Changed reduced_inf option to asymp_relative_inf - much clearer.

Automatically set t_hosp_offset to be 3 more than highest hospitalization days, singe this was not an accessible option on the command line.

docs/source/usage/how_to_run.rst

@@ -135,8 +135,9 @@ The following inputs specify the disease parameters:
     Probability of transmission given contact. There must be one entry for each disease strain.
 * ``disease.p_asymp`` (`list of float`, default ``0.4``)
     The fraction of cases that are asymptomatic. There must be one entry for each disease strain.
-* ``disease.reduced_inf`` (`list of float`, default ``0.75``)
-    The relative infectiousness of asymptomatic individuals. There must be one entry for each disease strain.
+* ``disease.asymp_relative_inf`` (`list of float`, default ``0.75``)
+    The relative infectiousness of asymptomatic individuals, from 0 to 1. There must be one entry for each disease strain.
+    `This is not yet implemented`.
 * ``disease.vac_eff`` (`float`, default ``0``)
     The vaccine efficacy - the probability of transmission will be multiplied by one minus this factor.
     `Vaccination is not yet implemented, so this factor must be left at 0`.

examples/inputs.defaults

@@ -90,8 +90,8 @@ disease.nstrain = 1
 disease.p_trans = 0.2
 # Probability of being asymptomatic.
 disease.p_asymp = 0.4
-# Relative infectiousness of asymptomatic indivudals.
-disease.reduced_inf = 0.75
+# Relative infectiousness of asymptomatic indivudals. Curnently not implemented.
+disease.asymp_relative_inf = 0.75
 # Vaccine efficacy. Not yet implemented; leave at 0.
 disease.vac_eff = 0
 # Mean length in days that agents are immune after recovery from an infection.
@@ -107,9 +107,9 @@ disease.infectious_length_mean = 6.0
 # Standard deviation in days.
 disease.infectious_length_std = 1.0
 # Mean length in days from the time of infectioun untli symptoms develop.
-disease.incution_length_mean = 5.0
+disease.incubation_length_mean = 5.0
 # Standard deviation in days.
-disease.incution_length_std = 1.0
+disease.incubation_length_std = 1.0
 
 # Number of days in hospital for the age groups under 50, 50 to 64 and over 64.
 disease.hospitalization_days = 3 8 7

src/DiseaseParm.H

@@ -76,7 +76,7 @@ struct DiseaseParm
     int nstrain = 1;  /*!< Number of strains */
     Real p_trans[1] = {Real(0.20)};     /*!< probability of transimission given contact */
     Real p_asymp[1] = {Real(0.40)};     /*!< fraction of cases that are asymptomatic */
-    Real reduced_inf[1] = {Real(0.75)}; /*!< relative infectiousness of asymptomatic individuals */
+    Real asymp_relative_inf[1] = {Real(0.75)}; /*!< relative infectiousness of asymptomatic individuals */
 
     Real vac_eff = Real(0.0); /*!< Vaccine efficacy */
 
@@ -101,7 +101,8 @@ struct DiseaseParm
      *  used in other parts of the code (#AgeGroups) */
     Real m_t_hosp[AgeGroups_Hosp::total] = {Real(3), Real(8), Real(7)};
     /*! Offset to separate the timers for hospital, ICU, and ventilator;
-     * needs to be greater than the maximum of #DiseaseParm::m_t_hosp */
+     * needs to be greater than the maximum of #DiseaseParm::m_t_hosp
+     * Set automatically when the hospital days are set. */
     Real m_t_hosp_offset = 10;
 
     /*! sick -> hospital probabilities */

src/DiseaseParm.cpp

@@ -58,7 +58,7 @@ void DiseaseParm::readInputs ( const std::string& a_pp_str /*!< Parmparse string
 
     queryArray(pp, "p_trans", p_trans, nstrain);
     queryArray(pp, "p_asymp", p_asymp, nstrain);
-    queryArray(pp, "reduced_inf", reduced_inf, nstrain);
+    queryArray(pp, "asymp_relative_inf", asymp_relative_inf, nstrain);
 
     pp.query("vac_eff", vac_eff);
     // no support yet for vaccinations
@@ -78,9 +78,10 @@ void DiseaseParm::readInputs ( const std::string& a_pp_str /*!< Parmparse string
     pp.query("immune_length_mean", immune_length_mean);
     pp.query("immune_length_std", immune_length_std);
 
+    m_t_hosp_offset = 0;
     queryArray(pp, "hospitalization_days", m_t_hosp, AgeGroups_Hosp::total);
     for (int i = 0; i < AgeGroups_Hosp::total; i++) {
-        if (m_t_hosp[i] > m_t_hosp_offset) m_t_hosp_offset = m_t_hosp[i] + 1;
+        if (m_t_hosp[i] > m_t_hosp_offset) m_t_hosp_offset = m_t_hosp[i] + 3;
     }
 
     queryArray(pp, "CHR", m_CHR, AgeGroups::total);