbor.get_virus();
17456 
-
17457  };
-
17458 
-
17459 
-
17460  epiworld::UpdateFun<TSeq> update_infected = [](
-
17461  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
17462  ) -> void {
-
17463 
-
17464  auto state = p->get_state();
-
17465 
-
17466  if (state == ModelSIRCONN<TSeq>::INFECTED)
-
17467  {
-
17468 
-
17469 
-
17470  // Odd: Die, Even: Recover
-
17471  epiworld_fast_uint n_events = 0u;
-
17472  // Recover
-
17473  m->array_double_tmp[n_events++] =
-
17474  1.0 - (1.0 - p->get_virus()->get_prob_recovery(m)) *
-
17475  (1.0 - p->get_recovery_enhancer(p->get_virus(), m));
+
17457  #ifdef EPI_DEBUG
+
17458  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
+
17459  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
+
17460  #endif
+
17461 
+
17462  /* And it is a function of susceptibility_reduction as well */
+
17463  m->array_double_tmp[nviruses_tmp] =
+
17464  (1.0 - p->get_susceptibility_reduction(v, m)) *
+
17465  v->get_prob_infecting(m) *
+
17466  (1.0 - neighbor.get_transmission_reduction(v, m))
+
17467  ;
+
17468 
+
17469  m->array_virus_tmp[nviruses_tmp++] = &(*v);
+
17470 
+
17471  }
+
17472 
+
17473  // No virus to compute
+
17474  if (nviruses_tmp == 0u)
+
17475  return;
17476 
-
17477  #ifdef EPI_DEBUG
-
17478  if (n_events == 0u)
-
17479  {
-
17480  printf_epiworld(
-
17481  "[epi-debug] agent %i has 0 possible events!!\n",
-
17482  static_cast<int>(p->get_id())
-
17483  );
-
17484  throw std::logic_error("Zero events in exposed.");
-
17485  }
-
17486  #else
-
17487  if (n_events == 0u)
-
17488  return;
-
17489  #endif
-
17490 
-
17491 
-
17492  // Running the roulette
-
17493  int which = roulette(n_events, m);
-
17494 
-
17495  if (which < 0)
-
17496  return;
-
17497 
-
17498  // Which roulette happen?
-
17499  p->rm_virus(m);
-
17500 
-
17501  return ;
-
17502 
-
17503  } else
-
17504  throw std::logic_error(
-
17505  "This function can only be applied to infected individuals. (SIR)"
-
17506  ) ;
-
17507 
-
17508  return;
-
17509 
-
17510  };
-
17511 
-
17512  // state
-
17513  model.add_state("Susceptible", update_susceptible);
-
17514  model.add_state("Infected", update_infected);
-
17515  model.add_state("Recovered");
-
17516 
-
17517  // Setting up parameters
-
17518  model.add_param(contact_rate, "Contact rate");
-
17519  model.add_param(transmission_rate, "Transmission rate");
-
17520  model.add_param(recovery_rate, "Recovery rate");
-
17521  // model.add_param(prob_reinfection, "Prob. Reinfection");
-
17522 
-
17523  // Adding update function
-
17524  epiworld::GlobalFun<TSeq> update = [](epiworld::Model<TSeq> * m) -> void
-
17525  {
-
17526  ModelSIRCONN<TSeq> * model = dynamic_cast<ModelSIRCONN<TSeq> *>(m);
-
17527  model->update_infected();
-
17528 
-
17529  return;
-
17530  };
-
17531 
-
17532  model.add_globalevent(update, "Update infected individuals");
-
17533 
-
17534  // Preparing the virus -------------------------------------------
-
17535  epiworld::Virus<TSeq> virus(vname, prevalence, true);
-
17536  virus.set_state(1, 2, 2);
-
17537  virus.set_prob_infecting(&model("Transmission rate"));
-
17538  virus.set_prob_recovery(&model("Recovery rate"));
+
17477  // Running the roulette
+
17478  int which = roulette(nviruses_tmp, m);
+
17479 
+
17480  if (which < 0)
+
17481  return;
+
17482 
+
17483  p->set_virus(*m->array_virus_tmp[which], m);
+
17484 
+
17485  return;
+
17486 
+
17487  };
+
17488 
+
17489 
+
17490  epiworld::UpdateFun<TSeq> update_infected = [](
+
17491  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
17492  ) -> void {
+
17493 
+
17494  auto state = p->get_state();
+
17495 
+
17496  if (state == ModelSIRCONN<TSeq>::INFECTED)
+
17497  {
+
17498 
+
17499 
+
17500  // Odd: Die, Even: Recover
+
17501  epiworld_fast_uint n_events = 0u;
+
17502  // Recover
+
17503  m->array_double_tmp[n_events++] =
+
17504  1.0 - (1.0 - p->get_virus()->get_prob_recovery(m)) *
+
17505  (1.0 - p->get_recovery_enhancer(p->get_virus(), m));
+
17506 
+
17507  #ifdef EPI_DEBUG
+
17508  if (n_events == 0u)
+
17509  {
+
17510  printf_epiworld(
+
17511  "[epi-debug] agent %i has 0 possible events!!\n",
+
17512  static_cast<int>(p->get_id())
+
17513  );
+
17514  throw std::logic_error("Zero events in exposed.");
+
17515  }
+
17516  #else
+
17517  if (n_events == 0u)
+
17518  return;
+
17519  #endif
+
17520 
+
17521 
+
17522  // Running the roulette
+
17523  int which = roulette(n_events, m);
+
17524 
+
17525  if (which < 0)
+
17526  return;
+
17527 
+
17528  // Which roulette happen?
+
17529  p->rm_virus(m);
+
17530 
+
17531  return ;
+
17532 
+
17533  } else
+
17534  throw std::logic_error(
+
17535  "This function can only be applied to infected individuals. (SIR)"
+
17536  ) ;
+
17537 
+
17538  return;
17539 
-
17540  model.add_virus(virus);
+
17540  };
17541 
-
17542  model.queuing_off(); // No queuing need
-
17543 
-
17544  model.agents_empty_graph(n);
-
17545 
-
17546  model.set_name("Susceptible-Infected-Removed (SIR) (connected)");
-
17547 
-
17548  return;
-
17549 
-
17550 }
-
17551 
-
17552 template<typename TSeq>
-
17553 inline ModelSIRCONN<TSeq>::ModelSIRCONN(
-
17554  const std::string & vname,
-
17555  epiworld_fast_uint n,
-
17556  epiworld_double prevalence,
-
17557  epiworld_double contact_rate,
-
17558  epiworld_double transmission_rate,
-
17559  epiworld_double recovery_rate
-
17560  )
-
17561 {
-
17562 
-
17563  ModelSIRCONN(
-
17564  *this,
-
17565  vname,
-
17566  n,
-
17567  prevalence,
-
17568  contact_rate,
-
17569  transmission_rate,
-
17570  recovery_rate
-
17571  );
-
17572 
-
17573  return;
-
17574 
-
17575 }
-
17576 
-
17577 template<typename TSeq>
-
17578 inline ModelSIRCONN<TSeq> & ModelSIRCONN<TSeq>::initial_states(
-
17579  std::vector< double > proportions_,
-
17580  std::vector< int >
-
17581 ) {
-
17582 
-
17583  Model<TSeq>::initial_states_fun =
-
17584  create_init_function_sir<TSeq>(proportions_)
-
17585  ;
-
17586 
-
17587  return *this;
-
17588 
-
17589 }
-
17590 
-
17591 template<typename TSeq>
-
17592 inline std::vector< double > ModelSIRCONN<TSeq>::generation_time_expected(
-
17593  int max_days,
-
17594  int max_contacts
-
17595 ) const
-
17596 {
-
17597 
-
17598  // Retrieving total counts
-
17599  std::vector< int > h_date;
-
17600  std::vector< std::string > h_state;
-
17601  std::vector< int > h_counts;
-
17602  const auto this_const = dynamic_cast<const ModelSIRCONN<TSeq> *>(this);
-
17603  this_const->get_db().get_hist_total(
-
17604  &h_date,
-
17605  &h_state,
-
17606  &h_counts
-
17607  );
-
17608 
-
17609  // Retrieving information on susceptibles
-
17610  std::vector< double > S(this_const->get_ndays(), 0.0);
-
17611  for (size_t i = 0; i < h_date.size(); ++i)
-
17612  {
-
17613  if (h_state[i] == "Susceptible")
-
17614  S[h_date[i]] += h_counts[i];
-
17615  }
+
17542  // state
+
17543  model.add_state("Susceptible", update_susceptible);
+
17544  model.add_state("Infected", update_infected);
+
17545  model.add_state("Recovered");
+
17546 
+
17547  // Setting up parameters
+
17548  model.add_param(contact_rate, "Contact rate");
+
17549  model.add_param(transmission_rate, "Transmission rate");
+
17550  model.add_param(recovery_rate, "Recovery rate");
+
17551  // model.add_param(prob_reinfection, "Prob. Reinfection");
+
17552 
+
17553  // Adding update function
+
17554  epiworld::GlobalFun<TSeq> update = [](epiworld::Model<TSeq> * m) -> void
+
17555  {
+
17556  ModelSIRCONN<TSeq> * model = dynamic_cast<ModelSIRCONN<TSeq> *>(m);
+
17557  model->update_infected();
+
17558 
+
17559  return;
+
17560  };
+
17561 
+
17562  model.add_globalevent(update, "Update infected individuals");
+
17563 
+
17564  // Preparing the virus -------------------------------------------
+
17565  epiworld::Virus<TSeq> virus(vname, prevalence, true);
+
17566  virus.set_state(1, 2, 2);
+
17567  virus.set_prob_infecting(&model("Transmission rate"));
+
17568  virus.set_prob_recovery(&model("Recovery rate"));
+
17569 
+
17570  model.add_virus(virus);
+
17571 
+
17572  model.queuing_off(); // No queuing need
+
17573 
+
17574  model.agents_empty_graph(n);
+
17575 
+
17576  model.set_name("Susceptible-Infected-Removed (SIR) (connected)");
+
17577 
+
17578  return;
+
17579 
+
17580 }
+
17581 
+
17582 template<typename TSeq>
+
17583 inline ModelSIRCONN<TSeq>::ModelSIRCONN(
+
17584  const std::string & vname,
+
17585  epiworld_fast_uint n,
+
17586  epiworld_double prevalence,
+
17587  epiworld_double contact_rate,
+
17588  epiworld_double transmission_rate,
+
17589  epiworld_double recovery_rate
+
17590  )
+
17591 {
+
17592 
+
17593  ModelSIRCONN(
+
17594  *this,
+
17595  vname,
+
17596  n,
+
17597  prevalence,
+
17598  contact_rate,
+
17599  transmission_rate,
+
17600  recovery_rate
+
17601  );
+
17602 
+
17603  return;
+
17604 
+
17605 }
+
17606 
+
17607 template<typename TSeq>
+
17608 inline ModelSIRCONN<TSeq> & ModelSIRCONN<TSeq>::initial_states(
+
17609  std::vector< double > proportions_,
+
17610  std::vector< int >
+
17611 ) {
+
17612 
+
17613  Model<TSeq>::initial_states_fun =
+
17614  create_init_function_sir<TSeq>(proportions_)
+
17615  ;
17616 
-
17617  // The generation time in the SIR model starts from 1, as agents
-
17618  // spend at least one day in the infected state before starting
-
17619  // transmitting.
-
17620  std::vector< double > gen_times(this_const->get_ndays(), 1.0);
-
17621  double p_c = this_const->par("Contact rate")/this_const->size();
-
17622  double p_i = this_const->par("Transmission rate");
-
17623  double p_r = this_const->par("Recovery rate");
-
17624  for (size_t i = 0u; i < this_const->get_ndays(); ++i)
-
17625  {
-
17626  gen_times[i] = gen_int_mean(
-
17627  S[i],
-
17628  p_c,
-
17629  p_i,
-
17630  p_r,
-
17631  max_days,
-
17632  max_contacts
-
17633  );
-
17634 
-
17635  }
-
17636 
-
17637  return gen_times;
+
17617  return *this;
+
17618 
+
17619 }
+
17620 
+
17621 template<typename TSeq>
+
17622 inline std::vector< double > ModelSIRCONN<TSeq>::generation_time_expected(
+
17623  int max_days,
+
17624  int max_contacts
+
17625 ) const
+
17626 {
+
17627 
+
17628  // Retrieving total counts
+
17629  std::vector< int > h_date;
+
17630  std::vector< std::string > h_state;
+
17631  std::vector< int > h_counts;
+
17632  const auto this_const = dynamic_cast<const ModelSIRCONN<TSeq> *>(this);
+
17633  this_const->get_db().get_hist_total(
+
17634  &h_date,
+
17635  &h_state,
+
17636  &h_counts
+
17637  );
17638 
-
17639 }
-
17640 
-
17641 #endif
-
17642 /*//////////////////////////////////////////////////////////////////////////////
-
17644 
-
17645  End of -include/epiworld//models/sirconnected.hpp-
-
17646 
-
17649 
-
17650 
-
17651 /*//////////////////////////////////////////////////////////////////////////////
-
17653 
-
17654  Start of -include/epiworld//models/seirconnected.hpp-
-
17655 
-
17658 
-
17659 
-
17660 #ifndef EPIWORLD_MODELS_SEIRCONNECTED_HPP
-
17661 #define EPIWORLD_MODELS_SEIRCONNECTED_HPP
-
17662 
-
17663 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
17664 class ModelSEIRCONN : public epiworld::Model<TSeq>
-
17665 {
-
17666 private:
-
17667  std::vector< epiworld::Agent<TSeq> * > infected;
-
17668  void update_infected();
-
17669 
-
17670 public:
-
17671 
-
17672  static const int SUSCEPTIBLE = 0;
-
17673  static const int EXPOSED = 1;
-
17674  static const int INFECTED = 2;
-
17675  static const int RECOVERED = 3;
+
17639  // Retrieving information on susceptibles
+
17640  std::vector< double > S(this_const->get_ndays(), 0.0);
+
17641  for (size_t i = 0; i < h_date.size(); ++i)
+
17642  {
+
17643  if (h_state[i] == "Susceptible")
+
17644  S[h_date[i]] += h_counts[i];
+
17645  }
+
17646 
+
17647  // The generation time in the SIR model starts from 1, as agents
+
17648  // spend at least one day in the infected state before starting
+
17649  // transmitting.
+
17650  std::vector< double > gen_times(this_const->get_ndays(), 1.0);
+
17651  double p_c = this_const->par("Contact rate")/this_const->size();
+
17652  double p_i = this_const->par("Transmission rate");
+
17653  double p_r = this_const->par("Recovery rate");
+
17654  for (size_t i = 0u; i < this_const->get_ndays(); ++i)
+
17655  {
+
17656  gen_times[i] = gen_int_mean(
+
17657  S[i],
+
17658  p_c,
+
17659  p_i,
+
17660  p_r,
+
17661  max_days,
+
17662  max_contacts
+
17663  );
+
17664 
+
17665  }
+
17666 
+
17667  return gen_times;
+
17668 
+
17669 }
+
17670 
+
17671 #endif
+
17672 /*//////////////////////////////////////////////////////////////////////////////
+
17674 
+
17675  End of -include/epiworld//models/sirconnected.hpp-
17676 
-
17677 
-
17678  ModelSEIRCONN() {};
17679 
-
17680  ModelSEIRCONN(
-
17681  ModelSEIRCONN<TSeq> & model,
-
17682  const std::string & vname,
-
17683  epiworld_fast_uint n,
-
17684  epiworld_double prevalence,
-
17685  epiworld_double contact_rate,
-
17686  epiworld_double transmission_rate,
-
17687  epiworld_double avg_incubation_days,
-
17688  epiworld_double recovery_rate
-
17689  );
-
17690 
-
17691  ModelSEIRCONN(
-
17692  const std::string & vname,
-
17693  epiworld_fast_uint n,
-
17694  epiworld_double prevalence,
-
17695  epiworld_double contact_rate,
-
17696  epiworld_double transmission_rate,
-
17697  epiworld_double avg_incubation_days,
-
17698  epiworld_double recovery_rate
-
17699  );
-
17700 
-
17701  ModelSEIRCONN<TSeq> & run(
-
17702  epiworld_fast_uint ndays,
-
17703  int seed = -1
-
17704  );
-
17705 
-
17706  void reset();
+
17680 
+
17681 /*//////////////////////////////////////////////////////////////////////////////
+
17683 
+
17684  Start of -include/epiworld//models/seirconnected.hpp-
+
17685 
+
17688 
+
17689 
+
17690 #ifndef EPIWORLD_MODELS_SEIRCONNECTED_HPP
+
17691 #define EPIWORLD_MODELS_SEIRCONNECTED_HPP
+
17692 
+
17693 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
17694 class ModelSEIRCONN : public epiworld::Model<TSeq>
+
17695 {
+
17696 private:
+
17697  std::vector< epiworld::Agent<TSeq> * > infected;
+
17698  void update_infected();
+
17699 
+
17700 public:
+
17701 
+
17702  static const int SUSCEPTIBLE = 0;
+
17703  static const int EXPOSED = 1;
+
17704  static const int INFECTED = 2;
+
17705  static const int RECOVERED = 3;
+
17706 
17707 
-
17708  Model<TSeq> * clone_ptr();
+
17708  ModelSEIRCONN() {};
17709 
-
17715  ModelSEIRCONN<TSeq> & initial_states(
-
17716  std::vector< double > proportions_,
-
17717  std::vector< int > queue_ = {}
-
17718  );
-
17719 
-
17720  size_t get_n_infected() const { return infected.size(); }
-
17721 
-
17722  /***
-
17723  * @brief Compute expected generation time
-
17724  * @param max_days Maximum number of days.
-
17725  * @param max_contacts Maximum number of contacts.
-
17726  */
-
17727  std::vector< double > generation_time_expected(
-
17728  int max_days = 200,
-
17729  int max_contacts = 200
-
17730  ) const;
-
17731 
-
17732 };
-
17733 
-
17734 template<typename TSeq>
-
17735 inline void ModelSEIRCONN<TSeq>::update_infected()
-
17736 {
-
17737 
-
17738  infected.clear();
-
17739  infected.reserve(this->size());
-
17740 
-
17741  for (auto & p : this->get_agents())
-
17742  {
-
17743  if (p.get_state() == ModelSEIRCONN<TSeq>::INFECTED)
-
17744  {
-
17745  infected.push_back(&p);
-
17746  }
-
17747  }
-
17748 
-
17749  Model<TSeq>::set_rand_binom(
-
17750  this->get_n_infected(),
-
17751  static_cast<double>(Model<TSeq>::par("Contact rate"))/
-
17752  static_cast<double>(Model<TSeq>::size())
-
17753  );
-
17754 
-
17755  return;
-
17756 
-
17757 }
-
17758 
-
17759 template<typename TSeq>
-
17760 inline ModelSEIRCONN<TSeq> & ModelSEIRCONN<TSeq>::run(
-
17761  epiworld_fast_uint ndays,
-
17762  int seed
-
17763 )
-
17764 {
-
17765 
-
17766  Model<TSeq>::run(ndays, seed);
+
17710  ModelSEIRCONN(
+
17711  ModelSEIRCONN<TSeq> & model,
+
17712  const std::string & vname,
+
17713  epiworld_fast_uint n,
+
17714  epiworld_double prevalence,
+
17715  epiworld_double contact_rate,
+
17716  epiworld_double transmission_rate,
+
17717  epiworld_double avg_incubation_days,
+
17718  epiworld_double recovery_rate
+
17719  );
+
17720 
+
17721  ModelSEIRCONN(
+
17722  const std::string & vname,
+
17723  epiworld_fast_uint n,
+
17724  epiworld_double prevalence,
+
17725  epiworld_double contact_rate,
+
17726  epiworld_double transmission_rate,
+
17727  epiworld_double avg_incubation_days,
+
17728  epiworld_double recovery_rate
+
17729  );
+
17730 
+
17731  ModelSEIRCONN<TSeq> & run(
+
17732  epiworld_fast_uint ndays,
+
17733  int seed = -1
+
17734  );
+
17735 
+
17736  void reset();
+
17737 
+
17738  Model<TSeq> * clone_ptr();
+
17739 
+
17745  ModelSEIRCONN<TSeq> & initial_states(
+
17746  std::vector< double > proportions_,
+
17747  std::vector< int > queue_ = {}
+
17748  );
+
17749 
+
17750  size_t get_n_infected() const { return infected.size(); }
+
17751 
+
17752  /***
+
17753  * @brief Compute expected generation time
+
17754  * @param max_days Maximum number of days.
+
17755  * @param max_contacts Maximum number of contacts.
+
17756  */
+
17757  std::vector< double > generation_time_expected(
+
17758  int max_days = 200,
+
17759  int max_contacts = 200
+
17760  ) const;
+
17761 
+
17762 };
+
17763 
+
17764 template<typename TSeq>
+
17765 inline void ModelSEIRCONN<TSeq>::update_infected()
+
17766 {
17767 
-
17768  return *this;
-
17769 
-
17770 }
-
17771 
-
17772 template<typename TSeq>
-
17773 inline void ModelSEIRCONN<TSeq>::reset()
-
17774 {
-
17775 
-
17776  Model<TSeq>::reset();
-
17777  this->update_infected();
+
17768  infected.clear();
+
17769  infected.reserve(this->size());
+
17770 
+
17771  for (auto & p : this->get_agents())
+
17772  {
+
17773  if (p.get_state() == ModelSEIRCONN<TSeq>::INFECTED)
+
17774  {
+
17775  infected.push_back(&p);
+
17776  }
+
17777  }
17778 
-
17779  return;
-
17780 
-
17781 }
-
17782 
-
17783 template<typename TSeq>
-
17784 inline Model<TSeq> * ModelSEIRCONN<TSeq>::clone_ptr()
-
17785 {
-
17786 
-
17787  ModelSEIRCONN<TSeq> * ptr = new ModelSEIRCONN<TSeq>(
-
17788  *dynamic_cast<const ModelSEIRCONN<TSeq>*>(this)
-
17789  );
-
17790 
-
17791  return dynamic_cast< Model<TSeq> *>(ptr);
-
17792 
-
17793 }
-
17794 
-
17805 template<typename TSeq>
-
17806 inline ModelSEIRCONN<TSeq>::ModelSEIRCONN(
-
17807  ModelSEIRCONN<TSeq> & model,
-
17808  const std::string & vname,
-
17809  epiworld_fast_uint n,
-
17810  epiworld_double prevalence,
-
17811  epiworld_double contact_rate,
-
17812  epiworld_double transmission_rate,
-
17813  epiworld_double avg_incubation_days,
-
17814  epiworld_double recovery_rate
-
17815  // epiworld_double prob_reinfection
-
17816  )
-
17817 {
-
17818 
-
17819  epiworld::UpdateFun<TSeq> update_susceptible = [](
-
17820  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
17821  ) -> void
-
17822  {
-
17823 
-
17824  // Sampling how many individuals
-
17825  int ndraw = m->rbinom();
-
17826 
-
17827  if (ndraw == 0)
-
17828  return;
-
17829 
-
17830  ModelSEIRCONN<TSeq> * model = dynamic_cast<ModelSEIRCONN<TSeq> *>(m);
-
17831  size_t ninfected = model->get_n_infected();
-
17832 
-
17833  // Drawing from the set
-
17834  int nviruses_tmp = 0;
-
17835  for (int i = 0; i < ndraw; ++i)
-
17836  {
-
17837  // Now selecting who is transmitting the disease
-
17838  int which = static_cast<int>(
-
17839  std::floor(ninfected * m->runif())
-
17840  );
-
17841 
-
17842  /* There is a bug in which runif() returns 1.0. It is rare, but
-
17843  * we saw it here. See the Notes section in the C++ manual
-
17844  * https://en.cppreference.com/mwiki/index.php?title=cpp/numeric/random/uniform_real_distribution&oldid=133329
-
17845  * And the reported bug in GCC:
-
17846  * https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63176
-
17847  *
-
17848  */
-
17849  if (which == static_cast<int>(ninfected))
-
17850  --which;
-
17851 
-
17852  epiworld::Agent<TSeq> & neighbor = *model->infected[which];
+
17779  Model<TSeq>::set_rand_binom(
+
17780  this->get_n_infected(),
+
17781  static_cast<double>(Model<TSeq>::par("Contact rate"))/
+
17782  static_cast<double>(Model<TSeq>::size())
+
17783  );
+
17784 
+
17785  return;
+
17786 
+
17787 }
+
17788 
+
17789 template<typename TSeq>
+
17790 inline ModelSEIRCONN<TSeq> & ModelSEIRCONN<TSeq>::run(
+
17791  epiworld_fast_uint ndays,
+
17792  int seed
+
17793 )
+
17794 {
+
17795 
+
17796  Model<TSeq>::run(ndays, seed);
+
17797 
+
17798  return *this;
+
17799 
+
17800 }
+
17801 
+
17802 template<typename TSeq>
+
17803 inline void ModelSEIRCONN<TSeq>::reset()
+
17804 {
+
17805 
+
17806  Model<TSeq>::reset();
+
17807  this->update_infected();
+
17808 
+
17809  return;
+
17810 
+
17811 }
+
17812 
+
17813 template<typename TSeq>
+
17814 inline Model<TSeq> * ModelSEIRCONN<TSeq>::clone_ptr()
+
17815 {
+
17816 
+
17817  ModelSEIRCONN<TSeq> * ptr = new ModelSEIRCONN<TSeq>(
+
17818  *dynamic_cast<const ModelSEIRCONN<TSeq>*>(this)
+
17819  );
+
17820 
+
17821  return dynamic_cast< Model<TSeq> *>(ptr);
+
17822 
+
17823 }
+
17824 
+
17835 template<typename TSeq>
+
17836 inline ModelSEIRCONN<TSeq>::ModelSEIRCONN(
+
17837  ModelSEIRCONN<TSeq> & model,
+
17838  const std::string & vname,
+
17839  epiworld_fast_uint n,
+
17840  epiworld_double prevalence,
+
17841  epiworld_double contact_rate,
+
17842  epiworld_double transmission_rate,
+
17843  epiworld_double avg_incubation_days,
+
17844  epiworld_double recovery_rate
+
17845  // epiworld_double prob_reinfection
+
17846  )
+
17847 {
+
17848 
+
17849  epiworld::UpdateFun<TSeq> update_susceptible = [](
+
17850  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
17851  ) -> void
+
17852  {
17853 
-
17854  // Can't sample itself
-
17855  if (neighbor.get_id() == p->get_id())
-
17856  continue;
-
17857 
-
17858  // The neighbor is infected by construction
-
17859  auto & v = neighbor.get_virus();
-
17860 
-
17861  #ifdef EPI_DEBUG
-
17862  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
-
17863  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
-
17864  #endif
-
17865 
-
17866  /* And it is a function of susceptibility_reduction as well */
-
17867  m->array_double_tmp[nviruses_tmp] =
-
17868  (1.0 - p->get_susceptibility_reduction(v, m)) *
-
17869  v->get_prob_infecting(m) *
-
17870  (1.0 - neighbor.get_transmission_reduction(v, m))
-
17871  ;
-
17872 
-
17873  m->array_virus_tmp[nviruses_tmp++] = &(*v);
-
17874 
-
17875  }
-
17876 
-
17877  // No virus to compute
-
17878  if (nviruses_tmp == 0u)
-
17879  return;
-
17880 
-
17881  // Running the roulette
-
17882  int which = roulette(nviruses_tmp, m);
+
17854  // Sampling how many individuals
+
17855  int ndraw = m->rbinom();
+
17856 
+
17857  if (ndraw == 0)
+
17858  return;
+
17859 
+
17860  ModelSEIRCONN<TSeq> * model = dynamic_cast<ModelSEIRCONN<TSeq> *>(m);
+
17861  size_t ninfected = model->get_n_infected();
+
17862 
+
17863  // Drawing from the set
+
17864  int nviruses_tmp = 0;
+
17865  for (int i = 0; i < ndraw; ++i)
+
17866  {
+
17867  // Now selecting who is transmitting the disease
+
17868  int which = static_cast<int>(
+
17869  std::floor(ninfected * m->runif())
+
17870  );
+
17871 
+
17872  /* There is a bug in which runif() returns 1.0. It is rare, but
+
17873  * we saw it here. See the Notes section in the C++ manual
+
17874  * https://en.cppreference.com/mwiki/index.php?title=cpp/numeric/random/uniform_real_distribution&oldid=133329
+
17875  * And the reported bug in GCC:
+
17876  * https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63176
+
17877  *
+
17878  */
+
17879  if (which == static_cast<int>(ninfected))
+
17880  --which;
+
17881 
+
17882  epiworld::Agent<TSeq> & neighbor = *model->infected[which];
17883 
-
17884  if (which < 0)
-
17885  return;
-
17886 
-
17887  p->set_virus(
-
17888  *m->array_virus_tmp[which],
-
17889  m,
-
17890  ModelSEIRCONN<TSeq>::EXPOSED
-
17891  );
-
17892 
-
17893  return;
-
17894 
-
17895  };
-
17896 
-
17897  epiworld::UpdateFun<TSeq> update_infected = [](
-
17898  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
17899  ) -> void {
-
17900 
-
17901  auto state = p->get_state();
-
17902 
-
17903  if (state == ModelSEIRCONN<TSeq>::EXPOSED)
-
17904  {
-
17905 
-
17906  // Getting the virus
-
17907  auto & v = p->get_virus();
-
17908 
-
17909  // Does the agent become infected?
-
17910  if (m->runif() < 1.0/(v->get_incubation(m)))
-
17911  {
-
17912 
-
17913  p->change_state(m, ModelSEIRCONN<TSeq>::INFECTED);
-
17914  return;
-
17915 
-
17916  }
-
17917 
-
17918 
-
17919  } else if (state == ModelSEIRCONN<TSeq>::INFECTED)
-
17920  {
-
17921 
+
17884  // Can't sample itself
+
17885  if (neighbor.get_id() == p->get_id())
+
17886  continue;
+
17887 
+
17888  // The neighbor is infected by construction
+
17889  auto & v = neighbor.get_virus();
+
17890 
+
17891  #ifdef EPI_DEBUG
+
17892  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
+
17893  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
+
17894  #endif
+
17895 
+
17896  /* And it is a function of susceptibility_reduction as well */
+
17897  m->array_double_tmp[nviruses_tmp] =
+
17898  (1.0 - p->get_susceptibility_reduction(v, m)) *
+
17899  v->get_prob_infecting(m) *
+
17900  (1.0 - neighbor.get_transmission_reduction(v, m))
+
17901  ;
+
17902 
+
17903  m->array_virus_tmp[nviruses_tmp++] = &(*v);
+
17904 
+
17905  }
+
17906 
+
17907  // No virus to compute
+
17908  if (nviruses_tmp == 0u)
+
17909  return;
+
17910 
+
17911  // Running the roulette
+
17912  int which = roulette(nviruses_tmp, m);
+
17913 
+
17914  if (which < 0)
+
17915  return;
+
17916 
+
17917  p->set_virus(
+
17918  *m->array_virus_tmp[which],
+
17919  m,
+
17920  ModelSEIRCONN<TSeq>::EXPOSED
+
17921  );
17922 
-
17923  // Odd: Die, Even: Recover
-
17924  epiworld_fast_uint n_events = 0u;
-
17925  const auto & v = p->get_virus();
+
17923  return;
+
17924 
+
17925  };
17926 
-
17927  // Recover
-
17928  m->array_double_tmp[n_events++] =
-
17929  1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m));
+
17927  epiworld::UpdateFun<TSeq> update_infected = [](
+
17928  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
17929  ) -> void {
17930 
-
17931  #ifdef EPI_DEBUG
-
17932  if (n_events == 0u)
-
17933  {
-
17934  printf_epiworld(
-
17935  "[epi-debug] agent %i has 0 possible events!!\n",
-
17936  static_cast<int>(p->get_id())
-
17937  );
-
17938  throw std::logic_error("Zero events in exposed.");
-
17939  }
-
17940  #else
-
17941  if (n_events == 0u)
-
17942  return;
-
17943  #endif
-
17944 
+
17931  auto state = p->get_state();
+
17932 
+
17933  if (state == ModelSEIRCONN<TSeq>::EXPOSED)
+
17934  {
+
17935 
+
17936  // Getting the virus
+
17937  auto & v = p->get_virus();
+
17938 
+
17939  // Does the agent become infected?
+
17940  if (m->runif() < 1.0/(v->get_incubation(m)))
+
17941  {
+
17942 
+
17943  p->change_state(m, ModelSEIRCONN<TSeq>::INFECTED);
+
17944  return;
17945 
-
17946  // Running the roulette
-
17947  int which = roulette(n_events, m);
+
17946  }
+
17947 
17948 
-
17949  if (which < 0)
-
17950  return;
+
17949  } else if (state == ModelSEIRCONN<TSeq>::INFECTED)
+
17950  {
17951 
-
17952  // Which roulette happen?
-
17953  p->rm_virus(m);
-
17954 
-
17955  return ;
+
17952 
+
17953  // Odd: Die, Even: Recover
+
17954  epiworld_fast_uint n_events = 0u;
+
17955  const auto & v = p->get_virus();
17956 
-
17957  } else
-
17958  throw std::logic_error("This function can only be applied to exposed or infected individuals. (SEIR)") ;
-
17959 
-
17960  return;
-
17961 
-
17962  };
-
17963 
-
17964  // Setting up parameters
-
17965  model.add_param(contact_rate, "Contact rate");
-
17966  model.add_param(transmission_rate, "Prob. Transmission");
-
17967  model.add_param(recovery_rate, "Prob. Recovery");
-
17968  model.add_param(avg_incubation_days, "Avg. Incubation days");
-
17969 
-
17970  // state
-
17971  model.add_state("Susceptible", update_susceptible);
-
17972  model.add_state("Exposed", update_infected);
-
17973  model.add_state("Infected", update_infected);
-
17974  model.add_state("Recovered");
+
17957  // Recover
+
17958  m->array_double_tmp[n_events++] =
+
17959  1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m));
+
17960 
+
17961  #ifdef EPI_DEBUG
+
17962  if (n_events == 0u)
+
17963  {
+
17964  printf_epiworld(
+
17965  "[epi-debug] agent %i has 0 possible events!!\n",
+
17966  static_cast<int>(p->get_id())
+
17967  );
+
17968  throw std::logic_error("Zero events in exposed.");
+
17969  }
+
17970  #else
+
17971  if (n_events == 0u)
+
17972  return;
+
17973  #endif
+
17974 
17975 
-
17976  // Adding update function
-
17977  epiworld::GlobalFun<TSeq> update = [](
-
17978  epiworld::Model<TSeq> * m
-
17979  ) -> void
-
17980  {
+
17976  // Running the roulette
+
17977  int which = roulette(n_events, m);
+
17978 
+
17979  if (which < 0)
+
17980  return;
17981 
-
17982  ModelSEIRCONN<TSeq> * model = dynamic_cast<ModelSEIRCONN<TSeq> *>(m);
-
17983 
-
17984  model->update_infected();
-
17985 
-
17986  return;
-
17987 
-
17988  };
+
17982  // Which roulette happen?
+
17983  p->rm_virus(m);
+
17984 
+
17985  return ;
+
17986 
+
17987  } else
+
17988  throw std::logic_error("This function can only be applied to exposed or infected individuals. (SEIR)") ;
17989 
-
17990  model.add_globalevent(update, "Update infected individuals");
+
17990  return;
17991 
-
17992 
-
17993  // Preparing the virus -------------------------------------------
-
17994  epiworld::Virus<TSeq> virus(vname, prevalence, true);
-
17995  virus.set_state(
-
17996  ModelSEIRCONN<TSeq>::EXPOSED,
-
17997  ModelSEIRCONN<TSeq>::RECOVERED,
-
17998  ModelSEIRCONN<TSeq>::RECOVERED
-
17999  );
-
18000 
-
18001  virus.set_prob_infecting(&model("Prob. Transmission"));
-
18002  virus.set_prob_recovery(&model("Prob. Recovery"));
-
18003  virus.set_incubation(&model("Avg. Incubation days"));
-
18004 
-
18005  model.add_virus(virus);
-
18006 
-
18007  model.queuing_off(); // No queuing need
-
18008 
-
18009  // Adding the empty population
-
18010  model.agents_empty_graph(n);
+
17992  };
+
17993 
+
17994  // Setting up parameters
+
17995  model.add_param(contact_rate, "Contact rate");
+
17996  model.add_param(transmission_rate, "Prob. Transmission");
+
17997  model.add_param(recovery_rate, "Prob. Recovery");
+
17998  model.add_param(avg_incubation_days, "Avg. Incubation days");
+
17999 
+
18000  // state
+
18001  model.add_state("Susceptible", update_susceptible);
+
18002  model.add_state("Exposed", update_infected);
+
18003  model.add_state("Infected", update_infected);
+
18004  model.add_state("Recovered");
+
18005 
+
18006  // Adding update function
+
18007  epiworld::GlobalFun<TSeq> update = [](
+
18008  epiworld::Model<TSeq> * m
+
18009  ) -> void
+
18010  {
18011 
-
18012  model.set_name("Susceptible-Exposed-Infected-Removed (SEIR) (connected)");
+
18012  ModelSEIRCONN<TSeq> * model = dynamic_cast<ModelSEIRCONN<TSeq> *>(m);
18013 
-
18014  return;
+
18014  model->update_infected();
18015 
-
18016 }
+
18016  return;
18017 
-
18018 template<typename TSeq>
-
18019 inline ModelSEIRCONN<TSeq>::ModelSEIRCONN(
-
18020  const std::string & vname,
-
18021  epiworld_fast_uint n,
-
18022  epiworld_double prevalence,
-
18023  epiworld_double contact_rate,
-
18024  epiworld_double transmission_rate,
-
18025  epiworld_double avg_incubation_days,
-
18026  epiworld_double recovery_rate
-
18027  )
-
18028 {
-
18029 
-
18030  ModelSEIRCONN(
-
18031  *this,
-
18032  vname,
-
18033  n,
-
18034  prevalence,
-
18035  contact_rate,
-
18036  transmission_rate,
-
18037  avg_incubation_days,
-
18038  recovery_rate
-
18039  );
-
18040 
-
18041  return;
-
18042 
-
18043 }
-
18044 
-
18045 template<typename TSeq>
-
18046 inline ModelSEIRCONN<TSeq> & ModelSEIRCONN<TSeq>::initial_states(
-
18047  std::vector< double > proportions_,
-
18048  std::vector< int > /* queue_ */
-
18049 )
-
18050 {
-
18051 
-
18052  Model<TSeq>::initial_states_fun =
-
18053  create_init_function_seir<TSeq>(proportions_)
-
18054  ;
-
18055 
-
18056  return *this;
-
18057 
-
18058 }
+
18018  };
+
18019 
+
18020  model.add_globalevent(update, "Update infected individuals");
+
18021 
+
18022 
+
18023  // Preparing the virus -------------------------------------------
+
18024  epiworld::Virus<TSeq> virus(vname, prevalence, true);
+
18025  virus.set_state(
+
18026  ModelSEIRCONN<TSeq>::EXPOSED,
+
18027  ModelSEIRCONN<TSeq>::RECOVERED,
+
18028  ModelSEIRCONN<TSeq>::RECOVERED
+
18029  );
+
18030 
+
18031  virus.set_prob_infecting(&model("Prob. Transmission"));
+
18032  virus.set_prob_recovery(&model("Prob. Recovery"));
+
18033  virus.set_incubation(&model("Avg. Incubation days"));
+
18034 
+
18035  model.add_virus(virus);
+
18036 
+
18037  model.queuing_off(); // No queuing need
+
18038 
+
18039  // Adding the empty population
+
18040  model.agents_empty_graph(n);
+
18041 
+
18042  model.set_name("Susceptible-Exposed-Infected-Removed (SEIR) (connected)");
+
18043 
+
18044  return;
+
18045 
+
18046 }
+
18047 
+
18048 template<typename TSeq>
+
18049 inline ModelSEIRCONN<TSeq>::ModelSEIRCONN(
+
18050  const std::string & vname,
+
18051  epiworld_fast_uint n,
+
18052  epiworld_double prevalence,
+
18053  epiworld_double contact_rate,
+
18054  epiworld_double transmission_rate,
+
18055  epiworld_double avg_incubation_days,
+
18056  epiworld_double recovery_rate
+
18057  )
+
18058 {
18059 
-
18060 template<typename TSeq>
-
18061 inline std::vector< double > ModelSEIRCONN<TSeq>::generation_time_expected(
-
18062  int max_days,
-
18063  int max_contacts
-
18064 ) const
-
18065 {
-
18066 
-
18067  // Retrieving total counts
-
18068  std::vector< int > h_date;
-
18069  std::vector< std::string > h_state;
-
18070  std::vector< int > h_counts;
-
18071  const auto this_const = dynamic_cast<const ModelSEIRCONN<TSeq> *>(this);
-
18072  this_const->get_db().get_hist_total(
-
18073  &h_date,
-
18074  &h_state,
-
18075  &h_counts
-
18076  );
-
18077 
-
18078  // Retrieving information on susceptibles
-
18079  std::vector< double > S(this_const->get_ndays(), 0.0);
-
18080  for (size_t i = 0; i < h_date.size(); ++i)
-
18081  {
-
18082  if (h_state[i] == "Susceptible")
-
18083  S[h_date[i]] += h_counts[i];
-
18084  }
+
18060  ModelSEIRCONN(
+
18061  *this,
+
18062  vname,
+
18063  n,
+
18064  prevalence,
+
18065  contact_rate,
+
18066  transmission_rate,
+
18067  avg_incubation_days,
+
18068  recovery_rate
+
18069  );
+
18070 
+
18071  return;
+
18072 
+
18073 }
+
18074 
+
18075 template<typename TSeq>
+
18076 inline ModelSEIRCONN<TSeq> & ModelSEIRCONN<TSeq>::initial_states(
+
18077  std::vector< double > proportions_,
+
18078  std::vector< int > /* queue_ */
+
18079 )
+
18080 {
+
18081 
+
18082  Model<TSeq>::initial_states_fun =
+
18083  create_init_function_seir<TSeq>(proportions_)
+
18084  ;
18085 
-
18086  // Computing the expected number of days in exposed
-
18087  double days_exposed = this_const->par("Avg. Incubation days");
-
18088 
-
18089  // The generation time in the SEIR model starts from 2, as agents
-
18090  // spend at least one day in the exposed state, and 1 day in the
-
18091  // infectious state before starting transmitting.
-
18092  std::vector< double > gen_times(
-
18093  this_const->get_ndays(), 1.0 + days_exposed
-
18094  );
-
18095 
-
18096  double p_c = this_const->par("Contact rate")/this_const->size();
-
18097  double p_i = this_const->par("Prob. Transmission");
-
18098  double p_r = this_const->par("Prob. Recovery");
-
18099 
-
18100  for (size_t i = 0u; i < this_const->get_ndays(); ++i)
-
18101  {
-
18102  gen_times[i] += gen_int_mean(
-
18103  S[i],
-
18104  p_c,
-
18105  p_i,
-
18106  p_r,
-
18107  max_days,
-
18108  max_contacts
-
18109  );
-
18110 
-
18111  }
-
18112 
-
18113  return gen_times;
-
18114 
-
18115 }
-
18116 
-
18117 #endif
-
18118 /*//////////////////////////////////////////////////////////////////////////////
-
18120 
-
18121  End of -include/epiworld//models/seirconnected.hpp-
-
18122 
-
18125 
-
18126 
-
18127 /*//////////////////////////////////////////////////////////////////////////////
-
18129 
-
18130  Start of -include/epiworld//models/sird.hpp-
-
18131 
-
18134 
-
18135 
-
18136 #ifndef EPIWORLD_SIRD_H
-
18137 #define EPIWORLD_SIRD_H
-
18138 
-
18142 template<typename TSeq = int>
-
18143 class ModelSIRD : public epiworld::Model<TSeq>
-
18144 {
-
18145 public:
-
18146 
-
18147  ModelSIRD() {};
-
18148 
-
18149 
-
18161  ModelSIRD(
-
18162  ModelSIRD<TSeq> & model,
-
18163  const std::string & vname,
-
18164  epiworld_double prevalence,
-
18165  epiworld_double transmission_rate,
-
18166  epiworld_double recovery_rate,
-
18167  epiworld_double death_rate
-
18168  );
-
18169 
-
18170  ModelSIRD(
-
18171  const std::string & vname,
-
18172  epiworld_double prevalence,
-
18173  epiworld_double transmission_rate,
-
18174  epiworld_double recovery_rate,
-
18175  epiworld_double death_rate
-
18176  );
+
18086  return *this;
+
18087 
+
18088 }
+
18089 
+
18090 template<typename TSeq>
+
18091 inline std::vector< double > ModelSEIRCONN<TSeq>::generation_time_expected(
+
18092  int max_days,
+
18093  int max_contacts
+
18094 ) const
+
18095 {
+
18096 
+
18097  // Retrieving total counts
+
18098  std::vector< int > h_date;
+
18099  std::vector< std::string > h_state;
+
18100  std::vector< int > h_counts;
+
18101  const auto this_const = dynamic_cast<const ModelSEIRCONN<TSeq> *>(this);
+
18102  this_const->get_db().get_hist_total(
+
18103  &h_date,
+
18104  &h_state,
+
18105  &h_counts
+
18106  );
+
18107 
+
18108  // Retrieving information on susceptibles
+
18109  std::vector< double > S(this_const->get_ndays(), 0.0);
+
18110  for (size_t i = 0; i < h_date.size(); ++i)
+
18111  {
+
18112  if (h_state[i] == "Susceptible")
+
18113  S[h_date[i]] += h_counts[i];
+
18114  }
+
18115 
+
18116  // Computing the expected number of days in exposed
+
18117  double days_exposed = this_const->par("Avg. Incubation days");
+
18118 
+
18119  // The generation time in the SEIR model starts from 2, as agents
+
18120  // spend at least one day in the exposed state, and 1 day in the
+
18121  // infectious state before starting transmitting.
+
18122  std::vector< double > gen_times(
+
18123  this_const->get_ndays(), 1.0 + days_exposed
+
18124  );
+
18125 
+
18126  double p_c = this_const->par("Contact rate")/this_const->size();
+
18127  double p_i = this_const->par("Prob. Transmission");
+
18128  double p_r = this_const->par("Prob. Recovery");
+
18129 
+
18130  for (size_t i = 0u; i < this_const->get_ndays(); ++i)
+
18131  {
+
18132  gen_times[i] += gen_int_mean(
+
18133  S[i],
+
18134  p_c,
+
18135  p_i,
+
18136  p_r,
+
18137  max_days,
+
18138  max_contacts
+
18139  );
+
18140 
+
18141  }
+
18142 
+
18143  return gen_times;
+
18144 
+
18145 }
+
18146 
+
18147 #endif
+
18148 /*//////////////////////////////////////////////////////////////////////////////
+
18150 
+
18151  End of -include/epiworld//models/seirconnected.hpp-
+
18152 
+
18155 
+
18156 
+
18157 /*//////////////////////////////////////////////////////////////////////////////
+
18159 
+
18160  Start of -include/epiworld//models/sird.hpp-
+
18161 
+
18164 
+
18165 
+
18166 #ifndef EPIWORLD_SIRD_H
+
18167 #define EPIWORLD_SIRD_H
+
18168 
+
18172 template<typename TSeq = int>
+
18173 class ModelSIRD : public epiworld::Model<TSeq>
+
18174 {
+
18175 public:
+
18176 
+
18177  ModelSIRD() {};
18178 
-
18185  ModelSIRD<TSeq> & initial_states(
-
18186  std::vector< double > proportions_,
-
18187  std::vector< int > queue_ = {}
-
18188  );
-
18189 
-
18190 };
-
18191 
-
18192 template<typename TSeq>
-
18193 inline ModelSIRD<TSeq>::ModelSIRD(
-
18194  ModelSIRD<TSeq> & model,
-
18195  const std::string & vname,
-
18196  epiworld_double prevalence,
-
18197  epiworld_double transmission_rate,
-
18198  epiworld_double recovery_rate,
-
18199  epiworld_double death_rate
-
18200  )
-
18201 {
-
18202 
-
18203  // Adding statuses
-
18204  model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
-
18205  model.add_state("Infected", epiworld::default_update_exposed<TSeq>);
-
18206  model.add_state("Recovered"),
-
18207  model.add_state("Deceased")
-
18208  ;
-
18209 
-
18210  // Setting up parameters
-
18211  model.add_param(recovery_rate, "Recovery rate");
-
18212  model.add_param(transmission_rate, "Transmission rate"),
-
18213  model.add_param(death_rate, "Death rate");
-
18214 
-
18215  // Preparing the virus -------------------------------------------
-
18216  epiworld::Virus<TSeq> virus(vname, prevalence, true);
-
18217  virus.set_state(1,2,3);
-
18218  virus.set_prob_recovery(&model("Recovery rate"));
-
18219  virus.set_prob_infecting(&model("Transmission rate"));
-
18220  virus.set_prob_death(&model("Death rate"));
-
18221 
-
18222  model.add_virus(virus);
-
18223 
-
18224  model.set_name("Susceptible-Infected-Recovered-Deceased (SIRD)");
-
18225 
-
18226  return;
-
18227 
-
18228 }
-
18229 
-
18230 template<typename TSeq>
-
18231 inline ModelSIRD<TSeq>::ModelSIRD(
-
18232  const std::string & vname,
-
18233  epiworld_double prevalence,
-
18234  epiworld_double transmission_rate,
-
18235  epiworld_double recovery_rate,
-
18236  epiworld_double death_rate
-
18237  )
-
18238 {
+
18179 
+
18191  ModelSIRD(
+
18192  ModelSIRD<TSeq> & model,
+
18193  const std::string & vname,
+
18194  epiworld_double prevalence,
+
18195  epiworld_double transmission_rate,
+
18196  epiworld_double recovery_rate,
+
18197  epiworld_double death_rate
+
18198  );
+
18199 
+
18200  ModelSIRD(
+
18201  const std::string & vname,
+
18202  epiworld_double prevalence,
+
18203  epiworld_double transmission_rate,
+
18204  epiworld_double recovery_rate,
+
18205  epiworld_double death_rate
+
18206  );
+
18208 
+
18215  ModelSIRD<TSeq> & initial_states(
+
18216  std::vector< double > proportions_,
+
18217  std::vector< int > queue_ = {}
+
18218  );
+
18219 
+
18220 };
+
18221 
+
18222 template<typename TSeq>
+
18223 inline ModelSIRD<TSeq>::ModelSIRD(
+
18224  ModelSIRD<TSeq> & model,
+
18225  const std::string & vname,
+
18226  epiworld_double prevalence,
+
18227  epiworld_double transmission_rate,
+
18228  epiworld_double recovery_rate,
+
18229  epiworld_double death_rate
+
18230  )
+
18231 {
+
18232 
+
18233  // Adding statuses
+
18234  model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
+
18235  model.add_state("Infected", epiworld::default_update_exposed<TSeq>);
+
18236  model.add_state("Recovered"),
+
18237  model.add_state("Deceased")
+
18238  ;
18239 
-
18240  ModelSIRD<TSeq>(
-
18241  *this,
-
18242  vname,
-
18243  prevalence,
-
18244  transmission_rate,
-
18245  recovery_rate,
-
18246  death_rate
-
18247  );
-
18248 
-
18249  return;
-
18250 
-
18251 }
-
18252 
-
18253 template<typename TSeq>
-
18254 inline ModelSIRD<TSeq> & ModelSIRD<TSeq>::initial_states(
-
18255  std::vector< double > proportions_,
-
18256  std::vector< int > /**/
-
18257 ) {
-
18258 
-
18259  Model<TSeq>::initial_states_fun =
-
18260  create_init_function_sird<TSeq>(proportions_)
-
18261  ;
-
18262 
-
18263  return *this;
-
18264 
-
18265 }
-
18266 
-
18267 #endif
-
18268 /*//////////////////////////////////////////////////////////////////////////////
-
18270 
-
18271  End of -include/epiworld//models/sird.hpp-
-
18272 
-
18275 
-
18276 
-
18277 /*//////////////////////////////////////////////////////////////////////////////
-
18279 
-
18280  Start of -include/epiworld//models/sisd.hpp-
-
18281 
-
18284 
-
18285 
-
18286 #ifndef EPIWORLD_MODELS_SISD_HPP
-
18287 #define EPIWORLD_MODELS_SISD_HPP
-
18288 
-
18298 template<typename TSeq = int>
-
18299 class ModelSISD : public epiworld::Model<TSeq>
-
18300 {
-
18301 
-
18302 public:
-
18303 
-
18304  ModelSISD() {};
+
18240  // Setting up parameters
+
18241  model.add_param(recovery_rate, "Recovery rate");
+
18242  model.add_param(transmission_rate, "Transmission rate"),
+
18243  model.add_param(death_rate, "Death rate");
+
18244 
+
18245  // Preparing the virus -------------------------------------------
+
18246  epiworld::Virus<TSeq> virus(vname, prevalence, true);
+
18247  virus.set_state(1,2,3);
+
18248  virus.set_prob_recovery(&model("Recovery rate"));
+
18249  virus.set_prob_infecting(&model("Transmission rate"));
+
18250  virus.set_prob_death(&model("Death rate"));
+
18251 
+
18252  model.add_virus(virus);
+
18253 
+
18254  model.set_name("Susceptible-Infected-Recovered-Deceased (SIRD)");
+
18255 
+
18256  return;
+
18257 
+
18258 }
+
18259 
+
18260 template<typename TSeq>
+
18261 inline ModelSIRD<TSeq>::ModelSIRD(
+
18262  const std::string & vname,
+
18263  epiworld_double prevalence,
+
18264  epiworld_double transmission_rate,
+
18265  epiworld_double recovery_rate,
+
18266  epiworld_double death_rate
+
18267  )
+
18268 {
+
18269 
+
18270  ModelSIRD<TSeq>(
+
18271  *this,
+
18272  vname,
+
18273  prevalence,
+
18274  transmission_rate,
+
18275  recovery_rate,
+
18276  death_rate
+
18277  );
+
18278 
+
18279  return;
+
18280 
+
18281 }
+
18282 
+
18283 template<typename TSeq>
+
18284 inline ModelSIRD<TSeq> & ModelSIRD<TSeq>::initial_states(
+
18285  std::vector< double > proportions_,
+
18286  std::vector< int > /**/
+
18287 ) {
+
18288 
+
18289  Model<TSeq>::initial_states_fun =
+
18290  create_init_function_sird<TSeq>(proportions_)
+
18291  ;
+
18292 
+
18293  return *this;
+
18294 
+
18295 }
+
18296 
+
18297 #endif
+
18298 /*//////////////////////////////////////////////////////////////////////////////
+
18300 
+
18301  End of -include/epiworld//models/sird.hpp-
+
18302 
18305 
-
18306  ModelSISD(
-
18307  ModelSISD<TSeq> & model,
-
18308  const std::string & vname,
-
18309  epiworld_double prevalence,
-
18310  epiworld_double transmission_rate,
-
18311  epiworld_double recovery_rate,
-
18312  epiworld_double death_rate
-
18313  );
+
18306 
+
18307 /*//////////////////////////////////////////////////////////////////////////////
+
18309 
+
18310  Start of -include/epiworld//models/sisd.hpp-
+
18311 
18314 
-
18315  ModelSISD(
-
18316  const std::string & vname,
-
18317  epiworld_double prevalence,
-
18318  epiworld_double transmission_rate,
-
18319  epiworld_double recovery_rate,
-
18320  epiworld_double death_rate
-
18321  );
-
18322 
-
18323 };
-
18324 
-
18325 template<typename TSeq>
-
18326 inline ModelSISD<TSeq>::ModelSISD(
-
18327  ModelSISD<TSeq> & model,
-
18328  const std::string & vname,
-
18329  epiworld_double prevalence,
-
18330  epiworld_double transmission_rate,
-
18331  epiworld_double recovery_rate,
-
18332  epiworld_double death_rate
-
18333  )
-
18334 {
+
18315 
+
18316 #ifndef EPIWORLD_MODELS_SISD_HPP
+
18317 #define EPIWORLD_MODELS_SISD_HPP
+
18318 
+
18328 template<typename TSeq = int>
+
18329 class ModelSISD : public epiworld::Model<TSeq>
+
18330 {
+
18331 
+
18332 public:
+
18333 
+
18334  ModelSISD() {};
18335 
-
18336  model.set_name("Susceptible-Infected-Susceptible-Deceased (SISD)");
-
18337 
-
18338  // Adding statuses
-
18339  model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
-
18340  model.add_state("Infected", epiworld::default_update_exposed<TSeq>);
-
18341  model.add_state("Deceased");
-
18342 
-
18343  // Setting up parameters
-
18344  model.add_param(transmission_rate, "Transmission rate");
-
18345  model.add_param(recovery_rate, "Recovery rate");
-
18346  model.add_param(death_rate, "Death rate");
-
18347 
-
18348  // Preparing the virus -------------------------------------------
-
18349  epiworld::Virus<TSeq> virus(vname, prevalence, true);
-
18350  virus.set_state(1,0,2);
-
18351 
-
18352  virus.set_prob_infecting(&model("Transmission rate"));
-
18353  virus.set_prob_recovery(&model("Recovery rate"));
-
18354  virus.set_prob_death(0.01);
-
18355 
-
18356  model.add_virus(virus);
-
18357 
-
18358  return;
-
18359 
-
18360 }
-
18361 
-
18362 template<typename TSeq>
-
18363 inline ModelSISD<TSeq>::ModelSISD(
-
18364  const std::string & vname,
-
18365  epiworld_double prevalence,
-
18366  epiworld_double transmission_rate,
-
18367  epiworld_double recovery_rate,
-
18368  epiworld_double death_rate
-
18369  )
-
18370 {
-
18371 
-
18372  ModelSISD<TSeq>(
-
18373  *this,
-
18374  vname,
-
18375  prevalence,
-
18376  transmission_rate,
-
18377  recovery_rate,
-
18378  death_rate
-
18379  );
-
18380 
-
18381  return;
-
18382 
-
18383 }
-
18384 
-
18385 #endif
-
18386 /*//////////////////////////////////////////////////////////////////////////////
-
18388 
-
18389  End of -include/epiworld//models/sisd.hpp-
-
18390 
-
18393 
-
18394 
-
18395 /*//////////////////////////////////////////////////////////////////////////////
-
18397 
-
18398  Start of -include/epiworld//models/seird.hpp-
-
18399 
-
18402 
-
18403 
-
18404 #ifndef EPIWORLD_MODELS_SEIRD_HPP
-
18405 #define EPIWORLD_MODELS_SEIRD_HPP
-
18406 
-
18410 template<typename TSeq = int>
-
18411 class ModelSEIRD : public epiworld::Model<TSeq>
-
18412 {
-
18413 
-
18414 public:
-
18415  static const int SUSCEPTIBLE = 0;
-
18416  static const int EXPOSED = 1;
-
18417  static const int INFECTED = 2;
-
18418  static const int REMOVED = 3;
-
18419  static const int DECEASED = 4;
-
18420 
-
18421  ModelSEIRD() {};
-
18422 
-
18435  ModelSEIRD(
-
18436  ModelSEIRD<TSeq> & model,
-
18437  const std::string & vname,
-
18438  epiworld_double prevalence,
-
18439  epiworld_double transmission_rate,
-
18440  epiworld_double avg_incubation_days,
-
18441  epiworld_double recovery_rate,
-
18442  epiworld_double death_rate
-
18443  );
-
18444 
-
18455  ModelSEIRD(
-
18456  const std::string & vname,
-
18457  epiworld_double prevalence,
-
18458  epiworld_double transmission_rate,
-
18459  epiworld_double avg_incubation_days,
-
18460  epiworld_double recovery_rate,
-
18461  epiworld_double death_rate
-
18462  );
-
18463 
-
18464  epiworld::UpdateFun<TSeq> update_exposed_seir = [](
-
18465  epiworld::Agent<TSeq> * p,
-
18466  epiworld::Model<TSeq> * m
-
18467  ) -> void {
-
18468 
-
18469  // Getting the virus
-
18470  auto v = p->get_virus();
-
18471 
-
18472  // Does the agent become infected?
-
18473  if (m->runif() < 1.0/(v->get_incubation(m)))
-
18474  p->change_state(m, ModelSEIRD<TSeq>::INFECTED);
-
18475 
-
18476  return;
-
18477  };
-
18478 
-
18479 
-
18480  epiworld::UpdateFun<TSeq> update_infected = [](
-
18481  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
18482  ) -> void {
-
18483 
-
18484  // Odd: Die, Even: Recover
-
18485  epiworld_fast_uint n_events = 0u;
-
18486 
-
18487  const auto & v = p->get_virus();
-
18488 
-
18489  // Die
-
18490  m->array_double_tmp[n_events++] =
-
18491  v->get_prob_death(m) * (1.0 - p->get_death_reduction(v, m));
-
18492 
-
18493  // Recover
-
18494  m->array_double_tmp[n_events++] =
-
18495  1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m));
-
18496 
-
18497 
-
18498 #ifdef EPI_DEBUG
-
18499  if (n_events == 0u)
-
18500  {
-
18501  printf_epiworld(
-
18502  "[epi-debug] agent %i has 0 possible events!!\n",
-
18503  static_cast<int>(p->get_id())
-
18504  );
-
18505  throw std::logic_error("Zero events in exposed.");
-
18506  }
-
18507 #else
-
18508  if (n_events == 0u)
-
18509  return;
-
18510 #endif
-
18511 
-
18512 
-
18513  // Running the roulette
-
18514  int which = roulette(n_events, m);
-
18515 
-
18516  if (which < 0)
-
18517  return;
-
18518 
-
18519  // Which roulette happen?
-
18520  if ((which % 2) == 0) // If odd
-
18521  {
-
18522 
-
18523  p->rm_agent_by_virus(m);
-
18524 
-
18525  } else {
-
18526 
-
18527  p->rm_virus(m);
-
18528 
-
18529  }
-
18530 
-
18531  return ;
-
18532 
-
18533 
-
18534 
-
18535  return;
-
18536 
-
18537  };
-
18538 
-
18539  ModelSEIRD<TSeq> & initial_states(
-
18540  std::vector< double > proportions_,
-
18541  std::vector< int > queue_ = {}
-
18542  );
-
18543 
-
18544 };
-
18545 
-
18546 
-
18547 
-
18548 template<typename TSeq>
-
18549 inline ModelSEIRD<TSeq>::ModelSEIRD(
-
18550  ModelSEIRD<TSeq> & model,
-
18551  const std::string & vname,
-
18552  epiworld_double prevalence,
-
18553  epiworld_double transmission_rate,
-
18554  epiworld_double avg_incubation_days,
-
18555  epiworld_double recovery_rate,
-
18556  epiworld_double death_rate
-
18557 )
-
18558 {
-
18559 
-
18560  // Adding statuses
-
18561  model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
-
18562  model.add_state("Exposed", model.update_exposed_seir);
-
18563  model.add_state("Infected", model.update_infected);
-
18564  model.add_state("Removed");
-
18565  model.add_state("Deceased");
-
18566 
-
18567  // Setting up parameters
-
18568  model.add_param(transmission_rate, "Transmission rate");
-
18569  model.add_param(avg_incubation_days, "Incubation days");
-
18570  model.add_param(recovery_rate, "Recovery rate");
-
18571  model.add_param(death_rate, "Death rate");
-
18572 
-
18573  // Preparing the virus -------------------------------------------
-
18574  epiworld::Virus<TSeq> virus(vname, prevalence, true);
-
18575  virus.set_state(ModelSEIRD<TSeq>::EXPOSED, ModelSEIRD<TSeq>::REMOVED, ModelSEIRD<TSeq>::DECEASED);
-
18576 
-
18577  virus.set_prob_infecting(&model("Transmission rate"));
-
18578  virus.set_incubation(&model("Incubation days"));
-
18579  virus.set_prob_death(&model("Death rate"));
-
18580  virus.set_prob_recovery(&model("Recovery rate"));
-
18581 
-
18582  // Adding the tool and the virus
-
18583  model.add_virus(virus);
-
18584 
-
18585  model.set_name("Susceptible-Exposed-Infected-Removed-Deceased (SEIRD)");
-
18586 
-
18587  return;
-
18588 
-
18589 }
-
18590 
-
18591 template<typename TSeq>
-
18592 inline ModelSEIRD<TSeq>::ModelSEIRD(
-
18593  const std::string & vname,
-
18594  epiworld_double prevalence,
-
18595  epiworld_double transmission_rate,
-
18596  epiworld_double avg_incubation_days,
-
18597  epiworld_double recovery_rate,
-
18598  epiworld_double death_rate
-
18599 )
-
18600 {
-
18601 
-
18602  ModelSEIRD<TSeq>(
-
18603  *this,
-
18604  vname,
-
18605  prevalence,
-
18606  transmission_rate,
-
18607  avg_incubation_days,
-
18608  recovery_rate,
-
18609  death_rate
-
18610  );
+
18336  ModelSISD(
+
18337  ModelSISD<TSeq> & model,
+
18338  const std::string & vname,
+
18339  epiworld_double prevalence,
+
18340  epiworld_double transmission_rate,
+
18341  epiworld_double recovery_rate,
+
18342  epiworld_double death_rate
+
18343  );
+
18344 
+
18345  ModelSISD(
+
18346  const std::string & vname,
+
18347  epiworld_double prevalence,
+
18348  epiworld_double transmission_rate,
+
18349  epiworld_double recovery_rate,
+
18350  epiworld_double death_rate
+
18351  );
+
18352 
+
18353 };
+
18354 
+
18355 template<typename TSeq>
+
18356 inline ModelSISD<TSeq>::ModelSISD(
+
18357  ModelSISD<TSeq> & model,
+
18358  const std::string & vname,
+
18359  epiworld_double prevalence,
+
18360  epiworld_double transmission_rate,
+
18361  epiworld_double recovery_rate,
+
18362  epiworld_double death_rate
+
18363  )
+
18364 {
+
18365 
+
18366  model.set_name("Susceptible-Infected-Susceptible-Deceased (SISD)");
+
18367 
+
18368  // Adding statuses
+
18369  model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
+
18370  model.add_state("Infected", epiworld::default_update_exposed<TSeq>);
+
18371  model.add_state("Deceased");
+
18372 
+
18373  // Setting up parameters
+
18374  model.add_param(transmission_rate, "Transmission rate");
+
18375  model.add_param(recovery_rate, "Recovery rate");
+
18376  model.add_param(death_rate, "Death rate");
+
18377 
+
18378  // Preparing the virus -------------------------------------------
+
18379  epiworld::Virus<TSeq> virus(vname, prevalence, true);
+
18380  virus.set_state(1,0,2);
+
18381 
+
18382  virus.set_prob_infecting(&model("Transmission rate"));
+
18383  virus.set_prob_recovery(&model("Recovery rate"));
+
18384  virus.set_prob_death(0.01);
+
18385 
+
18386  model.add_virus(virus);
+
18387 
+
18388  return;
+
18389 
+
18390 }
+
18391 
+
18392 template<typename TSeq>
+
18393 inline ModelSISD<TSeq>::ModelSISD(
+
18394  const std::string & vname,
+
18395  epiworld_double prevalence,
+
18396  epiworld_double transmission_rate,
+
18397  epiworld_double recovery_rate,
+
18398  epiworld_double death_rate
+
18399  )
+
18400 {
+
18401 
+
18402  ModelSISD<TSeq>(
+
18403  *this,
+
18404  vname,
+
18405  prevalence,
+
18406  transmission_rate,
+
18407  recovery_rate,
+
18408  death_rate
+
18409  );
+
18410 
+
18411  return;
+
18412 
+
18413 }
+
18414 
+
18415 #endif
+
18416 /*//////////////////////////////////////////////////////////////////////////////
+
18418 
+
18419  End of -include/epiworld//models/sisd.hpp-
+
18420 
+
18423 
+
18424 
+
18425 /*//////////////////////////////////////////////////////////////////////////////
+
18427 
+
18428  Start of -include/epiworld//models/seird.hpp-
+
18429 
+
18432 
+
18433 
+
18434 #ifndef EPIWORLD_MODELS_SEIRD_HPP
+
18435 #define EPIWORLD_MODELS_SEIRD_HPP
+
18436 
+
18440 template<typename TSeq = int>
+
18441 class ModelSEIRD : public epiworld::Model<TSeq>
+
18442 {
+
18443 
+
18444 public:
+
18445  static const int SUSCEPTIBLE = 0;
+
18446  static const int EXPOSED = 1;
+
18447  static const int INFECTED = 2;
+
18448  static const int REMOVED = 3;
+
18449  static const int DECEASED = 4;
+
18450 
+
18451  ModelSEIRD() {};
+
18452 
+
18465  ModelSEIRD(
+
18466  ModelSEIRD<TSeq> & model,
+
18467  const std::string & vname,
+
18468  epiworld_double prevalence,
+
18469  epiworld_double transmission_rate,
+
18470  epiworld_double avg_incubation_days,
+
18471  epiworld_double recovery_rate,
+
18472  epiworld_double death_rate
+
18473  );
+
18474 
+
18485  ModelSEIRD(
+
18486  const std::string & vname,
+
18487  epiworld_double prevalence,
+
18488  epiworld_double transmission_rate,
+
18489  epiworld_double avg_incubation_days,
+
18490  epiworld_double recovery_rate,
+
18491  epiworld_double death_rate
+
18492  );
+
18493 
+
18494  epiworld::UpdateFun<TSeq> update_exposed_seir = [](
+
18495  epiworld::Agent<TSeq> * p,
+
18496  epiworld::Model<TSeq> * m
+
18497  ) -> void {
+
18498 
+
18499  // Getting the virus
+
18500  auto v = p->get_virus();
+
18501 
+
18502  // Does the agent become infected?
+
18503  if (m->runif() < 1.0/(v->get_incubation(m)))
+
18504  p->change_state(m, ModelSEIRD<TSeq>::INFECTED);
+
18505 
+
18506  return;
+
18507  };
+
18508 
+
18509 
+
18510  epiworld::UpdateFun<TSeq> update_infected = [](
+
18511  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
18512  ) -> void {
+
18513 
+
18514  // Odd: Die, Even: Recover
+
18515  epiworld_fast_uint n_events = 0u;
+
18516 
+
18517  const auto & v = p->get_virus();
+
18518 
+
18519  // Die
+
18520  m->array_double_tmp[n_events++] =
+
18521  v->get_prob_death(m) * (1.0 - p->get_death_reduction(v, m));
+
18522 
+
18523  // Recover
+
18524  m->array_double_tmp[n_events++] =
+
18525  1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m));
+
18526 
+
18527 
+
18528 #ifdef EPI_DEBUG
+
18529  if (n_events == 0u)
+
18530  {
+
18531  printf_epiworld(
+
18532  "[epi-debug] agent %i has 0 possible events!!\n",
+
18533  static_cast<int>(p->get_id())
+
18534  );
+
18535  throw std::logic_error("Zero events in exposed.");
+
18536  }
+
18537 #else
+
18538  if (n_events == 0u)
+
18539  return;
+
18540 #endif
+
18541 
+
18542 
+
18543  // Running the roulette
+
18544  int which = roulette(n_events, m);
+
18545 
+
18546  if (which < 0)
+
18547  return;
+
18548 
+
18549  // Which roulette happen?
+
18550  if ((which % 2) == 0) // If odd
+
18551  {
+
18552 
+
18553  p->rm_agent_by_virus(m);
+
18554 
+
18555  } else {
+
18556 
+
18557  p->rm_virus(m);
+
18558 
+
18559  }
+
18560 
+
18561  return ;
+
18562 
+
18563 
+
18564 
+
18565  return;
+
18566 
+
18567  };
+
18568 
+
18569  ModelSEIRD<TSeq> & initial_states(
+
18570  std::vector< double > proportions_,
+
18571  std::vector< int > queue_ = {}
+
18572  );
+
18573 
+
18574 };
+
18575 
+
18576 
+
18577 
+
18578 template<typename TSeq>
+
18579 inline ModelSEIRD<TSeq>::ModelSEIRD(
+
18580  ModelSEIRD<TSeq> & model,
+
18581  const std::string & vname,
+
18582  epiworld_double prevalence,
+
18583  epiworld_double transmission_rate,
+
18584  epiworld_double avg_incubation_days,
+
18585  epiworld_double recovery_rate,
+
18586  epiworld_double death_rate
+
18587 )
+
18588 {
+
18589 
+
18590  // Adding statuses
+
18591  model.add_state("Susceptible", epiworld::default_update_susceptible<TSeq>);
+
18592  model.add_state("Exposed", model.update_exposed_seir);
+
18593  model.add_state("Infected", model.update_infected);
+
18594  model.add_state("Removed");
+
18595  model.add_state("Deceased");
+
18596 
+
18597  // Setting up parameters
+
18598  model.add_param(transmission_rate, "Transmission rate");
+
18599  model.add_param(avg_incubation_days, "Incubation days");
+
18600  model.add_param(recovery_rate, "Recovery rate");
+
18601  model.add_param(death_rate, "Death rate");
+
18602 
+
18603  // Preparing the virus -------------------------------------------
+
18604  epiworld::Virus<TSeq> virus(vname, prevalence, true);
+
18605  virus.set_state(ModelSEIRD<TSeq>::EXPOSED, ModelSEIRD<TSeq>::REMOVED, ModelSEIRD<TSeq>::DECEASED);
+
18606 
+
18607  virus.set_prob_infecting(&model("Transmission rate"));
+
18608  virus.set_incubation(&model("Incubation days"));
+
18609  virus.set_prob_death(&model("Death rate"));
+
18610  virus.set_prob_recovery(&model("Recovery rate"));
18611 
-
18612  return;
-
18613 
-
18614 }
-
18615 
-
18616 template<typename TSeq>
-
18617 inline ModelSEIRD<TSeq> & ModelSEIRD<TSeq>::initial_states(
-
18618  std::vector< double > proportions_,
-
18619  std::vector< int > /**/
-
18620 ) {
-
18621 
-
18622  Model<TSeq>::initial_states_fun =
-
18623  create_init_function_seird<TSeq>(proportions_)
-
18624  ;
-
18625 
-
18626  return *this;
-
18627 
-
18628 }
-
18629 
-
18630 
-
18631 #endif
-
18632 /*//////////////////////////////////////////////////////////////////////////////
-
18634 
-
18635  End of -include/epiworld//models/seird.hpp-
-
18636 
-
18639 
-
18640 
-
18641 /*//////////////////////////////////////////////////////////////////////////////
-
18643 
-
18644  Start of -include/epiworld//models/sirdconnected.hpp-
+
18612  // Adding the tool and the virus
+
18613  model.add_virus(virus);
+
18614 
+
18615  model.set_name("Susceptible-Exposed-Infected-Removed-Deceased (SEIRD)");
+
18616 
+
18617  return;
+
18618 
+
18619 }
+
18620 
+
18621 template<typename TSeq>
+
18622 inline ModelSEIRD<TSeq>::ModelSEIRD(
+
18623  const std::string & vname,
+
18624  epiworld_double prevalence,
+
18625  epiworld_double transmission_rate,
+
18626  epiworld_double avg_incubation_days,
+
18627  epiworld_double recovery_rate,
+
18628  epiworld_double death_rate
+
18629 )
+
18630 {
+
18631 
+
18632  ModelSEIRD<TSeq>(
+
18633  *this,
+
18634  vname,
+
18635  prevalence,
+
18636  transmission_rate,
+
18637  avg_incubation_days,
+
18638  recovery_rate,
+
18639  death_rate
+
18640  );
+
18641 
+
18642  return;
+
18643 
+
18644 }
18645 
-
18648 
-
18649 
-
18650 #ifndef EPIWORLD_MODELS_SIRDCONNECTED_HPP
-
18651 #define EPIWORLD_MODELS_SIRDCONNECTED_HPP
-
18652 
-
18653 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
18654 class ModelSIRDCONN : public epiworld::Model<TSeq>
-
18655 {
-
18656 public:
-
18657  static const int SUSCEPTIBLE = 0;
-
18658  static const int INFECTED = 1;
-
18659  static const int RECOVERED = 2;
-
18660  static const int DECEASED = 3;
-
18661 
-
18662  ModelSIRDCONN() {
-
18663 
-
18664  // tracked_agents_infected.reserve(1e4);
-
18665  // tracked_agents_infected_next.reserve(1e4);
+
18646 template<typename TSeq>
+
18647 inline ModelSEIRD<TSeq> & ModelSEIRD<TSeq>::initial_states(
+
18648  std::vector< double > proportions_,
+
18649  std::vector< int > /**/
+
18650 ) {
+
18651 
+
18652  Model<TSeq>::initial_states_fun =
+
18653  create_init_function_seird<TSeq>(proportions_)
+
18654  ;
+
18655 
+
18656  return *this;
+
18657 
+
18658 }
+
18659 
+
18660 
+
18661 #endif
+
18662 /*//////////////////////////////////////////////////////////////////////////////
+
18664 
+
18665  End of -include/epiworld//models/seird.hpp-
18666 
-
18667  };
-
18668 
-
18669  ModelSIRDCONN(
-
18670  ModelSIRDCONN<TSeq> & model,
-
18671  const std::string & vname,
-
18672  epiworld_fast_uint n,
-
18673  epiworld_double prevalence,
-
18674  epiworld_double contact_rate,
-
18675  epiworld_double transmission_rate,
-
18676  epiworld_double recovery_rate,
-
18677  epiworld_double death_rate
-
18678  );
+
18669 
+
18670 
+
18671 /*//////////////////////////////////////////////////////////////////////////////
+
18673 
+
18674  Start of -include/epiworld//models/sirdconnected.hpp-
+
18675 
+
18678 
18679 
-
18680  ModelSIRDCONN(
-
18681  const std::string & vname,
-
18682  epiworld_fast_uint n,
-
18683  epiworld_double prevalence,
-
18684  epiworld_double contact_rate,
-
18685  epiworld_double transmission_rate,
-
18686  epiworld_double recovery_rate,
-
18687  epiworld_double death_rate
-
18688  );
-
18689 
-
18690  // Tracking who is infected and who is not
-
18691  // std::vector< epiworld::Agent<TSeq>* > tracked_agents_infected = {};
-
18692  // std::vector< epiworld::Agent<TSeq>* > tracked_agents_infected_next = {};
-
18693  // std::vector< epiworld_double > tracked_agents_weight = {};
-
18694  // std::vector< epiworld_double > tracked_agents_weight_next = {};
-
18695 
-
18696  // int tracked_ninfected = 0;
-
18697  // int tracked_ninfected_next = 0;
-
18698  // epiworld_double tracked_current_infect_prob = 0.0;
-
18699 
-
18700  ModelSIRDCONN<TSeq> & run(
-
18701  epiworld_fast_uint ndays,
-
18702  int seed = -1
-
18703  );
-
18704 
-
18705  void reset();
-
18706 
-
18707  Model<TSeq> * clone_ptr();
-
18708 
+
18680 #ifndef EPIWORLD_MODELS_SIRDCONNECTED_HPP
+
18681 #define EPIWORLD_MODELS_SIRDCONNECTED_HPP
+
18682 
+
18683 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
18684 class ModelSIRDCONN : public epiworld::Model<TSeq>
+
18685 {
+
18686 public:
+
18687  static const int SUSCEPTIBLE = 0;
+
18688  static const int INFECTED = 1;
+
18689  static const int RECOVERED = 2;
+
18690  static const int DECEASED = 3;
+
18691 
+
18692  ModelSIRDCONN() {
+
18693 
+
18694  // tracked_agents_infected.reserve(1e4);
+
18695  // tracked_agents_infected_next.reserve(1e4);
+
18696 
+
18697  };
+
18698 
+
18699  ModelSIRDCONN(
+
18700  ModelSIRDCONN<TSeq> & model,
+
18701  const std::string & vname,
+
18702  epiworld_fast_uint n,
+
18703  epiworld_double prevalence,
+
18704  epiworld_double contact_rate,
+
18705  epiworld_double transmission_rate,
+
18706  epiworld_double recovery_rate,
+
18707  epiworld_double death_rate
+
18708  );
18709 
-
18710 };
-
18711 
-
18712 template<typename TSeq>
-
18713 inline ModelSIRDCONN<TSeq> & ModelSIRDCONN<TSeq>::run(
-
18714  epiworld_fast_uint ndays,
-
18715  int seed
-
18716 )
-
18717 {
-
18718 
-
18719  Model<TSeq>::run(ndays, seed);
-
18720 
-
18721  return *this;
-
18722 
-
18723 }
-
18724 
-
18725 template<typename TSeq>
-
18726 inline void ModelSIRDCONN<TSeq>::reset()
-
18727 {
-
18728 
-
18729  Model<TSeq>::reset();
-
18730 
-
18731  // Model<TSeq>::set_rand_binom(
-
18732  // Model<TSeq>::size(),
-
18733  // static_cast<double>(
-
18734  // Model<TSeq>::par("Contact rate"))/
-
18735  // static_cast<double>(Model<TSeq>::size())
-
18736  // );
-
18737 
-
18738  return;
+
18710  ModelSIRDCONN(
+
18711  const std::string & vname,
+
18712  epiworld_fast_uint n,
+
18713  epiworld_double prevalence,
+
18714  epiworld_double contact_rate,
+
18715  epiworld_double transmission_rate,
+
18716  epiworld_double recovery_rate,
+
18717  epiworld_double death_rate
+
18718  );
+
18719 
+
18720  // Tracking who is infected and who is not
+
18721  // std::vector< epiworld::Agent<TSeq>* > tracked_agents_infected = {};
+
18722  // std::vector< epiworld::Agent<TSeq>* > tracked_agents_infected_next = {};
+
18723  // std::vector< epiworld_double > tracked_agents_weight = {};
+
18724  // std::vector< epiworld_double > tracked_agents_weight_next = {};
+
18725 
+
18726  // int tracked_ninfected = 0;
+
18727  // int tracked_ninfected_next = 0;
+
18728  // epiworld_double tracked_current_infect_prob = 0.0;
+
18729 
+
18730  ModelSIRDCONN<TSeq> & run(
+
18731  epiworld_fast_uint ndays,
+
18732  int seed = -1
+
18733  );
+
18734 
+
18735  void reset();
+
18736 
+
18737  Model<TSeq> * clone_ptr();
+
18738 
18739 
-
18740 }
+
18740 };
18741 
18742 template<typename TSeq>
-
18743 inline Model<TSeq> * ModelSIRDCONN<TSeq>::clone_ptr()
-
18744 {
-
18745 
-
18746  ModelSIRDCONN<TSeq> * ptr = new ModelSIRDCONN<TSeq>(
-
18747  *dynamic_cast<const ModelSIRDCONN<TSeq>*>(this)
-
18748  );
-
18749 
-
18750  return dynamic_cast< Model<TSeq> *>(ptr);
-
18751 
-
18752 }
-
18753 
-
18765 template<typename TSeq>
-
18766 inline ModelSIRDCONN<TSeq>::ModelSIRDCONN(
-
18767  ModelSIRDCONN<TSeq> & model,
-
18768  const std::string & vname,
-
18769  epiworld_fast_uint n,
-
18770  epiworld_double prevalence,
-
18771  epiworld_double contact_rate,
-
18772  epiworld_double transmission_rate,
-
18773  epiworld_double recovery_rate,
-
18774  epiworld_double death_rate
-
18775  // epiworld_double prob_reinfection
-
18776  )
-
18777 {
-
18778 
+
18743 inline ModelSIRDCONN<TSeq> & ModelSIRDCONN<TSeq>::run(
+
18744  epiworld_fast_uint ndays,
+
18745  int seed
+
18746 )
+
18747 {
+
18748 
+
18749  Model<TSeq>::run(ndays, seed);
+
18750 
+
18751  return *this;
+
18752 
+
18753 }
+
18754 
+
18755 template<typename TSeq>
+
18756 inline void ModelSIRDCONN<TSeq>::reset()
+
18757 {
+
18758 
+
18759  Model<TSeq>::reset();
+
18760 
+
18761  // Model<TSeq>::set_rand_binom(
+
18762  // Model<TSeq>::size(),
+
18763  // static_cast<double>(
+
18764  // Model<TSeq>::par("Contact rate"))/
+
18765  // static_cast<double>(Model<TSeq>::size())
+
18766  // );
+
18767 
+
18768  return;
+
18769 
+
18770 }
+
18771 
+
18772 template<typename TSeq>
+
18773 inline Model<TSeq> * ModelSIRDCONN<TSeq>::clone_ptr()
+
18774 {
+
18775 
+
18776  ModelSIRDCONN<TSeq> * ptr = new ModelSIRDCONN<TSeq>(
+
18777  *dynamic_cast<const ModelSIRDCONN<TSeq>*>(this)
+
18778  );
18779 
-
18780 
-
18781  epiworld::UpdateFun<TSeq> update_susceptible = [](
-
18782  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
18783  ) -> void
-
18784  {
-
18785 
-
18786  // Sampling how many individuals
-
18787  m->set_rand_binom(
-
18788  m->size(),
-
18789  static_cast<double>(
-
18790  m->par("Contact rate"))/
-
18791  static_cast<double>(m->size())
-
18792  );
-
18793 
-
18794  int ndraw = m->rbinom();
-
18795 
-
18796  if (ndraw == 0)
-
18797  return;
-
18798 
-
18799  // Drawing from the set
-
18800  int nviruses_tmp = 0;
-
18801  for (int i = 0; i < ndraw; ++i)
-
18802  {
-
18803  // Now selecting who is transmitting the disease
-
18804  int which = static_cast<int>(
-
18805  std::floor(m->size() * m->runif())
-
18806  );
-
18807 
-
18808  /* There is a bug in which runif() returns 1.0. It is rare, but
-
18809  * we saw it here. See the Notes section in the C++ manual
-
18810  * https://en.cppreference.com/mwiki/index.php?title=cpp/numeric/random/uniform_real_distribution&oldid=133329
-
18811  * And the reported bug in GCC:
-
18812  * https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63176
-
18813  *
-
18814  */
-
18815  if (which == static_cast<int>(m->size()))
-
18816  --which;
-
18817 
-
18818  // Can't sample itself
-
18819  if (which == static_cast<int>(p->get_id()))
-
18820  continue;
-
18821 
-
18822  // If the neighbor is infected, then proceed
-
18823  auto & neighbor = m->get_agents()[which];
-
18824  if (neighbor.get_state() == ModelSIRDCONN<TSeq>::INFECTED)
-
18825  {
-
18826 
-
18827  const auto & v = neighbor.get_virus();
-
18828 
-
18829  #ifdef EPI_DEBUG
-
18830  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
-
18831  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
-
18832  #endif
-
18833 
-
18834  /* And it is a function of susceptibility_reduction as well */
-
18835  m->array_double_tmp[nviruses_tmp] =
-
18836  (1.0 - p->get_susceptibility_reduction(v, m)) *
-
18837  v->get_prob_infecting(m) *
-
18838  (1.0 - neighbor.get_transmission_reduction(v, m))
-
18839  ;
-
18840 
-
18841  m->array_virus_tmp[nviruses_tmp++] = &(*v);
-
18842 
-
18843  }
-
18844  }
-
18845 
-
18846  // No virus to compute
-
18847  if (nviruses_tmp == 0u)
-
18848  return;
-
18849 
-
18850  // Running the roulette
-
18851  int which = roulette(nviruses_tmp, m);
-
18852 
-
18853  if (which < 0)
-
18854  return;
-
18855 
-
18856  p->set_virus(*m->array_virus_tmp[which], m);
-
18857 
-
18858  return;
-
18859 
-
18860  };
-
18861 
-
18862 
-
18863  epiworld::UpdateFun<TSeq> update_infected = [](
-
18864  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
18865  ) -> void {
-
18866 
-
18867  auto state = p->get_state();
-
18868 
-
18869  if (state == ModelSIRDCONN<TSeq>::INFECTED)
-
18870  {
-
18871 
+
18780  return dynamic_cast< Model<TSeq> *>(ptr);
+
18781 
+
18782 }
+
18783 
+
18795 template<typename TSeq>
+
18796 inline ModelSIRDCONN<TSeq>::ModelSIRDCONN(
+
18797  ModelSIRDCONN<TSeq> & model,
+
18798  const std::string & vname,
+
18799  epiworld_fast_uint n,
+
18800  epiworld_double prevalence,
+
18801  epiworld_double contact_rate,
+
18802  epiworld_double transmission_rate,
+
18803  epiworld_double recovery_rate,
+
18804  epiworld_double death_rate
+
18805  // epiworld_double prob_reinfection
+
18806  )
+
18807 {
+
18808 
+
18809 
+
18810 
+
18811  epiworld::UpdateFun<TSeq> update_susceptible = [](
+
18812  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
18813  ) -> void
+
18814  {
+
18815 
+
18816  // Sampling how many individuals
+
18817  m->set_rand_binom(
+
18818  m->size(),
+
18819  static_cast<double>(
+
18820  m->par("Contact rate"))/
+
18821  static_cast<double>(m->size())
+
18822  );
+
18823 
+
18824  int ndraw = m->rbinom();
+
18825 
+
18826  if (ndraw == 0)
+
18827  return;
+
18828 
+
18829  // Drawing from the set
+
18830  int nviruses_tmp = 0;
+
18831  for (int i = 0; i < ndraw; ++i)
+
18832  {
+
18833  // Now selecting who is transmitting the disease
+
18834  int which = static_cast<int>(
+
18835  std::floor(m->size() * m->runif())
+
18836  );
+
18837 
+
18838  /* There is a bug in which runif() returns 1.0. It is rare, but
+
18839  * we saw it here. See the Notes section in the C++ manual
+
18840  * https://en.cppreference.com/mwiki/index.php?title=cpp/numeric/random/uniform_real_distribution&oldid=133329
+
18841  * And the reported bug in GCC:
+
18842  * https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63176
+
18843  *
+
18844  */
+
18845  if (which == static_cast<int>(m->size()))
+
18846  --which;
+
18847 
+
18848  // Can't sample itself
+
18849  if (which == static_cast<int>(p->get_id()))
+
18850  continue;
+
18851 
+
18852  // If the neighbor is infected, then proceed
+
18853  auto & neighbor = m->get_agents()[which];
+
18854  if (neighbor.get_state() == ModelSIRDCONN<TSeq>::INFECTED)
+
18855  {
+
18856 
+
18857  const auto & v = neighbor.get_virus();
+
18858 
+
18859  #ifdef EPI_DEBUG
+
18860  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
+
18861  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
+
18862  #endif
+
18863 
+
18864  /* And it is a function of susceptibility_reduction as well */
+
18865  m->array_double_tmp[nviruses_tmp] =
+
18866  (1.0 - p->get_susceptibility_reduction(v, m)) *
+
18867  v->get_prob_infecting(m) *
+
18868  (1.0 - neighbor.get_transmission_reduction(v, m))
+
18869  ;
+
18870 
+
18871  m->array_virus_tmp[nviruses_tmp++] = &(*v);
18872 
-
18873  // Odd: Die, Even: Recover
-
18874  epiworld_fast_uint n_events = 0u;
-
18875  const auto & v = p->get_virus();
-
18876 
-
18877  // Die
-
18878  m->array_double_tmp[n_events++] =
-
18879  v->get_prob_death(m) * (1.0 - p->get_death_reduction(v, m));
-
18880 
-
18881  // Recover
-
18882  m->array_double_tmp[n_events++] =
-
18883  1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m));
-
18884 
-
18885  #ifdef EPI_DEBUG
-
18886  if (n_events == 0u)
-
18887  {
-
18888  printf_epiworld(
-
18889  "[epi-debug] agent %i has 0 possible events!!\n",
-
18890  static_cast<int>(p->get_id())
-
18891  );
-
18892  throw std::logic_error("Zero events in exposed.");
-
18893  }
-
18894  #else
-
18895  if (n_events == 0u)
-
18896  return;
-
18897  #endif
-
18898 
-
18899 
-
18900  // Running the roulette
-
18901  int which = roulette(n_events, m);
-
18902 
-
18903  if (which < 0)
-
18904  return;
-
18905 
-
18906  // Which roulette happen?
-
18907  if ((which % 2) == 0) // If odd
-
18908  {
-
18909 
-
18910  p->rm_agent_by_virus(m);
-
18911 
-
18912  } else {
-
18913 
-
18914  p->rm_virus(m);
-
18915 
-
18916  }
-
18917 
-
18918  return ;
-
18919 
-
18920  } else
-
18921  throw std::logic_error("This function can only be applied to infected individuals. (SIR)") ;
-
18922 
-
18923  return;
-
18924 
-
18925  };
-
18926 
-
18927  // state
-
18928  model.add_state("Susceptible", update_susceptible);
-
18929  model.add_state("Infected", update_infected);
-
18930  model.add_state("Recovered");
-
18931  model.add_state("Deceased");
-
18932 
-
18933 
-
18934  // Setting up parameters
-
18935  model.add_param(contact_rate, "Contact rate");
-
18936  model.add_param(transmission_rate, "Transmission rate");
-
18937  model.add_param(recovery_rate, "Recovery rate");
-
18938  model.add_param(death_rate, "Death rate");
-
18939  // model.add_param(prob_reinfection, "Prob. Reinfection");
-
18940 
-
18941  // Preparing the virus -------------------------------------------
-
18942  epiworld::Virus<TSeq> virus(vname, prevalence, true);
-
18943  virus.set_state(1, 2, 3);
-
18944  virus.set_prob_infecting(&model("Transmission rate"));
-
18945  virus.set_prob_recovery(&model("Recovery rate"));
-
18946  virus.set_prob_death(&model("Death rate"));
-
18947 
-
18948  model.add_virus(virus);
+
18873  }
+
18874  }
+
18875 
+
18876  // No virus to compute
+
18877  if (nviruses_tmp == 0u)
+
18878  return;
+
18879 
+
18880  // Running the roulette
+
18881  int which = roulette(nviruses_tmp, m);
+
18882 
+
18883  if (which < 0)
+
18884  return;
+
18885 
+
18886  p->set_virus(*m->array_virus_tmp[which], m);
+
18887 
+
18888  return;
+
18889 
+
18890  };
+
18891 
+
18892 
+
18893  epiworld::UpdateFun<TSeq> update_infected = [](
+
18894  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
18895  ) -> void {
+
18896 
+
18897  auto state = p->get_state();
+
18898 
+
18899  if (state == ModelSIRDCONN<TSeq>::INFECTED)
+
18900  {
+
18901 
+
18902 
+
18903  // Odd: Die, Even: Recover
+
18904  epiworld_fast_uint n_events = 0u;
+
18905  const auto & v = p->get_virus();
+
18906 
+
18907  // Die
+
18908  m->array_double_tmp[n_events++] =
+
18909  v->get_prob_death(m) * (1.0 - p->get_death_reduction(v, m));
+
18910 
+
18911  // Recover
+
18912  m->array_double_tmp[n_events++] =
+
18913  1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m));
+
18914 
+
18915  #ifdef EPI_DEBUG
+
18916  if (n_events == 0u)
+
18917  {
+
18918  printf_epiworld(
+
18919  "[epi-debug] agent %i has 0 possible events!!\n",
+
18920  static_cast<int>(p->get_id())
+
18921  );
+
18922  throw std::logic_error("Zero events in exposed.");
+
18923  }
+
18924  #else
+
18925  if (n_events == 0u)
+
18926  return;
+
18927  #endif
+
18928 
+
18929 
+
18930  // Running the roulette
+
18931  int which = roulette(n_events, m);
+
18932 
+
18933  if (which < 0)
+
18934  return;
+
18935 
+
18936  // Which roulette happen?
+
18937  if ((which % 2) == 0) // If odd
+
18938  {
+
18939 
+
18940  p->rm_agent_by_virus(m);
+
18941 
+
18942  } else {
+
18943 
+
18944  p->rm_virus(m);
+
18945 
+
18946  }
+
18947 
+
18948  return ;
18949 
-
18950  model.queuing_off(); // No queuing need
-
18951 
-
18952  model.agents_empty_graph(n);
-
18953 
-
18954  model.set_name("Susceptible-Infected-Removed-Deceased (SIRD) (connected)");
-
18955 
-
18956  return;
-
18957 
-
18958 }
-
18959 
-
18960 template<typename TSeq>
-
18961 inline ModelSIRDCONN<TSeq>::ModelSIRDCONN(
-
18962  const std::string & vname,
-
18963  epiworld_fast_uint n,
-
18964  epiworld_double prevalence,
-
18965  epiworld_double contact_rate,
-
18966  epiworld_double transmission_rate,
-
18967  epiworld_double recovery_rate,
-
18968  epiworld_double death_rate
-
18969  )
-
18970 {
-
18971 
-
18972  ModelSIRDCONN(
-
18973  *this,
-
18974  vname,
-
18975  n,
-
18976  prevalence,
-
18977  contact_rate,
-
18978  transmission_rate,
-
18979  recovery_rate,
-
18980  death_rate
-
18981  );
-
18982 
-
18983  return;
-
18984 
-
18985 }
-
18986 
+
18950  } else
+
18951  throw std::logic_error("This function can only be applied to infected individuals. (SIR)") ;
+
18952 
+
18953  return;
+
18954 
+
18955  };
+
18956 
+
18957  // state
+
18958  model.add_state("Susceptible", update_susceptible);
+
18959  model.add_state("Infected", update_infected);
+
18960  model.add_state("Recovered");
+
18961  model.add_state("Deceased");
+
18962 
+
18963 
+
18964  // Setting up parameters
+
18965  model.add_param(contact_rate, "Contact rate");
+
18966  model.add_param(transmission_rate, "Transmission rate");
+
18967  model.add_param(recovery_rate, "Recovery rate");
+
18968  model.add_param(death_rate, "Death rate");
+
18969  // model.add_param(prob_reinfection, "Prob. Reinfection");
+
18970 
+
18971  // Preparing the virus -------------------------------------------
+
18972  epiworld::Virus<TSeq> virus(vname, prevalence, true);
+
18973  virus.set_state(1, 2, 3);
+
18974  virus.set_prob_infecting(&model("Transmission rate"));
+
18975  virus.set_prob_recovery(&model("Recovery rate"));
+
18976  virus.set_prob_death(&model("Death rate"));
+
18977 
+
18978  model.add_virus(virus);
+
18979 
+
18980  model.queuing_off(); // No queuing need
+
18981 
+
18982  model.agents_empty_graph(n);
+
18983 
+
18984  model.set_name("Susceptible-Infected-Removed-Deceased (SIRD) (connected)");
+
18985 
+
18986  return;
18987 
-
18988 #endif
-
18989 /*//////////////////////////////////////////////////////////////////////////////
-
18991 
-
18992  End of -include/epiworld//models/sirdconnected.hpp-
-
18993 
-
18996 
-
18997 
-
18998 /*//////////////////////////////////////////////////////////////////////////////
-
19000 
-
19001  Start of -include/epiworld//models/seirdconnected.hpp-
-
19002 
-
19005 
-
19006 
-
19007 #ifndef EPIWORLD_MODELS_SEIRDCONNECTED_HPP
-
19008 #define EPIWORLD_MODELS_SEIRDCONNECTED_HPP
-
19009 
-
19010 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
19011 class ModelSEIRDCONN : public epiworld::Model<TSeq>
-
19012 {
-
19013 private:
-
19014  std::vector< epiworld::Agent<TSeq> * > infected;
-
19015  void update_infected();
-
19016 
-
19017 public:
-
19018 
-
19019  static const int SUSCEPTIBLE = 0;
-
19020  static const int EXPOSED = 1;
-
19021  static const int INFECTED = 2;
-
19022  static const int REMOVED = 3;
-
19023  static const int DECEASED = 4;
-
19024 
-
19025  ModelSEIRDCONN() {};
+
18988 }
+
18989 
+
18990 template<typename TSeq>
+
18991 inline ModelSIRDCONN<TSeq>::ModelSIRDCONN(
+
18992  const std::string & vname,
+
18993  epiworld_fast_uint n,
+
18994  epiworld_double prevalence,
+
18995  epiworld_double contact_rate,
+
18996  epiworld_double transmission_rate,
+
18997  epiworld_double recovery_rate,
+
18998  epiworld_double death_rate
+
18999  )
+
19000 {
+
19001 
+
19002  ModelSIRDCONN(
+
19003  *this,
+
19004  vname,
+
19005  n,
+
19006  prevalence,
+
19007  contact_rate,
+
19008  transmission_rate,
+
19009  recovery_rate,
+
19010  death_rate
+
19011  );
+
19012 
+
19013  return;
+
19014 
+
19015 }
+
19016 
+
19017 
+
19018 #endif
+
19019 /*//////////////////////////////////////////////////////////////////////////////
+
19021 
+
19022  End of -include/epiworld//models/sirdconnected.hpp-
+
19023 
19026 
-
19027  ModelSEIRDCONN(
-
19028  ModelSEIRDCONN<TSeq> & model,
-
19029  const std::string & vname,
-
19030  epiworld_fast_uint n,
-
19031  epiworld_double prevalence,
-
19032  epiworld_double contact_rate,
-
19033  epiworld_double transmission_rate,
-
19034  epiworld_double avg_incubation_days,
-
19035  epiworld_double recovery_rate,
-
19036  epiworld_double death_rate
-
19037  );
-
19038 
-
19039  ModelSEIRDCONN(
-
19040  const std::string & vname,
-
19041  epiworld_fast_uint n,
-
19042  epiworld_double prevalence,
-
19043  epiworld_double contact_rate,
-
19044  epiworld_double transmission_rate,
-
19045  epiworld_double avg_incubation_days,
-
19046  epiworld_double recovery_rate,
-
19047  epiworld_double death_rate
-
19048  );
-
19049 
-
19050  ModelSEIRDCONN<TSeq> & run(
-
19051  epiworld_fast_uint ndays,
-
19052  int seed = -1
-
19053  );
+
19027 
+
19028 /*//////////////////////////////////////////////////////////////////////////////
+
19030 
+
19031  Start of -include/epiworld//models/seirdconnected.hpp-
+
19032 
+
19035 
+
19036 
+
19037 #ifndef EPIWORLD_MODELS_SEIRDCONNECTED_HPP
+
19038 #define EPIWORLD_MODELS_SEIRDCONNECTED_HPP
+
19039 
+
19040 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
19041 class ModelSEIRDCONN : public epiworld::Model<TSeq>
+
19042 {
+
19043 private:
+
19044  std::vector< epiworld::Agent<TSeq> * > infected;
+
19045  void update_infected();
+
19046 
+
19047 public:
+
19048 
+
19049  static const int SUSCEPTIBLE = 0;
+
19050  static const int EXPOSED = 1;
+
19051  static const int INFECTED = 2;
+
19052  static const int REMOVED = 3;
+
19053  static const int DECEASED = 4;
19054 
-
19055  void reset();
+
19055  ModelSEIRDCONN() {};
19056 
-
19057  Model<TSeq> * clone_ptr();
-
19058 
-
19065  ModelSEIRDCONN<TSeq> & initial_states(
-
19066  std::vector< double > proportions_,
-
19067  std::vector< int > queue_ = {}
-
19068  );
-
19069 
-
19070  size_t get_n_infected() const
-
19071  {
-
19072  return infected.size();
-
19073  }
-
19074 
-
19075 };
-
19076 
-
19077 template<typename TSeq>
-
19078 inline void ModelSEIRDCONN<TSeq>::update_infected()
-
19079 {
-
19080  infected.clear();
-
19081  infected.reserve(this->size());
-
19082 
-
19083  for (auto & p : this->get_agents())
-
19084  {
-
19085  if (p.get_state() == ModelSEIRDCONN<TSeq>::INFECTED)
-
19086  {
-
19087  infected.push_back(&p);
-
19088  }
-
19089  }
-
19090 
-
19091  Model<TSeq>::set_rand_binom(
-
19092  this->get_n_infected(),
-
19093  static_cast<double>(Model<TSeq>::par("Contact rate"))/
-
19094  static_cast<double>(Model<TSeq>::size())
-
19095  );
-
19096 
-
19097  return;
-
19098 }
+
19057  ModelSEIRDCONN(
+
19058  ModelSEIRDCONN<TSeq> & model,
+
19059  const std::string & vname,
+
19060  epiworld_fast_uint n,
+
19061  epiworld_double prevalence,
+
19062  epiworld_double contact_rate,
+
19063  epiworld_double transmission_rate,
+
19064  epiworld_double avg_incubation_days,
+
19065  epiworld_double recovery_rate,
+
19066  epiworld_double death_rate
+
19067  );
+
19068 
+
19069  ModelSEIRDCONN(
+
19070  const std::string & vname,
+
19071  epiworld_fast_uint n,
+
19072  epiworld_double prevalence,
+
19073  epiworld_double contact_rate,
+
19074  epiworld_double transmission_rate,
+
19075  epiworld_double avg_incubation_days,
+
19076  epiworld_double recovery_rate,
+
19077  epiworld_double death_rate
+
19078  );
+
19079 
+
19080  ModelSEIRDCONN<TSeq> & run(
+
19081  epiworld_fast_uint ndays,
+
19082  int seed = -1
+
19083  );
+
19084 
+
19085  void reset();
+
19086 
+
19087  Model<TSeq> * clone_ptr();
+
19088 
+
19095  ModelSEIRDCONN<TSeq> & initial_states(
+
19096  std::vector< double > proportions_,
+
19097  std::vector< int > queue_ = {}
+
19098  );
19099 
-
19100 template<typename TSeq>
-
19101 inline ModelSEIRDCONN<TSeq> & ModelSEIRDCONN<TSeq>::run(
-
19102  epiworld_fast_uint ndays,
-
19103  int seed
-
19104 )
-
19105 {
-
19106 
-
19107  Model<TSeq>::run(ndays, seed);
-
19108 
-
19109  return *this;
-
19110 
-
19111 }
+
19100  size_t get_n_infected() const
+
19101  {
+
19102  return infected.size();
+
19103  }
+
19104 
+
19105 };
+
19106 
+
19107 template<typename TSeq>
+
19108 inline void ModelSEIRDCONN<TSeq>::update_infected()
+
19109 {
+
19110  infected.clear();
+
19111  infected.reserve(this->size());
19112 
-
19113 template<typename TSeq>
-
19114 inline void ModelSEIRDCONN<TSeq>::reset()
-
19115 {
-
19116 
-
19117  Model<TSeq>::reset();
-
19118 
-
19119  this->update_infected();
+
19113  for (auto & p : this->get_agents())
+
19114  {
+
19115  if (p.get_state() == ModelSEIRDCONN<TSeq>::INFECTED)
+
19116  {
+
19117  infected.push_back(&p);
+
19118  }
+
19119  }
19120 
-
19121  return;
-
19122 
-
19123 }
-
19124 
-
19125 template<typename TSeq>
-
19126 inline Model<TSeq> * ModelSEIRDCONN<TSeq>::clone_ptr()
-
19127 {
-
19128 
-
19129  ModelSEIRDCONN<TSeq> * ptr = new ModelSEIRDCONN<TSeq>(
-
19130  *dynamic_cast<const ModelSEIRDCONN<TSeq>*>(this)
-
19131  );
-
19132 
-
19133  return dynamic_cast< Model<TSeq> *>(ptr);
-
19134 
-
19135 }
-
19136 
-
19148 template<typename TSeq>
-
19149 inline ModelSEIRDCONN<TSeq>::ModelSEIRDCONN(
-
19150  ModelSEIRDCONN<TSeq> & model,
-
19151  const std::string & vname,
-
19152  epiworld_fast_uint n,
-
19153  epiworld_double prevalence,
-
19154  epiworld_double contact_rate,
-
19155  epiworld_double transmission_rate,
-
19156  epiworld_double avg_incubation_days,
-
19157  epiworld_double recovery_rate,
-
19158  epiworld_double death_rate
-
19159  // epiworld_double prob_reinfection
-
19160  )
-
19161 {
+
19121  Model<TSeq>::set_rand_binom(
+
19122  this->get_n_infected(),
+
19123  static_cast<double>(Model<TSeq>::par("Contact rate"))/
+
19124  static_cast<double>(Model<TSeq>::size())
+
19125  );
+
19126 
+
19127  return;
+
19128 }
+
19129 
+
19130 template<typename TSeq>
+
19131 inline ModelSEIRDCONN<TSeq> & ModelSEIRDCONN<TSeq>::run(
+
19132  epiworld_fast_uint ndays,
+
19133  int seed
+
19134 )
+
19135 {
+
19136 
+
19137  Model<TSeq>::run(ndays, seed);
+
19138 
+
19139  return *this;
+
19140 
+
19141 }
+
19142 
+
19143 template<typename TSeq>
+
19144 inline void ModelSEIRDCONN<TSeq>::reset()
+
19145 {
+
19146 
+
19147  Model<TSeq>::reset();
+
19148 
+
19149  this->update_infected();
+
19150 
+
19151  return;
+
19152 
+
19153 }
+
19154 
+
19155 template<typename TSeq>
+
19156 inline Model<TSeq> * ModelSEIRDCONN<TSeq>::clone_ptr()
+
19157 {
+
19158 
+
19159  ModelSEIRDCONN<TSeq> * ptr = new ModelSEIRDCONN<TSeq>(
+
19160  *dynamic_cast<const ModelSEIRDCONN<TSeq>*>(this)
+
19161  );
19162 
-
19163  epiworld::UpdateFun<TSeq> update_susceptible = [](
-
19164  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
19165  ) -> void
-
19166  {
-
19167 
-
19168  // Sampling how many individuals
-
19169  int ndraw = m->rbinom();
-
19170 
-
19171  if (ndraw == 0)
-
19172  return;
-
19173 
-
19174  ModelSEIRDCONN<TSeq> * model = dynamic_cast<ModelSEIRDCONN<TSeq> *>(
-
19175  m
-
19176  );
-
19177 
-
19178  size_t ninfected = model->get_n_infected();
-
19179 
-
19180  // Drawing from the set
-
19181  int nviruses_tmp = 0;
-
19182  for (int i = 0; i < ndraw; ++i)
-
19183  {
-
19184  // Now selecting who is transmitting the disease
-
19185  int which = static_cast<int>(
-
19186  std::floor(ninfected * m->runif())
-
19187  );
-
19188 
-
19189  /* There is a bug in which runif() returns 1.0. It is rare, but
-
19190  * we saw it here. See the Notes section in the C++ manual
-
19191  * https://en.cppreference.com/mwiki/index.php?title=cpp/numeric/random/uniform_real_distribution&oldid=133329
-
19192  * And the reported bug in GCC:
-
19193  * https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63176
-
19194  *
-
19195  */
-
19196  if (which == static_cast<int>(ninfected))
-
19197  --which;
-
19198 
-
19199  epiworld::Agent<TSeq> & neighbor = *model->infected[which];
-
19200 
-
19201  // Can't sample itself
-
19202  if (neighbor.get_id() == p->get_id())
-
19203  continue;
-
19204 
-
19205  // All neighbors in this set are infected by construction
-
19206  const auto & v = neighbor.get_virus();
-
19207 
-
19208  #ifdef EPI_DEBUG
-
19209  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
-
19210  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
-
19211  #endif
-
19212 
-
19213  /* And it is a function of susceptibility_reduction as well */
-
19214  m->array_double_tmp[nviruses_tmp] =
-
19215  (1.0 - p->get_susceptibility_reduction(v, m)) *
-
19216  v->get_prob_infecting(m) *
-
19217  (1.0 - neighbor.get_transmission_reduction(v, m))
-
19218  ;
-
19219 
-
19220  m->array_virus_tmp[nviruses_tmp++] = &(*v);
-
19221  }
-
19222 
-
19223  // No virus to compute
-
19224  if (nviruses_tmp == 0u)
-
19225  return;
-
19226 
-
19227  // Running the roulette
-
19228  int which = roulette(nviruses_tmp, m);
-
19229 
-
19230  if (which < 0)
-
19231  return;
-
19232 
-
19233  p->set_virus(
-
19234  *m->array_virus_tmp[which],
-
19235  m,
-
19236  ModelSEIRDCONN<TSeq>::EXPOSED
-
19237  );
-
19238 
-
19239  return;
-
19240 
-
19241  };
-
19242 
-
19243  epiworld::UpdateFun<TSeq> update_infected = [](
-
19244  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
19245  ) -> void {
-
19246 
-
19247  auto state = p->get_state();
-
19248 
-
19249  if (state == ModelSEIRDCONN<TSeq>::EXPOSED)
-
19250  {
-
19251 
-
19252  // Getting the virus
-
19253  auto & v = p->get_virus();
-
19254 
-
19255  // Does the agent become infected?
-
19256  if (m->runif() < 1.0/(v->get_incubation(m)))
-
19257  {
-
19258 
-
19259  p->change_state(m, ModelSEIRDCONN<TSeq>::INFECTED);
-
19260  return;
-
19261 
-
19262  }
-
19263 
-
19264 
-
19265  } else if (state == ModelSEIRDCONN<TSeq>::INFECTED)
-
19266  {
-
19267 
-
19268  // Odd: Die, Even: Recover
-
19269  epiworld_fast_uint n_events = 0u;
-
19270  const auto & v = p->get_virus();
-
19271 
-
19272  // Die
-
19273  m->array_double_tmp[n_events++] =
-
19274  v->get_prob_death(m) * (1.0 - p->get_death_reduction(v, m));
-
19275 
-
19276  // Recover
-
19277  m->array_double_tmp[n_events++] =
-
19278  1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m));
-
19279 
-
19280  #ifdef EPI_DEBUG
-
19281  if (n_events == 0u)
-
19282  {
-
19283  printf_epiworld(
-
19284  "[epi-debug] agent %i has 0 possible events!!\n",
-
19285  static_cast<int>(p->get_id())
-
19286  );
-
19287  throw std::logic_error("Zero events in exposed.");
-
19288  }
-
19289  #else
-
19290  if (n_events == 0u)
-
19291  return;
-
19292  #endif
-
19293 
-
19294 
-
19295  // Running the roulette
-
19296  int which = roulette(n_events, m);
-
19297 
-
19298  if (which < 0)
-
19299  return;
-
19300 
-
19301  // Which roulette happen?
-
19302  if ((which % 2) == 0) // If odd
-
19303  {
-
19304 
-
19305  p->rm_agent_by_virus(m);
-
19306 
-
19307  } else {
-
19308 
-
19309  p->rm_virus(m);
-
19310 
-
19311  }
-
19312 
-
19313  return ;
-
19314 
-
19315  } else
-
19316  throw std::logic_error("This function can only be applied to exposed or infected individuals. (SEIRD)") ;
-
19317 
-
19318  return;
-
19319 
-
19320  };
-
19321 
-
19322  // Setting up parameters
-
19323  model.add_param(contact_rate, "Contact rate");
-
19324  model.add_param(transmission_rate, "Prob. Transmission");
-
19325  model.add_param(recovery_rate, "Prob. Recovery");
-
19326  model.add_param(avg_incubation_days, "Avg. Incubation days");
-
19327  model.add_param(death_rate, "Death rate");
-
19328 
-
19329  // state
-
19330  model.add_state("Susceptible", update_susceptible);
-
19331  model.add_state("Exposed", update_infected);
-
19332  model.add_state("Infected", update_infected);
-
19333  model.add_state("Removed");
-
19334  model.add_state("Deceased");
-
19335 
-
19336 
-
19337  // Adding update function
-
19338  epiworld::GlobalFun<TSeq> update = [](epiworld::Model<TSeq> * m) -> void
-
19339  {
-
19340  ModelSEIRDCONN<TSeq> * model = dynamic_cast<ModelSEIRDCONN<TSeq> *>(m);
-
19341  model->update_infected();
-
19342 
-
19343  return;
-
19344  };
-
19345 
-
19346  model.add_globalevent(update, "Update infected individuals");
+
19163  return dynamic_cast< Model<TSeq> *>(ptr);
+
19164 
+
19165 }
+
19166 
+
19178 template<typename TSeq>
+
19179 inline ModelSEIRDCONN<TSeq>::ModelSEIRDCONN(
+
19180  ModelSEIRDCONN<TSeq> & model,
+
19181  const std::string & vname,
+
19182  epiworld_fast_uint n,
+
19183  epiworld_double prevalence,
+
19184  epiworld_double contact_rate,
+
19185  epiworld_double transmission_rate,
+
19186  epiworld_double avg_incubation_days,
+
19187  epiworld_double recovery_rate,
+
19188  epiworld_double death_rate
+
19189  // epiworld_double prob_reinfection
+
19190  )
+
19191 {
+
19192 
+
19193  epiworld::UpdateFun<TSeq> update_susceptible = [](
+
19194  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
19195  ) -> void
+
19196  {
+
19197 
+
19198  // Sampling how many individuals
+
19199  int ndraw = m->rbinom();
+
19200 
+
19201  if (ndraw == 0)
+
19202  return;
+
19203 
+
19204  ModelSEIRDCONN<TSeq> * model = dynamic_cast<ModelSEIRDCONN<TSeq> *>(
+
19205  m
+
19206  );
+
19207 
+
19208  size_t ninfected = model->get_n_infected();
+
19209 
+
19210  // Drawing from the set
+
19211  int nviruses_tmp = 0;
+
19212  for (int i = 0; i < ndraw; ++i)
+
19213  {
+
19214  // Now selecting who is transmitting the disease
+
19215  int which = static_cast<int>(
+
19216  std::floor(ninfected * m->runif())
+
19217  );
+
19218 
+
19219  /* There is a bug in which runif() returns 1.0. It is rare, but
+
19220  * we saw it here. See the Notes section in the C++ manual
+
19221  * https://en.cppreference.com/mwiki/index.php?title=cpp/numeric/random/uniform_real_distribution&oldid=133329
+
19222  * And the reported bug in GCC:
+
19223  * https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63176
+
19224  *
+
19225  */
+
19226  if (which == static_cast<int>(ninfected))
+
19227  --which;
+
19228 
+
19229  epiworld::Agent<TSeq> & neighbor = *model->infected[which];
+
19230 
+
19231  // Can't sample itself
+
19232  if (neighbor.get_id() == p->get_id())
+
19233  continue;
+
19234 
+
19235  // All neighbors in this set are infected by construction
+
19236  const auto & v = neighbor.get_virus();
+
19237 
+
19238  #ifdef EPI_DEBUG
+
19239  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
+
19240  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
+
19241  #endif
+
19242 
+
19243  /* And it is a function of susceptibility_reduction as well */
+
19244  m->array_double_tmp[nviruses_tmp] =
+
19245  (1.0 - p->get_susceptibility_reduction(v, m)) *
+
19246  v->get_prob_infecting(m) *
+
19247  (1.0 - neighbor.get_transmission_reduction(v, m))
+
19248  ;
+
19249 
+
19250  m->array_virus_tmp[nviruses_tmp++] = &(*v);
+
19251  }
+
19252 
+
19253  // No virus to compute
+
19254  if (nviruses_tmp == 0u)
+
19255  return;
+
19256 
+
19257  // Running the roulette
+
19258  int which = roulette(nviruses_tmp, m);
+
19259 
+
19260  if (which < 0)
+
19261  return;
+
19262 
+
19263  p->set_virus(
+
19264  *m->array_virus_tmp[which],
+
19265  m,
+
19266  ModelSEIRDCONN<TSeq>::EXPOSED
+
19267  );
+
19268 
+
19269  return;
+
19270 
+
19271  };
+
19272 
+
19273  epiworld::UpdateFun<TSeq> update_infected = [](
+
19274  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
19275  ) -> void {
+
19276 
+
19277  auto state = p->get_state();
+
19278 
+
19279  if (state == ModelSEIRDCONN<TSeq>::EXPOSED)
+
19280  {
+
19281 
+
19282  // Getting the virus
+
19283  auto & v = p->get_virus();
+
19284 
+
19285  // Does the agent become infected?
+
19286  if (m->runif() < 1.0/(v->get_incubation(m)))
+
19287  {
+
19288 
+
19289  p->change_state(m, ModelSEIRDCONN<TSeq>::INFECTED);
+
19290  return;
+
19291 
+
19292  }
+
19293 
+
19294 
+
19295  } else if (state == ModelSEIRDCONN<TSeq>::INFECTED)
+
19296  {
+
19297 
+
19298  // Odd: Die, Even: Recover
+
19299  epiworld_fast_uint n_events = 0u;
+
19300  const auto & v = p->get_virus();
+
19301 
+
19302  // Die
+
19303  m->array_double_tmp[n_events++] =
+
19304  v->get_prob_death(m) * (1.0 - p->get_death_reduction(v, m));
+
19305 
+
19306  // Recover
+
19307  m->array_double_tmp[n_events++] =
+
19308  1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m));
+
19309 
+
19310  #ifdef EPI_DEBUG
+
19311  if (n_events == 0u)
+
19312  {
+
19313  printf_epiworld(
+
19314  "[epi-debug] agent %i has 0 possible events!!\n",
+
19315  static_cast<int>(p->get_id())
+
19316  );
+
19317  throw std::logic_error("Zero events in exposed.");
+
19318  }
+
19319  #else
+
19320  if (n_events == 0u)
+
19321  return;
+
19322  #endif
+
19323 
+
19324 
+
19325  // Running the roulette
+
19326  int which = roulette(n_events, m);
+
19327 
+
19328  if (which < 0)
+
19329  return;
+
19330 
+
19331  // Which roulette happen?
+
19332  if ((which % 2) == 0) // If odd
+
19333  {
+
19334 
+
19335  p->rm_agent_by_virus(m);
+
19336 
+
19337  } else {
+
19338 
+
19339  p->rm_virus(m);
+
19340 
+
19341  }
+
19342 
+
19343  return ;
+
19344 
+
19345  } else
+
19346  throw std::logic_error("This function can only be applied to exposed or infected individuals. (SEIRD)") ;
19347 
-
19348 
-
19349  // Preparing the virus -------------------------------------------
-
19350  epiworld::Virus<TSeq> virus(vname, prevalence, true);
-
19351  virus.set_state(
-
19352  ModelSEIRDCONN<TSeq>::EXPOSED,
-
19353  ModelSEIRDCONN<TSeq>::REMOVED,
-
19354  ModelSEIRDCONN<TSeq>::DECEASED
-
19355  );
-
19356 
-
19357  virus.set_prob_infecting(&model("Prob. Transmission"));
-
19358  virus.set_prob_recovery(&model("Prob. Recovery"));
-
19359  virus.set_incubation(&model("Avg. Incubation days"));
-
19360  virus.set_prob_death(&model("Death rate"));
-
19361  model.add_virus(virus);
-
19362 
-
19363  model.queuing_off(); // No queuing need
-
19364 
-
19365  // Adding the empty population
-
19366  model.agents_empty_graph(n);
-
19367 
-
19368  model.set_name("Susceptible-Exposed-Infected-Removed-Deceased (SEIRD) (connected)");
-
19369 
-
19370  return;
-
19371 
-
19372 }
-
19373 
-
19374 template<typename TSeq>
-
19375 inline ModelSEIRDCONN<TSeq>::ModelSEIRDCONN(
-
19376  const std::string & vname,
-
19377  epiworld_fast_uint n,
-
19378  epiworld_double prevalence,
-
19379  epiworld_double contact_rate,
-
19380  epiworld_double transmission_rate,
-
19381  epiworld_double avg_incubation_days,
-
19382  epiworld_double recovery_rate,
-
19383  epiworld_double death_rate
-
19384  )
-
19385 {
+
19348  return;
+
19349 
+
19350  };
+
19351 
+
19352  // Setting up parameters
+
19353  model.add_param(contact_rate, "Contact rate");
+
19354  model.add_param(transmission_rate, "Prob. Transmission");
+
19355  model.add_param(recovery_rate, "Prob. Recovery");
+
19356  model.add_param(avg_incubation_days, "Avg. Incubation days");
+
19357  model.add_param(death_rate, "Death rate");
+
19358 
+
19359  // state
+
19360  model.add_state("Susceptible", update_susceptible);
+
19361  model.add_state("Exposed", update_infected);
+
19362  model.add_state("Infected", update_infected);
+
19363  model.add_state("Removed");
+
19364  model.add_state("Deceased");
+
19365 
+
19366 
+
19367  // Adding update function
+
19368  epiworld::GlobalFun<TSeq> update = [](epiworld::Model<TSeq> * m) -> void
+
19369  {
+
19370  ModelSEIRDCONN<TSeq> * model = dynamic_cast<ModelSEIRDCONN<TSeq> *>(m);
+
19371  model->update_infected();
+
19372 
+
19373  return;
+
19374  };
+
19375 
+
19376  model.add_globalevent(update, "Update infected individuals");
+
19377 
+
19378 
+
19379  // Preparing the virus -------------------------------------------
+
19380  epiworld::Virus<TSeq> virus(vname, prevalence, true);
+
19381  virus.set_state(
+
19382  ModelSEIRDCONN<TSeq>::EXPOSED,
+
19383  ModelSEIRDCONN<TSeq>::REMOVED,
+
19384  ModelSEIRDCONN<TSeq>::DECEASED
+
19385  );
19386 
-
19387  ModelSEIRDCONN(
-
19388  *this,
-
19389  vname,
-
19390  n,
-
19391  prevalence,
-
19392  contact_rate,
-
19393  transmission_rate,
-
19394  avg_incubation_days,
-
19395  recovery_rate,
-
19396  death_rate
-
19397  );
-
19398 
-
19399  return;
-
19400 
-
19401 }
-
19402 
-
19403 template<typename TSeq>
-
19404 inline ModelSEIRDCONN<TSeq> & ModelSEIRDCONN<TSeq>::initial_states(
-
19405  std::vector< double > proportions_,
-
19406  std::vector< int >
-
19407 ) {
-
19408 
-
19409  Model<TSeq>::initial_states_fun =
-
19410  create_init_function_seird<TSeq>(proportions_)
-
19411  ;
-
19412 
-
19413  return *this;
-
19414 
-
19415 }
+
19387  virus.set_prob_infecting(&model("Prob. Transmission"));
+
19388  virus.set_prob_recovery(&model("Prob. Recovery"));
+
19389  virus.set_incubation(&model("Avg. Incubation days"));
+
19390  virus.set_prob_death(&model("Death rate"));
+
19391  model.add_virus(virus);
+
19392 
+
19393  model.queuing_off(); // No queuing need
+
19394 
+
19395  // Adding the empty population
+
19396  model.agents_empty_graph(n);
+
19397 
+
19398  model.set_name("Susceptible-Exposed-Infected-Removed-Deceased (SEIRD) (connected)");
+
19399 
+
19400  return;
+
19401 
+
19402 }
+
19403 
+
19404 template<typename TSeq>
+
19405 inline ModelSEIRDCONN<TSeq>::ModelSEIRDCONN(
+
19406  const std::string & vname,
+
19407  epiworld_fast_uint n,
+
19408  epiworld_double prevalence,
+
19409  epiworld_double contact_rate,
+
19410  epiworld_double transmission_rate,
+
19411  epiworld_double avg_incubation_days,
+
19412  epiworld_double recovery_rate,
+
19413  epiworld_double death_rate
+
19414  )
+
19415 {
19416 
-
19417 #endif
-
19418 /*//////////////////////////////////////////////////////////////////////////////
-
19420 
-
19421  End of -include/epiworld//models/seirdconnected.hpp-
-
19422 
-
19425 
-
19426 
-
19427 /*//////////////////////////////////////////////////////////////////////////////
-
19429 
-
19430  Start of -include/epiworld//models/sirlogit.hpp-
-
19431 
-
19434 
-
19435 
-
19436 // #include "../epiworld.hpp"
-
19437 
-
19438 #ifndef EPIWORLD_MODELS_SIRLOGIT_HPP
-
19439 #define EPIWORLD_MODELS_SIRLOGIT_HPP
-
19440 
-
19441 
-
19469 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
19470 class ModelSIRLogit : public epiworld::Model<TSeq>
-
19471 {
-
19472 private:
-
19473  static const int SUSCEPTIBLE = 0;
-
19474  static const int INFECTED = 1;
-
19475  static const int RECOVERED = 2;
-
19476 
-
19477 public:
-
19478 
-
19479  ModelSIRLogit() {};
-
19480 
-
19490  ModelSIRLogit(
-
19491  ModelSIRLogit<TSeq> & model,
-
19492  const std::string & vname,
-
19493  double * data,
-
19494  size_t ncols,
-
19495  std::vector< double > coefs_infect,
-
19496  std::vector< double > coefs_recover,
-
19497  std::vector< size_t > coef_infect_cols,
-
19498  std::vector< size_t > coef_recover_cols,
-
19499  epiworld_double transmission_rate,
-
19500  epiworld_double recovery_rate,
-
19501  epiworld_double prevalence
-
19502  );
-
19503 
-
19504  ModelSIRLogit(
-
19505  const std::string & vname,
-
19506  double * data,
-
19507  size_t ncols,
-
19508  std::vector< double > coefs_infect,
-
19509  std::vector< double > coefs_recover,
-
19510  std::vector< size_t > coef_infect_cols,
-
19511  std::vector< size_t > coef_recover_cols,
-
19512  epiworld_double transmission_rate,
-
19513  epiworld_double recovery_rate,
-
19514  epiworld_double prevalence
-
19515  );
-
19516 
-
19517  ModelSIRLogit<TSeq> & run(
-
19518  epiworld_fast_uint ndays,
-
19519  int seed = -1
-
19520  );
-
19521 
-
19522  Model<TSeq> * clone_ptr();
-
19523 
-
19524  void reset();
-
19525 
-
19526  std::vector< double > coefs_infect;
-
19527  std::vector< double > coefs_recover;
-
19528  std::vector< size_t > coef_infect_cols;
-
19529  std::vector< size_t > coef_recover_cols;
-
19530 
-
19531 };
-
19532 
+
19417  ModelSEIRDCONN(
+
19418  *this,
+
19419  vname,
+
19420  n,
+
19421  prevalence,
+
19422  contact_rate,
+
19423  transmission_rate,
+
19424  avg_incubation_days,
+
19425  recovery_rate,
+
19426  death_rate
+
19427  );
+
19428 
+
19429  return;
+
19430 
+
19431 }
+
19432 
+
19433 template<typename TSeq>
+
19434 inline ModelSEIRDCONN<TSeq> & ModelSEIRDCONN<TSeq>::initial_states(
+
19435  std::vector< double > proportions_,
+
19436  std::vector< int >
+
19437 ) {
+
19438 
+
19439  Model<TSeq>::initial_states_fun =
+
19440  create_init_function_seird<TSeq>(proportions_)
+
19441  ;
+
19442 
+
19443  return *this;
+
19444 
+
19445 }
+
19446 
+
19447 #endif
+
19448 /*//////////////////////////////////////////////////////////////////////////////
+
19450 
+
19451  End of -include/epiworld//models/seirdconnected.hpp-
+
19452 
+
19455 
+
19456 
+
19457 /*//////////////////////////////////////////////////////////////////////////////
+
19459 
+
19460  Start of -include/epiworld//models/sirlogit.hpp-
+
19461 
+
19464 
+
19465 
+
19466 // #include "../epiworld.hpp"
+
19467 
+
19468 #ifndef EPIWORLD_MODELS_SIRLOGIT_HPP
+
19469 #define EPIWORLD_MODELS_SIRLOGIT_HPP
+
19470 
+
19471 
+
19499 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
19500 class ModelSIRLogit : public epiworld::Model<TSeq>
+
19501 {
+
19502 private:
+
19503  static const int SUSCEPTIBLE = 0;
+
19504  static const int INFECTED = 1;
+
19505  static const int RECOVERED = 2;
+
19506 
+
19507 public:
+
19508 
+
19509  ModelSIRLogit() {};
+
19510 
+
19520  ModelSIRLogit(
+
19521  ModelSIRLogit<TSeq> & model,
+
19522  const std::string & vname,
+
19523  double * data,
+
19524  size_t ncols,
+
19525  std::vector< double > coefs_infect,
+
19526  std::vector< double > coefs_recover,
+
19527  std::vector< size_t > coef_infect_cols,
+
19528  std::vector< size_t > coef_recover_cols,
+
19529  epiworld_double transmission_rate,
+
19530  epiworld_double recovery_rate,
+
19531  epiworld_double prevalence
+
19532  );
19533 
-
19534 
-
19535 template<typename TSeq>
-
19536 inline ModelSIRLogit<TSeq> & ModelSIRLogit<TSeq>::run(
-
19537  epiworld_fast_uint ndays,
-
19538  int seed
-
19539 )
-
19540 {
-
19541 
-
19542  Model<TSeq>::run(ndays, seed);
-
19543  return *this;
-
19544 
-
19545 }
+
19534  ModelSIRLogit(
+
19535  const std::string & vname,
+
19536  double * data,
+
19537  size_t ncols,
+
19538  std::vector< double > coefs_infect,
+
19539  std::vector< double > coefs_recover,
+
19540  std::vector< size_t > coef_infect_cols,
+
19541  std::vector< size_t > coef_recover_cols,
+
19542  epiworld_double transmission_rate,
+
19543  epiworld_double recovery_rate,
+
19544  epiworld_double prevalence
+
19545  );
19546 
-
19547 template<typename TSeq>
-
19548 inline Model<TSeq> * ModelSIRLogit<TSeq>::clone_ptr()
-
19549 {
-
19550 
-
19551  ModelSIRLogit<TSeq> * ptr = new ModelSIRLogit<TSeq>(
-
19552  *dynamic_cast<const ModelSIRLogit<TSeq>*>(this)
-
19553  );
-
19554 
-
19555  return dynamic_cast< Model<TSeq> *>(ptr);
-
19556 
-
19557 }
-
19558 
-
19559 template<typename TSeq>
-
19560 inline void ModelSIRLogit<TSeq>::reset()
-
19561 {
+
19547  ModelSIRLogit<TSeq> & run(
+
19548  epiworld_fast_uint ndays,
+
19549  int seed = -1
+
19550  );
+
19551 
+
19552  Model<TSeq> * clone_ptr();
+
19553 
+
19554  void reset();
+
19555 
+
19556  std::vector< double > coefs_infect;
+
19557  std::vector< double > coefs_recover;
+
19558  std::vector< size_t > coef_infect_cols;
+
19559  std::vector< size_t > coef_recover_cols;
+
19560 
+
19561 };
19562 
-
19563  /* Checking specified columns in the model */
-
19564  for (const auto & c : coef_infect_cols)
-
19565  {
-
19566  if (c >= Model<TSeq>::agents_data_ncols)
-
19567  throw std::range_error("Columns specified in coef_infect_cols out of range.");
-
19568  }
-
19569 
-
19570  for (const auto & c : coef_recover_cols)
-
19571  {
-
19572  if (c >= Model<TSeq>::agents_data_ncols)
-
19573  throw std::range_error("Columns specified in coef_recover_cols out of range.");
-
19574  }
-
19575 
-
19576  /* Checking attributes */
-
19577  if (coefs_infect.size() != (coef_infect_cols.size() + 1u))
-
19578  throw std::logic_error(
-
19579  "The number of coefficients (infection) doesn't match the number of features. It must be as many features of the agents plus 1 (exposure.)"
-
19580  );
-
19581 
-
19582  if (coefs_recover.size() != coef_recover_cols.size())
-
19583  throw std::logic_error(
-
19584  "The number of coefficients (recovery) doesn't match the number of features. It must be as many features of the agents."
-
19585  );
-
19586 
-
19587  Model<TSeq>::reset();
-
19588 
-
19589  return;
-
19590 
-
19591 }
-
19592 
-
19603 template<typename TSeq>
-
19604 inline ModelSIRLogit<TSeq>::ModelSIRLogit(
-
19605  ModelSIRLogit<TSeq> & model,
-
19606  const std::string & vname,
-
19607  double * data,
-
19608  size_t ncols,
-
19609  std::vector< double > coefs_infect,
-
19610  std::vector< double > coefs_recover,
-
19611  std::vector< size_t > coef_infect_cols,
-
19612  std::vector< size_t > coef_recover_cols,
-
19613  epiworld_double transmission_rate,
-
19614  epiworld_double recovery_rate,
-
19615  epiworld_double prevalence
-
19616  )
-
19617 {
+
19563 
+
19564 
+
19565 template<typename TSeq>
+
19566 inline ModelSIRLogit<TSeq> & ModelSIRLogit<TSeq>::run(
+
19567  epiworld_fast_uint ndays,
+
19568  int seed
+
19569 )
+
19570 {
+
19571 
+
19572  Model<TSeq>::run(ndays, seed);
+
19573  return *this;
+
19574 
+
19575 }
+
19576 
+
19577 template<typename TSeq>
+
19578 inline Model<TSeq> * ModelSIRLogit<TSeq>::clone_ptr()
+
19579 {
+
19580 
+
19581  ModelSIRLogit<TSeq> * ptr = new ModelSIRLogit<TSeq>(
+
19582  *dynamic_cast<const ModelSIRLogit<TSeq>*>(this)
+
19583  );
+
19584 
+
19585  return dynamic_cast< Model<TSeq> *>(ptr);
+
19586 
+
19587 }
+
19588 
+
19589 template<typename TSeq>
+
19590 inline void ModelSIRLogit<TSeq>::reset()
+
19591 {
+
19592 
+
19593  /* Checking specified columns in the model */
+
19594  for (const auto & c : coef_infect_cols)
+
19595  {
+
19596  if (c >= Model<TSeq>::agents_data_ncols)
+
19597  throw std::range_error("Columns specified in coef_infect_cols out of range.");
+
19598  }
+
19599 
+
19600  for (const auto & c : coef_recover_cols)
+
19601  {
+
19602  if (c >= Model<TSeq>::agents_data_ncols)
+
19603  throw std::range_error("Columns specified in coef_recover_cols out of range.");
+
19604  }
+
19605 
+
19606  /* Checking attributes */
+
19607  if (coefs_infect.size() != (coef_infect_cols.size() + 1u))
+
19608  throw std::logic_error(
+
19609  "The number of coefficients (infection) doesn't match the number of features. It must be as many features of the agents plus 1 (exposure.)"
+
19610  );
+
19611 
+
19612  if (coefs_recover.size() != coef_recover_cols.size())
+
19613  throw std::logic_error(
+
19614  "The number of coefficients (recovery) doesn't match the number of features. It must be as many features of the agents."
+
19615  );
+
19616 
+
19617  Model<TSeq>::reset();
19618 
-
19619  if (coef_infect_cols.size() == 0u)
-
19620  throw std::logic_error("No columns specified for coef_infect_cols.");
-
19621 
-
19622  if (coef_recover_cols.size() == 0u)
-
19623  throw std::logic_error("No columns specified for coef_recover_cols.");
-
19624 
-
19625  // Saving the variables
-
19626  model.set_agents_data(
-
19627  data, ncols
-
19628  );
-
19629 
-
19630  model.coefs_infect = coefs_infect;
-
19631  model.coefs_recover = coefs_recover;
-
19632  model.coef_infect_cols = coef_infect_cols;
-
19633  model.coef_recover_cols = coef_recover_cols;
-
19634 
-
19635  epiworld::UpdateFun<TSeq> update_susceptible = [](
-
19636  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
19637  ) -> void
-
19638  {
-
19639 
-
19640  // Getting the right type
-
19641  ModelSIRLogit<TSeq> * _m = dynamic_cast<ModelSIRLogit<TSeq>*>(m);
-
19642 
-
19643  // Exposure coefficient
-
19644  const double coef_exposure = _m->coefs_infect[0u];
-
19645 
-
19646  // This computes the prob of getting any neighbor variant
-
19647  size_t nviruses_tmp = 0u;
+
19619  return;
+
19620 
+
19621 }
+
19622 
+
19633 template<typename TSeq>
+
19634 inline ModelSIRLogit<TSeq>::ModelSIRLogit(
+
19635  ModelSIRLogit<TSeq> & model,
+
19636  const std::string & vname,
+
19637  double * data,
+
19638  size_t ncols,
+
19639  std::vector< double > coefs_infect,
+
19640  std::vector< double > coefs_recover,
+
19641  std::vector< size_t > coef_infect_cols,
+
19642  std::vector< size_t > coef_recover_cols,
+
19643  epiworld_double transmission_rate,
+
19644  epiworld_double recovery_rate,
+
19645  epiworld_double prevalence
+
19646  )
+
19647 {
19648 
-
19649  double baseline = 0.0;
-
19650  for (size_t k = 0u; k < _m->coef_infect_cols.size(); ++k)
-
19651  baseline += p->operator[](k) * _m->coefs_infect[k + 1u];
-
19652 
-
19653  for (auto & neighbor: p->get_neighbors())
-
19654  {
-
19655 
-
19656  if (neighbor->get_virus() == nullptr)
-
19657  continue;
-
19658 
-
19659  auto & v = neighbor->get_virus();
-
19660 
-
19661  #ifdef EPI_DEBUG
-
19662  if (nviruses_tmp >= m->array_virus_tmp.size())
-
19663  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
-
19664  #endif
-
19665 
-
19666  /* And it is a function of susceptibility_reduction as well */
-
19667  m->array_double_tmp[nviruses_tmp] =
-
19668  baseline +
-
19669  (1.0 - p->get_susceptibility_reduction(v, m)) *
-
19670  v->get_prob_infecting(m) *
-
19671  (1.0 - neighbor->get_transmission_reduction(v, m)) *
-
19672  coef_exposure
-
19673  ;
-
19674 
-
19675  // Applying the plogis function
-
19676  m->array_double_tmp[nviruses_tmp] = 1.0/
-
19677  (1.0 + std::exp(-m->array_double_tmp[nviruses_tmp]));
-
19678 
-
19679  m->array_virus_tmp[nviruses_tmp++] = &(*v);
-
19680 
-
19681  }
+
19649  if (coef_infect_cols.size() == 0u)
+
19650  throw std::logic_error("No columns specified for coef_infect_cols.");
+
19651 
+
19652  if (coef_recover_cols.size() == 0u)
+
19653  throw std::logic_error("No columns specified for coef_recover_cols.");
+
19654 
+
19655  // Saving the variables
+
19656  model.set_agents_data(
+
19657  data, ncols
+
19658  );
+
19659 
+
19660  model.coefs_infect = coefs_infect;
+
19661  model.coefs_recover = coefs_recover;
+
19662  model.coef_infect_cols = coef_infect_cols;
+
19663  model.coef_recover_cols = coef_recover_cols;
+
19664 
+
19665  epiworld::UpdateFun<TSeq> update_susceptible = [](
+
19666  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
19667  ) -> void
+
19668  {
+
19669 
+
19670  // Getting the right type
+
19671  ModelSIRLogit<TSeq> * _m = dynamic_cast<ModelSIRLogit<TSeq>*>(m);
+
19672 
+
19673  // Exposure coefficient
+
19674  const double coef_exposure = _m->coefs_infect[0u];
+
19675 
+
19676  // This computes the prob of getting any neighbor variant
+
19677  size_t nviruses_tmp = 0u;
+
19678 
+
19679  double baseline = 0.0;
+
19680  for (size_t k = 0u; k < _m->coef_infect_cols.size(); ++k)
+
19681  baseline += p->operator[](k) * _m->coefs_infect[k + 1u];
19682 
-
19683  // No virus to compute
-
19684  if (nviruses_tmp == 0u)
-
19685  return;
-
19686 
-
19687  // Running the roulette
-
19688  int which = roulette(nviruses_tmp, m);
-
19689 
-
19690  if (which < 0)
-
19691  return;
-
19692 
-
19693  p->set_virus(*m->array_virus_tmp[which], m);
-
19694 
-
19695  return;
-
19696 
-
19697  };
-
19698 
-
19699  epiworld::UpdateFun<TSeq> update_infected = [](
-
19700  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
19701  ) -> void
-
19702  {
-
19703 
-
19704  // Getting the right type
-
19705  ModelSIRLogit<TSeq> * _m = dynamic_cast<ModelSIRLogit<TSeq>*>(m);
-
19706 
-
19707  // Computing recovery probability once
-
19708  double prob = 0.0;
-
19709  #if defined(__OPENMP) || defined(_OPENMP)
-
19710  #pragma omp simd reduction(+:prob)
-
19711  #endif
-
19712  for (size_t i = 0u; i < _m->coefs_recover.size(); ++i)
-
19713  prob += p->operator[](i) * _m->coefs_recover[i];
-
19714 
-
19715  // Computing logis
-
19716  prob = 1.0/(1.0 + std::exp(-prob));
-
19717 
-
19718  if (prob > m->runif())
-
19719  p->rm_virus(m);
-
19720 
-
19721  return;
+
19683  for (auto & neighbor: p->get_neighbors())
+
19684  {
+
19685 
+
19686  if (neighbor->get_virus() == nullptr)
+
19687  continue;
+
19688 
+
19689  auto & v = neighbor->get_virus();
+
19690 
+
19691  #ifdef EPI_DEBUG
+
19692  if (nviruses_tmp >= m->array_virus_tmp.size())
+
19693  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
+
19694  #endif
+
19695 
+
19696  /* And it is a function of susceptibility_reduction as well */
+
19697  m->array_double_tmp[nviruses_tmp] =
+
19698  baseline +
+
19699  (1.0 - p->get_susceptibility_reduction(v, m)) *
+
19700  v->get_prob_infecting(m) *
+
19701  (1.0 - neighbor->get_transmission_reduction(v, m)) *
+
19702  coef_exposure
+
19703  ;
+
19704 
+
19705  // Applying the plogis function
+
19706  m->array_double_tmp[nviruses_tmp] = 1.0/
+
19707  (1.0 + std::exp(-m->array_double_tmp[nviruses_tmp]));
+
19708 
+
19709  m->array_virus_tmp[nviruses_tmp++] = &(*v);
+
19710 
+
19711  }
+
19712 
+
19713  // No virus to compute
+
19714  if (nviruses_tmp == 0u)
+
19715  return;
+
19716 
+
19717  // Running the roulette
+
19718  int which = roulette(nviruses_tmp, m);
+
19719 
+
19720  if (which < 0)
+
19721  return;
19722 
-
19723  };
+
19723  p->set_virus(*m->array_virus_tmp[which], m);
19724 
-
19725  // state
-
19726  model.add_state("Susceptible", update_susceptible);
-
19727  model.add_state("Infected", update_infected);
-
19728  model.add_state("Recovered");
-
19729 
-
19730  // Setting up parameters
-
19731  // model.add_param(contact_rate, "Contact rate");
-
19732  model.add_param(transmission_rate, "Transmission rate");
-
19733  model.add_param(recovery_rate, "Recovery rate");
-
19734  // model.add_param(prob_reinfection, "Prob. Reinfection");
-
19735 
-
19736  // Preparing the virus -------------------------------------------
-
19737  epiworld::Virus<TSeq> virus(vname, prevalence, true);
-
19738  virus.set_state(
-
19739  ModelSIRLogit<TSeq>::INFECTED,
-
19740  ModelSIRLogit<TSeq>::RECOVERED,
-
19741  ModelSIRLogit<TSeq>::RECOVERED
-
19742  );
-
19743 
-
19744  virus.set_prob_infecting(&model("Transmission rate"));
-
19745  virus.set_prob_recovery(&model("Recovery rate"));
-
19746 
-
19747  // virus.set_prob
-
19748 
-
19749  model.add_virus(virus);
-
19750 
-
19751  model.set_name("Susceptible-Infected-Removed (SIR) (logit)");
+
19725  return;
+
19726 
+
19727  };
+
19728 
+
19729  epiworld::UpdateFun<TSeq> update_infected = [](
+
19730  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
19731  ) -> void
+
19732  {
+
19733 
+
19734  // Getting the right type
+
19735  ModelSIRLogit<TSeq> * _m = dynamic_cast<ModelSIRLogit<TSeq>*>(m);
+
19736 
+
19737  // Computing recovery probability once
+
19738  double prob = 0.0;
+
19739  #if defined(__OPENMP) || defined(_OPENMP)
+
19740  #pragma omp simd reduction(+:prob)
+
19741  #endif
+
19742  for (size_t i = 0u; i < _m->coefs_recover.size(); ++i)
+
19743  prob += p->operator[](i) * _m->coefs_recover[i];
+
19744 
+
19745  // Computing logis
+
19746  prob = 1.0/(1.0 + std::exp(-prob));
+
19747 
+
19748  if (prob > m->runif())
+
19749  p->rm_virus(m);
+
19750 
+
19751  return;
19752 
-
19753  return;
+
19753  };
19754 
-
19755 }
-
19756 
-
19757 template<typename TSeq>
-
19758 inline ModelSIRLogit<TSeq>::ModelSIRLogit(
-
19759  const std::string & vname,
-
19760  double * data,
-
19761  size_t ncols,
-
19762  std::vector< double > coefs_infect,
-
19763  std::vector< double > coefs_recover,
-
19764  std::vector< size_t > coef_infect_cols,
-
19765  std::vector< size_t > coef_recover_cols,
-
19766  epiworld_double transmission_rate,
-
19767  epiworld_double recovery_rate,
-
19768  epiworld_double prevalence
-
19769  )
-
19770 {
-
19771 
-
19772  ModelSIRLogit(
-
19773  *this,
-
19774  vname,
-
19775  data,
-
19776  ncols,
-
19777  coefs_infect,
-
19778  coefs_recover,
-
19779  coef_infect_cols,
-
19780  coef_recover_cols,
-
19781  transmission_rate,
-
19782  recovery_rate,
-
19783  prevalence
-
19784  );
-
19785 
-
19786  return;
-
19787 
-
19788 }
-
19789 
-
19790 
-
19791 #endif
-
19792 /*//////////////////////////////////////////////////////////////////////////////
-
19794 
-
19795  End of -include/epiworld//models/sirlogit.hpp-
-
19796 
-
19799 
-
19800 
-
19801 /*//////////////////////////////////////////////////////////////////////////////
-
19803 
-
19804  Start of -include/epiworld//models/diffnet.hpp-
-
19805 
-
19808 
-
19809 
-
19810 #ifndef EPIWORLD_DIFFNET_H
-
19811 #define EPIWORLD_DIFFNET_H
-
19812 
-
19822 template<typename TSeq = int>
-
19823 class ModelDiffNet : public epiworld::Model<TSeq>
-
19824 {
-
19825 private:
-
19826 public:
-
19827 
-
19828  ModelDiffNet() {};
+
19755  // state
+
19756  model.add_state("Susceptible", update_susceptible);
+
19757  model.add_state("Infected", update_infected);
+
19758  model.add_state("Recovered");
+
19759 
+
19760  // Setting up parameters
+
19761  // model.add_param(contact_rate, "Contact rate");
+
19762  model.add_param(transmission_rate, "Transmission rate");
+
19763  model.add_param(recovery_rate, "Recovery rate");
+
19764  // model.add_param(prob_reinfection, "Prob. Reinfection");
+
19765 
+
19766  // Preparing the virus -------------------------------------------
+
19767  epiworld::Virus<TSeq> virus(vname, prevalence, true);
+
19768  virus.set_state(
+
19769  ModelSIRLogit<TSeq>::INFECTED,
+
19770  ModelSIRLogit<TSeq>::RECOVERED,
+
19771  ModelSIRLogit<TSeq>::RECOVERED
+
19772  );
+
19773 
+
19774  virus.set_prob_infecting(&model("Transmission rate"));
+
19775  virus.set_prob_recovery(&model("Recovery rate"));
+
19776 
+
19777  // virus.set_prob
+
19778 
+
19779  model.add_virus(virus);
+
19780 
+
19781  model.set_name("Susceptible-Infected-Removed (SIR) (logit)");
+
19782 
+
19783  return;
+
19784 
+
19785 }
+
19786 
+
19787 template<typename TSeq>
+
19788 inline ModelSIRLogit<TSeq>::ModelSIRLogit(
+
19789  const std::string & vname,
+
19790  double * data,
+
19791  size_t ncols,
+
19792  std::vector< double > coefs_infect,
+
19793  std::vector< double > coefs_recover,
+
19794  std::vector< size_t > coef_infect_cols,
+
19795  std::vector< size_t > coef_recover_cols,
+
19796  epiworld_double transmission_rate,
+
19797  epiworld_double recovery_rate,
+
19798  epiworld_double prevalence
+
19799  )
+
19800 {
+
19801 
+
19802  ModelSIRLogit(
+
19803  *this,
+
19804  vname,
+
19805  data,
+
19806  ncols,
+
19807  coefs_infect,
+
19808  coefs_recover,
+
19809  coef_infect_cols,
+
19810  coef_recover_cols,
+
19811  transmission_rate,
+
19812  recovery_rate,
+
19813  prevalence
+
19814  );
+
19815 
+
19816  return;
+
19817 
+
19818 }
+
19819 
+
19820 
+
19821 #endif
+
19822 /*//////////////////////////////////////////////////////////////////////////////
+
19824 
+
19825  End of -include/epiworld//models/sirlogit.hpp-
+
19826 
19829 
-
19830  ModelDiffNet(
-
19831  ModelDiffNet<TSeq> & model,
-
19832  const std::string & innovation_name,
-
19833  epiworld_double prevalence,
-
19834  epiworld_double prob_adopt,
-
19835  bool normalize_exposure = true,
-
19836  double * agents_data = nullptr,
-
19837  size_t data_ncols = 0u,
-
19838  std::vector< size_t > data_cols = {},
-
19839  std::vector< double > params = {}
-
19840  );
-
19841 
-
19842  ModelDiffNet(
-
19843  const std::string & innovation_name,
-
19844  epiworld_double prevalence,
-
19845  epiworld_double prob_adopt,
-
19846  bool normalize_exposure = true,
-
19847  double * agents_data = nullptr,
-
19848  size_t data_ncols = 0u,
-
19849  std::vector< size_t > data_cols = {},
-
19850  std::vector< double > params = {}
-
19851  );
-
19852 
-
19853  static const int NONADOPTER = 0;
-
19854  static const int ADOPTER = 1;
-
19855 
-
19856  bool normalize_exposure = true;
-
19857  std::vector< size_t > data_cols;
-
19858  std::vector< double > params;
-
19859 };
-
19860 
-
19861 template<typename TSeq>
-
19862 inline ModelDiffNet<TSeq>::ModelDiffNet(
-
19863  ModelDiffNet<TSeq> & model,
-
19864  const std::string & innovation_name,
-
19865  epiworld_double prevalence,
-
19866  epiworld_double prob_adopt,
-
19867  bool normalize_exposure,
-
19868  double * agents_data,
-
19869  size_t data_ncols,
-
19870  std::vector< size_t > data_cols,
-
19871  std::vector< double > params
-
19872  )
-
19873 {
-
19874 
-
19875  // Adding additional parameters
-
19876  this->normalize_exposure = normalize_exposure;
-
19877  this->data_cols = data_cols;
-
19878  this->params = params;
-
19879 
-
19880  epiworld::UpdateFun<TSeq> update_non_adopters = [](
-
19881  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
19882  ) -> void {
-
19883 
-
19884  // Measuring exposure
-
19885  // If the neighbor is infected, then proceed
-
19886  size_t nviruses = m->get_n_viruses();
-
19887  std::vector< Virus<TSeq>* > innovations(nviruses, {});
-
19888  std::vector< bool > stored(nviruses, false);
-
19889  std::vector< double > exposure(nviruses, 0.0);
+
19830 
+
19831 /*//////////////////////////////////////////////////////////////////////////////
+
19833 
+
19834  Start of -include/epiworld//models/diffnet.hpp-
+
19835 
+
19838 
+
19839 
+
19840 #ifndef EPIWORLD_DIFFNET_H
+
19841 #define EPIWORLD_DIFFNET_H
+
19842 
+
19852 template<typename TSeq = int>
+
19853 class ModelDiffNet : public epiworld::Model<TSeq>
+
19854 {
+
19855 private:
+
19856 public:
+
19857 
+
19858  ModelDiffNet() {};
+
19859 
+
19860  ModelDiffNet(
+
19861  ModelDiffNet<TSeq> & model,
+
19862  const std::string & innovation_name,
+
19863  epiworld_double prevalence,
+
19864  epiworld_double prob_adopt,
+
19865  bool normalize_exposure = true,
+
19866  double * agents_data = nullptr,
+
19867  size_t data_ncols = 0u,
+
19868  std::vector< size_t > data_cols = {},
+
19869  std::vector< double > params = {}
+
19870  );
+
19871 
+
19872  ModelDiffNet(
+
19873  const std::string & innovation_name,
+
19874  epiworld_double prevalence,
+
19875  epiworld_double prob_adopt,
+
19876  bool normalize_exposure = true,
+
19877  double * agents_data = nullptr,
+
19878  size_t data_ncols = 0u,
+
19879  std::vector< size_t > data_cols = {},
+
19880  std::vector< double > params = {}
+
19881  );
+
19882 
+
19883  static const int NONADOPTER = 0;
+
19884  static const int ADOPTER = 1;
+
19885 
+
19886  bool normalize_exposure = true;
+
19887  std::vector< size_t > data_cols;
+
19888  std::vector< double > params;
+
19889 };
19890 
-
19891  ModelDiffNet<TSeq> * diffmodel = dynamic_cast<ModelDiffNet<TSeq>*>(m);
-
19892 
-
19893  Agent<TSeq> & agent = *p;
-
19894 
-
19895  // For each one of the possible innovations, we have to compute
-
19896  // the adoption probability, which is a function of exposure
-
19897  for (auto & neighbor: agent.get_neighbors())
-
19898  {
-
19899 
-
19900  if (neighbor->get_state() == ModelDiffNet<TSeq>::ADOPTER)
-
19901  {
-
19902 
-
19903  auto & v = neighbor->get_virus();
-
19904 
-
19905  if (v == nullptr)
-
19906  continue;
-
19907 
-
19908  /* And it is a function of susceptibility_reduction as well */
-
19909  double p_i =
-
19910  (1.0 - agent.get_susceptibility_reduction(v, m)) *
-
19911  (1.0 - agent.get_transmission_reduction(v, m))
-
19912  ;
-
19913 
-
19914  size_t vid = v->get_id();
-
19915  if (!stored[vid])
-
19916  {
-
19917  stored[vid] = true;
-
19918  innovations[vid] = &(*v);
-
19919  }
-
19920  exposure[vid] += p_i;
-
19921 
-
19922 
-
19923  }
-
19924 
-
19925  }
-
19926 
-
19927  // Computing probability of adoption
-
19928  for (size_t i = 0u; i < nviruses; ++i)
-
19929  {
-
19930 
-
19931  if (diffmodel->normalize_exposure)
-
19932  exposure.at(i) /= agent.get_n_neighbors();
-
19933 
-
19934  for (auto & j: diffmodel->data_cols)
-
19935  exposure.at(i) += agent(j) * diffmodel->params.at(j);
-
19936 
-
19937  // Baseline probability of adoption
-
19938  double p = m->get_viruses()[i]->get_prob_infecting(m);
-
19939  exposure.at(i) += std::log(p) - std::log(1.0 - p);
-
19940 
-
19941  // Computing as log
-
19942  exposure.at(i) = 1.0/(1.0 + std::exp(-exposure.at(i)));
-
19943 
-
19944  }
-
19945 
-
19946  // Running the roulette to see is an innovation is adopted
-
19947  int which = roulette<int>(exposure, m);
-
19948 
-
19949  // No innovation was adopted
-
19950  if (which < 0)
-
19951  return;
+
19891 template<typename TSeq>
+
19892 inline ModelDiffNet<TSeq>::ModelDiffNet(
+
19893  ModelDiffNet<TSeq> & model,
+
19894  const std::string & innovation_name,
+
19895  epiworld_double prevalence,
+
19896  epiworld_double prob_adopt,
+
19897  bool normalize_exposure,
+
19898  double * agents_data,
+
19899  size_t data_ncols,
+
19900  std::vector< size_t > data_cols,
+
19901  std::vector< double > params
+
19902  )
+
19903 {
+
19904 
+
19905  // Adding additional parameters
+
19906  this->normalize_exposure = normalize_exposure;
+
19907  this->data_cols = data_cols;
+
19908  this->params = params;
+
19909 
+
19910  epiworld::UpdateFun<TSeq> update_non_adopters = [](
+
19911  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
19912  ) -> void {
+
19913 
+
19914  // Measuring exposure
+
19915  // If the neighbor is infected, then proceed
+
19916  size_t nviruses = m->get_n_viruses();
+
19917  std::vector< Virus<TSeq>* > innovations(nviruses, {});
+
19918  std::vector< bool > stored(nviruses, false);
+
19919  std::vector< double > exposure(nviruses, 0.0);
+
19920 
+
19921  ModelDiffNet<TSeq> * diffmodel = dynamic_cast<ModelDiffNet<TSeq>*>(m);
+
19922 
+
19923  Agent<TSeq> & agent = *p;
+
19924 
+
19925  // For each one of the possible innovations, we have to compute
+
19926  // the adoption probability, which is a function of exposure
+
19927  for (auto & neighbor: agent.get_neighbors())
+
19928  {
+
19929 
+
19930  if (neighbor->get_state() == ModelDiffNet<TSeq>::ADOPTER)
+
19931  {
+
19932 
+
19933  auto & v = neighbor->get_virus();
+
19934 
+
19935  if (v == nullptr)
+
19936  continue;
+
19937 
+
19938  /* And it is a function of susceptibility_reduction as well */
+
19939  double p_i =
+
19940  (1.0 - agent.get_susceptibility_reduction(v, m)) *
+
19941  (1.0 - agent.get_transmission_reduction(v, m))
+
19942  ;
+
19943 
+
19944  size_t vid = v->get_id();
+
19945  if (!stored[vid])
+
19946  {
+
19947  stored[vid] = true;
+
19948  innovations[vid] = &(*v);
+
19949  }
+
19950  exposure[vid] += p_i;
+
19951 
19952 
-
19953  // Otherwise, it is adopted from any of the neighbors
-
19954  agent.set_virus(
-
19955  *innovations.at(which),
-
19956  m,
-
19957  ModelDiffNet::ADOPTER
-
19958  );
-
19959 
-
19960  return;
-
19961 
-
19962  };
+
19953  }
+
19954 
+
19955  }
+
19956 
+
19957  // Computing probability of adoption
+
19958  for (size_t i = 0u; i < nviruses; ++i)
+
19959  {
+
19960 
+
19961  if (diffmodel->normalize_exposure)
+
19962  exposure.at(i) /= agent.get_n_neighbors();
19963 
-
19964  // Adding agents data
-
19965  model.set_agents_data(agents_data, data_ncols);
-
19966 
-
19967  // Adding statuses
-
19968  model.add_state("Non adopters", update_non_adopters);
-
19969  model.add_state("Adopters");
+
19964  for (auto & j: diffmodel->data_cols)
+
19965  exposure.at(i) += agent(j) * diffmodel->params.at(j);
+
19966 
+
19967  // Baseline probability of adoption
+
19968  double p = m->get_viruses()[i]->get_prob_infecting(m);
+
19969  exposure.at(i) += std::log(p) - std::log(1.0 - p);
19970 
-
19971  // Adding parameters
-
19972  std::string parname = std::string("Prob. Adopting ") + innovation_name;
-
19973  model.add_param(prob_adopt, parname);
-
19974 
-
19975  // Preparing the virus -------------------------------------------
-
19976  epiworld::Virus<TSeq> innovation(innovation_name, prevalence, true);
-
19977  innovation.set_state(1,1,1);
-
19978 
-
19979  innovation.set_prob_infecting(&model(parname));
-
19980 
-
19981  model.add_virus(innovation);
+
19971  // Computing as log
+
19972  exposure.at(i) = 1.0/(1.0 + std::exp(-exposure.at(i)));
+
19973 
+
19974  }
+
19975 
+
19976  // Running the roulette to see is an innovation is adopted
+
19977  int which = roulette<int>(exposure, m);
+
19978 
+
19979  // No innovation was adopted
+
19980  if (which < 0)
+
19981  return;
19982 
-
19983  model.set_name(
-
19984  std::string("Diffusion of Innovations - ") + innovation_name);
-
19985 
-
19986  return;
-
19987 
-
19988 }
+
19983  // Otherwise, it is adopted from any of the neighbors
+
19984  agent.set_virus(
+
19985  *innovations.at(which),
+
19986  m,
+
19987  ModelDiffNet::ADOPTER
+
19988  );
19989 
-
19990 template<typename TSeq>
-
19991 inline ModelDiffNet<TSeq>::ModelDiffNet(
-
19992  const std::string & innovation_name,
-
19993  epiworld_double prevalence,
-
19994  epiworld_double prob_adopt,
-
19995  bool normalize_exposure,
-
19996  double * agents_data,
-
19997  size_t data_ncols,
-
19998  std::vector< size_t > data_cols,
-
19999  std::vector< double > params
-
20000  )
-
20001 {
-
20002 
-
20003  ModelDiffNet<TSeq>(
-
20004  *this,
-
20005  innovation_name,
-
20006  prevalence,
-
20007  prob_adopt,
-
20008  normalize_exposure,
-
20009  agents_data,
-
20010  data_ncols,
-
20011  data_cols,
-
20012  params
-
20013  );
-
20014 
-
20015  return;
-
20016 
-
20017 }
-
20018 
-
20019 #endif
-
20020 /*//////////////////////////////////////////////////////////////////////////////
-
20022 
-
20023  End of -include/epiworld//models/diffnet.hpp-
-
20024 
-
20027 
-
20028 
-
20029 /*//////////////////////////////////////////////////////////////////////////////
-
20031 
-
20032  Start of -include/epiworld//models/seirmixing.hpp-
-
20033 
-
20036 
-
20037 
-
20038 #ifndef EPIWORLD_MODELS_SEIRMIXING_HPP
-
20039 #define EPIWORLD_MODELS_SEIRMIXING_HPP
-
20040 
-
20045 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
20046 class ModelSEIRMixing : public epiworld::Model<TSeq>
-
20047 {
-
20048 private:
-
20049  std::vector< std::vector< epiworld::Agent<TSeq> * > > infected;
-
20050  void update_infected();
-
20051  std::vector< epiworld::Agent<TSeq> * > sampled_agents;
-
20052  size_t sample_agents(
-
20053  epiworld::Agent<TSeq> * agent,
-
20054  std::vector< epiworld::Agent<TSeq> * > & sampled_agents
-
20055  );
-
20056  double adjusted_contact_rate;
-
20057  std::vector< double > contact_matrix;
+
19990  return;
+
19991 
+
19992  };
+
19993 
+
19994  // Adding agents data
+
19995  model.set_agents_data(agents_data, data_ncols);
+
19996 
+
19997  // Adding statuses
+
19998  model.add_state("Non adopters", update_non_adopters);
+
19999  model.add_state("Adopters");
+
20000 
+
20001  // Adding parameters
+
20002  std::string parname = std::string("Prob. Adopting ") + innovation_name;
+
20003  model.add_param(prob_adopt, parname);
+
20004 
+
20005  // Preparing the virus -------------------------------------------
+
20006  epiworld::Virus<TSeq> innovation(innovation_name, prevalence, true);
+
20007  innovation.set_state(1,1,1);
+
20008 
+
20009  innovation.set_prob_infecting(&model(parname));
+
20010 
+
20011  model.add_virus(innovation);
+
20012 
+
20013  model.set_name(
+
20014  std::string("Diffusion of Innovations - ") + innovation_name);
+
20015 
+
20016  return;
+
20017 
+
20018 }
+
20019 
+
20020 template<typename TSeq>
+
20021 inline ModelDiffNet<TSeq>::ModelDiffNet(
+
20022  const std::string & innovation_name,
+
20023  epiworld_double prevalence,
+
20024  epiworld_double prob_adopt,
+
20025  bool normalize_exposure,
+
20026  double * agents_data,
+
20027  size_t data_ncols,
+
20028  std::vector< size_t > data_cols,
+
20029  std::vector< double > params
+
20030  )
+
20031 {
+
20032 
+
20033  ModelDiffNet<TSeq>(
+
20034  *this,
+
20035  innovation_name,
+
20036  prevalence,
+
20037  prob_adopt,
+
20038  normalize_exposure,
+
20039  agents_data,
+
20040  data_ncols,
+
20041  data_cols,
+
20042  params
+
20043  );
+
20044 
+
20045  return;
+
20046 
+
20047 }
+
20048 
+
20049 #endif
+
20050 /*//////////////////////////////////////////////////////////////////////////////
+
20052 
+
20053  End of -include/epiworld//models/diffnet.hpp-
+
20054 
+
20057 
20058 
-
20059  size_t index(size_t i, size_t j, size_t n) {
-
20060  return j * n + i;
-
20061  }
-
20062 
-
20063 public:
-
20064 
-
20065  static const int SUSCEPTIBLE = 0;
-
20066  static const int EXPOSED = 1;
-
20067  static const int INFECTED = 2;
-
20068  static const int RECOVERED = 3;
-
20069 
-
20070  ModelSEIRMixing() {};
-
20071 
-
20086  ModelSEIRMixing(
-
20087  ModelSEIRMixing<TSeq> & model,
-
20088  const std::string & vname,
-
20089  epiworld_fast_uint n,
-
20090  epiworld_double prevalence,
-
20091  epiworld_double contact_rate,
-
20092  epiworld_double transmission_rate,
-
20093  epiworld_double avg_incubation_days,
-
20094  epiworld_double recovery_rate,
-
20095  std::vector< double > contact_matrix
-
20096  );
-
20097 
-
20110  ModelSEIRMixing(
-
20111  const std::string & vname,
-
20112  epiworld_fast_uint n,
-
20113  epiworld_double prevalence,
-
20114  epiworld_double contact_rate,
-
20115  epiworld_double transmission_rate,
-
20116  epiworld_double avg_incubation_days,
-
20117  epiworld_double recovery_rate,
-
20118  std::vector< double > contact_matrix
-
20119  );
-
20120 
-
20121  ModelSEIRMixing<TSeq> & run(
-
20122  epiworld_fast_uint ndays,
-
20123  int seed = -1
-
20124  );
-
20125 
-
20126  void reset();
-
20127 
-
20128  Model<TSeq> * clone_ptr();
-
20129 
-
20135  ModelSEIRMixing<TSeq> & initial_states(
-
20136  std::vector< double > proportions_,
-
20137  std::vector< int > queue_ = {}
-
20138  );
-
20139 
-
20140  size_t get_n_infected(size_t group) const
-
20141  {
-
20142  return infected[group].size();
-
20143  }
-
20144 
-
20145  void set_contact_matrix(std::vector< double > cmat)
-
20146  {
-
20147  contact_matrix = cmat;
-
20148  return;
-
20149  };
+
20059 /*//////////////////////////////////////////////////////////////////////////////
+
20061 
+
20062  Start of -include/epiworld//models/seirmixing.hpp-
+
20063 
+
20066 
+
20067 
+
20068 #ifndef EPIWORLD_MODELS_SEIRMIXING_HPP
+
20069 #define EPIWORLD_MODELS_SEIRMIXING_HPP
+
20070 
+
20075 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
20076 class ModelSEIRMixing : public epiworld::Model<TSeq>
+
20077 {
+
20078 private:
+
20079  std::vector< std::vector< epiworld::Agent<TSeq> * > > infected;
+
20080  void update_infected();
+
20081  std::vector< epiworld::Agent<TSeq> * > sampled_agents;
+
20082  size_t sample_agents(
+
20083  epiworld::Agent<TSeq> * agent,
+
20084  std::vector< epiworld::Agent<TSeq> * > & sampled_agents
+
20085  );
+
20086  double adjusted_contact_rate;
+
20087  std::vector< double > contact_matrix;
+
20088 
+
20089  size_t index(size_t i, size_t j, size_t n) {
+
20090  return j * n + i;
+
20091  }
+
20092 
+
20093 public:
+
20094 
+
20095  static const int SUSCEPTIBLE = 0;
+
20096  static const int EXPOSED = 1;
+
20097  static const int INFECTED = 2;
+
20098  static const int RECOVERED = 3;
+
20099 
+
20100  ModelSEIRMixing() {};
+
20101 
+
20116  ModelSEIRMixing(
+
20117  ModelSEIRMixing<TSeq> & model,
+
20118  const std::string & vname,
+
20119  epiworld_fast_uint n,
+
20120  epiworld_double prevalence,
+
20121  epiworld_double contact_rate,
+
20122  epiworld_double transmission_rate,
+
20123  epiworld_double avg_incubation_days,
+
20124  epiworld_double recovery_rate,
+
20125  std::vector< double > contact_matrix
+
20126  );
+
20127 
+
20140  ModelSEIRMixing(
+
20141  const std::string & vname,
+
20142  epiworld_fast_uint n,
+
20143  epiworld_double prevalence,
+
20144  epiworld_double contact_rate,
+
20145  epiworld_double transmission_rate,
+
20146  epiworld_double avg_incubation_days,
+
20147  epiworld_double recovery_rate,
+
20148  std::vector< double > contact_matrix
+
20149  );
20150 
-
20151 };
-
20152 
-
20153 template<typename TSeq>
-
20154 inline void ModelSEIRMixing<TSeq>::update_infected()
-
20155 {
-
20156 
-
20157  auto & agents = Model<TSeq>::get_agents();
-
20158  auto & entities = Model<TSeq>::get_entities();
+
20151  ModelSEIRMixing<TSeq> & run(
+
20152  epiworld_fast_uint ndays,
+
20153  int seed = -1
+
20154  );
+
20155 
+
20156  void reset();
+
20157 
+
20158  Model<TSeq> * clone_ptr();
20159 
-
20160  infected.resize(entities.size());
-
20161  sampled_agents.resize(agents.size());
-
20162 
-
20163  // Checking contact matrix's rows add to one
-
20164  size_t nentities = entities.size();
-
20165  if (this->contact_matrix.size() != nentities*nentities)
-
20166  throw std::length_error(
-
20167  std::string("The contact matrix must be a square matrix of size ") +
-
20168  std::string("nentities x nentities. ") +
-
20169  std::to_string(this->contact_matrix.size()) +
-
20170  std::string(" != ") + std::to_string(nentities*nentities) +
-
20171  std::string(".")
-
20172  );
-
20173 
-
20174  for (size_t i = 0u; i < entities.size(); ++i)
-
20175  {
-
20176  double sum = 0.0;
-
20177  for (size_t j = 0u; j < entities.size(); ++j)
-
20178  {
-
20179  if (this->contact_matrix[index(i, j, nentities)] < 0.0)
-
20180  throw std::range_error(
-
20181  std::string("The contact matrix must be non-negative. ") +
-
20182  std::to_string(this->contact_matrix[index(i, j, nentities)]) +
-
20183  std::string(" < 0.")
-
20184  );
-
20185  sum += this->contact_matrix[index(i, j, nentities)];
-
20186  }
-
20187  if (sum < 0.999 || sum > 1.001)
-
20188  throw std::range_error(
-
20189  std::string("The contact matrix must have rows that add to one. ") +
-
20190  std::to_string(sum) +
-
20191  std::string(" != 1.")
-
20192  );
-
20193  }
-
20194 
-
20195  for (size_t i = 0; i < entities.size(); ++i)
-
20196  {
-
20197  infected[i].clear();
-
20198  infected[i].reserve(agents.size());
-
20199  }
-
20200 
-
20201  for (auto & a : agents)
-
20202  {
+
20165  ModelSEIRMixing<TSeq> & initial_states(
+
20166  std::vector< double > proportions_,
+
20167  std::vector< int > queue_ = {}
+
20168  );
+
20169 
+
20170  size_t get_n_infected(size_t group) const
+
20171  {
+
20172  return infected[group].size();
+
20173  }
+
20174 
+
20175  void set_contact_matrix(std::vector< double > cmat)
+
20176  {
+
20177  contact_matrix = cmat;
+
20178  return;
+
20179  };
+
20180 
+
20181 };
+
20182 
+
20183 template<typename TSeq>
+
20184 inline void ModelSEIRMixing<TSeq>::update_infected()
+
20185 {
+
20186 
+
20187  auto & agents = Model<TSeq>::get_agents();
+
20188  auto & entities = Model<TSeq>::get_entities();
+
20189 
+
20190  infected.resize(entities.size());
+
20191  sampled_agents.resize(agents.size());
+
20192 
+
20193  // Checking contact matrix's rows add to one
+
20194  size_t nentities = entities.size();
+
20195  if (this->contact_matrix.size() != nentities*nentities)
+
20196  throw std::length_error(
+
20197  std::string("The contact matrix must be a square matrix of size ") +
+
20198  std::string("nentities x nentities. ") +
+
20199  std::to_string(this->contact_matrix.size()) +
+
20200  std::string(" != ") + std::to_string(nentities*nentities) +
+
20201  std::string(".")
+
20202  );
20203 
-
20204  if (a.get_state() == ModelSEIRMixing<TSeq>::INFECTED)
-
20205  {
-
20206  if (a.get_n_entities() > 0u)
-
20207  infected[a.get_entity(0u).get_id()].push_back(&a);
-
20208  }
-
20209 
-
20210  }
-
20211 
-
20212  // Adjusting contact rate
-
20213  adjusted_contact_rate = Model<TSeq>::get_param("Contact rate") /
-
20214  agents.size();
-
20215 
-
20216  return;
-
20217 
-
20218 }
-
20219 
-
20220 template<typename TSeq>
-
20221 inline size_t ModelSEIRMixing<TSeq>::sample_agents(
-
20222  epiworld::Agent<TSeq> * agent,
-
20223  std::vector< epiworld::Agent<TSeq> * > & sampled_agents
-
20224  )
-
20225 {
-
20226 
-
20227  size_t agent_group_id = agent->get_entity(0u).get_id();
-
20228  size_t ngroups = infected.size();
-
20229 
-
20230  int samp_id = 0;
-
20231  for (size_t g = 0; g < infected.size(); ++g)
+
20204  for (size_t i = 0u; i < entities.size(); ++i)
+
20205  {
+
20206  double sum = 0.0;
+
20207  for (size_t j = 0u; j < entities.size(); ++j)
+
20208  {
+
20209  if (this->contact_matrix[index(i, j, nentities)] < 0.0)
+
20210  throw std::range_error(
+
20211  std::string("The contact matrix must be non-negative. ") +
+
20212  std::to_string(this->contact_matrix[index(i, j, nentities)]) +
+
20213  std::string(" < 0.")
+
20214  );
+
20215  sum += this->contact_matrix[index(i, j, nentities)];
+
20216  }
+
20217  if (sum < 0.999 || sum > 1.001)
+
20218  throw std::range_error(
+
20219  std::string("The contact matrix must have rows that add to one. ") +
+
20220  std::to_string(sum) +
+
20221  std::string(" != 1.")
+
20222  );
+
20223  }
+
20224 
+
20225  for (size_t i = 0; i < entities.size(); ++i)
+
20226  {
+
20227  infected[i].clear();
+
20228  infected[i].reserve(agents.size());
+
20229  }
+
20230 
+
20231  for (auto & a : agents)
20232  {
20233 
-
20234  // How many from this entity?
-
20235  int nsamples = epiworld::Model<TSeq>::rbinom(
-
20236  infected[g].size(),
-
20237  adjusted_contact_rate * contact_matrix[
-
20238  index(agent_group_id, g, ngroups)
-
20239  ]
-
20240  );
+
20234  if (a.get_state() == ModelSEIRMixing<TSeq>::INFECTED)
+
20235  {
+
20236  if (a.get_n_entities() > 0u)
+
20237  infected[a.get_entity(0u).get_id()].push_back(&a);
+
20238  }
+
20239 
+
20240  }
20241 
-
20242  if (nsamples == 0)
-
20243  continue;
-
20244 
-
20245  // Sampling from the entity
-
20246  for (int s = 0; s < nsamples; ++s)
-
20247  {
-
20248 
-
20249  // Randomly selecting an agent
-
20250  int which = epiworld::Model<TSeq>::runif() * infected[g].size();
-
20251 
-
20252  // Correcting overflow error
-
20253  if (which >= static_cast<int>(infected[g].size()))
-
20254  which = static_cast<int>(infected[g].size()) - 1;
-
20255 
-
20256  auto & a = infected[g][which];
-
20257 
-
20258  // Can't sample itself
-
20259  if (a->get_id() == agent->get_id())
-
20260  continue;
-
20261 
-
20262  sampled_agents[samp_id++] = a;
-
20263 
-
20264  }
-
20265 
-
20266  }
-
20267 
-
20268  return samp_id;
-
20269 
-
20270 }
+
20242  // Adjusting contact rate
+
20243  adjusted_contact_rate = Model<TSeq>::get_param("Contact rate") /
+
20244  agents.size();
+
20245 
+
20246  return;
+
20247 
+
20248 }
+
20249 
+
20250 template<typename TSeq>
+
20251 inline size_t ModelSEIRMixing<TSeq>::sample_agents(
+
20252  epiworld::Agent<TSeq> * agent,
+
20253  std::vector< epiworld::Agent<TSeq> * > & sampled_agents
+
20254  )
+
20255 {
+
20256 
+
20257  size_t agent_group_id = agent->get_entity(0u).get_id();
+
20258  size_t ngroups = infected.size();
+
20259 
+
20260  int samp_id = 0;
+
20261  for (size_t g = 0; g < infected.size(); ++g)
+
20262  {
+
20263 
+
20264  // How many from this entity?
+
20265  int nsamples = epiworld::Model<TSeq>::rbinom(
+
20266  infected[g].size(),
+
20267  adjusted_contact_rate * contact_matrix[
+
20268  index(agent_group_id, g, ngroups)
+
20269  ]
+
20270  );
20271 
-
20272 template<typename TSeq>
-
20273 inline ModelSEIRMixing<TSeq> & ModelSEIRMixing<TSeq>::run(
-
20274  epiworld_fast_uint ndays,
-
20275  int seed
-
20276 )
-
20277 {
+
20272  if (nsamples == 0)
+
20273  continue;
+
20274 
+
20275  // Sampling from the entity
+
20276  for (int s = 0; s < nsamples; ++s)
+
20277  {
20278 
-
20279  Model<TSeq>::run(ndays, seed);
-
20280  return *this;
+
20279  // Randomly selecting an agent
+
20280  int which = epiworld::Model<TSeq>::runif() * infected[g].size();
20281 
-
20282 }
-
20283 
-
20284 template<typename TSeq>
-
20285 inline void ModelSEIRMixing<TSeq>::reset()
-
20286 {
+
20282  // Correcting overflow error
+
20283  if (which >= static_cast<int>(infected[g].size()))
+
20284  which = static_cast<int>(infected[g].size()) - 1;
+
20285 
+
20286  auto & a = infected[g][which];
20287 
-
20288  Model<TSeq>::reset();
-
20289  this->update_infected();
-
20290 
-
20291  return;
-
20292 
-
20293 }
-
20294 
-
20295 template<typename TSeq>
-
20296 inline Model<TSeq> * ModelSEIRMixing<TSeq>::clone_ptr()
-
20297 {
-
20298 
-
20299  ModelSEIRMixing<TSeq> * ptr = new ModelSEIRMixing<TSeq>(
-
20300  *dynamic_cast<const ModelSEIRMixing<TSeq>*>(this)
-
20301  );
-
20302 
-
20303  return dynamic_cast< Model<TSeq> *>(ptr);
-
20304 
-
20305 }
-
20306 
-
20307 
-
20318 template<typename TSeq>
-
20319 inline ModelSEIRMixing<TSeq>::ModelSEIRMixing(
-
20320  ModelSEIRMixing<TSeq> & model,
-
20321  const std::string & vname,
-
20322  epiworld_fast_uint n,
-
20323  epiworld_double prevalence,
-
20324  epiworld_double contact_rate,
-
20325  epiworld_double transmission_rate,
-
20326  epiworld_double avg_incubation_days,
-
20327  epiworld_double recovery_rate,
-
20328  std::vector< double > contact_matrix
-
20329  )
-
20330 {
-
20331 
-
20332  // Setting up the contact matrix
-
20333  this->contact_matrix = contact_matrix;
+
20288  // Can't sample itself
+
20289  if (a->get_id() == agent->get_id())
+
20290  continue;
+
20291 
+
20292  sampled_agents[samp_id++] = a;
+
20293 
+
20294  }
+
20295 
+
20296  }
+
20297 
+
20298  return samp_id;
+
20299 
+
20300 }
+
20301 
+
20302 template<typename TSeq>
+
20303 inline ModelSEIRMixing<TSeq> & ModelSEIRMixing<TSeq>::run(
+
20304  epiworld_fast_uint ndays,
+
20305  int seed
+
20306 )
+
20307 {
+
20308 
+
20309  Model<TSeq>::run(ndays, seed);
+
20310  return *this;
+
20311 
+
20312 }
+
20313 
+
20314 template<typename TSeq>
+
20315 inline void ModelSEIRMixing<TSeq>::reset()
+
20316 {
+
20317 
+
20318  Model<TSeq>::reset();
+
20319  this->update_infected();
+
20320 
+
20321  return;
+
20322 
+
20323 }
+
20324 
+
20325 template<typename TSeq>
+
20326 inline Model<TSeq> * ModelSEIRMixing<TSeq>::clone_ptr()
+
20327 {
+
20328 
+
20329  ModelSEIRMixing<TSeq> * ptr = new ModelSEIRMixing<TSeq>(
+
20330  *dynamic_cast<const ModelSEIRMixing<TSeq>*>(this)
+
20331  );
+
20332 
+
20333  return dynamic_cast< Model<TSeq> *>(ptr);
20334 
-
20335  epiworld::UpdateFun<TSeq> update_susceptible = [](
-
20336  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
20337  ) -> void
-
20338  {
-
20339 
-
20340  if (p->get_n_entities() == 0)
-
20341  return;
-
20342 
-
20343  // Downcasting to retrieve the sampler attached to the
-
20344  // class
-
20345  ModelSEIRMixing<TSeq> * m_down =
-
20346  dynamic_cast<ModelSEIRMixing<TSeq> *>(m);
-
20347 
-
20348  size_t ndraws = m_down->sample_agents(p, m_down->sampled_agents);
-
20349 
-
20350  if (ndraws == 0u)
-
20351  return;
-
20352 
-
20353 
-
20354  // Drawing from the set
-
20355  int nviruses_tmp = 0;
-
20356  for (size_t n = 0u; n < ndraws; ++n)
-
20357  {
-
20358 
-
20359  auto & neighbor = m_down->sampled_agents[n];
-
20360 
-
20361  auto & v = neighbor->get_virus();
-
20362 
-
20363  #ifdef EPI_DEBUG
-
20364  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
-
20365  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
-
20366  #endif
-
20367 
-
20368  /* And it is a function of susceptibility_reduction as well */
-
20369  m->array_double_tmp[nviruses_tmp] =
-
20370  (1.0 - p->get_susceptibility_reduction(v, m)) *
-
20371  v->get_prob_infecting(m) *
-
20372  (1.0 - neighbor->get_transmission_reduction(v, m))
-
20373  ;
-
20374 
-
20375  m->array_virus_tmp[nviruses_tmp++] = &(*v);
-
20376 
-
20377  }
-
20378 
-
20379  // Running the roulette
-
20380  int which = roulette(nviruses_tmp, m);
-
20381 
-
20382  if (which < 0)
-
20383  return;
-
20384 
-
20385  p->set_virus(
-
20386  *m->array_virus_tmp[which],
-
20387  m,
-
20388  ModelSEIRMixing<TSeq>::EXPOSED
-
20389  );
-
20390 
-
20391  return;
-
20392 
-
20393  };
-
20394 
-
20395  epiworld::UpdateFun<TSeq> update_infected = [](
-
20396  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
20397  ) -> void {
-
20398 
-
20399  auto state = p->get_state();
-
20400 
-
20401  if (state == ModelSEIRMixing<TSeq>::EXPOSED)
-
20402  {
-
20403 
-
20404  // Getting the virus
-
20405  auto & v = p->get_virus();
+
20335 }
+
20336 
+
20337 
+
20348 template<typename TSeq>
+
20349 inline ModelSEIRMixing<TSeq>::ModelSEIRMixing(
+
20350  ModelSEIRMixing<TSeq> & model,
+
20351  const std::string & vname,
+
20352  epiworld_fast_uint n,
+
20353  epiworld_double prevalence,
+
20354  epiworld_double contact_rate,
+
20355  epiworld_double transmission_rate,
+
20356  epiworld_double avg_incubation_days,
+
20357  epiworld_double recovery_rate,
+
20358  std::vector< double > contact_matrix
+
20359  )
+
20360 {
+
20361 
+
20362  // Setting up the contact matrix
+
20363  this->contact_matrix = contact_matrix;
+
20364 
+
20365  epiworld::UpdateFun<TSeq> update_susceptible = [](
+
20366  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
20367  ) -> void
+
20368  {
+
20369 
+
20370  if (p->get_n_entities() == 0)
+
20371  return;
+
20372 
+
20373  // Downcasting to retrieve the sampler attached to the
+
20374  // class
+
20375  ModelSEIRMixing<TSeq> * m_down =
+
20376  dynamic_cast<ModelSEIRMixing<TSeq> *>(m);
+
20377 
+
20378  size_t ndraws = m_down->sample_agents(p, m_down->sampled_agents);
+
20379 
+
20380  if (ndraws == 0u)
+
20381  return;
+
20382 
+
20383 
+
20384  // Drawing from the set
+
20385  int nviruses_tmp = 0;
+
20386  for (size_t n = 0u; n < ndraws; ++n)
+
20387  {
+
20388 
+
20389  auto & neighbor = m_down->sampled_agents[n];
+
20390 
+
20391  auto & v = neighbor->get_virus();
+
20392 
+
20393  #ifdef EPI_DEBUG
+
20394  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
+
20395  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
+
20396  #endif
+
20397 
+
20398  /* And it is a function of susceptibility_reduction as well */
+
20399  m->array_double_tmp[nviruses_tmp] =
+
20400  (1.0 - p->get_susceptibility_reduction(v, m)) *
+
20401  v->get_prob_infecting(m) *
+
20402  (1.0 - neighbor->get_transmission_reduction(v, m))
+
20403  ;
+
20404 
+
20405  m->array_virus_tmp[nviruses_tmp++] = &(*v);
20406 
-
20407  // Does the agent become infected?
-
20408  if (m->runif() < 1.0/(v->get_incubation(m)))
-
20409  {
-
20410 
-
20411  p->change_state(m, ModelSEIRMixing<TSeq>::INFECTED);
-
20412  return;
-
20413 
-
20414  }
-
20415 
-
20416 
-
20417  } else if (state == ModelSEIRMixing<TSeq>::INFECTED)
-
20418  {
-
20419 
+
20407  }
+
20408 
+
20409  // Running the roulette
+
20410  int which = roulette(nviruses_tmp, m);
+
20411 
+
20412  if (which < 0)
+
20413  return;
+
20414 
+
20415  p->set_virus(
+
20416  *m->array_virus_tmp[which],
+
20417  m,
+
20418  ModelSEIRMixing<TSeq>::EXPOSED
+
20419  );
20420 
-
20421  // Odd: Die, Even: Recover
-
20422  epiworld_fast_uint n_events = 0u;
-
20423  const auto & v = p->get_virus();
+
20421  return;
+
20422 
+
20423  };
20424 
-
20425  // Recover
-
20426  m->array_double_tmp[n_events++] =
-
20427  1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m));
+
20425  epiworld::UpdateFun<TSeq> update_infected = [](
+
20426  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
20427  ) -> void {
20428 
-
20429  #ifdef EPI_DEBUG
-
20430  if (n_events == 0u)
-
20431  {
-
20432  printf_epiworld(
-
20433  "[epi-debug] agent %i has 0 possible events!!\n",
-
20434  static_cast<int>(p->get_id())
-
20435  );
-
20436  throw std::logic_error("Zero events in exposed.");
-
20437  }
-
20438  #else
-
20439  if (n_events == 0u)
-
20440  return;
-
20441  #endif
-
20442 
+
20429  auto state = p->get_state();
+
20430 
+
20431  if (state == ModelSEIRMixing<TSeq>::EXPOSED)
+
20432  {
+
20433 
+
20434  // Getting the virus
+
20435  auto & v = p->get_virus();
+
20436 
+
20437  // Does the agent become infected?
+
20438  if (m->runif() < 1.0/(v->get_incubation(m)))
+
20439  {
+
20440 
+
20441  p->change_state(m, ModelSEIRMixing<TSeq>::INFECTED);
+
20442  return;
20443 
-
20444  // Running the roulette
-
20445  int which = roulette(n_events, m);
+
20444  }
+
20445 
20446 
-
20447  if (which < 0)
-
20448  return;
+
20447  } else if (state == ModelSEIRMixing<TSeq>::INFECTED)
+
20448  {
20449 
-
20450  // Which roulette happen?
-
20451  p->rm_virus(m);
-
20452 
-
20453  return ;
+
20450 
+
20451  // Odd: Die, Even: Recover
+
20452  epiworld_fast_uint n_events = 0u;
+
20453  const auto & v = p->get_virus();
20454 
-
20455  } else
-
20456  throw std::logic_error("This function can only be applied to exposed or infected individuals. (SEIR)") ;
-
20457 
-
20458  return;
-
20459 
-
20460  };
-
20461 
-
20462  // Setting up parameters
-
20463  model.add_param(contact_rate, "Contact rate");
-
20464  model.add_param(transmission_rate, "Prob. Transmission");
-
20465  model.add_param(recovery_rate, "Prob. Recovery");
-
20466  model.add_param(avg_incubation_days, "Avg. Incubation days");
-
20467 
-
20468  // state
-
20469  model.add_state("Susceptible", update_susceptible);
-
20470  model.add_state("Exposed", update_infected);
-
20471  model.add_state("Infected", update_infected);
-
20472  model.add_state("Recovered");
+
20455  // Recover
+
20456  m->array_double_tmp[n_events++] =
+
20457  1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m));
+
20458 
+
20459  #ifdef EPI_DEBUG
+
20460  if (n_events == 0u)
+
20461  {
+
20462  printf_epiworld(
+
20463  "[epi-debug] agent %i has 0 possible events!!\n",
+
20464  static_cast<int>(p->get_id())
+
20465  );
+
20466  throw std::logic_error("Zero events in exposed.");
+
20467  }
+
20468  #else
+
20469  if (n_events == 0u)
+
20470  return;
+
20471  #endif
+
20472 
20473 
-
20474  // Global function
-
20475  epiworld::GlobalFun<TSeq> update = [](epiworld::Model<TSeq> * m) -> void
-
20476  {
-
20477 
-
20478  ModelSEIRMixing<TSeq> * m_down =
-
20479  dynamic_cast<ModelSEIRMixing<TSeq> *>(m);
-
20480 
-
20481  m_down->update_infected();
+
20474  // Running the roulette
+
20475  int which = roulette(n_events, m);
+
20476 
+
20477  if (which < 0)
+
20478  return;
+
20479 
+
20480  // Which roulette happen?
+
20481  p->rm_virus(m);
20482 
-
20483  return;
+
20483  return ;
20484 
-
20485  };
-
20486 
-
20487  model.add_globalevent(update, "Update infected individuals");
-
20488 
+
20485  } else
+
20486  throw std::logic_error("This function can only be applied to exposed or infected individuals. (SEIR)") ;
+
20487 
+
20488  return;
20489 
-
20490  // Preparing the virus -------------------------------------------
-
20491  epiworld::Virus<TSeq> virus(vname, prevalence, true);
-
20492  virus.set_state(
-
20493  ModelSEIRMixing<TSeq>::EXPOSED,
-
20494  ModelSEIRMixing<TSeq>::RECOVERED,
-
20495  ModelSEIRMixing<TSeq>::RECOVERED
-
20496  );
-
20497 
-
20498  virus.set_prob_infecting(&model("Prob. Transmission"));
-
20499  virus.set_prob_recovery(&model("Prob. Recovery"));
-
20500  virus.set_incubation(&model("Avg. Incubation days"));
-
20501 
-
20502  model.add_virus(virus);
+
20490  };
+
20491 
+
20492  // Setting up parameters
+
20493  model.add_param(contact_rate, "Contact rate");
+
20494  model.add_param(transmission_rate, "Prob. Transmission");
+
20495  model.add_param(recovery_rate, "Prob. Recovery");
+
20496  model.add_param(avg_incubation_days, "Avg. Incubation days");
+
20497 
+
20498  // state
+
20499  model.add_state("Susceptible", update_susceptible);
+
20500  model.add_state("Exposed", update_infected);
+
20501  model.add_state("Infected", update_infected);
+
20502  model.add_state("Recovered");
20503 
-
20504  model.queuing_off(); // No queuing need
-
20505 
-
20506  // Adding the empty population
-
20507  model.agents_empty_graph(n);
-
20508 
-
20509  model.set_name("Susceptible-Exposed-Infected-Removed (SEIR) with Mixing");
+
20504  // Global function
+
20505  epiworld::GlobalFun<TSeq> update = [](epiworld::Model<TSeq> * m) -> void
+
20506  {
+
20507 
+
20508  ModelSEIRMixing<TSeq> * m_down =
+
20509  dynamic_cast<ModelSEIRMixing<TSeq> *>(m);
20510 
-
20511  return;
+
20511  m_down->update_infected();
20512 
-
20513 }
+
20513  return;
20514 
-
20515 template<typename TSeq>
-
20516 inline ModelSEIRMixing<TSeq>::ModelSEIRMixing(
-
20517  const std::string & vname,
-
20518  epiworld_fast_uint n,
-
20519  epiworld_double prevalence,
-
20520  epiworld_double contact_rate,
-
20521  epiworld_double transmission_rate,
-
20522  epiworld_double avg_incubation_days,
-
20523  epiworld_double recovery_rate,
-
20524  std::vector< double > contact_matrix
-
20525  )
-
20526 {
+
20515  };
+
20516 
+
20517  model.add_globalevent(update, "Update infected individuals");
+
20518 
+
20519 
+
20520  // Preparing the virus -------------------------------------------
+
20521  epiworld::Virus<TSeq> virus(vname, prevalence, true);
+
20522  virus.set_state(
+
20523  ModelSEIRMixing<TSeq>::EXPOSED,
+
20524  ModelSEIRMixing<TSeq>::RECOVERED,
+
20525  ModelSEIRMixing<TSeq>::RECOVERED
+
20526  );
20527 
-
20528  this->contact_matrix = contact_matrix;
-
20529 
-
20530  ModelSEIRMixing(
-
20531  *this,
-
20532  vname,
-
20533  n,
-
20534  prevalence,
-
20535  contact_rate,
-
20536  transmission_rate,
-
20537  avg_incubation_days,
-
20538  recovery_rate,
-
20539  contact_matrix
-
20540  );
-
20541 
-
20542  return;
-
20543 
-
20544 }
-
20545 
-
20546 template<typename TSeq>
-
20547 inline ModelSEIRMixing<TSeq> & ModelSEIRMixing<TSeq>::initial_states(
-
20548  std::vector< double > proportions_,
-
20549  std::vector< int > /* queue_ */
-
20550 )
-
20551 {
-
20552 
-
20553  Model<TSeq>::initial_states_fun =
-
20554  create_init_function_seir<TSeq>(proportions_)
-
20555  ;
-
20556 
-
20557  return *this;
-
20558 
-
20559 }
-
20560 
-
20561 #endif
-
20562 /*//////////////////////////////////////////////////////////////////////////////
-
20564 
-
20565  End of -include/epiworld//models/seirmixing.hpp-
-
20566 
-
20569 
-
20570 
-
20571 /*//////////////////////////////////////////////////////////////////////////////
-
20573 
-
20574  Start of -include/epiworld//models/sirmixing.hpp-
-
20575 
-
20578 
-
20579 
-
20580 #ifndef EPIWORLD_MODELS_SIRMIXING_HPP
-
20581 #define EPIWORLD_MODELS_SIRMIXING_HPP
-
20582 
-
20587 template<typename TSeq = EPI_DEFAULT_TSEQ>
-
20588 class ModelSIRMixing : public epiworld::Model<TSeq>
-
20589 {
-
20590 private:
-
20591  std::vector< std::vector< epiworld::Agent<TSeq> * > > infected;
-
20592  void update_infected_list();
-
20593  std::vector< epiworld::Agent<TSeq> * > sampled_agents;
-
20594  size_t sample_agents(
-
20595  epiworld::Agent<TSeq> * agent,
-
20596  std::vector< epiworld::Agent<TSeq> * > & sampled_agents
-
20597  );
-
20598  double adjusted_contact_rate;
-
20599  std::vector< double > contact_matrix;
+
20528  virus.set_prob_infecting(&model("Prob. Transmission"));
+
20529  virus.set_prob_recovery(&model("Prob. Recovery"));
+
20530  virus.set_incubation(&model("Avg. Incubation days"));
+
20531 
+
20532  model.add_virus(virus);
+
20533 
+
20534  model.queuing_off(); // No queuing need
+
20535 
+
20536  // Adding the empty population
+
20537  model.agents_empty_graph(n);
+
20538 
+
20539  model.set_name("Susceptible-Exposed-Infected-Removed (SEIR) with Mixing");
+
20540 
+
20541  return;
+
20542 
+
20543 }
+
20544 
+
20545 template<typename TSeq>
+
20546 inline ModelSEIRMixing<TSeq>::ModelSEIRMixing(
+
20547  const std::string & vname,
+
20548  epiworld_fast_uint n,
+
20549  epiworld_double prevalence,
+
20550  epiworld_double contact_rate,
+
20551  epiworld_double transmission_rate,
+
20552  epiworld_double avg_incubation_days,
+
20553  epiworld_double recovery_rate,
+
20554  std::vector< double > contact_matrix
+
20555  )
+
20556 {
+
20557 
+
20558  this->contact_matrix = contact_matrix;
+
20559 
+
20560  ModelSEIRMixing(
+
20561  *this,
+
20562  vname,
+
20563  n,
+
20564  prevalence,
+
20565  contact_rate,
+
20566  transmission_rate,
+
20567  avg_incubation_days,
+
20568  recovery_rate,
+
20569  contact_matrix
+
20570  );
+
20571 
+
20572  return;
+
20573 
+
20574 }
+
20575 
+
20576 template<typename TSeq>
+
20577 inline ModelSEIRMixing<TSeq> & ModelSEIRMixing<TSeq>::initial_states(
+
20578  std::vector< double > proportions_,
+
20579  std::vector< int > /* queue_ */
+
20580 )
+
20581 {
+
20582 
+
20583  Model<TSeq>::initial_states_fun =
+
20584  create_init_function_seir<TSeq>(proportions_)
+
20585  ;
+
20586 
+
20587  return *this;
+
20588 
+
20589 }
+
20590 
+
20591 #endif
+
20592 /*//////////////////////////////////////////////////////////////////////////////
+
20594 
+
20595  End of -include/epiworld//models/seirmixing.hpp-
+
20596 
+
20599 
20600 
-
20601  size_t index(size_t i, size_t j, size_t n) {
-
20602  return j * n + i;
-
20603  }
-
20604 
-
20605 public:
-
20606 
-
20607  static const int SUSCEPTIBLE = 0;
-
20608  static const int INFECTED = 1;
-
20609  static const int RECOVERED = 2;
-
20610 
-
20611  ModelSIRMixing() {};
-
20612 
-
20625  ModelSIRMixing(
-
20626  ModelSIRMixing<TSeq> & model,
-
20627  const std::string & vname,
-
20628  epiworld_fast_uint n,
-
20629  epiworld_double prevalence,
-
20630  epiworld_double contact_rate,
-
20631  epiworld_double transmission_rate,
-
20632  epiworld_double recovery_rate,
-
20633  std::vector< double > contact_matrix
-
20634  );
-
20635 
-
20647  ModelSIRMixing(
-
20648  const std::string & vname,
-
20649  epiworld_fast_uint n,
-
20650  epiworld_double prevalence,
-
20651  epiworld_double contact_rate,
-
20652  epiworld_double transmission_rate,
-
20653  epiworld_double recovery_rate,
-
20654  std::vector< double > contact_matrix
-
20655  );
-
20656 
-
20657  ModelSIRMixing<TSeq> & run(
-
20658  epiworld_fast_uint ndays,
-
20659  int seed = -1
-
20660  );
-
20661 
-
20662  void reset();
-
20663 
-
20664  Model<TSeq> * clone_ptr();
-
20665 
-
20671  ModelSIRMixing<TSeq> & initial_states(
-
20672  std::vector< double > proportions_,
-
20673  std::vector< int > queue_ = {}
-
20674  );
-
20675 
-
20676  size_t get_n_infected(size_t group) const
-
20677  {
-
20678  return infected[group].size();
-
20679  }
-
20680 
-
20681  void set_contact_matrix(std::vector< double > cmat)
-
20682  {
-
20683  contact_matrix = cmat;
-
20684  return;
-
20685  };
+
20601 /*//////////////////////////////////////////////////////////////////////////////
+
20603 
+
20604  Start of -include/epiworld//models/sirmixing.hpp-
+
20605 
+
20608 
+
20609 
+
20610 #ifndef EPIWORLD_MODELS_SIRMIXING_HPP
+
20611 #define EPIWORLD_MODELS_SIRMIXING_HPP
+
20612 
+
20617 template<typename TSeq = EPI_DEFAULT_TSEQ>
+
20618 class ModelSIRMixing : public epiworld::Model<TSeq>
+
20619 {
+
20620 private:
+
20621  std::vector< std::vector< epiworld::Agent<TSeq> * > > infected;
+
20622  void update_infected_list();
+
20623  std::vector< epiworld::Agent<TSeq> * > sampled_agents;
+
20624  size_t sample_agents(
+
20625  epiworld::Agent<TSeq> * agent,
+
20626  std::vector< epiworld::Agent<TSeq> * > & sampled_agents
+
20627  );
+
20628  double adjusted_contact_rate;
+
20629  std::vector< double > contact_matrix;
+
20630 
+
20631  size_t index(size_t i, size_t j, size_t n) {
+
20632  return j * n + i;
+
20633  }
+
20634 
+
20635 public:
+
20636 
+
20637  static const int SUSCEPTIBLE = 0;
+
20638  static const int INFECTED = 1;
+
20639  static const int RECOVERED = 2;
+
20640 
+
20641  ModelSIRMixing() {};
+
20642 
+
20655  ModelSIRMixing(
+
20656  ModelSIRMixing<TSeq> & model,
+
20657  const std::string & vname,
+
20658  epiworld_fast_uint n,
+
20659  epiworld_double prevalence,
+
20660  epiworld_double contact_rate,
+
20661  epiworld_double transmission_rate,
+
20662  epiworld_double recovery_rate,
+
20663  std::vector< double > contact_matrix
+
20664  );
+
20665 
+
20677  ModelSIRMixing(
+
20678  const std::string & vname,
+
20679  epiworld_fast_uint n,
+
20680  epiworld_double prevalence,
+
20681  epiworld_double contact_rate,
+
20682  epiworld_double transmission_rate,
+
20683  epiworld_double recovery_rate,
+
20684  std::vector< double > contact_matrix
+
20685  );
20686 
-
20687 };
-
20688 
-
20689 template<typename TSeq>
-
20690 inline void ModelSIRMixing<TSeq>::update_infected_list()
-
20691 {
-
20692 
-
20693  auto & agents = Model<TSeq>::get_agents();
-
20694  auto & entities = Model<TSeq>::get_entities();
+
20687  ModelSIRMixing<TSeq> & run(
+
20688  epiworld_fast_uint ndays,
+
20689  int seed = -1
+
20690  );
+
20691 
+
20692  void reset();
+
20693 
+
20694  Model<TSeq> * clone_ptr();
20695 
-
20696  infected.resize(entities.size());
-
20697  sampled_agents.resize(agents.size());
-
20698 
-
20699  // Checking contact matrix's rows add to one
-
20700  size_t nentities = entities.size();
-
20701  if (this->contact_matrix.size() != nentities*nentities)
-
20702  throw std::length_error(
-
20703  std::string("The contact matrix must be a square matrix of size ") +
-
20704  std::string("nentities x nentities. ") +
-
20705  std::to_string(this->contact_matrix.size()) +
-
20706  std::string(" != ") + std::to_string(nentities*nentities) +
-
20707  std::string(".")
-
20708  );
-
20709 
-
20710  for (size_t i = 0u; i < entities.size(); ++i)
-
20711  {
-
20712  double sum = 0.0;
-
20713  for (size_t j = 0u; j < entities.size(); ++j)
-
20714  {
-
20715  if (this->contact_matrix[index(i, j, nentities)] < 0.0)
-
20716  throw std::range_error(
-
20717  std::string("The contact matrix must be non-negative. ") +
-
20718  std::to_string(this->contact_matrix[index(i, j, nentities)]) +
-
20719  std::string(" < 0.")
-
20720  );
-
20721  sum += this->contact_matrix[index(i, j, nentities)];
-
20722  }
-
20723  if (sum < 0.999 || sum > 1.001)
-
20724  throw std::range_error(
-
20725  std::string("The contact matrix must have rows that add to one. ") +
-
20726  std::to_string(sum) +
-
20727  std::string(" != 1.")
-
20728  );
-
20729  }
-
20730 
-
20731  for (size_t i = 0; i < entities.size(); ++i)
-
20732  {
-
20733  infected[i].clear();
-
20734  infected[i].reserve(agents.size());
-
20735  }
-
20736 
-
20737  for (auto & a : agents)
-
20738  {
+
20701  ModelSIRMixing<TSeq> & initial_states(
+
20702  std::vector< double > proportions_,
+
20703  std::vector< int > queue_ = {}
+
20704  );
+
20705 
+
20706  size_t get_n_infected(size_t group) const
+
20707  {
+
20708  return infected[group].size();
+
20709  }
+
20710 
+
20711  void set_contact_matrix(std::vector< double > cmat)
+
20712  {
+
20713  contact_matrix = cmat;
+
20714  return;
+
20715  };
+
20716 
+
20717 };
+
20718 
+
20719 template<typename TSeq>
+
20720 inline void ModelSIRMixing<TSeq>::update_infected_list()
+
20721 {
+
20722 
+
20723  auto & agents = Model<TSeq>::get_agents();
+
20724  auto & entities = Model<TSeq>::get_entities();
+
20725 
+
20726  infected.resize(entities.size());
+
20727  sampled_agents.resize(agents.size());
+
20728 
+
20729  // Checking contact matrix's rows add to one
+
20730  size_t nentities = entities.size();
+
20731  if (this->contact_matrix.size() != nentities*nentities)
+
20732  throw std::length_error(
+
20733  std::string("The contact matrix must be a square matrix of size ") +
+
20734  std::string("nentities x nentities. ") +
+
20735  std::to_string(this->contact_matrix.size()) +
+
20736  std::string(" != ") + std::to_string(nentities*nentities) +
+
20737  std::string(".")
+
20738  );
20739 
-
20740  if (a.get_state() == ModelSIRMixing<TSeq>::INFECTED)
-
20741  {
-
20742  if (a.get_n_entities() > 0u)
-
20743  infected[a.get_entity(0u).get_id()].push_back(&a);
-
20744  }
-
20745 
-
20746  }
-
20747 
-
20748  // Adjusting contact rate
-
20749  adjusted_contact_rate = Model<TSeq>::get_param("Contact rate") /
-
20750  agents.size();
-
20751 
-
20752  return;
-
20753 
-
20754 }
-
20755 
-
20756 template<typename TSeq>
-
20757 inline size_t ModelSIRMixing<TSeq>::sample_agents(
-
20758  epiworld::Agent<TSeq> * agent,
-
20759  std::vector< epiworld::Agent<TSeq> * > & sampled_agents
-
20760  )
-
20761 {
-
20762 
-
20763  size_t agent_group_id = agent->get_entity(0u).get_id();
-
20764  size_t ngroups = infected.size();
-
20765 
-
20766  int samp_id = 0;
-
20767  for (size_t g = 0; g < infected.size(); ++g)
+
20740  for (size_t i = 0u; i < entities.size(); ++i)
+
20741  {
+
20742  double sum = 0.0;
+
20743  for (size_t j = 0u; j < entities.size(); ++j)
+
20744  {
+
20745  if (this->contact_matrix[index(i, j, nentities)] < 0.0)
+
20746  throw std::range_error(
+
20747  std::string("The contact matrix must be non-negative. ") +
+
20748  std::to_string(this->contact_matrix[index(i, j, nentities)]) +
+
20749  std::string(" < 0.")
+
20750  );
+
20751  sum += this->contact_matrix[index(i, j, nentities)];
+
20752  }
+
20753  if (sum < 0.999 || sum > 1.001)
+
20754  throw std::range_error(
+
20755  std::string("The contact matrix must have rows that add to one. ") +
+
20756  std::to_string(sum) +
+
20757  std::string(" != 1.")
+
20758  );
+
20759  }
+
20760 
+
20761  for (size_t i = 0; i < entities.size(); ++i)
+
20762  {
+
20763  infected[i].clear();
+
20764  infected[i].reserve(agents.size());
+
20765  }
+
20766 
+
20767  for (auto & a : agents)
20768  {
20769 
-
20770  // How many from this entity?
-
20771  int nsamples = epiworld::Model<TSeq>::rbinom(
-
20772  infected[g].size(),
-
20773  adjusted_contact_rate * contact_matrix[
-
20774  index(agent_group_id, g, ngroups)
-
20775  ]
-
20776  );
+
20770  if (a.get_state() == ModelSIRMixing<TSeq>::INFECTED)
+
20771  {
+
20772  if (a.get_n_entities() > 0u)
+
20773  infected[a.get_entity(0u).get_id()].push_back(&a);
+
20774  }
+
20775 
+
20776  }
20777 
-
20778  if (nsamples == 0)
-
20779  continue;
-
20780 
-
20781  // Sampling from the entity
-
20782  for (int s = 0; s < nsamples; ++s)
-
20783  {
-
20784 
-
20785  // Randomly selecting an agent
-
20786  int which = epiworld::Model<TSeq>::runif() * infected[g].size();
-
20787 
-
20788  // Correcting overflow error
-
20789  if (which >= static_cast<int>(infected[g].size()))
-
20790  which = static_cast<int>(infected[g].size()) - 1;
-
20791 
-
20792  auto & a = infected[g][which];
-
20793 
-
20794  // Can't sample itself
-
20795  if (a->get_id() == agent->get_id())
-
20796  continue;
-
20797 
-
20798  sampled_agents[samp_id++] = a;
-
20799 
-
20800  }
-
20801 
-
20802  }
-
20803 
-
20804  return samp_id;
-
20805 
-
20806 }
+
20778  // Adjusting contact rate
+
20779  adjusted_contact_rate = Model<TSeq>::get_param("Contact rate") /
+
20780  agents.size();
+
20781 
+
20782  return;
+
20783 
+
20784 }
+
20785 
+
20786 template<typename TSeq>
+
20787 inline size_t ModelSIRMixing<TSeq>::sample_agents(
+
20788  epiworld::Agent<TSeq> * agent,
+
20789  std::vector< epiworld::Agent<TSeq> * > & sampled_agents
+
20790  )
+
20791 {
+
20792 
+
20793  size_t agent_group_id = agent->get_entity(0u).get_id();
+
20794  size_t ngroups = infected.size();
+
20795 
+
20796  int samp_id = 0;
+
20797  for (size_t g = 0; g < infected.size(); ++g)
+
20798  {
+
20799 
+
20800  // How many from this entity?
+
20801  int nsamples = epiworld::Model<TSeq>::rbinom(
+
20802  infected[g].size(),
+
20803  adjusted_contact_rate * contact_matrix[
+
20804  index(agent_group_id, g, ngroups)
+
20805  ]
+
20806  );
20807 
-
20808 template<typename TSeq>
-
20809 inline ModelSIRMixing<TSeq> & ModelSIRMixing<TSeq>::run(
-
20810  epiworld_fast_uint ndays,
-
20811  int seed
-
20812 )
-
20813 {
-
20814 
-
20815  Model<TSeq>::run(ndays, seed);
-
20816  return *this;
+
20808  if (nsamples == 0)
+
20809  continue;
+
20810 
+
20811  // Sampling from the entity
+
20812  for (int s = 0; s < nsamples; ++s)
+
20813  {
+
20814 
+
20815  // Randomly selecting an agent
+
20816  int which = epiworld::Model<TSeq>::runif() * infected[g].size();
20817 
-
20818 }
-
20819 
-
20820 template<typename TSeq>
-
20821 inline void ModelSIRMixing<TSeq>::reset()
-
20822 {
+
20818  // Correcting overflow error
+
20819  if (which >= static_cast<int>(infected[g].size()))
+
20820  which = static_cast<int>(infected[g].size()) - 1;
+
20821 
+
20822  auto & a = infected[g][which];
20823 
-
20824  Model<TSeq>::reset();
-
20825  this->update_infected_list();
-
20826 
-
20827  return;
-
20828 
-
20829 }
-
20830 
-
20831 template<typename TSeq>
-
20832 inline Model<TSeq> * ModelSIRMixing<TSeq>::clone_ptr()
-
20833 {
-
20834 
-
20835  ModelSIRMixing<TSeq> * ptr = new ModelSIRMixing<TSeq>(
-
20836  *dynamic_cast<const ModelSIRMixing<TSeq>*>(this)
-
20837  );
-
20838 
-
20839  return dynamic_cast< Model<TSeq> *>(ptr);
-
20840 
-
20841 }
-
20842 
-
20843 
-
20854 template<typename TSeq>
-
20855 inline ModelSIRMixing<TSeq>::ModelSIRMixing(
-
20856  ModelSIRMixing<TSeq> & model,
-
20857  const std::string & vname,
-
20858  epiworld_fast_uint n,
-
20859  epiworld_double prevalence,
-
20860  epiworld_double contact_rate,
-
20861  epiworld_double transmission_rate,
-
20862  epiworld_double recovery_rate,
-
20863  std::vector< double > contact_matrix
-
20864  )
-
20865 {
-
20866 
-
20867  // Setting up the contact matrix
-
20868  this->contact_matrix = contact_matrix;
-
20869 
-
20870  epiworld::UpdateFun<TSeq> update_susceptible = [](
-
20871  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
20872  ) -> void
-
20873  {
-
20874 
-
20875  if (p->get_n_entities() == 0)
-
20876  return;
-
20877 
-
20878  // Downcasting to retrieve the sampler attached to the
-
20879  // class
-
20880  ModelSIRMixing<TSeq> * m_down =
-
20881  dynamic_cast<ModelSIRMixing<TSeq> *>(m);
-
20882 
-
20883  size_t ndraws = m_down->sample_agents(p, m_down->sampled_agents);
-
20884 
-
20885  if (ndraws == 0u)
-
20886  return;
-
20887 
-
20888 
-
20889  // Drawing from the set
-
20890  int nviruses_tmp = 0;
-
20891  for (size_t n = 0u; n < ndraws; ++n)
-
20892  {
-
20893 
-
20894  auto & neighbor = m_down->sampled_agents[n];
-
20895 
-
20896  auto & v = neighbor->get_virus();
-
20897 
-
20898  #ifdef EPI_DEBUG
-
20899  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
-
20900  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
-
20901  #endif
-
20902 
-
20903  /* And it is a function of susceptibility_reduction as well */
-
20904  m->array_double_tmp[nviruses_tmp] =
-
20905  (1.0 - p->get_susceptibility_reduction(v, m)) *
-
20906  v->get_prob_infecting(m) *
-
20907  (1.0 - neighbor->get_transmission_reduction(v, m))
-
20908  ;
-
20909 
-
20910  m->array_virus_tmp[nviruses_tmp++] = &(*v);
-
20911 
-
20912  }
-
20913 
-
20914  // Running the roulette
-
20915  int which = roulette(nviruses_tmp, m);
-
20916 
-
20917  if (which < 0)
-
20918  return;
-
20919 
-
20920  p->set_virus(
-
20921  *m->array_virus_tmp[which],
-
20922  m,
-
20923  ModelSIRMixing<TSeq>::INFECTED
-
20924  );
-
20925 
-
20926  return;
-
20927 
-
20928  };
-
20929 
-
20930  epiworld::UpdateFun<TSeq> update_infected = [](
-
20931  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
-
20932  ) -> void {
-
20933 
-
20934  auto state = p->get_state();
-
20935 
-
20936  if (state == ModelSIRMixing<TSeq>::INFECTED)
-
20937  {
-
20938 
-
20939 
-
20940  // Odd: Die, Even: Recover
-
20941  epiworld_fast_uint n_events = 0u;
-
20942  const auto & v = p->get_virus();
+
20824  // Can't sample itself
+
20825  if (a->get_id() == agent->get_id())
+
20826  continue;
+
20827 
+
20828  sampled_agents[samp_id++] = a;
+
20829 
+
20830  }
+
20831 
+
20832  }
+
20833 
+
20834  return samp_id;
+
20835 
+
20836 }
+
20837 
+
20838 template<typename TSeq>
+
20839 inline ModelSIRMixing<TSeq> & ModelSIRMixing<TSeq>::run(
+
20840  epiworld_fast_uint ndays,
+
20841  int seed
+
20842 )
+
20843 {
+
20844 
+
20845  Model<TSeq>::run(ndays, seed);
+
20846  return *this;
+
20847 
+
20848 }
+
20849 
+
20850 template<typename TSeq>
+
20851 inline void ModelSIRMixing<TSeq>::reset()
+
20852 {
+
20853 
+
20854  Model<TSeq>::reset();
+
20855  this->update_infected_list();
+
20856 
+
20857  return;
+
20858 
+
20859 }
+
20860 
+
20861 template<typename TSeq>
+
20862 inline Model<TSeq> * ModelSIRMixing<TSeq>::clone_ptr()
+
20863 {
+
20864 
+
20865  ModelSIRMixing<TSeq> * ptr = new ModelSIRMixing<TSeq>(
+
20866  *dynamic_cast<const ModelSIRMixing<TSeq>*>(this)
+
20867  );
+
20868 
+
20869  return dynamic_cast< Model<TSeq> *>(ptr);
+
20870 
+
20871 }
+
20872 
+
20873 
+
20884 template<typename TSeq>
+
20885 inline ModelSIRMixing<TSeq>::ModelSIRMixing(
+
20886  ModelSIRMixing<TSeq> & model,
+
20887  const std::string & vname,
+
20888  epiworld_fast_uint n,
+
20889  epiworld_double prevalence,
+
20890  epiworld_double contact_rate,
+
20891  epiworld_double transmission_rate,
+
20892  epiworld_double recovery_rate,
+
20893  std::vector< double > contact_matrix
+
20894  )
+
20895 {
+
20896 
+
20897  // Setting up the contact matrix
+
20898  this->contact_matrix = contact_matrix;
+
20899 
+
20900  epiworld::UpdateFun<TSeq> update_susceptible = [](
+
20901  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
20902  ) -> void
+
20903  {
+
20904 
+
20905  if (p->get_n_entities() == 0)
+
20906  return;
+
20907 
+
20908  // Downcasting to retrieve the sampler attached to the
+
20909  // class
+
20910  ModelSIRMixing<TSeq> * m_down =
+
20911  dynamic_cast<ModelSIRMixing<TSeq> *>(m);
+
20912 
+
20913  size_t ndraws = m_down->sample_agents(p, m_down->sampled_agents);
+
20914 
+
20915  if (ndraws == 0u)
+
20916  return;
+
20917 
+
20918 
+
20919  // Drawing from the set
+
20920  int nviruses_tmp = 0;
+
20921  for (size_t n = 0u; n < ndraws; ++n)
+
20922  {
+
20923 
+
20924  auto & neighbor = m_down->sampled_agents[n];
+
20925 
+
20926  auto & v = neighbor->get_virus();
+
20927 
+
20928  #ifdef EPI_DEBUG
+
20929  if (nviruses_tmp >= static_cast<int>(m->array_virus_tmp.size()))
+
20930  throw std::logic_error("Trying to add an extra element to a temporal array outside of the range.");
+
20931  #endif
+
20932 
+
20933  /* And it is a function of susceptibility_reduction as well */
+
20934  m->array_double_tmp[nviruses_tmp] =
+
20935  (1.0 - p->get_susceptibility_reduction(v, m)) *
+
20936  v->get_prob_infecting(m) *
+
20937  (1.0 - neighbor->get_transmission_reduction(v, m))
+
20938  ;
+
20939 
+
20940  m->array_virus_tmp[nviruses_tmp++] = &(*v);
+
20941 
+
20942  }
20943 
-
20944  // Recover
-
20945  m->array_double_tmp[n_events++] =
-
20946  1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m));
-
20947 
-
20948  #ifdef EPI_DEBUG
-
20949  if (n_events == 0u)
-
20950  {
-
20951  printf_epiworld(
-
20952  "[epi-debug] agent %i has 0 possible events!!\n",
-
20953  static_cast<int>(p->get_id())
-
20954  );
-
20955  throw std::logic_error("Zero events in infected.");
-
20956  }
-
20957  #else
-
20958  if (n_events == 0u)
-
20959  return;
-
20960  #endif
-
20961 
-
20962 
-
20963  // Running the roulette
-
20964  int which = roulette(n_events, m);
+
20944  // Running the roulette
+
20945  int which = roulette(nviruses_tmp, m);
+
20946 
+
20947  if (which < 0)
+
20948  return;
+
20949 
+
20950  p->set_virus(
+
20951  *m->array_virus_tmp[which],
+
20952  m,
+
20953  ModelSIRMixing<TSeq>::INFECTED
+
20954  );
+
20955 
+
20956  return;
+
20957 
+
20958  };
+
20959 
+
20960  epiworld::UpdateFun<TSeq> update_infected = [](
+
20961  epiworld::Agent<TSeq> * p, epiworld::Model<TSeq> * m
+
20962  ) -> void {
+
20963 
+
20964  auto state = p->get_state();
20965 
-
20966  if (which < 0)
-
20967  return;
+
20966  if (state == ModelSIRMixing<TSeq>::INFECTED)
+
20967  {
20968 
-
20969  // Which roulette happen?
-
20970  p->rm_virus(m);
-
20971 
-
20972  return ;
+
20969 
+
20970  // Odd: Die, Even: Recover
+
20971  epiworld_fast_uint n_events = 0u;
+
20972  const auto & v = p->get_virus();
20973 
-
20974  } else
-
20975  throw std::logic_error("This function can only be applied to infected individuals. (SIR)") ;
-
20976 
-
20977  return;
-
20978 
-
20979  };
-
20980 
-
20981  // Setting up parameters
-
20982  model.add_param(contact_rate, "Contact rate");
-
20983  model.add_param(transmission_rate, "Prob. Transmission");
-
20984  model.add_param(recovery_rate, "Prob. Recovery");
-
20985 
-
20986  // state
-
20987  model.add_state("Susceptible", update_susceptible);
-
20988  model.add_state("Infected", update_infected);
-
20989  model.add_state("Recovered");
-
20990 
-
20991  // Global function
-
20992  epiworld::GlobalFun<TSeq> update = [](epiworld::Model<TSeq> * m) -> void
-
20993  {
-
20994 
-
20995  ModelSIRMixing<TSeq> * m_down =
-
20996  dynamic_cast<ModelSIRMixing<TSeq> *>(m);
-
20997 
-
20998  m_down->update_infected_list();
-
20999 
-
21000  return;
+
20974  // Recover
+
20975  m->array_double_tmp[n_events++] =
+
20976  1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m));
+
20977 
+
20978  #ifdef EPI_DEBUG
+
20979  if (n_events == 0u)
+
20980  {
+
20981  printf_epiworld(
+
20982  "[epi-debug] agent %i has 0 possible events!!\n",
+
20983  static_cast<int>(p->get_id())
+
20984  );
+
20985  throw std::logic_error("Zero events in infected.");
+
20986  }
+
20987  #else
+
20988  if (n_events == 0u)
+
20989  return;
+
20990  #endif
+
20991 
+
20992 
+
20993  // Running the roulette
+
20994  int which = roulette(n_events, m);
+
20995 
+
20996  if (which < 0)
+
20997  return;
+
20998 
+
20999  // Which roulette happen?
+
21000  p->rm_virus(m);
21001 
-
21002  };
+
21002  return ;
21003 
-
21004  model.add_globalevent(update, "Update infected individuals");
-
21005 
+
21004  } else
+
21005  throw std::logic_error("This function can only be applied to infected individuals. (SIR)") ;
21006 
-
21007  // Preparing the virus -------------------------------------------
-
21008  epiworld::Virus<TSeq> virus(vname, prevalence, true);
-
21009  virus.set_state(
-
21010  ModelSIRMixing<TSeq>::INFECTED,
-
21011  ModelSIRMixing<TSeq>::RECOVERED,
-
21012  ModelSIRMixing<TSeq>::RECOVERED
-
21013  );
-
21014 
-
21015  virus.set_prob_infecting(&model("Prob. Transmission"));
-
21016  virus.set_prob_recovery(&model("Prob. Recovery"));
-
21017 
-
21018  model.add_virus(virus);
-
21019 
-
21020  model.queuing_off(); // No queuing need
-
21021 
-
21022  // Adding the empty population
-
21023  model.agents_empty_graph(n);
+
21007  return;
+
21008 
+
21009  };
+
21010 
+
21011  // Setting up parameters
+
21012  model.add_param(contact_rate, "Contact rate");
+
21013  model.add_param(transmission_rate, "Prob. Transmission");
+
21014  model.add_param(recovery_rate, "Prob. Recovery");
+
21015 
+
21016  // state
+
21017  model.add_state("Susceptible", update_susceptible);
+
21018  model.add_state("Infected", update_infected);
+
21019  model.add_state("Recovered");
+
21020 
+
21021  // Global function
+
21022  epiworld::GlobalFun<TSeq> update = [](epiworld::Model<TSeq> * m) -> void
+
21023  {
21024 
-
21025  model.set_name("Susceptible-Infected-Removed (SIR) with Mixing");
-
21026 
-
21027  return;
-
21028 
-
21029 }
-
21030 
-
21031 template<typename TSeq>
-
21032 inline ModelSIRMixing<TSeq>::ModelSIRMixing(
-
21033  const std::string & vname,
-
21034  epiworld_fast_uint n,
-
21035  epiworld_double prevalence,
-
21036  epiworld_double contact_rate,
-
21037  epiworld_double transmission_rate,
-
21038  epiworld_double recovery_rate,
-
21039  std::vector< double > contact_matrix
-
21040  )
-
21041 {
-
21042 
-
21043  this->contact_matrix = contact_matrix;
+
21025  ModelSIRMixing<TSeq> * m_down =
+
21026  dynamic_cast<ModelSIRMixing<TSeq> *>(m);
+
21027 
+
21028  m_down->update_infected_list();
+
21029 
+
21030  return;
+
21031 
+
21032  };
+
21033 
+
21034  model.add_globalevent(update, "Update infected individuals");
+
21035 
+
21036 
+
21037  // Preparing the virus -------------------------------------------
+
21038  epiworld::Virus<TSeq> virus(vname, prevalence, true);
+
21039  virus.set_state(
+
21040  ModelSIRMixing<TSeq>::INFECTED,
+
21041  ModelSIRMixing<TSeq>::RECOVERED,
+
21042  ModelSIRMixing<TSeq>::RECOVERED
+
21043  );
21044 
-
21045  ModelSIRMixing(
-
21046  *this,
-
21047  vname,
-
21048  n,
-
21049  prevalence,
-
21050  contact_rate,
-
21051  transmission_rate,
-
21052  recovery_rate,
-
21053  contact_matrix
-
21054  );
-
21055 
-
21056  return;
-
21057 
-
21058 }
-
21059 
-
21060 template<typename TSeq>
-
21061 inline ModelSIRMixing<TSeq> & ModelSIRMixing<TSeq>::initial_states(
-
21062  std::vector< double > proportions_,
-
21063  std::vector< int > /* queue_ */
-
21064 )
-
21065 {
-
21066 
-
21067  Model<TSeq>::initial_states_fun =
-
21068  create_init_function_sir<TSeq>(proportions_)
-
21069  ;
-
21070 
-
21071  return *this;
+
21045  virus.set_prob_infecting(&model("Prob. Transmission"));
+
21046  virus.set_prob_recovery(&model("Prob. Recovery"));
+
21047 
+
21048  model.add_virus(virus);
+
21049 
+
21050  model.queuing_off(); // No queuing need
+
21051 
+
21052  // Adding the empty population
+
21053  model.agents_empty_graph(n);
+
21054 
+
21055  model.set_name("Susceptible-Infected-Removed (SIR) with Mixing");
+
21056 
+
21057  return;
+
21058 
+
21059 }
+
21060 
+
21061 template<typename TSeq>
+
21062 inline ModelSIRMixing<TSeq>::ModelSIRMixing(
+
21063  const std::string & vname,
+
21064  epiworld_fast_uint n,
+
21065  epiworld_double prevalence,
+
21066  epiworld_double contact_rate,
+
21067  epiworld_double transmission_rate,
+
21068  epiworld_double recovery_rate,
+
21069  std::vector< double > contact_matrix
+
21070  )
+
21071 {
21072 
-
21073 }
+
21073  this->contact_matrix = contact_matrix;
21074 
-
21075 #endif
-
21076 /*//////////////////////////////////////////////////////////////////////////////
-
21078 
-
21079  End of -include/epiworld//models/sirmixing.hpp-
-
21080 
-
21083 
-
21084 
-
21085 
-
21086 
-
21087 }
-
21088 
-
21089 #endif
-
21090 /*//////////////////////////////////////////////////////////////////////////////
-
21092 
-
21093  End of -include/epiworld/models/models.hpp-
-
21094 
-
21097 
-
21098 
-
21099 
-
21100 }
-
21101 
-
21102 #endif
+
21075  ModelSIRMixing(
+
21076  *this,
+
21077  vname,
+
21078  n,
+
21079  prevalence,
+
21080  contact_rate,
+
21081  transmission_rate,
+
21082  recovery_rate,
+
21083  contact_matrix
+
21084  );
+
21085 
+
21086  return;
+
21087 
+
21088 }
+
21089 
+
21090 template<typename TSeq>
+
21091 inline ModelSIRMixing<TSeq> & ModelSIRMixing<TSeq>::initial_states(
+
21092  std::vector< double > proportions_,
+
21093  std::vector< int > /* queue_ */
+
21094 )
+
21095 {
+
21096 
+
21097  Model<TSeq>::initial_states_fun =
+
21098  create_init_function_sir<TSeq>(proportions_)
+
21099  ;
+
21100 
+
21101  return *this;
+
21102 
+
21103 }
+
21104 
+
21105 #endif
+
21106 /*//////////////////////////////////////////////////////////////////////////////
+
21108 
+
21109  End of -include/epiworld//models/sirmixing.hpp-
+
21110 
+
21113 
+
21114 
+
21115 
+
21116 
+
21117 }
+
21118 
+
21119 #endif
+
21120 /*//////////////////////////////////////////////////////////////////////////////
+
21122 
+
21123  End of -include/epiworld/models/models.hpp-
+
21124 
+
21127 
+
21128 
+
21129 
+
21130 }
+
21131 
+
21132 #endif
AdjList
Definition: adjlist-bones.hpp:4
AdjList::vcount
size_t vcount() const
Number of vertices/nodes in the network.
Definition: adjlist-meat.hpp:203
AdjList::read_edgelist
void read_edgelist(std::string fn, int size, int skip=0, bool directed=true)
Read an edgelist.
Definition: adjlist-meat.hpp:92
@@ -19317,56 +19347,56 @@
Tools_const
Set of Tools (const) (useful for iterators)
Definition: tools-bones.hpp:117
Tools
Set of tools (useful for building iterators)
Definition: tools-bones.hpp:18
Virus
Virus.
Definition: virus-bones.hpp:24
-
epiworld::AdjList
Definition: epiworld.hpp:5019
-
epiworld::Agent
Agent (agents)
Definition: epiworld.hpp:13643
-
epiworld::Agent::get_id
int get_id() const
Id of the individual.
Definition: epiworld.hpp:14670
-
epiworld::Agent::rm_agent_by_virus
void rm_agent_by_virus(Model< TSeq > *model, epiworld_fast_int state_new=-99, epiworld_fast_int queue=-99)
Agent removed by virus.
Definition: epiworld.hpp:14619
-
epiworld::DataBase
Statistical data about the process.
Definition: epiworld.hpp:2890
-
epiworld::Entity
Definition: epiworld.hpp:12218
-
epiworld::GlobalEvent
Template for a Global Event.
Definition: epiworld.hpp:6052
-
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6296
-
epiworld::Model::get_agents
std::vector< Agent< TSeq > > & get_agents()
Returns a reference to the vector of agents.
Definition: epiworld.hpp:7517
-
epiworld::Model::load_agents_entities_ties
void load_agents_entities_ties(const std::vector< int > &agents_ids, const std::vector< int > &entities_ids)
Associate agents-entities from data.
Definition: epiworld.hpp:8030
-
epiworld::Model::rm_globalevent
void rm_globalevent(size_t i)
Remove a global action by index.
Definition: epiworld.hpp:9537
-
epiworld::Model::get_agents_viruses
std::vector< Viruses_const< TSeq > > get_agents_viruses() const
Returns a const vector with the viruses of the agents.
Definition: epiworld.hpp:7539
-
epiworld::Model::set_agents_data
void set_agents_data(double *data_, size_t ncols_)
Set the agents data object.
Definition: epiworld.hpp:9622
-
epiworld::Model::queuing_on
void queuing_on()
Activates the queuing system (default.)
Definition: epiworld.hpp:9562
-
epiworld::Model::is_queuing_on
bool is_queuing_on() const
Query if the queuing system is on.
Definition: epiworld.hpp:9575
-
epiworld::Model::run_multiple
void run_multiple(epiworld_fast_uint ndays, epiworld_fast_uint nexperiments, int seed_=-1, std::function< void(size_t, Model< TSeq > *)> fun=make_save_run< TSeq >(), bool reset=true, bool verbose=true, int nthreads=1)
Definition: epiworld.hpp:8334
-
epiworld::Model::get_queue
Queue< TSeq > & get_queue()
Retrieve the Queue object.
Definition: epiworld.hpp:9581
-
epiworld::Model::set_name
void set_name(std::string name)
Set the name object.
Definition: epiworld.hpp:9640
-
epiworld::Model::load_agents_entities_ties
void load_agents_entities_ties(std::string fn, int skip)
Associate agents-entities from a file.
Definition: epiworld.hpp:7972
-
epiworld::Model::get_n_tools
size_t get_n_tools() const
Number of tools in the model.
Definition: epiworld.hpp:8603
-
epiworld::Model::add_globalevent
void add_globalevent(std::function< void(Model< TSeq > *)> fun, std::string name="A global action", int date=-99)
Set a global action.
Definition: epiworld.hpp:9463
-
epiworld::Model::write_data
void write_data(std::string fn_virus_info, std::string fn_virus_hist, std::string fn_tool_info, std::string fn_tool_hist, std::string fn_total_hist, std::string fn_transmission, std::string fn_transition, std::string fn_reproductive_number, std::string fn_generation_time) const
Wrapper of DataBase::write_data
Definition: epiworld.hpp:8674
-
epiworld::Model::events_run
void events_run()
Executes the stored action.
Definition: epiworld.hpp:7151
-
epiworld::Model::queuing_off
Model< TSeq > & queuing_off()
Deactivates the queuing system.
Definition: epiworld.hpp:9568
-
epiworld::Model::reset
virtual void reset()
Reset the model.
Definition: epiworld.hpp:8778
-
epiworld::Model::get_agents_states
std::vector< epiworld_fast_uint > get_agents_states() const
Returns a vector with the states of the agents.
Definition: epiworld.hpp:7529
-
epiworld::Model::get_globalevent
GlobalEvent< TSeq > & get_globalevent(size_t i)
Retrieve a global action by index.
Definition: epiworld.hpp:9503
-
epiworld::Model::today
int today() const
The current time of the model.
Definition: epiworld.hpp:8200
-
epiworld::Model::run
virtual Model< TSeq > & run(epiworld_fast_uint ndays, int seed=-1)
Runs the simulation (after initialization)
Definition: epiworld.hpp:8222
-
epiworld::Model::get_n_viruses
size_t get_n_viruses() const
Number of viruses in the model.
Definition: epiworld.hpp:8598
-
epiworld::Model::rm_globalevent
void rm_globalevent(std::string name)
Remove a global action by name.
Definition: epiworld.hpp:9517
-
epiworld::Model::get_agents_viruses
std::vector< Viruses< TSeq > > get_agents_viruses()
Returns a vector with the viruses of the agents.
Definition: epiworld.hpp:7552
-
epiworld::Model::set_user_data
void set_user_data(std::vector< std::string > names)
[@
Definition: epiworld.hpp:9439
-
epiworld::Model::get_globalevent
GlobalEvent< TSeq > & get_globalevent(std::string name)
Retrieve a global action by name.
Definition: epiworld.hpp:9489
-
epiworld::Model::events_add
void events_add(Agent< TSeq > *agent_, VirusPtr< TSeq > virus_, ToolPtr< TSeq > tool_, Entity< TSeq > *entity_, epiworld_fast_int new_state_, epiworld_fast_int queue_, EventFun< TSeq > call_, int idx_agent_, int idx_object_)
Construct a new Event object.
Definition: epiworld.hpp:7100
-
epiworld::Model::clone_ptr
virtual Model< TSeq > * clone_ptr()
Advanced usage: Makes a copy of data and returns it as undeleted pointer.
Definition: epiworld.hpp:7301
+
epiworld::AdjList
Definition: epiworld.hpp:5049
+
epiworld::Agent
Agent (agents)
Definition: epiworld.hpp:13673
+
epiworld::Agent::get_id
int get_id() const
Id of the individual.
Definition: epiworld.hpp:14700
+
epiworld::Agent::rm_agent_by_virus
void rm_agent_by_virus(Model< TSeq > *model, epiworld_fast_int state_new=-99, epiworld_fast_int queue=-99)
Agent removed by virus.
Definition: epiworld.hpp:14649
+
epiworld::DataBase
Statistical data about the process.
Definition: epiworld.hpp:2920
+
epiworld::Entity
Definition: epiworld.hpp:12248
+
epiworld::GlobalEvent
Template for a Global Event.
Definition: epiworld.hpp:6082
+
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6326
+
epiworld::Model::get_agents
std::vector< Agent< TSeq > > & get_agents()
Returns a reference to the vector of agents.
Definition: epiworld.hpp:7547
+
epiworld::Model::load_agents_entities_ties
void load_agents_entities_ties(const std::vector< int > &agents_ids, const std::vector< int > &entities_ids)
Associate agents-entities from data.
Definition: epiworld.hpp:8060
+
epiworld::Model::rm_globalevent
void rm_globalevent(size_t i)
Remove a global action by index.
Definition: epiworld.hpp:9567
+
epiworld::Model::get_agents_viruses
std::vector< Viruses_const< TSeq > > get_agents_viruses() const
Returns a const vector with the viruses of the agents.
Definition: epiworld.hpp:7569
+
epiworld::Model::set_agents_data
void set_agents_data(double *data_, size_t ncols_)
Set the agents data object.
Definition: epiworld.hpp:9652
+
epiworld::Model::queuing_on
void queuing_on()
Activates the queuing system (default.)
Definition: epiworld.hpp:9592
+
epiworld::Model::is_queuing_on
bool is_queuing_on() const
Query if the queuing system is on.
Definition: epiworld.hpp:9605
+
epiworld::Model::run_multiple
void run_multiple(epiworld_fast_uint ndays, epiworld_fast_uint nexperiments, int seed_=-1, std::function< void(size_t, Model< TSeq > *)> fun=make_save_run< TSeq >(), bool reset=true, bool verbose=true, int nthreads=1)
Definition: epiworld.hpp:8364
+
epiworld::Model::get_queue
Queue< TSeq > & get_queue()
Retrieve the Queue object.
Definition: epiworld.hpp:9611
+
epiworld::Model::set_name
void set_name(std::string name)
Set the name object.
Definition: epiworld.hpp:9670
+
epiworld::Model::load_agents_entities_ties
void load_agents_entities_ties(std::string fn, int skip)
Associate agents-entities from a file.
Definition: epiworld.hpp:8002
+
epiworld::Model::get_n_tools
size_t get_n_tools() const
Number of tools in the model.
Definition: epiworld.hpp:8633
+
epiworld::Model::add_globalevent
void add_globalevent(std::function< void(Model< TSeq > *)> fun, std::string name="A global action", int date=-99)
Set a global action.
Definition: epiworld.hpp:9493
+
epiworld::Model::write_data
void write_data(std::string fn_virus_info, std::string fn_virus_hist, std::string fn_tool_info, std::string fn_tool_hist, std::string fn_total_hist, std::string fn_transmission, std::string fn_transition, std::string fn_reproductive_number, std::string fn_generation_time) const
Wrapper of DataBase::write_data
Definition: epiworld.hpp:8704
+
epiworld::Model::events_run
void events_run()
Executes the stored action.
Definition: epiworld.hpp:7181
+
epiworld::Model::queuing_off
Model< TSeq > & queuing_off()
Deactivates the queuing system.
Definition: epiworld.hpp:9598
+
epiworld::Model::reset
virtual void reset()
Reset the model.
Definition: epiworld.hpp:8808
+
epiworld::Model::get_agents_states
std::vector< epiworld_fast_uint > get_agents_states() const
Returns a vector with the states of the agents.
Definition: epiworld.hpp:7559
+
epiworld::Model::get_globalevent
GlobalEvent< TSeq > & get_globalevent(size_t i)
Retrieve a global action by index.
Definition: epiworld.hpp:9533
+
epiworld::Model::today
int today() const
The current time of the model.
Definition: epiworld.hpp:8230
+
epiworld::Model::run
virtual Model< TSeq > & run(epiworld_fast_uint ndays, int seed=-1)
Runs the simulation (after initialization)
Definition: epiworld.hpp:8252
+
epiworld::Model::get_n_viruses
size_t get_n_viruses() const
Number of viruses in the model.
Definition: epiworld.hpp:8628
+
epiworld::Model::rm_globalevent
void rm_globalevent(std::string name)
Remove a global action by name.
Definition: epiworld.hpp:9547
+
epiworld::Model::get_agents_viruses
std::vector< Viruses< TSeq > > get_agents_viruses()
Returns a vector with the viruses of the agents.
Definition: epiworld.hpp:7582
+
epiworld::Model::set_user_data
void set_user_data(std::vector< std::string > names)
[@
Definition: epiworld.hpp:9469
+
epiworld::Model::get_globalevent
GlobalEvent< TSeq > & get_globalevent(std::string name)
Retrieve a global action by name.
Definition: epiworld.hpp:9519
+
epiworld::Model::events_add
void events_add(Agent< TSeq > *agent_, VirusPtr< TSeq > virus_, ToolPtr< TSeq > tool_, Entity< TSeq > *entity_, epiworld_fast_int new_state_, epiworld_fast_int queue_, EventFun< TSeq > call_, int idx_agent_, int idx_object_)
Construct a new Event object.
Definition: epiworld.hpp:7130
+
epiworld::Model::clone_ptr
virtual Model< TSeq > * clone_ptr()
Advanced usage: Makes a copy of data and returns it as undeleted pointer.
Definition: epiworld.hpp:7331
epiworld::Progress
A simple progress bar.
Definition: epiworld.hpp:765
-
epiworld::Queue
Controls which agents are verified at each step.
Definition: epiworld.hpp:5912
-
epiworld::Tool
Tools for defending the agent against the virus.
Definition: epiworld.hpp:11409
-
epiworld::UserData
Personalized data by the user.
Definition: epiworld.hpp:2406
-
epiworld::Virus
Virus.
Definition: epiworld.hpp:10105
-
epiworld::epimodels::ModelSEIRCONN
Definition: epiworld.hpp:17665
-
epiworld::epimodels::ModelSEIRDCONN
Definition: epiworld.hpp:19012
-
epiworld::epimodels::ModelSEIRMixing
Definition: epiworld.hpp:20047
-
epiworld::epimodels::ModelSIRCONN
Definition: epiworld.hpp:17224
-
epiworld::epimodels::ModelSIRDCONN
Definition: epiworld.hpp:18655
-
epiworld::epimodels::ModelSIRLogit
Template for a Susceptible-Infected-Removed (SIR) model.
Definition: epiworld.hpp:19471
-
epiworld::epimodels::ModelSIRMixing
Definition: epiworld.hpp:20589
-
epiworld::sampler::sample_virus_single
Virus< TSeq > * sample_virus_single(Agent< TSeq > *p, Model< TSeq > *m)
Sample from neighbors pool of viruses (at most one)
Definition: epiworld.hpp:13409
-
epiworld::sampler::make_sample_virus_neighbors
std::function< Virus< TSeq > *(Agent< TSeq > *, Model< TSeq > *)> make_sample_virus_neighbors(std::vector< epiworld_fast_uint > exclude={})
Make a function to sample from neighbors.
Definition: epiworld.hpp:13241
+
epiworld::Queue
Controls which agents are verified at each step.
Definition: epiworld.hpp:5942
+
epiworld::Tool
Tools for defending the agent against the virus.
Definition: epiworld.hpp:11439
+
epiworld::UserData
Personalized data by the user.
Definition: epiworld.hpp:2436
+
epiworld::Virus
Virus.
Definition: epiworld.hpp:10135
+
epiworld::epimodels::ModelSEIRCONN
Definition: epiworld.hpp:17695
+
epiworld::epimodels::ModelSEIRDCONN
Definition: epiworld.hpp:19042
+
epiworld::epimodels::ModelSEIRMixing
Definition: epiworld.hpp:20077
+
epiworld::epimodels::ModelSIRCONN
Definition: epiworld.hpp:17254
+
epiworld::epimodels::ModelSIRDCONN
Definition: epiworld.hpp:18685
+
epiworld::epimodels::ModelSIRLogit
Template for a Susceptible-Infected-Removed (SIR) model.
Definition: epiworld.hpp:19501
+
epiworld::epimodels::ModelSIRMixing
Definition: epiworld.hpp:20619
+
epiworld::sampler::sample_virus_single
Virus< TSeq > * sample_virus_single(Agent< TSeq > *p, Model< TSeq > *m)
Sample from neighbors pool of viruses (at most one)
Definition: epiworld.hpp:13439
+
epiworld::sampler::make_sample_virus_neighbors
std::function< Virus< TSeq > *(Agent< TSeq > *, Model< TSeq > *)> make_sample_virus_neighbors(std::vector< epiworld_fast_uint > exclude={})
Make a function to sample from neighbors.
Definition: epiworld.hpp:13271
sampler
Functions for sampling viruses.
Definition: agent-meat-virus-sampling.hpp:8
diff --git a/include_2epiworld_2epiworld_8hpp_source.html b/include_2epiworld_2epiworld_8hpp_source.html index 88a64f881..5c50d572e 100644 --- a/include_2epiworld_2epiworld_8hpp_source.html +++ b/include_2epiworld_2epiworld_8hpp_source.html @@ -90,8 +90,8 @@
18 
19 /* Versioning */
20 #define EPIWORLD_VERSION_MAJOR 0
-
21 #define EPIWORLD_VERSION_MINOR 4
-
22 #define EPIWORLD_VERSION_PATCH 3
+
21 #define EPIWORLD_VERSION_MINOR 5
+
22 #define EPIWORLD_VERSION_PATCH 0
23 
24 static const int epiworld_version_major = EPIWORLD_VERSION_MAJOR;
25 static const int epiworld_version_minor = EPIWORLD_VERSION_MINOR;
diff --git a/init-functions_8hpp_source.html b/init-functions_8hpp_source.html index d57ec2c24..5ef9349c1 100644 --- a/init-functions_8hpp_source.html +++ b/init-functions_8hpp_source.html @@ -385,8 +385,8 @@
329 
330 #endif
Queue
Controls which agents are verified at each step.
Definition: queue-bones.hpp:16
-
epiworld::AgentsSample
Sample of agents.
Definition: epiworld.hpp:15221
-
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6296
+
epiworld::AgentsSample
Sample of agents.
Definition: epiworld.hpp:15251
+
epiworld::Model
Core class of epiworld.
Definition: epiworld.hpp:6326
diff --git a/latex/agent-meat-state_8hpp__dep__incl.pdf b/latex/agent-meat-state_8hpp__dep__incl.pdf index 582ea3dfb098dbe0c70df82e0b5d61e3b986d710..74b66b814a5f8a8508d6dcf87c76d0197504a0f0 100644 GIT binary patch delta 21 ccmbPaKFNGTnIwmik%57ssgdR8I!O^G07%&d&j0`b delta 21 ccmbPaKFNGTnIwmyrJ;$jiK)frI!O^G07+~G-2eap diff --git a/latex/agent-meat-state_8hpp__incl.pdf b/latex/agent-meat-state_8hpp__incl.pdf index cd698d152b268c7b29550a45d66870f47374b28f..37141f800d9c72b08810c52410e1a6b2563e4ddb 100644 GIT binary patch delta 21 ccmca-a?fN#mIQ~9k%57ssgdR8B8fMQ095n`9smFU delta 21 ccmca-a?fN#mIQ~PrJ;$jiK)frB8fMQ09A(vEC2ui diff --git a/latex/class_l_f_m_c_m_c.tex b/latex/class_l_f_m_c_m_c.tex index 43330bc12..504713cce 100644 --- a/latex/class_l_f_m_c_m_c.tex +++ b/latex/class_l_f_m_c_m_c.tex @@ -72,6 +72,12 @@ \mbox{\Hypertarget{class_l_f_m_c_m_c_ad3cba41457c38a50bc16b5783a3b3fb5}\label{class_l_f_m_c_m_c_ad3cba41457c38a50bc16b5783a3b3fb5}} std\+::vector$<$ TData $>$ $\ast$ {\bfseries get\+\_\+sampled\+\_\+data} () \item +\mbox{\Hypertarget{class_l_f_m_c_m_c_a798c3bf3bb2c601be3456c907d5a6ea1}\label{class_l_f_m_c_m_c_a798c3bf3bb2c601be3456c907d5a6ea1}} +const std\+::vector$<$ epiworld\+\_\+double $>$ \& {\bfseries get\+\_\+accepted\+\_\+params} () +\item +\mbox{\Hypertarget{class_l_f_m_c_m_c_afa81c1f9d53945f97d0a3b4742cf96ec}\label{class_l_f_m_c_m_c_afa81c1f9d53945f97d0a3b4742cf96ec}} +const std\+::vector$<$ epiworld\+\_\+double $>$ \& {\bfseries get\+\_\+accepted\+\_\+stats} () +\item \mbox{\Hypertarget{class_l_f_m_c_m_c_a7e626ab23d03daac688c7ce51e44ba23}\label{class_l_f_m_c_m_c_a7e626ab23d03daac688c7ce51e44ba23}} void {\bfseries set\+\_\+par\+\_\+names} (std\+::vector$<$ std\+::string $>$ names) \item @@ -84,8 +90,8 @@ \mbox{\Hypertarget{class_l_f_m_c_m_c_a43e3232efd453703869544b6876ee9ae}\label{class_l_f_m_c_m_c_a43e3232efd453703869544b6876ee9ae}} std\+::vector$<$ epiworld\+\_\+double $>$ {\bfseries get\+\_\+stats\+\_\+mean} () \item -\mbox{\Hypertarget{class_l_f_m_c_m_c_adf46ba06d7e03b3f71aa5d9e0de44c78}\label{class_l_f_m_c_m_c_adf46ba06d7e03b3f71aa5d9e0de44c78}} -void {\bfseries print} () +\mbox{\Hypertarget{class_l_f_m_c_m_c_aa3030ef8d08f00fdec8b2fbfa8a33628}\label{class_l_f_m_c_m_c_aa3030ef8d08f00fdec8b2fbfa8a33628}} +void {\bfseries print} (size\+\_\+t burnin=0u) const \end{DoxyCompactItemize} \begin{Indent}\textbf{ Random number generation}\par {\em diff --git a/latex/class_model__coll__graph.pdf b/latex/class_model__coll__graph.pdf index b0b946da962fae5fb5d316b0b8a1d4d0ebb9bfc7..f665788b398e3900964ad18641b316c3e9d93d08 100644 GIT binary patch delta 21 ccmZqDZ_?k;C(2=DWME)uYGk>2n&=xw07!5Ko&W#< delta 21 ccmZqDZ_?k;C(2=HX=q|>VrsE@n&=xw07(M|tN;K2 diff --git a/latex/class_model_diff_net__coll__graph.pdf b/latex/class_model_diff_net__coll__graph.pdf index 650ced1f1b63bdbe01b9b60d570d8338090c053f..0f4fc17b5c64e48cd9c2315925be5fd30113891e 100644 GIT binary patch delta 21 ccmdnwyvcckkvxZyk%57ssgdPoEBOj00851i4*&oF 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get\+\_\+sampled\+\_\+data} () \item +\mbox{\Hypertarget{classepiworld_1_1_l_f_m_c_m_c_ad4fc7c8a7531c28b934fb71a076b88b9}\label{classepiworld_1_1_l_f_m_c_m_c_ad4fc7c8a7531c28b934fb71a076b88b9}} +const std\+::vector$<$ epiworld\+\_\+double $>$ \& {\bfseries get\+\_\+accepted\+\_\+params} () +\item +\mbox{\Hypertarget{classepiworld_1_1_l_f_m_c_m_c_afbaeb759dea2596fd678f698df1566ab}\label{classepiworld_1_1_l_f_m_c_m_c_afbaeb759dea2596fd678f698df1566ab}} +const std\+::vector$<$ epiworld\+\_\+double $>$ \& {\bfseries get\+\_\+accepted\+\_\+stats} () +\item \mbox{\Hypertarget{classepiworld_1_1_l_f_m_c_m_c_a7e626ab23d03daac688c7ce51e44ba23}\label{classepiworld_1_1_l_f_m_c_m_c_a7e626ab23d03daac688c7ce51e44ba23}} void {\bfseries set\+\_\+par\+\_\+names} (std\+::vector$<$ std\+::string $>$ names) \item @@ -84,8 +90,8 @@ \mbox{\Hypertarget{classepiworld_1_1_l_f_m_c_m_c_a43e3232efd453703869544b6876ee9ae}\label{classepiworld_1_1_l_f_m_c_m_c_a43e3232efd453703869544b6876ee9ae}} std\+::vector$<$ epiworld\+\_\+double $>$ {\bfseries get\+\_\+stats\+\_\+mean} () \item -\mbox{\Hypertarget{classepiworld_1_1_l_f_m_c_m_c_adf46ba06d7e03b3f71aa5d9e0de44c78}\label{classepiworld_1_1_l_f_m_c_m_c_adf46ba06d7e03b3f71aa5d9e0de44c78}} -void {\bfseries print} () +\mbox{\Hypertarget{classepiworld_1_1_l_f_m_c_m_c_aa3030ef8d08f00fdec8b2fbfa8a33628}\label{classepiworld_1_1_l_f_m_c_m_c_aa3030ef8d08f00fdec8b2fbfa8a33628}} +void {\bfseries print} (size\+\_\+t burnin=0u) const \end{DoxyCompactItemize} \begin{Indent}\textbf{ Random number generation}\par {\em diff --git a/latex/classepiworld_1_1_model__coll__graph.pdf b/latex/classepiworld_1_1_model__coll__graph.pdf index b50a3ee85e9cbf43ffd6eb84d12bd552d366af87..16916ee0e779523db1059ecc7b4370356e2d4424 100644 GIT binary patch delta 20 ccmdmMxYuyQNilXKBLf3NQ=`on#NILj08niQRsaA1 delta 20 ccmdmMxYuyQNilXqOG6W56VuHX#NILj08sY_WdHyG diff --git a/latex/classepiworld_1_1epimodels_1_1_model_diff_net__coll__graph.pdf 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-\hypertarget{md__r_e_a_d_m_e_old_autotoc_md48}{}\doxysection{Disease dynamics}\label{md__r_e_a_d_m_e_old_autotoc_md48} +\hypertarget{md__r_e_a_d_m_e_old_autotoc_md50}{}\doxysection{Disease dynamics}\label{md__r_e_a_d_m_e_old_autotoc_md50} Diseases continuously evolve in time. Changes in their genetic sequence make them more or less resistant to the particular version of the vaccine. Mutations also affect the transmissibility level and mortality rate of the disease. Using this approach allows making vaccination efficacy a function of compatibility between the variant and the vaccine. -When an individual becomes infected, the disease accumulates mutations in the new host. Ultimately, there is no single version of the disease present in the model, but rather an infinite number of them, each slightly different from the other.\hypertarget{md__r_e_a_d_m_e_old_autotoc_md49}{}\doxysection{Network dynamics}\label{md__r_e_a_d_m_e_old_autotoc_md49} -We can assume that the Population is organized in fully connected blocks for the first version of the model. Block sizes and the number of connections between blocks are Poisson random variables. Individuals interact with all the members of their blocks, and bridging individuals allow the disease to move across blocks.\hypertarget{md__r_e_a_d_m_e_old_autotoc_md50}{}\doxysection{Contagion dynamics}\label{md__r_e_a_d_m_e_old_autotoc_md50} -The transmission of the disease will be governed by the number of vaccinated, infected, and recovered within each block. Transmission between blocks will be treated in the same way, although individuals bridging the block will only interact with others within the block and their direct connections across the blocks.\hypertarget{md__r_e_a_d_m_e_old_autotoc_md51}{}\doxysection{Time dynamics}\label{md__r_e_a_d_m_e_old_autotoc_md51} +When an individual becomes infected, the disease accumulates mutations in the new host. Ultimately, there is no single version of the disease present in the model, but rather an infinite number of them, each slightly different from the other.\hypertarget{md__r_e_a_d_m_e_old_autotoc_md51}{}\doxysection{Network dynamics}\label{md__r_e_a_d_m_e_old_autotoc_md51} +We can assume that the Population is organized in fully connected blocks for the first version of the model. Block sizes and the number of connections between blocks are Poisson random variables. Individuals interact with all the members of their blocks, and bridging individuals allow the disease to move across blocks.\hypertarget{md__r_e_a_d_m_e_old_autotoc_md52}{}\doxysection{Contagion dynamics}\label{md__r_e_a_d_m_e_old_autotoc_md52} +The transmission of the disease will be governed by the number of vaccinated, infected, and recovered within each block. Transmission between blocks will be treated in the same way, although individuals bridging the block will only interact with others within the block and their direct connections across the blocks.\hypertarget{md__r_e_a_d_m_e_old_autotoc_md53}{}\doxysection{Time dynamics}\label{md__r_e_a_d_m_e_old_autotoc_md53} Time dynamics has two components, how biology evolves and how agents react. The model develops as a continuous-\/time Markov process. Each block of individuals takes action at rates {\ttfamily L(i$\vert$N(i))} function of the local number of infections. This way, if ~\newline -\hypertarget{md__r_e_a_d_m_e_old_autotoc_md52}{}\doxysection{Updating agent\textquotesingle{}s status}\label{md__r_e_a_d_m_e_old_autotoc_md52} +\hypertarget{md__r_e_a_d_m_e_old_autotoc_md54}{}\doxysection{Updating agent\textquotesingle{}s status}\label{md__r_e_a_d_m_e_old_autotoc_md54} Like most other components, updating agents\textquotesingle{} states can be personalized. A naive approach allows agents to get infected with a single virus or stay as-\/is. The probability of this event is conditional on acquiring at most one virus. Since these are independent events, the conditional probability is computed as follows\+: @@ -30,7 +30,7 @@ \end{DoxyCode} -Furthermore, the (Variant, Person) pairs are treated independently.\hypertarget{md__r_e_a_d_m_e_old_autotoc_md53}{}\doxysubsection{Other parameters}\label{md__r_e_a_d_m_e_old_autotoc_md53} +Furthermore, the (Variant, Person) pairs are treated independently.\hypertarget{md__r_e_a_d_m_e_old_autotoc_md55}{}\doxysubsection{Other parameters}\label{md__r_e_a_d_m_e_old_autotoc_md55} \begin{DoxyItemize} \item Who did you get the infection from. diff --git a/latex/md_paper_mixing.tex b/latex/md_paper_mixing.tex index a706119ce..651330f03 100644 --- a/latex/md_paper_mixing.tex +++ b/latex/md_paper_mixing.tex @@ -1,4 +1,4 @@ -George G. Vega Yon, Ph.\+D. 2024-\/04-\/25\hypertarget{md_paper_mixing_autotoc_md38}{}\doxysection{Case 1\+: No grouping}\label{md_paper_mixing_autotoc_md38} +George G. Vega Yon, Ph.\+D. 2024-\/04-\/25\hypertarget{md_paper_mixing_autotoc_md40}{}\doxysection{Case 1\+: No grouping}\label{md_paper_mixing_autotoc_md40} We will look into the probability of drawing infected individuals to simplify the algorithm. There are \$I\$ infected individuals at any time in the simulation; thus, instead of drawing from \$\+Bern(c/N, N)\$, we will be drawing from \$\+Bern(c/N, I)\$. The next step is to check which infected individuals should be drawn. Let’s compare the distributions using the hypergeometric as an example\+: @@ -56,7 +56,7 @@ -These two approaches are equivalent, but the second one is more efficient from the computational perspective.\hypertarget{md_paper_mixing_autotoc_md39}{}\doxysection{Case 2\+: Grouping}\label{md_paper_mixing_autotoc_md39} +These two approaches are equivalent, but the second one is more efficient from the computational perspective.\hypertarget{md_paper_mixing_autotoc_md41}{}\doxysection{Case 2\+: Grouping}\label{md_paper_mixing_autotoc_md41} This explores the case when we have mixing across groups. The question is if we can replicate the effect at the group level. diff --git a/latex/namespaceepiworld_1_1sampler.tex b/latex/namespaceepiworld_1_1sampler.tex index 6a0dcaba1..3d4acaa49 100644 --- a/latex/namespaceepiworld_1_1sampler.tex +++ b/latex/namespaceepiworld_1_1sampler.tex @@ -8,11 +8,11 @@ \doxysubsection*{Functions} \begin{DoxyCompactItemize} \item -{\footnotesize template$<$typename TSeq $>$ }\\std\+::function$<$ void(\mbox{\hyperlink{classepiworld_1_1_agent}{Agent}}$<$ TSeq $>$ $\ast$, \mbox{\hyperlink{classepiworld_1_1_model}{Model}}$<$ TSeq $>$ $\ast$)$>$ \mbox{\hyperlink{namespaceepiworld_1_1sampler_af58114de37befaa5de5450e3d4414b22}{make\+\_\+update\+\_\+susceptible}} (std\+::vector$<$ epiworld\+\_\+fast\+\_\+uint $>$ exclude=\{\}) +{\footnotesize template$<$typename TSeq = EPI\+\_\+\+DEFAULT\+\_\+\+TSEQ$>$ }\\std\+::function$<$ void(\mbox{\hyperlink{classepiworld_1_1_agent}{Agent}}$<$ TSeq $>$ $\ast$, \mbox{\hyperlink{classepiworld_1_1_model}{Model}}$<$ TSeq $>$ $\ast$)$>$ \mbox{\hyperlink{namespaceepiworld_1_1sampler_af58114de37befaa5de5450e3d4414b22}{make\+\_\+update\+\_\+susceptible}} (std\+::vector$<$ epiworld\+\_\+fast\+\_\+uint $>$ exclude=\{\}) \begin{DoxyCompactList}\small\item\em Make a function to sample from neighbors. \end{DoxyCompactList}\item -{\footnotesize template$<$typename TSeq = int$>$ }\\std\+::function$<$ \mbox{\hyperlink{classepiworld_1_1_virus}{Virus}}$<$ TSeq $>$ $\ast$(\mbox{\hyperlink{classepiworld_1_1_agent}{Agent}}$<$ TSeq $>$ $\ast$, \mbox{\hyperlink{classepiworld_1_1_model}{Model}}$<$ TSeq $>$ $\ast$)$>$ \mbox{\hyperlink{namespaceepiworld_1_1sampler_a058e471163798e71719e9580b016692f}{make\+\_\+sample\+\_\+virus\+\_\+neighbors}} (std\+::vector$<$ epiworld\+\_\+fast\+\_\+uint $>$ exclude=\{\}) +{\footnotesize template$<$typename TSeq = EPI\+\_\+\+DEFAULT\+\_\+\+TSEQ$>$ }\\std\+::function$<$ \mbox{\hyperlink{classepiworld_1_1_virus}{Virus}}$<$ TSeq $>$ $\ast$(\mbox{\hyperlink{classepiworld_1_1_agent}{Agent}}$<$ TSeq $>$ $\ast$, \mbox{\hyperlink{classepiworld_1_1_model}{Model}}$<$ TSeq $>$ $\ast$)$>$ \mbox{\hyperlink{namespaceepiworld_1_1sampler_a058e471163798e71719e9580b016692f}{make\+\_\+sample\+\_\+virus\+\_\+neighbors}} (std\+::vector$<$ epiworld\+\_\+fast\+\_\+uint $>$ exclude=\{\}) \begin{DoxyCompactList}\small\item\em Make a function to sample from neighbors. \end{DoxyCompactList}\item -{\footnotesize template$<$typename TSeq = int$>$ }\\\mbox{\hyperlink{classepiworld_1_1_virus}{Virus}}$<$ TSeq $>$ $\ast$ \mbox{\hyperlink{namespaceepiworld_1_1sampler_a021132a942bb59db17289b6454315b4e}{sample\+\_\+virus\+\_\+single}} (\mbox{\hyperlink{classepiworld_1_1_agent}{Agent}}$<$ TSeq $>$ $\ast$p, \mbox{\hyperlink{classepiworld_1_1_model}{Model}}$<$ TSeq $>$ $\ast$m) +{\footnotesize template$<$typename TSeq = EPI\+\_\+\+DEFAULT\+\_\+\+TSEQ$>$ }\\\mbox{\hyperlink{classepiworld_1_1_virus}{Virus}}$<$ TSeq $>$ $\ast$ \mbox{\hyperlink{namespaceepiworld_1_1sampler_a021132a942bb59db17289b6454315b4e}{sample\+\_\+virus\+\_\+single}} (\mbox{\hyperlink{classepiworld_1_1_agent}{Agent}}$<$ TSeq $>$ $\ast$p, \mbox{\hyperlink{classepiworld_1_1_model}{Model}}$<$ TSeq $>$ $\ast$m) \begin{DoxyCompactList}\small\item\em Sample from neighbors pool of viruses (at most one) \end{DoxyCompactList}\end{DoxyCompactItemize} @@ -24,7 +24,7 @@ \index{epiworld::sampler@{epiworld::sampler}!make\_sample\_virus\_neighbors@{make\_sample\_virus\_neighbors}} \index{make\_sample\_virus\_neighbors@{make\_sample\_virus\_neighbors}!epiworld::sampler@{epiworld::sampler}} \doxysubsubsection{\texorpdfstring{make\_sample\_virus\_neighbors()}{make\_sample\_virus\_neighbors()}} -{\footnotesize\ttfamily template$<$typename TSeq = int$>$ \\ +{\footnotesize\ttfamily template$<$typename TSeq = EPI\+\_\+\+DEFAULT\+\_\+\+TSEQ$>$ \\ std\+::function$<$\mbox{\hyperlink{classepiworld_1_1_virus}{Virus}}$<$TSeq$>$$\ast$(\mbox{\hyperlink{classepiworld_1_1_agent}{Agent}}$<$TSeq$>$$\ast$,\mbox{\hyperlink{classepiworld_1_1_model}{Model}}$<$TSeq$>$$\ast$)$>$ epiworld\+::sampler\+::make\+\_\+sample\+\_\+virus\+\_\+neighbors (\begin{DoxyParamCaption}\item[{std\+::vector$<$ epiworld\+\_\+fast\+\_\+uint $>$}]{exclude = {\ttfamily \{\}} }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} @@ -50,7 +50,7 @@ \index{epiworld::sampler@{epiworld::sampler}!make\_update\_susceptible@{make\_update\_susceptible}} \index{make\_update\_susceptible@{make\_update\_susceptible}!epiworld::sampler@{epiworld::sampler}} \doxysubsubsection{\texorpdfstring{make\_update\_susceptible()}{make\_update\_susceptible()}} -{\footnotesize\ttfamily template$<$typename TSeq $>$ \\ +{\footnotesize\ttfamily template$<$typename TSeq = EPI\+\_\+\+DEFAULT\+\_\+\+TSEQ$>$ \\ std\+::function$<$void(\mbox{\hyperlink{classepiworld_1_1_agent}{Agent}}$<$TSeq$>$$\ast$,\mbox{\hyperlink{classepiworld_1_1_model}{Model}}$<$TSeq$>$$\ast$)$>$ epiworld\+::sampler\+::make\+\_\+update\+\_\+susceptible (\begin{DoxyParamCaption}\item[{std\+::vector$<$ epiworld\+\_\+fast\+\_\+uint $>$}]{exclude = {\ttfamily \{\}} }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} @@ -76,7 +76,7 @@ \index{epiworld::sampler@{epiworld::sampler}!sample\_virus\_single@{sample\_virus\_single}} \index{sample\_virus\_single@{sample\_virus\_single}!epiworld::sampler@{epiworld::sampler}} \doxysubsubsection{\texorpdfstring{sample\_virus\_single()}{sample\_virus\_single()}} -{\footnotesize\ttfamily template$<$typename TSeq = int$>$ \\ +{\footnotesize\ttfamily template$<$typename TSeq = EPI\+\_\+\+DEFAULT\+\_\+\+TSEQ$>$ \\ \mbox{\hyperlink{classepiworld_1_1_virus}{Virus}}$<$TSeq$>$$\ast$ epiworld\+::sampler\+::sample\+\_\+virus\+\_\+single (\begin{DoxyParamCaption}\item[{\mbox{\hyperlink{classepiworld_1_1_agent}{Agent}}$<$ TSeq $>$ $\ast$}]{p, }\item[{\mbox{\hyperlink{classepiworld_1_1_model}{Model}}$<$ TSeq $>$ $\ast$}]{m }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} diff --git a/latex/namespacesampler.tex b/latex/namespacesampler.tex index ad7d67768..04c68ab09 100644 --- a/latex/namespacesampler.tex +++ b/latex/namespacesampler.tex @@ -8,11 +8,11 @@ \doxysubsection*{Functions} \begin{DoxyCompactItemize} \item -{\footnotesize template$<$typename TSeq $>$ }\\std\+::function$<$ void(\mbox{\hyperlink{class_agent}{Agent}}$<$ TSeq $>$ $\ast$, \mbox{\hyperlink{class_model}{Model}}$<$ TSeq $>$ $\ast$)$>$ \mbox{\hyperlink{namespacesampler_a9f4c303b5e9016b050dd008fec902448}{make\+\_\+update\+\_\+susceptible}} (std\+::vector$<$ epiworld\+\_\+fast\+\_\+uint $>$ exclude=\{\}) +{\footnotesize template$<$typename TSeq = EPI\+\_\+\+DEFAULT\+\_\+\+TSEQ$>$ }\\std\+::function$<$ void(\mbox{\hyperlink{class_agent}{Agent}}$<$ TSeq $>$ $\ast$, \mbox{\hyperlink{class_model}{Model}}$<$ TSeq $>$ $\ast$)$>$ \mbox{\hyperlink{namespacesampler_a9f4c303b5e9016b050dd008fec902448}{make\+\_\+update\+\_\+susceptible}} (std\+::vector$<$ epiworld\+\_\+fast\+\_\+uint $>$ exclude=\{\}) \begin{DoxyCompactList}\small\item\em Make a function to sample from neighbors. \end{DoxyCompactList}\item -{\footnotesize template$<$typename TSeq = int$>$ }\\std\+::function$<$ \mbox{\hyperlink{class_virus}{Virus}}$<$ TSeq $>$ $\ast$(\mbox{\hyperlink{class_agent}{Agent}}$<$ TSeq $>$ $\ast$, \mbox{\hyperlink{class_model}{Model}}$<$ TSeq $>$ $\ast$)$>$ \mbox{\hyperlink{namespacesampler_a4cafc444e0a6c563f34ed5f9b5366ae4}{make\+\_\+sample\+\_\+virus\+\_\+neighbors}} (std\+::vector$<$ epiworld\+\_\+fast\+\_\+uint $>$ exclude=\{\}) +{\footnotesize template$<$typename TSeq = EPI\+\_\+\+DEFAULT\+\_\+\+TSEQ$>$ }\\std\+::function$<$ \mbox{\hyperlink{class_virus}{Virus}}$<$ TSeq $>$ $\ast$(\mbox{\hyperlink{class_agent}{Agent}}$<$ TSeq $>$ $\ast$, \mbox{\hyperlink{class_model}{Model}}$<$ TSeq $>$ $\ast$)$>$ \mbox{\hyperlink{namespacesampler_a4cafc444e0a6c563f34ed5f9b5366ae4}{make\+\_\+sample\+\_\+virus\+\_\+neighbors}} (std\+::vector$<$ epiworld\+\_\+fast\+\_\+uint $>$ exclude=\{\}) \begin{DoxyCompactList}\small\item\em Make a function to sample from neighbors. \end{DoxyCompactList}\item -{\footnotesize template$<$typename TSeq = int$>$ }\\\mbox{\hyperlink{class_virus}{Virus}}$<$ TSeq $>$ $\ast$ \mbox{\hyperlink{namespacesampler_ab33532e84aba976673b13d0f6758e95b}{sample\+\_\+virus\+\_\+single}} (\mbox{\hyperlink{class_agent}{Agent}}$<$ TSeq $>$ $\ast$p, \mbox{\hyperlink{class_model}{Model}}$<$ TSeq $>$ $\ast$m) +{\footnotesize template$<$typename TSeq = EPI\+\_\+\+DEFAULT\+\_\+\+TSEQ$>$ }\\\mbox{\hyperlink{class_virus}{Virus}}$<$ TSeq $>$ $\ast$ \mbox{\hyperlink{namespacesampler_ab33532e84aba976673b13d0f6758e95b}{sample\+\_\+virus\+\_\+single}} (\mbox{\hyperlink{class_agent}{Agent}}$<$ TSeq $>$ $\ast$p, \mbox{\hyperlink{class_model}{Model}}$<$ TSeq $>$ $\ast$m) \begin{DoxyCompactList}\small\item\em Sample from neighbors pool of viruses (at most one) \end{DoxyCompactList}\end{DoxyCompactItemize} @@ -24,7 +24,7 @@ \index{sampler@{sampler}!make\_sample\_virus\_neighbors@{make\_sample\_virus\_neighbors}} \index{make\_sample\_virus\_neighbors@{make\_sample\_virus\_neighbors}!sampler@{sampler}} \doxysubsubsection{\texorpdfstring{make\_sample\_virus\_neighbors()}{make\_sample\_virus\_neighbors()}} -{\footnotesize\ttfamily template$<$typename TSeq = int$>$ \\ +{\footnotesize\ttfamily template$<$typename TSeq = EPI\+\_\+\+DEFAULT\+\_\+\+TSEQ$>$ \\ std\+::function$<$\mbox{\hyperlink{class_virus}{Virus}}$<$TSeq$>$$\ast$(\mbox{\hyperlink{class_agent}{Agent}}$<$TSeq$>$$\ast$,\mbox{\hyperlink{class_model}{Model}}$<$TSeq$>$$\ast$)$>$ sampler\+::make\+\_\+sample\+\_\+virus\+\_\+neighbors (\begin{DoxyParamCaption}\item[{std\+::vector$<$ epiworld\+\_\+fast\+\_\+uint $>$}]{exclude = {\ttfamily \{\}} }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} @@ -50,7 +50,7 @@ \index{sampler@{sampler}!make\_update\_susceptible@{make\_update\_susceptible}} \index{make\_update\_susceptible@{make\_update\_susceptible}!sampler@{sampler}} \doxysubsubsection{\texorpdfstring{make\_update\_susceptible()}{make\_update\_susceptible()}} -{\footnotesize\ttfamily template$<$typename TSeq $>$ \\ +{\footnotesize\ttfamily template$<$typename TSeq = EPI\+\_\+\+DEFAULT\+\_\+\+TSEQ$>$ \\ std\+::function$<$void(\mbox{\hyperlink{class_agent}{Agent}}$<$TSeq$>$$\ast$,\mbox{\hyperlink{class_model}{Model}}$<$TSeq$>$$\ast$)$>$ sampler\+::make\+\_\+update\+\_\+susceptible (\begin{DoxyParamCaption}\item[{std\+::vector$<$ epiworld\+\_\+fast\+\_\+uint $>$}]{exclude = {\ttfamily \{\}} }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} @@ -76,7 +76,7 @@ \index{sampler@{sampler}!sample\_virus\_single@{sample\_virus\_single}} \index{sample\_virus\_single@{sample\_virus\_single}!sampler@{sampler}} \doxysubsubsection{\texorpdfstring{sample\_virus\_single()}{sample\_virus\_single()}} -{\footnotesize\ttfamily template$<$typename TSeq = int$>$ \\ +{\footnotesize\ttfamily template$<$typename TSeq = EPI\+\_\+\+DEFAULT\+\_\+\+TSEQ$>$ \\ \mbox{\hyperlink{class_virus}{Virus}}$<$TSeq$>$$\ast$ sampler\+::sample\+\_\+virus\+\_\+single (\begin{DoxyParamCaption}\item[{\mbox{\hyperlink{class_agent}{Agent}}$<$ TSeq $>$ $\ast$}]{p, }\item[{\mbox{\hyperlink{class_model}{Model}}$<$ TSeq $>$ $\ast$}]{m }\end{DoxyParamCaption})\hspace{0.3cm}{\ttfamily [inline]}} diff --git a/latex/refman.aux b/latex/refman.aux index 47ff89a44..9d179f42d 100644 --- a/latex/refman.aux +++ b/latex/refman.aux @@ -84,25 +84,25 @@ \@writefile{lot}{\addvspace {10\p@ }} \newlabel{md_paper_mixing}{{8}{19}{Mixing probabilities in connected model}{chapter.8}{}} \@writefile{toc}{\contentsline {section}{\numberline {8.1}Case 1\discretionary {\mbox {\scriptsize $\hookleftarrow $}}{}{}: No 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./class_model_s_i_r_logit__coll__graph.pdf): PDF inclusion: multiple pdfs with page group included in a single page > - + File: class_model_s_i_r_logit__coll__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_model_s_i_r_logit__coll__graph.pdf used on inpu @@ -2936,7 +2936,7 @@ pdfTeX warning: pdflatex (file ./classepiworld_1_1epimodels_1_1_model_s_i_r_mix ing__inherit__graph.pdf): PDF inclusion: multiple pdfs with page group included in a single page > - File: classepiworld_1_1epimodels_1_1_model_s_i_r_mixing__inherit__graph.pdf Gra phic file (type pdf) @@ -2950,7 +2950,7 @@ pdfTeX warning: pdflatex (file ./classepiworld_1_1epimodels_1_1_model_s_i_r_mix ing__coll__graph.pdf): PDF inclusion: multiple pdfs with page group included in a single page > - File: classepiworld_1_1epimodels_1_1_model_s_i_r_mixing__coll__graph.pdf Graphi c file (type pdf) @@ -2985,7 +2985,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): pdfTeX warning: pdflatex (file ./class_model_s_i_r_mixing__inherit__graph.pdf): PDF inclusion: multiple pdfs with page group included in a single page > - File: class_model_s_i_r_mixing__inherit__graph.pdf Graphic file (type pdf) @@ -2997,7 +2997,7 @@ input line 10. pdfTeX warning: pdflatex (file ./class_model_s_i_r_mixing__coll__graph.pdf): PD F inclusion: multiple pdfs with page group included in a single page > - + File: class_model_s_i_r_mixing__coll__graph.pdf Graphic file (type pdf) @@ -3036,7 +3036,7 @@ pdfTeX warning: pdflatex (file ./classepiworld_1_1epimodels_1_1_model_s_i_s__in herit__graph.pdf): PDF inclusion: multiple pdfs with page group included in a s ingle page > - File: classepiworld_1_1epimodels_1_1_model_s_i_s__inherit__graph.pdf Graphic fi le (type pdf) @@ -3050,7 +3050,7 @@ pdfTeX warning: pdflatex (file ./classepiworld_1_1epimodels_1_1_model_s_i_s__co ll__graph.pdf): PDF inclusion: multiple pdfs with page group included in a sing le page > - File: classepiworld_1_1epimodels_1_1_model_s_i_s__coll__graph.pdf Graphic file (type pdf) @@ -3076,7 +3076,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. <./class_model_s_i_s__inherit__graph.pdf> - + File: class_model_s_i_s__inherit__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_model_s_i_s__inherit__graph.pdf used on input l @@ -3087,7 +3087,7 @@ ine 19. pdfTeX warning: pdflatex (file ./class_model_s_i_s__coll__graph.pdf): PDF inclu sion: multiple pdfs with page group included in a single page > - + File: class_model_s_i_s__coll__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_model_s_i_s__coll__graph.pdf used on input line @@ -3111,7 +3111,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. <./classepiworld_1_1epimodels_1_1_model_s_i_s_d__inherit__graph.pdf> - File: classepiworld_1_1epimodels_1_1_model_s_i_s_d__inherit__graph.pdf Graphic file (type pdf) @@ -3125,7 +3125,7 @@ pdfTeX warning: pdflatex (file ./classepiworld_1_1epimodels_1_1_model_s_i_s_d__ coll__graph.pdf): PDF inclusion: multiple pdfs with page group included in a si ngle page > - File: classepiworld_1_1epimodels_1_1_model_s_i_s_d__coll__graph.pdf Graphic fil e (type pdf) @@ -3158,7 +3158,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. <./class_model_s_i_s_d__inherit__graph.pdf> - + File: class_model_s_i_s_d__inherit__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_model_s_i_s_d__inherit__graph.pdf used on input @@ -3169,7 +3169,7 @@ Package pdftex.def Info: class_model_s_i_s_d__inherit__graph.pdf used on input pdfTeX warning: pdflatex (file ./class_model_s_i_s_d__coll__graph.pdf): PDF inc lusion: multiple pdfs with page group included in a single page > - + File: class_model_s_i_s_d__coll__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_model_s_i_s_d__coll__graph.pdf used on input li @@ -3200,7 +3200,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. <./classepiworld_1_1epimodels_1_1_model_s_u_r_v__inherit__graph.pdf> - File: classepiworld_1_1epimodels_1_1_model_s_u_r_v__inherit__graph.pdf Graphic file (type pdf) @@ -3214,7 +3214,7 @@ pdfTeX warning: pdflatex (file ./classepiworld_1_1epimodels_1_1_model_s_u_r_v__ coll__graph.pdf): PDF inclusion: multiple pdfs with page group included in a si ngle page > - File: classepiworld_1_1epimodels_1_1_model_s_u_r_v__coll__graph.pdf Graphic fil e (type pdf) @@ -3256,7 +3256,7 @@ Package hyperref Warning: Token not allowed in a PDF string (Unicode): (hyperref) removing `math shift' on input line 1. <./class_model_s_u_r_v__inherit__graph.pdf> - + File: class_model_s_u_r_v__inherit__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_model_s_u_r_v__inherit__graph.pdf used on input @@ -3267,7 +3267,7 @@ Package pdftex.def Info: class_model_s_u_r_v__inherit__graph.pdf used on input pdfTeX warning: pdflatex (file ./class_model_s_u_r_v__coll__graph.pdf): PDF inc lusion: multiple pdfs with page group included in a single page > - + File: class_model_s_u_r_v__coll__graph.pdf Graphic file (type pdf) Package pdftex.def Info: class_model_s_u_r_v__coll__graph.pdf used on input li @@ -3706,7 +3706,7 @@ Chapter 16. pdfTeX warning: pdflatex (file ./agent-meat-state_8hpp__incl.pdf): PDF inclusio n: multiple pdfs with page group included in a single page > - + File: agent-meat-state_8hpp__incl.pdf Graphic file (type pdf) Package pdftex.def Info: agent-meat-state_8hpp__incl.pdf used on input line 14 @@ -3717,7 +3717,7 @@ Package pdftex.def Info: agent-meat-state_8hpp__incl.pdf used on input line 14 pdfTeX warning: pdflatex (file ./agent-meat-state_8hpp__dep__incl.pdf): PDF inc lusion: multiple pdfs with page group included in a single page > - + File: agent-meat-state_8hpp__dep__incl.pdf Graphic file (type pdf) Package pdftex.def Info: agent-meat-state_8hpp__dep__incl.pdf used on input li @@ -3870,10 +3870,10 @@ LaTeX Warning: There were multiply-defined labels. ) Here is how much of TeX's memory you used: - 22105 strings out of 480478 - 462705 string characters out of 5905923 - 718327 words of memory out of 5000000 - 34931 multiletter control sequences out of 15000+600000 + 22113 strings out of 480478 + 463169 string characters out of 5905923 + 718539 words of memory out of 5000000 + 34935 multiletter control sequences out of 15000+600000 603446 words of font info for 114 fonts, out of 8000000 for 9000 1141 hyphenation exceptions out of 8191 55i,16n,96p,1988b,710s stack positions out of 5000i,500n,10000p,200000b,80000s @@ -3892,10 +3892,10 @@ b> -Output written on refman.pdf (229 pages, 1106313 bytes). +Output written on refman.pdf (229 pages, 1106768 bytes). 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    178  std::string * unit_abbr,
    179  bool print
    -
    180  );
    +
    180  ) const;
    181 
    182  void chrono_start();
    183  void chrono_end();
    @@ -247,17 +247,21 @@
    235  const std::vector< epiworld_double > & get_drawn_prob() {return drawn_prob;};
    236  std::vector< TData > * get_sampled_data() {return sampled_data;};
    237 
    -
    238  void set_par_names(std::vector< std::string > names);
    -
    239  void set_stats_names(std::vector< std::string > names);
    +
    238  const std::vector< epiworld_double > & get_accepted_params() {return accepted_params;};
    +
    239  const std::vector< epiworld_double > & get_accepted_stats() {return accepted_stats;};
    240 
    -
    241  std::vector< epiworld_double > get_params_mean();
    -
    242  std::vector< epiworld_double > get_stats_mean();
    -
    243 
    -
    244  void print() ;
    -
    245 
    -
    246 };
    +
    241 
    +
    242  void set_par_names(std::vector< std::string > names);
    +
    243  void set_stats_names(std::vector< std::string > names);
    +
    244 
    +
    245  std::vector< epiworld_double > get_params_mean();
    +
    246  std::vector< epiworld_double > get_stats_mean();
    247 
    -
    248 #endif
    +
    248  void print(size_t burnin = 0u) const;
    +
    249 
    +
    250 };
    +
    251 
    +
    252 #endif
    LFMCMC
    Likelihood-Free Markov Chain Monte Carlo.
    Definition: lfmcmc-bones.hpp:115
    diff --git a/lfmcmc-meat-print_8hpp_source.html b/lfmcmc-meat-print_8hpp_source.html index c2b2f01bf..5982a507a 100644 --- a/lfmcmc-meat-print_8hpp_source.html +++ b/lfmcmc-meat-print_8hpp_source.html @@ -74,208 +74,225 @@
    2 #define LFMCMC_MEAT_PRINT_HPP
    3 
    4 template<typename TData>
    -
    5 inline void LFMCMC<TData>::print()
    -
    6 {
    -
    7  std::vector< epiworld_double > summ_params(n_parameters * 3, 0.0);
    -
    8  std::vector< epiworld_double > summ_stats(n_statistics * 3, 0.0);
    -
    9 
    -
    10  for (size_t k = 0u; k < n_parameters; ++k)
    -
    11  {
    -
    12 
    -
    13  // Retrieving the relevant parameter
    -
    14  std::vector< epiworld_double > par_i(n_samples);
    -
    15  for (size_t i = 0u; i < n_samples; ++i)
    -
    16  {
    -
    17  par_i[i] = accepted_params[i * n_parameters + k];
    -
    18  summ_params[k * 3] += par_i[i]/n_samples;
    -
    19  }
    +
    5 inline void LFMCMC<TData>::print(size_t burnin) const
    +
    6 {
    +
    7 
    +
    8  std::vector< epiworld_double > summ_params(n_parameters * 3, 0.0);
    +
    9  std::vector< epiworld_double > summ_stats(n_statistics * 3, 0.0);
    +
    10 
    +
    11  size_t n_samples_print = n_samples;
    +
    12  if (burnin > 0)
    +
    13  {
    +
    14  if (burnin >= n_samples)
    +
    15  throw std::length_error(
    +
    16  "The burnin is greater than the number of samples."
    +
    17  );
    +
    18 
    +
    19  n_samples_print = n_samples - burnin;
    20 
    -
    21  // Computing the 95% Credible interval
    -
    22  std::sort(par_i.begin(), par_i.end());
    -
    23 
    -
    24  summ_params[k * 3 + 1u] =
    -
    25  par_i[std::floor(.025 * static_cast<epiworld_double>(n_samples))];
    -
    26  summ_params[k * 3 + 2u] =
    -
    27  par_i[std::floor(.975 * static_cast<epiworld_double>(n_samples))];
    -
    28 
    -
    29  }
    -
    30 
    -
    31  for (size_t k = 0u; k < n_statistics; ++k)
    -
    32  {
    -
    33 
    -
    34  // Retrieving the relevant parameter
    -
    35  std::vector< epiworld_double > stat_k(n_samples);
    -
    36  for (size_t i = 0u; i < n_samples; ++i)
    -
    37  {
    -
    38  stat_k[i] = accepted_stats[i * n_statistics + k];
    -
    39  summ_stats[k * 3] += stat_k[i]/n_samples;
    -
    40  }
    -
    41 
    -
    42  // Computing the 95% Credible interval
    -
    43  std::sort(stat_k.begin(), stat_k.end());
    -
    44 
    -
    45  summ_stats[k * 3 + 1u] =
    -
    46  stat_k[std::floor(.025 * static_cast<epiworld_double>(n_samples))];
    -
    47  summ_stats[k * 3 + 2u] =
    -
    48  stat_k[std::floor(.975 * static_cast<epiworld_double>(n_samples))];
    -
    49 
    -
    50  }
    -
    51 
    -
    52  printf_epiworld("___________________________________________\n\n");
    -
    53  printf_epiworld("LIKELIHOOD-FREE MARKOV CHAIN MONTE CARLO\n\n");
    -
    54 
    -
    55  printf_epiworld("N Samples : %zu\n", n_samples);
    -
    56 
    -
    57  std::string abbr;
    -
    58  epiworld_double elapsed;
    -
    59  get_elapsed("auto", &elapsed, &abbr, false);
    -
    60  printf_epiworld("Elapsed t : %.2f%s\n\n", elapsed, abbr.c_str());
    -
    61 
    -
    63  // PARAMETERS
    -
    65  printf_epiworld("Parameters:\n");
    +
    21  }
    +
    22 
    +
    23  epiworld_double n_samples_dbl = static_cast< epiworld_double >(
    +
    24  n_samples_print
    +
    25  );
    +
    26 
    +
    27  for (size_t k = 0u; k < n_parameters; ++k)
    +
    28  {
    +
    29 
    +
    30  // Retrieving the relevant parameter
    +
    31  std::vector< epiworld_double > par_i(n_samples_print);
    +
    32  for (size_t i = burnin; i < n_samples; ++i)
    +
    33  {
    +
    34  par_i[i] = accepted_params[i * n_parameters + k];
    +
    35  summ_params[k * 3] += par_i[i]/n_samples_dbl;
    +
    36  }
    +
    37 
    +
    38  // Computing the 95% Credible interval
    +
    39  std::sort(par_i.begin(), par_i.end());
    +
    40 
    +
    41  summ_params[k * 3 + 1u] =
    +
    42  par_i[std::floor(.025 * n_samples_dbl)];
    +
    43  summ_params[k * 3 + 2u] =
    +
    44  par_i[std::floor(.975 * n_samples_dbl)];
    +
    45 
    +
    46  }
    +
    47 
    +
    48  for (size_t k = 0u; k < n_statistics; ++k)
    +
    49  {
    +
    50 
    +
    51  // Retrieving the relevant parameter
    +
    52  std::vector< epiworld_double > stat_k(n_samples_print);
    +
    53  for (size_t i = burnin; i < n_samples; ++i)
    +
    54  {
    +
    55  stat_k[i] = accepted_stats[i * n_statistics + k];
    +
    56  summ_stats[k * 3] += stat_k[i]/n_samples_dbl;
    +
    57  }
    +
    58 
    +
    59  // Computing the 95% Credible interval
    +
    60  std::sort(stat_k.begin(), stat_k.end());
    +
    61 
    +
    62  summ_stats[k * 3 + 1u] =
    +
    63  stat_k[std::floor(.025 * n_samples_dbl)];
    +
    64  summ_stats[k * 3 + 2u] =
    +
    65  stat_k[std::floor(.975 * n_samples_dbl)];
    66 
    -
    67  // Figuring out format
    -
    68  std::string fmt_params;
    -
    69 
    -
    70  int nchar_par_num = 0;
    -
    71  for (auto & n : summ_params)
    -
    72  {
    -
    73 
    -
    74  int tmp_nchar = std::floor(std::log10(std::abs(n)));
    -
    75  if (nchar_par_num < tmp_nchar)
    -
    76  nchar_par_num = tmp_nchar;
    -
    77  }
    -
    78  nchar_par_num += 5; // 1 for neg padd, 2 for decimals, 1 the decimal point, and one b/c log(<10) < 1.
    -
    79  std::string charlen = std::to_string(nchar_par_num);
    -
    80 
    -
    81  if (names_parameters.size() != 0u)
    -
    82  {
    -
    83  int nchar_par = 0;
    -
    84  for (auto & n : names_parameters)
    -
    85  {
    -
    86  int tmp_nchar = n.length();
    -
    87  if (nchar_par < tmp_nchar)
    -
    88  nchar_par = tmp_nchar;
    -
    89  }
    -
    90 
    -
    91  fmt_params = std::string(" -%-") +
    -
    92  std::to_string(nchar_par) +
    -
    93  std::string("s : % ") + charlen +
    -
    94  std::string(".2f [% ") + charlen +
    -
    95  std::string(".2f, % ") + charlen +
    -
    96  std::string(".2f] (initial : % ") +
    -
    97  charlen + std::string(".2f)\n");
    -
    98 
    -
    99  for (size_t k = 0u; k < n_parameters; ++k)
    -
    100  {
    -
    101  printf_epiworld(
    -
    102  fmt_params.c_str(),
    -
    103  names_parameters[k].c_str(),
    -
    104  summ_params[k * 3],
    -
    105  summ_params[k * 3 + 1u],
    -
    106  summ_params[k * 3 + 2u],
    -
    107  params_init[k]
    -
    108  );
    -
    109  }
    -
    110 
    -
    111 
    -
    112  } else {
    -
    113 
    -
    114  fmt_params = std::string(" [%-2ld]: % ") + charlen +
    -
    115  std::string(".2f [% ") + charlen +
    -
    116  std::string(".2f, % ") + charlen +
    -
    117  std::string(".2f] (initial : % ") + charlen +
    -
    118  std::string(".2f)\n");
    -
    119 
    -
    120  for (size_t k = 0u; k < n_parameters; ++k)
    -
    121  {
    -
    122 
    -
    123  printf_epiworld(
    -
    124  fmt_params.c_str(),
    -
    125  k,
    -
    126  summ_params[k * 3],
    -
    127  summ_params[k * 3 + 1u],
    -
    128  summ_params[k * 3 + 2u],
    -
    129  params_init[k]
    -
    130  );
    -
    131  }
    -
    132 
    -
    133  }
    -
    134 
    -
    136  // Statistics
    -
    138  printf_epiworld("\nStatistics:\n");
    -
    139  int nchar = 0;
    -
    140  for (auto & s : summ_stats)
    -
    141  {
    -
    142  int tmp_nchar = std::floor(std::log10(std::abs(s)));
    -
    143  if (nchar < tmp_nchar)
    -
    144  nchar = tmp_nchar;
    -
    145  }
    -
    146 
    -
    147  nchar += 5; // See above
    -
    148 
    -
    149  std::string nchar_char = std::to_string(nchar);
    -
    150 
    -
    151  // Figuring out format
    -
    152  std::string fmt_stats;
    -
    153  if (names_statistics.size() != 0u)
    -
    154  {
    -
    155  int nchar_stats = 0;
    -
    156  for (auto & n : names_statistics)
    -
    157  {
    -
    158  int tmp_nchar = n.length();
    -
    159  if (nchar_stats < tmp_nchar)
    -
    160  nchar_stats = tmp_nchar;
    -
    161  }
    -
    162 
    -
    163  fmt_stats = std::string(" -%-") +
    -
    164  std::to_string(nchar_stats) +
    -
    165  std::string("s : % ") + nchar_char +
    -
    166  std::string(".2f [% ") + nchar_char +
    -
    167  std::string(".2f, % ") + nchar_char +
    -
    168  std::string(".2f] (Observed: % ") + nchar_char +
    -
    169  std::string(".2f)\n");
    -
    170 
    -
    171  for (size_t k = 0u; k < n_statistics; ++k)
    -
    172  {
    -
    173  printf_epiworld(
    -
    174  fmt_stats.c_str(),
    -
    175  names_statistics[k].c_str(),
    -
    176  summ_stats[k * 3],
    -
    177  summ_stats[k * 3 + 1u],
    -
    178  summ_stats[k * 3 + 2u],
    -
    179  observed_stats[k]
    -
    180  );
    -
    181  }
    -
    182 
    -
    183 
    -
    184  } else {
    -
    185 
    -
    186  fmt_stats = std::string(" [%-2ld] : % ") +
    -
    187  nchar_char +
    -
    188  std::string(".2f [% ") + nchar_char +
    -
    189  std::string(".2f, % ") + nchar_char +
    -
    190  std::string(".2f] (Observed: % ") + nchar_char +
    -
    191  std::string(".2f)\n");
    -
    192 
    -
    193  for (size_t k = 0u; k < n_statistics; ++k)
    -
    194  {
    -
    195  printf_epiworld(
    -
    196  fmt_stats.c_str(),
    -
    197  k,
    -
    198  summ_stats[k * 3],
    -
    199  summ_stats[k * 3 + 1u],
    -
    200  summ_stats[k * 3 + 2u],
    -
    201  observed_stats[k]
    -
    202  );
    -
    203  }
    -
    204 
    -
    205  }
    -
    206 
    -
    207  printf_epiworld("___________________________________________\n\n");
    -
    208 }
    +
    67  }
    +
    68 
    +
    69  printf_epiworld("___________________________________________\n\n");
    +
    70  printf_epiworld("LIKELIHOOD-FREE MARKOV CHAIN MONTE CARLO\n\n");
    +
    71 
    +
    72  printf_epiworld("N Samples : %zu\n", n_samples);
    +
    73 
    +
    74  std::string abbr;
    +
    75  epiworld_double elapsed;
    +
    76  get_elapsed("auto", &elapsed, &abbr, false);
    +
    77  printf_epiworld("Elapsed t : %.2f%s\n\n", elapsed, abbr.c_str());
    +
    78 
    +
    80  // PARAMETERS
    +
    82  printf_epiworld("Parameters:\n");
    +
    83 
    +
    84  // Figuring out format
    +
    85  std::string fmt_params;
    +
    86 
    +
    87  int nchar_par_num = 0;
    +
    88  for (auto & n : summ_params)
    +
    89  {
    +
    90 
    +
    91  int tmp_nchar = std::floor(std::log10(std::abs(n)));
    +
    92  if (nchar_par_num < tmp_nchar)
    +
    93  nchar_par_num = tmp_nchar;
    +
    94  }
    +
    95  nchar_par_num += 5; // 1 for neg padd, 2 for decimals, 1 the decimal point, and one b/c log(<10) < 1.
    +
    96  std::string charlen = std::to_string(nchar_par_num);
    +
    97 
    +
    98  if (names_parameters.size() != 0u)
    +
    99  {
    +
    100  int nchar_par = 0;
    +
    101  for (auto & n : names_parameters)
    +
    102  {
    +
    103  int tmp_nchar = n.length();
    +
    104  if (nchar_par < tmp_nchar)
    +
    105  nchar_par = tmp_nchar;
    +
    106  }
    +
    107 
    +
    108  fmt_params = std::string(" -%-") +
    +
    109  std::to_string(nchar_par) +
    +
    110  std::string("s : % ") + charlen +
    +
    111  std::string(".2f [% ") + charlen +
    +
    112  std::string(".2f, % ") + charlen +
    +
    113  std::string(".2f] (initial : % ") +
    +
    114  charlen + std::string(".2f)\n");
    +
    115 
    +
    116  for (size_t k = 0u; k < n_parameters; ++k)
    +
    117  {
    +
    118  printf_epiworld(
    +
    119  fmt_params.c_str(),
    +
    120  names_parameters[k].c_str(),
    +
    121  summ_params[k * 3],
    +
    122  summ_params[k * 3 + 1u],
    +
    123  summ_params[k * 3 + 2u],
    +
    124  params_init[k]
    +
    125  );
    +
    126  }
    +
    127 
    +
    128 
    +
    129  } else {
    +
    130 
    +
    131  fmt_params = std::string(" [%-2ld]: % ") + charlen +
    +
    132  std::string(".2f [% ") + charlen +
    +
    133  std::string(".2f, % ") + charlen +
    +
    134  std::string(".2f] (initial : % ") + charlen +
    +
    135  std::string(".2f)\n");
    +
    136 
    +
    137  for (size_t k = 0u; k < n_parameters; ++k)
    +
    138  {
    +
    139 
    +
    140  printf_epiworld(
    +
    141  fmt_params.c_str(),
    +
    142  k,
    +
    143  summ_params[k * 3],
    +
    144  summ_params[k * 3 + 1u],
    +
    145  summ_params[k * 3 + 2u],
    +
    146  params_init[k]
    +
    147  );
    +
    148  }
    +
    149 
    +
    150  }
    +
    151 
    +
    153  // Statistics
    +
    155  printf_epiworld("\nStatistics:\n");
    +
    156  int nchar = 0;
    +
    157  for (auto & s : summ_stats)
    +
    158  {
    +
    159  int tmp_nchar = std::floor(std::log10(std::abs(s)));
    +
    160  if (nchar < tmp_nchar)
    +
    161  nchar = tmp_nchar;
    +
    162  }
    +
    163 
    +
    164  nchar += 5; // See above
    +
    165 
    +
    166  std::string nchar_char = std::to_string(nchar);
    +
    167 
    +
    168  // Figuring out format
    +
    169  std::string fmt_stats;
    +
    170  if (names_statistics.size() != 0u)
    +
    171  {
    +
    172  int nchar_stats = 0;
    +
    173  for (auto & n : names_statistics)
    +
    174  {
    +
    175  int tmp_nchar = n.length();
    +
    176  if (nchar_stats < tmp_nchar)
    +
    177  nchar_stats = tmp_nchar;
    +
    178  }
    +
    179 
    +
    180  fmt_stats = std::string(" -%-") +
    +
    181  std::to_string(nchar_stats) +
    +
    182  std::string("s : % ") + nchar_char +
    +
    183  std::string(".2f [% ") + nchar_char +
    +
    184  std::string(".2f, % ") + nchar_char +
    +
    185  std::string(".2f] (Observed: % ") + nchar_char +
    +
    186  std::string(".2f)\n");
    +
    187 
    +
    188  for (size_t k = 0u; k < n_statistics; ++k)
    +
    189  {
    +
    190  printf_epiworld(
    +
    191  fmt_stats.c_str(),
    +
    192  names_statistics[k].c_str(),
    +
    193  summ_stats[k * 3],
    +
    194  summ_stats[k * 3 + 1u],
    +
    195  summ_stats[k * 3 + 2u],
    +
    196  observed_stats[k]
    +
    197  );
    +
    198  }
    +
    199 
    +
    200 
    +
    201  } else {
    +
    202 
    +
    203  fmt_stats = std::string(" [%-2ld] : % ") +
    +
    204  nchar_char +
    +
    205  std::string(".2f [% ") + nchar_char +
    +
    206  std::string(".2f, % ") + nchar_char +
    +
    207  std::string(".2f] (Observed: % ") + nchar_char +
    +
    208  std::string(".2f)\n");
    209 
    -
    210 #endif
    +
    210  for (size_t k = 0u; k < n_statistics; ++k)
    +
    211  {
    +
    212  printf_epiworld(
    +
    213  fmt_stats.c_str(),
    +
    214  k,
    +
    215  summ_stats[k * 3],
    +
    216  summ_stats[k * 3 + 1u],
    +
    217  summ_stats[k * 3 + 2u],
    +
    218  observed_stats[k]
    +
    219  );
    +
    220  }
    +
    221 
    +
    222  }
    +
    223 
    +
    224  printf_epiworld("___________________________________________\n\n");
    +
    225 }
    +
    226 
    +
    227 #endif
    LFMCMC
    Likelihood-Free Markov Chain Monte Carlo.
    Definition: lfmcmc-bones.hpp:115
    diff --git a/lfmcmc-meat_8hpp_source.html b/lfmcmc-meat_8hpp_source.html index cbd44d5b5..d8ad69d34 100644 --- a/lfmcmc-meat_8hpp_source.html +++ b/lfmcmc-meat_8hpp_source.html @@ -273,294 +273,299 @@
    249 
    250  std::vector< epiworld_double > proposed_stats_i;
    251  summary_fun(proposed_stats_i, data_i, this);
    -
    252  accepted_params_prob[0u] = kernel_fun(proposed_stats_i, observed_stats, epsilon, this);
    -
    253 
    -
    254  // Recording statistics
    -
    255  for (size_t i = 0u; i < n_statistics; ++i)
    -
    256  sampled_stats[i] = proposed_stats_i[i];
    -
    257 
    -
    258  for (size_t k = 0u; k < n_statistics; ++k)
    -
    259  accepted_params[k] = proposed_stats_i[k];
    -
    260 
    -
    261  for (size_t i = 1u; i < n_samples; ++i)
    -
    262  {
    -
    263  // Step 1: Generate a proposal and store it in params_now
    -
    264  proposal_fun(params_now, params_prev, this);
    -
    265 
    -
    266  // Step 2: Using params_now, simulate data
    -
    267  TData data_i = simulation_fun(params_now, this);
    -
    268 
    -
    269  // Are we storing the data?
    -
    270  if (sampled_data != nullptr)
    -
    271  sampled_data->operator[](i) = data_i;
    -
    272 
    -
    273  // Step 3: Generate the summary statistics of the data
    -
    274  summary_fun(proposed_stats_i, data_i, this);
    -
    275 
    -
    276  // Step 4: Compute the hastings ratio using the kernel function
    -
    277  epiworld_double hr = kernel_fun(proposed_stats_i, observed_stats, epsilon, this);
    -
    278  sampled_stats_prob[i] = hr;
    -
    279 
    -
    280  // Storing data
    -
    281  for (size_t k = 0u; k < n_statistics; ++k)
    -
    282  sampled_stats[i * n_statistics + k] = proposed_stats_i[k];
    -
    283 
    -
    284  // Running Hastings ratio
    -
    285  epiworld_double r = runif();
    -
    286  drawn_prob[i] = r;
    -
    287 
    -
    288  // Step 5: Update if likely
    -
    289  if (r < std::min(static_cast<epiworld_double>(1.0), hr / accepted_params_prob[i - 1u]))
    -
    290  {
    -
    291  accepted_params_prob[i] = hr;
    -
    292  sampled_accepted[i] = true;
    -
    293 
    -
    294  for (size_t k = 0u; k < n_statistics; ++k)
    -
    295  accepted_stats[i * n_statistics + k] =
    -
    296  proposed_stats_i[k];
    -
    297 
    -
    298  params_prev = params_now;
    -
    299 
    -
    300  } else
    -
    301  {
    +
    252  accepted_params_prob[0u] = kernel_fun(
    +
    253  proposed_stats_i, observed_stats, epsilon, this
    +
    254  );
    +
    255 
    +
    256  // Recording statistics
    +
    257  for (size_t i = 0u; i < n_statistics; ++i)
    +
    258  sampled_stats[i] = proposed_stats_i[i];
    +
    259 
    +
    260  for (size_t k = 0u; k < n_parameters; ++k)
    +
    261  accepted_params[k] = params_init[k];
    +
    262 
    +
    263  for (size_t i = 1u; i < n_samples; ++i)
    +
    264  {
    +
    265  // Step 1: Generate a proposal and store it in params_now
    +
    266  proposal_fun(params_now, params_prev, this);
    +
    267 
    +
    268  // Step 2: Using params_now, simulate data
    +
    269  TData data_i = simulation_fun(params_now, this);
    +
    270 
    +
    271  // Are we storing the data?
    +
    272  if (sampled_data != nullptr)
    +
    273  sampled_data->operator[](i) = data_i;
    +
    274 
    +
    275  // Step 3: Generate the summary statistics of the data
    +
    276  summary_fun(proposed_stats_i, data_i, this);
    +
    277 
    +
    278  // Step 4: Compute the hastings ratio using the kernel function
    +
    279  epiworld_double hr = kernel_fun(
    +
    280  proposed_stats_i, observed_stats, epsilon, this
    +
    281  );
    +
    282 
    +
    283  sampled_stats_prob[i] = hr;
    +
    284 
    +
    285  // Storing data
    +
    286  for (size_t k = 0u; k < n_statistics; ++k)
    +
    287  sampled_stats[i * n_statistics + k] = proposed_stats_i[k];
    +
    288 
    +
    289  // Running Hastings ratio
    +
    290  epiworld_double r = runif();
    +
    291  drawn_prob[i] = r;
    +
    292 
    +
    293  // Step 5: Update if likely
    +
    294  if (r < std::min(static_cast<epiworld_double>(1.0), hr / accepted_params_prob[i - 1u]))
    +
    295  {
    +
    296  accepted_params_prob[i] = hr;
    +
    297  sampled_accepted[i] = true;
    +
    298 
    +
    299  for (size_t k = 0u; k < n_statistics; ++k)
    +
    300  accepted_stats[i * n_statistics + k] =
    +
    301  proposed_stats_i[k];
    302 
    -
    303  for (size_t k = 0u; k < n_statistics; ++k)
    -
    304  accepted_stats[i * n_statistics + k] =
    -
    305  accepted_stats[(i - 1) * n_statistics + k];
    -
    306 
    -
    307  accepted_params_prob[i] = accepted_params_prob[i - 1u];
    -
    308  }
    -
    309 
    -
    310 
    -
    311  for (size_t k = 0u; k < n_parameters; ++k)
    -
    312  accepted_params[i * n_parameters + k] = params_prev[k];
    -
    313 
    -
    314  }
    +
    303  params_prev = params_now;
    +
    304 
    +
    305  } else
    +
    306  {
    +
    307 
    +
    308  for (size_t k = 0u; k < n_statistics; ++k)
    +
    309  accepted_stats[i * n_statistics + k] =
    +
    310  accepted_stats[(i - 1) * n_statistics + k];
    +
    311 
    +
    312  accepted_params_prob[i] = accepted_params_prob[i - 1u];
    +
    313  }
    +
    314 
    315 
    -
    316  // End timing
    -
    317  chrono_end();
    +
    316  for (size_t k = 0u; k < n_parameters; ++k)
    +
    317  accepted_params[i * n_parameters + k] = params_prev[k];
    318 
    -
    319 }
    +
    319  }
    320 
    -
    321 
    -
    322 template<typename TData>
    -
    323 inline epiworld_double LFMCMC<TData>::runif()
    -
    324 {
    -
    325  return runifd->operator()(*engine);
    -
    326 }
    -
    327 
    -
    328 template<typename TData>
    -
    329 inline epiworld_double LFMCMC<TData>::runif(
    -
    330  epiworld_double lb,
    -
    331  epiworld_double ub
    -
    332 )
    -
    333 {
    -
    334  return runifd->operator()(*engine) * (ub - lb) + lb;
    -
    335 }
    -
    336 
    -
    337 template<typename TData>
    -
    338 inline epiworld_double LFMCMC<TData>::rnorm()
    -
    339 {
    -
    340  return rnormd->operator()(*engine);
    -
    341 }
    -
    342 
    -
    343 template<typename TData>
    -
    344 inline epiworld_double LFMCMC<TData>::rnorm(
    -
    345  epiworld_double mean,
    -
    346  epiworld_double sd
    -
    347  )
    -
    348 {
    -
    349  return (rnormd->operator()(*engine)) * sd + mean;
    -
    350 }
    -
    351 
    -
    352 template<typename TData>
    -
    353 inline epiworld_double LFMCMC<TData>::rgamma()
    -
    354 {
    -
    355  return rgammad->operator()(*engine);
    -
    356 }
    -
    357 
    -
    358 template<typename TData>
    -
    359 inline epiworld_double LFMCMC<TData>::rgamma(
    -
    360  epiworld_double alpha,
    -
    361  epiworld_double beta
    -
    362  )
    -
    363 {
    -
    364 
    -
    365  auto old_param = rgammad->param();
    -
    366 
    -
    367  rgammad->param(std::gamma_distribution<>::param_type(alpha, beta));
    -
    368 
    -
    369  epiworld_double ans = rgammad->operator()(*engine);
    -
    370 
    -
    371  rgammad->param(old_param);
    -
    372 
    -
    373  return ans;
    -
    374 
    -
    375 }
    -
    376 
    -
    377 template<typename TData>
    -
    378 inline void LFMCMC<TData>::seed(epiworld_fast_uint s) {
    +
    321  // End timing
    +
    322  chrono_end();
    +
    323 
    +
    324 }
    +
    325 
    +
    326 
    +
    327 template<typename TData>
    +
    328 inline epiworld_double LFMCMC<TData>::runif()
    +
    329 {
    +
    330  return runifd->operator()(*engine);
    +
    331 }
    +
    332 
    +
    333 template<typename TData>
    +
    334 inline epiworld_double LFMCMC<TData>::runif(
    +
    335  epiworld_double lb,
    +
    336  epiworld_double ub
    +
    337 )
    +
    338 {
    +
    339  return runifd->operator()(*engine) * (ub - lb) + lb;
    +
    340 }
    +
    341 
    +
    342 template<typename TData>
    +
    343 inline epiworld_double LFMCMC<TData>::rnorm()
    +
    344 {
    +
    345  return rnormd->operator()(*engine);
    +
    346 }
    +
    347 
    +
    348 template<typename TData>
    +
    349 inline epiworld_double LFMCMC<TData>::rnorm(
    +
    350  epiworld_double mean,
    +
    351  epiworld_double sd
    +
    352  )
    +
    353 {
    +
    354  return (rnormd->operator()(*engine)) * sd + mean;
    +
    355 }
    +
    356 
    +
    357 template<typename TData>
    +
    358 inline epiworld_double LFMCMC<TData>::rgamma()
    +
    359 {
    +
    360  return rgammad->operator()(*engine);
    +
    361 }
    +
    362 
    +
    363 template<typename TData>
    +
    364 inline epiworld_double LFMCMC<TData>::rgamma(
    +
    365  epiworld_double alpha,
    +
    366  epiworld_double beta
    +
    367  )
    +
    368 {
    +
    369 
    +
    370  auto old_param = rgammad->param();
    +
    371 
    +
    372  rgammad->param(std::gamma_distribution<>::param_type(alpha, beta));
    +
    373 
    +
    374  epiworld_double ans = rgammad->operator()(*engine);
    +
    375 
    +
    376  rgammad->param(old_param);
    +
    377 
    +
    378  return ans;
    379 
    -
    380  this->engine->seed(s);
    +
    380 }
    381 
    -
    382 }
    -
    383 
    -
    384 template<typename TData>
    -
    385 inline void LFMCMC<TData>::set_rand_engine(std::shared_ptr< std::mt19937 > & eng)
    -
    386 {
    -
    387  engine = eng;
    -
    388 }
    -
    389 
    -
    390 template<typename TData>
    -
    391 inline void LFMCMC<TData>::set_rand_gamma(epiworld_double alpha, epiworld_double beta)
    -
    392 {
    -
    393  rgammad = std::make_shared<std::gamma_distribution<>>(alpha,beta);
    -
    394 }
    -
    395 
    -
    396 template<typename TData>
    -
    397 inline std::shared_ptr< std::mt19937 > & LFMCMC<TData>::get_rand_endgine()
    -
    398 {
    -
    399  return engine;
    -
    400 }
    -
    401 
    -
    402 // Step 1: Simulate data
    -
    403 
    -
    404 // Step 2: Compute the sufficient statistics
    -
    405 
    -
    406 // Step 3: Compute the hastings-ratio
    -
    407 
    -
    408 // Step 4: Accept/reject, and go back to step 1
    -
    409 
    -
    410 #define DURCAST(tunit,txtunit) {\
    -
    411  elapsed = std::chrono::duration_cast<std::chrono:: tunit>(\
    -
    412  time_end - time_start).count(); \
    -
    413  abbr_unit = txtunit;}
    +
    382 template<typename TData>
    +
    383 inline void LFMCMC<TData>::seed(epiworld_fast_uint s) {
    +
    384 
    +
    385  this->engine->seed(s);
    +
    386 
    +
    387 }
    +
    388 
    +
    389 template<typename TData>
    +
    390 inline void LFMCMC<TData>::set_rand_engine(std::shared_ptr< std::mt19937 > & eng)
    +
    391 {
    +
    392  engine = eng;
    +
    393 }
    +
    394 
    +
    395 template<typename TData>
    +
    396 inline void LFMCMC<TData>::set_rand_gamma(epiworld_double alpha, epiworld_double beta)
    +
    397 {
    +
    398  rgammad = std::make_shared<std::gamma_distribution<>>(alpha,beta);
    +
    399 }
    +
    400 
    +
    401 template<typename TData>
    +
    402 inline std::shared_ptr< std::mt19937 > & LFMCMC<TData>::get_rand_endgine()
    +
    403 {
    +
    404  return engine;
    +
    405 }
    +
    406 
    +
    407 // Step 1: Simulate data
    +
    408 
    +
    409 // Step 2: Compute the sufficient statistics
    +
    410 
    +
    411 // Step 3: Compute the hastings-ratio
    +
    412 
    +
    413 // Step 4: Accept/reject, and go back to step 1
    414 
    -
    415 template<typename TData>
    -
    416 inline void LFMCMC<TData>::get_elapsed(
    -
    417  std::string unit,
    -
    418  epiworld_double * last_elapsed,
    -
    419  std::string * unit_abbr,
    -
    420  bool print
    -
    421 ) {
    -
    422 
    -
    423  // Preparing the result
    -
    424  epiworld_double elapsed;
    -
    425  std::string abbr_unit;
    -
    426 
    -
    427  // Figuring out the length
    -
    428  if (unit == "auto")
    -
    429  {
    -
    430 
    -
    431  size_t tlength = std::to_string(
    -
    432  static_cast<int>(floor(time_elapsed.count()))
    -
    433  ).length();
    -
    434 
    -
    435  if (tlength <= 1)
    -
    436  unit = "nanoseconds";
    -
    437  else if (tlength <= 3)
    -
    438  unit = "microseconds";
    -
    439  else if (tlength <= 6)
    -
    440  unit = "milliseconds";
    -
    441  else if (tlength <= 8)
    -
    442  unit = "seconds";
    -
    443  else if (tlength <= 9)
    -
    444  unit = "minutes";
    -
    445  else
    -
    446  unit = "hours";
    -
    447 
    -
    448  }
    -
    449 
    -
    450  if (unit == "nanoseconds") DURCAST(nanoseconds,"ns")
    -
    451  else if (unit == "microseconds") DURCAST(microseconds,"\xC2\xB5s")
    -
    452  else if (unit == "milliseconds") DURCAST(milliseconds,"ms")
    -
    453  else if (unit == "seconds") DURCAST(seconds,"s")
    -
    454  else if (unit == "minutes") DURCAST(minutes,"m")
    -
    455  else if (unit == "hours") DURCAST(hours,"h")
    -
    456  else
    -
    457  throw std::range_error("The time unit " + unit + " is not supported.");
    -
    458 
    -
    459 
    -
    460  if (last_elapsed != nullptr)
    -
    461  *last_elapsed = elapsed;
    -
    462  if (unit_abbr != nullptr)
    -
    463  *unit_abbr = abbr_unit;
    +
    415 #define DURCAST(tunit,txtunit) {\
    +
    416  elapsed = std::chrono::duration_cast<std::chrono:: tunit>(\
    +
    417  time_end - time_start).count(); \
    +
    418  abbr_unit = txtunit;}
    +
    419 
    +
    420 template<typename TData>
    +
    421 inline void LFMCMC<TData>::get_elapsed(
    +
    422  std::string unit,
    +
    423  epiworld_double * last_elapsed,
    +
    424  std::string * unit_abbr,
    +
    425  bool print
    +
    426 ) const {
    +
    427 
    +
    428  // Preparing the result
    +
    429  epiworld_double elapsed;
    +
    430  std::string abbr_unit;
    +
    431 
    +
    432  // Figuring out the length
    +
    433  if (unit == "auto")
    +
    434  {
    +
    435 
    +
    436  size_t tlength = std::to_string(
    +
    437  static_cast<int>(floor(time_elapsed.count()))
    +
    438  ).length();
    +
    439 
    +
    440  if (tlength <= 1)
    +
    441  unit = "nanoseconds";
    +
    442  else if (tlength <= 3)
    +
    443  unit = "microseconds";
    +
    444  else if (tlength <= 6)
    +
    445  unit = "milliseconds";
    +
    446  else if (tlength <= 8)
    +
    447  unit = "seconds";
    +
    448  else if (tlength <= 9)
    +
    449  unit = "minutes";
    +
    450  else
    +
    451  unit = "hours";
    +
    452 
    +
    453  }
    +
    454 
    +
    455  if (unit == "nanoseconds") DURCAST(nanoseconds,"ns")
    +
    456  else if (unit == "microseconds") DURCAST(microseconds,"\xC2\xB5s")
    +
    457  else if (unit == "milliseconds") DURCAST(milliseconds,"ms")
    +
    458  else if (unit == "seconds") DURCAST(seconds,"s")
    +
    459  else if (unit == "minutes") DURCAST(minutes,"m")
    +
    460  else if (unit == "hours") DURCAST(hours,"h")
    +
    461  else
    +
    462  throw std::range_error("The time unit " + unit + " is not supported.");
    +
    463 
    464 
    -
    465  if (!print)
    -
    466  return;
    -
    467 
    -
    468  printf_epiworld("Elapsed time : %.2f%s.\n", elapsed, abbr_unit.c_str());
    -
    469 }
    -
    470 
    -
    471 #undef DURCAST
    +
    465  if (last_elapsed != nullptr)
    +
    466  *last_elapsed = elapsed;
    +
    467  if (unit_abbr != nullptr)
    +
    468  *unit_abbr = abbr_unit;
    +
    469 
    +
    470  if (!print)
    +
    471  return;
    472 
    -
    473 #include "lfmcmc-meat-print.hpp"
    -
    474 
    -
    475 template<typename TData>
    -
    476 inline void LFMCMC<TData>::chrono_start() {
    -
    477  time_start = std::chrono::steady_clock::now();
    -
    478 }
    +
    473  printf_epiworld("Elapsed time : %.2f%s.\n", elapsed, abbr_unit.c_str());
    +
    474 }
    +
    475 
    +
    476 #undef DURCAST
    +
    477 
    +
    478 #include "lfmcmc-meat-print.hpp"
    479 
    480 template<typename TData>
    -
    481 inline void LFMCMC<TData>::chrono_end() {
    -
    482  time_end = std::chrono::steady_clock::now();
    -
    483  time_elapsed += (time_end - time_start);
    -
    484 }
    -
    485 
    -
    486 template<typename TData>
    -
    487 inline void LFMCMC<TData>::set_par_names(std::vector< std::string > names)
    -
    488 {
    -
    489 
    -
    490  if (names.size() != n_parameters)
    -
    491  throw std::length_error("The number of names to add differs from the number of parameters in the model.");
    -
    492 
    -
    493  names_parameters = names;
    +
    481 inline void LFMCMC<TData>::chrono_start() {
    +
    482  time_start = std::chrono::steady_clock::now();
    +
    483 }
    +
    484 
    +
    485 template<typename TData>
    +
    486 inline void LFMCMC<TData>::chrono_end() {
    +
    487  time_end = std::chrono::steady_clock::now();
    +
    488  time_elapsed += (time_end - time_start);
    +
    489 }
    +
    490 
    +
    491 template<typename TData>
    +
    492 inline void LFMCMC<TData>::set_par_names(std::vector< std::string > names)
    +
    493 {
    494 
    -
    495 }
    -
    496 template<typename TData>
    -
    497 inline void LFMCMC<TData>::set_stats_names(std::vector< std::string > names)
    -
    498 {
    +
    495  if (names.size() != n_parameters)
    +
    496  throw std::length_error("The number of names to add differs from the number of parameters in the model.");
    +
    497 
    +
    498  names_parameters = names;
    499 
    -
    500  if (names.size() != n_statistics)
    -
    501  throw std::length_error("The number of names to add differs from the number of statistics in the model.");
    -
    502 
    -
    503  names_statistics = names;
    +
    500 }
    +
    501 template<typename TData>
    +
    502 inline void LFMCMC<TData>::set_stats_names(std::vector< std::string > names)
    +
    503 {
    504 
    -
    505 }
    -
    506 
    -
    507 template<typename TData>
    -
    508 inline std::vector< epiworld_double > LFMCMC<TData>::get_params_mean()
    -
    509 {
    -
    510  std::vector< epiworld_double > res(this->n_parameters, 0.0);
    -
    511 
    -
    512  for (size_t k = 0u; k < n_parameters; ++k)
    -
    513  {
    -
    514  for (size_t i = 0u; i < n_samples; ++i)
    -
    515  res[k] += (this->accepted_params[k + n_parameters * i])/
    -
    516  static_cast< epiworld_double >(n_samples);
    -
    517  }
    -
    518 
    -
    519  return res;
    -
    520 
    -
    521 }
    -
    522 
    -
    523 template<typename TData>
    -
    524 inline std::vector< epiworld_double > LFMCMC<TData>::get_stats_mean()
    -
    525 {
    -
    526  std::vector< epiworld_double > res(this->n_statistics, 0.0);
    -
    527 
    -
    528  for (size_t k = 0u; k < n_statistics; ++k)
    -
    529  {
    -
    530  for (size_t i = 0u; i < n_samples; ++i)
    -
    531  res[k] += (this->accepted_stats[k + n_statistics * i])/
    -
    532  static_cast< epiworld_double >(n_samples);
    -
    533  }
    -
    534 
    -
    535  return res;
    -
    536 
    -
    537 }
    -
    538 
    -
    539 #endif
    +
    505  if (names.size() != n_statistics)
    +
    506  throw std::length_error("The number of names to add differs from the number of statistics in the model.");
    +
    507 
    +
    508  names_statistics = names;
    +
    509 
    +
    510 }
    +
    511 
    +
    512 template<typename TData>
    +
    513 inline std::vector< epiworld_double > LFMCMC<TData>::get_params_mean()
    +
    514 {
    +
    515  std::vector< epiworld_double > res(this->n_parameters, 0.0);
    +
    516 
    +
    517  for (size_t k = 0u; k < n_parameters; ++k)
    +
    518  {
    +
    519  for (size_t i = 0u; i < n_samples; ++i)
    +
    520  res[k] += (this->accepted_params[k + n_parameters * i])/
    +
    521  static_cast< epiworld_double >(n_samples);
    +
    522  }
    +
    523 
    +
    524  return res;
    +
    525 
    +
    526 }
    +
    527 
    +
    528 template<typename TData>
    +
    529 inline std::vector< epiworld_double > LFMCMC<TData>::get_stats_mean()
    +
    530 {
    +
    531  std::vector< epiworld_double > res(this->n_statistics, 0.0);
    +
    532 
    +
    533  for (size_t k = 0u; k < n_statistics; ++k)
    +
    534  {
    +
    535  for (size_t i = 0u; i < n_samples; ++i)
    +
    536  res[k] += (this->accepted_stats[k + n_statistics * i])/
    +
    537  static_cast< epiworld_double >(n_samples);
    +
    538  }
    +
    539 
    +
    540  return res;
    +
    541 
    +
    542 }
    +
    543 
    +
    544 #endif
    LFMCMC
    Likelihood-Free Markov Chain Monte Carlo.
    Definition: lfmcmc-bones.hpp:115
    diff --git a/md__r_e_a_d_m_e_old.html b/md__r_e_a_d_m_e_old.html index 665f9ac21..37aada525 100644 --- a/md__r_e_a_d_m_e_old.html +++ b/md__r_e_a_d_m_e_old.html @@ -66,22 +66,22 @@
    EPI Simulator
    -

    +

    Disease dynamics

    Diseases continuously evolve in time. Changes in their genetic sequence make them more or less resistant to the particular version of the vaccine. Mutations also affect the transmissibility level and mortality rate of the disease. Using this approach allows making vaccination efficacy a function of compatibility between the variant and the vaccine.

    When an individual becomes infected, the disease accumulates mutations in the new host. Ultimately, there is no single version of the disease present in the model, but rather an infinite number of them, each slightly different from the other.

    -

    +

    Network dynamics

    We can assume that the Population is organized in fully connected blocks for the first version of the model. Block sizes and the number of connections between blocks are Poisson random variables. Individuals interact with all the members of their blocks, and bridging individuals allow the disease to move across blocks.

    -

    +

    Contagion dynamics

    The transmission of the disease will be governed by the number of vaccinated, infected, and recovered within each block. Transmission between blocks will be treated in the same way, although individuals bridging the block will only interact with others within the block and their direct connections across the blocks.

    -

    +

    Time dynamics

    Time dynamics has two components, how biology evolves and how agents react.

    The model develops as a continuous-time Markov process. Each block of individuals takes action at rates L(i|N(i)) function of the local number of infections. This way, if

    -

    +

    Updating agent's status

    Like most other components, updating agents' states can be personalized. A naive approach allows agents to get infected with a single virus or stay as-is. The probability of this event is conditional on acquiring at most one virus. Since these are independent events, the conditional probability is computed as follows:

    P(Variant k|at most 1) = P(at most 1| Variant k) * P(Variant k)/P(at most 1)
    @@ -92,7 +92,7 @@

    P(at most 1) = P(None) + Sum(v in variants) P(v) * Prod(m != v) (1 - P(m))
    P(None) = Prod(v in variants) (1 - P(v))

    Furthermore, the (Variant, Person) pairs are treated independently.

    -

    +

    Other parameters

    • Who did you get the infection from.
      • diff --git a/md_paper_mixing.html b/md_paper_mixing.html index eba859318..97f3025c5 100644 --- a/md_paper_mixing.html +++ b/md_paper_mixing.html @@ -67,7 +67,7 @@

    George G. Vega Yon, Ph.D. 2024-04-25

    -

    +

    Case 1: No grouping

    We will look into the probability of drawing infected individuals to simplify the algorithm. There are $I$ infected individuals at any time in the simulation; thus, instead of drawing from $Bern(c/N, N)$, we will be drawing from $Bern(c/N, I)$. The next step is to check which infected individuals should be drawn. Let’s compare the distributions using the hypergeometric as an example:

    set.seed(132)
    @@ -102,7 +102,7 @@

    plotter(sim_complex, sim_simple)

    These two approaches are equivalent, but the second one is more efficient from the computational perspective.

    -

    +

    Case 2: Grouping

    This explores the case when we have mixing across groups. The question is if we can replicate the effect at the group level.

    set.seed(123133)
    diff --git a/misc_8hpp_source.html b/misc_8hpp_source.html index 6a1d4fa05..422d1b3d6 100644 --- a/misc_8hpp_source.html +++ b/misc_8hpp_source.html @@ -158,7 +158,7 @@
    111  return false;
    112 }
    113 
    -
    127 template<typename TSeq, typename TDbl>
    +
    127 template<typename TSeq = EPI_DEFAULT_TSEQ, typename TDbl = epiworld_double >
    128 inline int roulette(
    129  const std::vector< TDbl > & probs,
    130  Model<TSeq> * m
    diff --git a/model-meat_8hpp_source.html b/model-meat_8hpp_source.html index 2e8145903..411333ef6 100644 --- a/model-meat_8hpp_source.html +++ b/model-meat_8hpp_source.html @@ -759,7 +759,7 @@
    714 inline epiworld_double & Model<TSeq>::operator()(std::string pname) {
    715 
    716  if (parameters.find(pname) == parameters.end())
    -
    717  throw std::range_error("The parameter "+ pname + "is not in the model.");
    +
    717  throw std::range_error("The parameter '"+ pname + "' is not in the model.");
    718 
    719  return parameters[pname];
    720 
    diff --git a/namespaceepiworld_1_1sampler.html b/namespaceepiworld_1_1sampler.html index e921c1456..e67df5c19 100644 --- a/namespaceepiworld_1_1sampler.html +++ b/namespaceepiworld_1_1sampler.html @@ -78,15 +78,15 @@ - + - + - + @@ -100,7 +100,7 @@

    -template<typename TSeq = int>
    +template<typename TSeq = EPI_DEFAULT_TSEQ>

    Functions

    template<typename TSeq >
    template<typename TSeq = EPI_DEFAULT_TSEQ>
    std::function< void(Agent< TSeq > *, Model< TSeq > *)> make_update_susceptible (std::vector< epiworld_fast_uint > exclude={})
     Make a function to sample from neighbors. More...
     
    template<typename TSeq = int>
    template<typename TSeq = EPI_DEFAULT_TSEQ>
    std::function< Virus< TSeq > *(Agent< TSeq > *, Model< TSeq > *)> make_sample_virus_neighbors (std::vector< epiworld_fast_uint > exclude={})
     Make a function to sample from neighbors. More...
     
    template<typename TSeq = int>
    template<typename TSeq = EPI_DEFAULT_TSEQ>
    Virus< TSeq > * sample_virus_single (Agent< TSeq > *p, Model< TSeq > *m)
     Sample from neighbors pool of viruses (at most one) More...
     
    @@ -144,7 +144,7 @@

    -template<typename TSeq >
    +template<typename TSeq = EPI_DEFAULT_TSEQ>
    @@ -188,7 +188,7 @@

    -template<typename TSeq = int>
    +template<typename TSeq = EPI_DEFAULT_TSEQ>
    diff --git a/namespacesampler.html b/namespacesampler.html index b6927cbd1..aa4bfda40 100644 --- a/namespacesampler.html +++ b/namespacesampler.html @@ -74,15 +74,15 @@ - + - + - + @@ -96,7 +96,7 @@

    -template<typename TSeq = int>
    +template<typename TSeq = EPI_DEFAULT_TSEQ>

    Functions

    template<typename TSeq >
    template<typename TSeq = EPI_DEFAULT_TSEQ>
    std::function< void(Agent< TSeq > *, Model< TSeq > *)> make_update_susceptible (std::vector< epiworld_fast_uint > exclude={})
     Make a function to sample from neighbors. More...
     
    template<typename TSeq = int>
    template<typename TSeq = EPI_DEFAULT_TSEQ>
    std::function< Virus< TSeq > *(Agent< TSeq > *, Model< TSeq > *)> make_sample_virus_neighbors (std::vector< epiworld_fast_uint > exclude={})
     Make a function to sample from neighbors. More...
     
    template<typename TSeq = int>
    template<typename TSeq = EPI_DEFAULT_TSEQ>
    Virus< TSeq > * sample_virus_single (Agent< TSeq > *p, Model< TSeq > *m)
     Sample from neighbors pool of viruses (at most one) More...
     
    @@ -140,7 +140,7 @@

    -template<typename TSeq >
    +template<typename TSeq = EPI_DEFAULT_TSEQ>
    @@ -184,7 +184,7 @@

    -template<typename TSeq = int>
    +template<typename TSeq = EPI_DEFAULT_TSEQ>
    diff --git a/seir_8hpp_source.html b/seir_8hpp_source.html index a5cc9121e..c9b5871f0 100644 --- a/seir_8hpp_source.html +++ b/seir_8hpp_source.html @@ -217,9 +217,9 @@
    Model
    Core class of epiworld.
    Definition: model-bones.hpp:91
    ModelSEIR
    Template for a Susceptible-Exposed-Infected-Removed (SEIR) model.
    Definition: seir.hpp:16
    ModelSEIR::initial_states
    ModelSEIR< TSeq > & initial_states(std::vector< double > proportions_, std::vector< int > queue_={})
    Set up the initial states of the model.
    Definition: seir.hpp:147
    -
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13643
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13673
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/seirconnected_8hpp_source.html b/seirconnected_8hpp_source.html index b81bf52f3..11933b587 100644 --- a/seirconnected_8hpp_source.html +++ b/seirconnected_8hpp_source.html @@ -521,10 +521,10 @@
    ModelSEIRCONN::clone_ptr
    Model< TSeq > * clone_ptr()
    Advanced usage: Makes a copy of data and returns it as undeleted pointer.
    Definition: seirconnected.hpp:125
    ModelSEIRCONN::initial_states
    ModelSEIRCONN< TSeq > & initial_states(std::vector< double > proportions_, std::vector< int > queue_={})
    Set the initial states of the model.
    Definition: seirconnected.hpp:387
    ModelSEIRCONN::run
    ModelSEIRCONN< TSeq > & run(epiworld_fast_uint ndays, int seed=-1)
    Runs the simulation (after initialization)
    Definition: seirconnected.hpp:101
    -
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13643
    -
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14670
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13673
    +
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14700
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/seird_8hpp_source.html b/seird_8hpp_source.html index a0b7e266c..16437b3b1 100644 --- a/seird_8hpp_source.html +++ b/seird_8hpp_source.html @@ -275,11 +275,11 @@
    228 #endif
    Model
    Core class of epiworld.
    Definition: model-bones.hpp:91
    ModelSEIRD
    Template for a Susceptible-Exposed-Infected-Removed-Deceased (SEIRD) model.
    Definition: seird.hpp:9
    -
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13643
    -
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14670
    -
    epiworld::Agent::rm_agent_by_virus
    void rm_agent_by_virus(Model< TSeq > *model, epiworld_fast_int state_new=-99, epiworld_fast_int queue=-99)
    Agent removed by virus.
    Definition: epiworld.hpp:14619
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13673
    +
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14700
    +
    epiworld::Agent::rm_agent_by_virus
    void rm_agent_by_virus(Model< TSeq > *model, epiworld_fast_int state_new=-99, epiworld_fast_int queue=-99)
    Agent removed by virus.
    Definition: epiworld.hpp:14649
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/seirdconnected_8hpp_source.html b/seirdconnected_8hpp_source.html index 2e227dbb5..736c15d38 100644 --- a/seirdconnected_8hpp_source.html +++ b/seirdconnected_8hpp_source.html @@ -472,11 +472,11 @@
    ModelSEIRDCONN::initial_states
    ModelSEIRDCONN< TSeq > & initial_states(std::vector< double > proportions_, std::vector< int > queue_={})
    Set up the initial states of the model.
    Definition: seirdconnected.hpp:398
    ModelSEIRDCONN::run
    ModelSEIRDCONN< TSeq > & run(epiworld_fast_uint ndays, int seed=-1)
    Runs the simulation (after initialization)
    Definition: seirdconnected.hpp:95
    ModelSEIRDCONN::reset
    void reset()
    Reset the model.
    Definition: seirdconnected.hpp:108
    -
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13643
    -
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14670
    -
    epiworld::Agent::rm_agent_by_virus
    void rm_agent_by_virus(Model< TSeq > *model, epiworld_fast_int state_new=-99, epiworld_fast_int queue=-99)
    Agent removed by virus.
    Definition: epiworld.hpp:14619
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13673
    +
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14700
    +
    epiworld::Agent::rm_agent_by_virus
    void rm_agent_by_virus(Model< TSeq > *model, epiworld_fast_int state_new=-99, epiworld_fast_int queue=-99)
    Agent removed by virus.
    Definition: epiworld.hpp:14649
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/seirmixing_8hpp_source.html b/seirmixing_8hpp_source.html index 338f1ca1f..1bfe1f2ec 100644 --- a/seirmixing_8hpp_source.html +++ b/seirmixing_8hpp_source.html @@ -558,10 +558,10 @@
    ModelSEIRMixing::initial_states
    ModelSEIRMixing< TSeq > & initial_states(std::vector< double > proportions_, std::vector< int > queue_={})
    Set the initial states of the model.
    Definition: seirmixing.hpp:510
    ModelSEIRMixing::run
    ModelSEIRMixing< TSeq > & run(epiworld_fast_uint ndays, int seed=-1)
    Runs the simulation (after initialization)
    Definition: seirmixing.hpp:236
    ModelSEIRMixing::clone_ptr
    Model< TSeq > * clone_ptr()
    Advanced usage: Makes a copy of data and returns it as undeleted pointer.
    Definition: seirmixing.hpp:259
    -
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13643
    -
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14670
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13673
    +
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14700
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/sir_8hpp_source.html b/sir_8hpp_source.html index 51b6ea23c..96d941746 100644 --- a/sir_8hpp_source.html +++ b/sir_8hpp_source.html @@ -175,8 +175,8 @@
    Model
    Core class of epiworld.
    Definition: model-bones.hpp:91
    ModelSIR
    Template for a Susceptible-Infected-Removed (SIR) model.
    Definition: sir.hpp:15
    ModelSIR::initial_states
    ModelSIR< TSeq > & initial_states(std::vector< double > proportions_, std::vector< int > queue_={})
    Set the initial states of the model.
    Definition: sir.hpp:103
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/sirconnected_8hpp_source.html b/sirconnected_8hpp_source.html index 37f692257..5110e965f 100644 --- a/sirconnected_8hpp_source.html +++ b/sirconnected_8hpp_source.html @@ -483,10 +483,10 @@
    ModelSIRCONN::clone_ptr
    Model< TSeq > * clone_ptr()
    Advanced usage: Makes a copy of data and returns it as undeleted pointer.
    Definition: sirconnected.hpp:131
    ModelSIRCONN::initial_states
    ModelSIRCONN< TSeq > & initial_states(std::vector< double > proportions_, std::vector< int > queue_={})
    Set the initial states of the model.
    Definition: sirconnected.hpp:360
    ModelSIRCONN::reset
    void reset()
    Reset the model.
    Definition: sirconnected.hpp:119
    -
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13643
    -
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14670
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13673
    +
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14700
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/sird_8hpp_source.html b/sird_8hpp_source.html index 82f03e723..eb6a3f91f 100644 --- a/sird_8hpp_source.html +++ b/sird_8hpp_source.html @@ -184,8 +184,8 @@
    Model
    Core class of epiworld.
    Definition: model-bones.hpp:91
    ModelSIRD
    Template for a Susceptible-Infected-Removed-Deceased (SIRD) model.
    Definition: sird.hpp:9
    ModelSIRD::initial_states
    ModelSIRD< TSeq > & initial_states(std::vector< double > proportions_, std::vector< int > queue_={})
    Set the initial states of the model.
    Definition: sird.hpp:119
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/sirdconnected_8hpp_source.html b/sirdconnected_8hpp_source.html index 58e6abb8c..f2980c6ac 100644 --- a/sirdconnected_8hpp_source.html +++ b/sirdconnected_8hpp_source.html @@ -405,11 +405,11 @@
    ModelSIRDCONN::clone_ptr
    Model< TSeq > * clone_ptr()
    Advanced usage: Makes a copy of data and returns it as undeleted pointer.
    Definition: sirdconnected.hpp:94
    ModelSIRDCONN::reset
    void reset()
    Reset the model.
    Definition: sirdconnected.hpp:77
    ModelSIRDCONN::run
    ModelSIRDCONN< TSeq > & run(epiworld_fast_uint ndays, int seed=-1)
    Runs the simulation (after initialization)
    Definition: sirdconnected.hpp:64
    -
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13643
    -
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14670
    -
    epiworld::Agent::rm_agent_by_virus
    void rm_agent_by_virus(Model< TSeq > *model, epiworld_fast_int state_new=-99, epiworld_fast_int queue=-99)
    Agent removed by virus.
    Definition: epiworld.hpp:14619
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13673
    +
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14700
    +
    epiworld::Agent::rm_agent_by_virus
    void rm_agent_by_virus(Model< TSeq > *model, epiworld_fast_int state_new=-99, epiworld_fast_int queue=-99)
    Agent removed by virus.
    Definition: epiworld.hpp:14649
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/sirlogit_8hpp_source.html b/sirlogit_8hpp_source.html index 6a5fa2d3c..63d957522 100644 --- a/sirlogit_8hpp_source.html +++ b/sirlogit_8hpp_source.html @@ -387,9 +387,9 @@
    ModelSIRLogit::clone_ptr
    Model< TSeq > * clone_ptr()
    Advanced usage: Makes a copy of data and returns it as undeleted pointer.
    Definition: sirlogit.hpp:113
    ModelSIRLogit::reset
    void reset()
    Reset the model.
    Definition: sirlogit.hpp:125
    ModelSIRLogit::run
    ModelSIRLogit< TSeq > & run(epiworld_fast_uint ndays, int seed=-1)
    Runs the simulation (after initialization)
    Definition: sirlogit.hpp:101
    -
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13643
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13673
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/sirmixing_8hpp_source.html b/sirmixing_8hpp_source.html index 5f52d8056..8832dd974 100644 --- a/sirmixing_8hpp_source.html +++ b/sirmixing_8hpp_source.html @@ -533,10 +533,10 @@
    ModelSIRMixing::initial_states
    ModelSIRMixing< TSeq > & initial_states(std::vector< double > proportions_, std::vector< int > queue_={})
    Set the initial states of the model.
    Definition: sirmixing.hpp:482
    ModelSIRMixing::clone_ptr
    Model< TSeq > * clone_ptr()
    Advanced usage: Makes a copy of data and returns it as undeleted pointer.
    Definition: sirmixing.hpp:253
    ModelSIRMixing::reset
    void reset()
    Reset the model.
    Definition: sirmixing.hpp:242
    -
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13643
    -
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14670
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13673
    +
    epiworld::Agent::get_id
    int get_id() const
    Id of the individual.
    Definition: epiworld.hpp:14700
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/sis_8hpp_source.html b/sis_8hpp_source.html index e5e7ba3ec..7bd0003a3 100644 --- a/sis_8hpp_source.html +++ b/sis_8hpp_source.html @@ -158,8 +158,8 @@
    94 
    95 #endif
    ModelSIS
    Template for a Susceptible-Infected-Susceptible (SIS) model.
    Definition: sis.hpp:14
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/sisd_8hpp_source.html b/sisd_8hpp_source.html index 043eb74a4..18d916432 100644 --- a/sisd_8hpp_source.html +++ b/sisd_8hpp_source.html @@ -162,8 +162,8 @@
    99 
    100 #endif
    ModelSISD
    Template for a Susceptible-Infected-Susceptible-Deceased (SISD) model.
    Definition: sisd.hpp:15
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/surveillance_8hpp_source.html b/surveillance_8hpp_source.html index 0ff3cd67a..48d2d0296 100644 --- a/surveillance_8hpp_source.html +++ b/surveillance_8hpp_source.html @@ -419,10 +419,10 @@
    389 
    390 #endif
    ModelSURV
    Definition: surveillance.hpp:5
    -
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13643
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Tool
    Tools for defending the agent against the virus.
    Definition: epiworld.hpp:11409
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Agent
    Agent (agents)
    Definition: epiworld.hpp:13673
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Tool
    Tools for defending the agent against the virus.
    Definition: epiworld.hpp:11439
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135
    diff --git a/tests_8hpp_source.html b/tests_8hpp_source.html index 9ce1d3d0e..b9eafee19 100644 --- a/tests_8hpp_source.html +++ b/tests_8hpp_source.html @@ -159,9 +159,9 @@
    87 
    88 
    89 #endif
    -
    epiworld::Entity
    Definition: epiworld.hpp:12218
    -
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6296
    -
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10105
    +
    epiworld::Entity
    Definition: epiworld.hpp:12248
    +
    epiworld::Model
    Core class of epiworld.
    Definition: epiworld.hpp:6326
    +
    epiworld::Virus
    Virus.
    Definition: epiworld.hpp:10135

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