Adding new docker image for debugging. Fixed difference in rec rates

.Rbuildignore

@@ -33,3 +33,4 @@ README\.html
 \.gitattributes
 
 paper\..+
+docker

Makefile

@@ -1,8 +1,15 @@
+# Capture the current value of the version of the package in DESCRIPTION
+VERSION := $(shell grep Version DESCRIPTION | sed -e 's/Version: //')
+
 build: docs clean
 	cd .. && rm -f epiworldR_*.tar.gz & R CMD build epiworldR
 
 debug: clean
-	EPI_CONFIG="-DEPI_DEBUG -Wall -pedantic -g" R CMD INSTALL .
+	docker run --rm -ti -w/mnt -v $(PWD):/mnt uofuepibio/epiworldr:debug make docker-debug 
+
+docker-debug:
+	EPI_CONFIG="-DEPI_DEBUG -Wall -pedantic -g" R CMD INSTALL \
+		--no-docs --build .
 
 install: build 
 	which R
@@ -26,7 +33,7 @@ clean:
 docs:
 	Rscript --vanilla -e 'devtools::document()'
 
-.PHONY: build update check clean docs
+.PHONY: build update check clean docs docker-debug
 
 checkv: build
 	R CMD check --as-cran --use-valgrind epiworldR*.tar.gz

R/ModelSEIRD.R

@@ -45,8 +45,14 @@ ModelSEIRD <- function(
 ) {
 
   structure(
-    ModelSEIRD_cpp(name, prevalence, transmission_rate, incubation_days, 
-                  recovery_rate, death_rate),
+    ModelSEIRD_cpp(
+      name              = name,
+      prevalence        = prevalence,
+      transmission_rate = transmission_rate,
+      incubation_days   = incubation_days,
+      recovery_rate     = recovery_rate,
+      death_rate        = death_rate
+      ),
     class = c("epiworld_seird", "epiworld_model")
   )
 

docker/Dockerfile

@@ -0,0 +1,19 @@
+FROM rocker/r-base:latest
+
+RUN \
+  echo 'options(repos=c(CRAN="https://cloud.r-project.org"))' >> ~/.Rprofile && \
+  Rscript --vanilla -e 'getOption("repos")'
+
+
+RUN Rscript --vanilla -e "install.packages('cpp11', dependencies = TRUE, repos = 'https://cloud.r-project.org')"
+
+
+
+RUN mkdir ~/.R && \
+  echo "CXXFLAGS=-g -O0" > ~/.R/Makevars && \
+  echo "CXX14FLAGS=-g -O0" >> ~/.R/Makevars && \
+  echo "CXX17FLAGS=-g -O0" >> ~/.R/Makevars && \
+  echo "CXX11FLAGS=-g -O0" >> ~/.R/Makevars && \
+  echo "SAFE_FLAGS=-g -O0" >> ~/.R/Makevars
+
+CMD ["bash"]

docker/Makefile

@@ -0,0 +1,2 @@
+all:
+	docker build -t uofuepibio/epiworldr:debug -f Dockerfile .

inst/include/epiworld/models/seir.hpp

@@ -14,14 +14,13 @@
 template<typename TSeq = int>
 class ModelSEIR : public epiworld::Model<TSeq>
 {
-private:
+
+public:
     static const int SUSCEPTIBLE = 0;
     static const int EXPOSED     = 1;
     static const int INFECTED    = 2;
     static const int REMOVED     = 3;
 
-public:
-
     ModelSEIR() {};
 
     ModelSEIR(
@@ -99,6 +98,7 @@ inline ModelSEIR<TSeq>::ModelSEIR(
 
     virus.set_prob_infecting(&model("Transmission rate"));
     virus.set_incubation(&model("Incubation days"));
+    virus.set_prob_recovery(&model("Recovery rate"));
 
     // Adding the tool and the virus
     model.add_virus(virus, prevalence);

inst/include/epiworld/models/seird.hpp

@@ -15,15 +15,14 @@
 template<typename TSeq = int>
 class ModelSEIRD : public epiworld::Model<TSeq>
 {
-private:
+
+public:
   static const int SUSCEPTIBLE = 0;
   static const int EXPOSED     = 1;
   static const int INFECTED    = 2;
   static const int REMOVED     = 3;
   static const int DECEASED    = 4;
 
-public:
-
   ModelSEIRD() {};
 
   ModelSEIRD(
@@ -66,65 +65,60 @@ class ModelSEIRD : public epiworld::Model<TSeq>
   ) -> void {
 
     auto state = p->get_state();
-
-    if (state == ModelSEIRD<TSeq>::INFECTED)
+
+    // Odd: Die, Even: Recover
+    epiworld_fast_uint n_events = 0u;
+    for (const auto & v : p->get_viruses())
     {
 
+      // Die
+      m->array_double_tmp[n_events++] = 
+        v->get_prob_death(m) * (1.0 - p->get_death_reduction(v, m)); 
 
-      // Odd: Die, Even: Recover
-      epiworld_fast_uint n_events = 0u;
-      for (const auto & v : p->get_viruses())
-      {
-
-        // Die
-        m->array_double_tmp[n_events++] = 
-          v->get_prob_death(m) * (1.0 - p->get_death_reduction(v, m)); 
-
-        // Recover
-        m->array_double_tmp[n_events++] = 
-          1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m)); 
-
-      }
+      // Recover
+      m->array_double_tmp[n_events++] = 
+        1.0 - (1.0 - v->get_prob_recovery(m)) * (1.0 - p->get_recovery_enhancer(v, m)); 
 
+    }
+
 #ifdef EPI_DEBUG
-      if (n_events == 0u)
-      {
-        printf_epiworld(
-          "[epi-debug] agent %i has 0 possible events!!\n",
-          static_cast<int>(p->get_id())
-        );
-        throw std::logic_error("Zero events in exposed.");
-      }
+    if (n_events == 0u)
+    {
+      printf_epiworld(
+        "[epi-debug] agent %i has 0 possible events!!\n",
+        static_cast<int>(p->get_id())
+      );
+      throw std::logic_error("Zero events in exposed.");
+    }
 #else
-      if (n_events == 0u)
-        return;
+    if (n_events == 0u)
+      return;
 #endif
+
+
+    // Running the roulette
+    int which = roulette(n_events, m);
+
+    if (which < 0)
+      return;
+
+    // Which roulette happen?
+    if ((which % 2) == 0) // If odd
+    {
 
+      size_t which_v = std::ceil(which / 2);
+      p->rm_agent_by_virus(which_v, m);
 
-      // Running the roulette
-      int which = roulette(n_events, m);
-
-      if (which < 0)
-        return;
+    } else {
 
-      // Which roulette happen?
-      if ((which % 2) == 0) // If odd
-      {
-
-        size_t which_v = std::ceil(which / 2);
-        p->rm_agent_by_virus(which_v, m);
-
-      } else {
-
-        size_t which_v = std::floor(which / 2);
-        p->rm_virus(which_v, m);
-
-      }
+      size_t which_v = std::floor(which / 2);
+      p->rm_virus(which_v, m);
 
-      return ;
+    }
+
+    return ;
 
-    } else
-      throw std::logic_error("This function can only be applied to exposed or infected individuals. (SEIRD)") ;
+
 
     return;
 
@@ -165,6 +159,7 @@ inline ModelSEIRD<TSeq>::ModelSEIRD(
   virus.set_prob_infecting(&model("Transmission rate"));
   virus.set_incubation(&model("Incubation days"));
   virus.set_prob_death(&model("Death rate"));
+  virus.set_prob_recovery(&model("Recovery rate"));
 
   // Adding the tool and the virus
   model.add_virus(virus, prevalence);