Apply suggestions from code review

Co-authored-by: Martin J. Kühn <62713180+mknaranja@users.noreply.github.com>

Author: lenaploetzke

cpp/models/ide_secir/model.cpp

@@ -67,12 +67,12 @@ void Model::initialize(ScalarType dt)
             m_populations[Eigen::Index(0)][Eigen::Index(InfectionState::Dead)];
     }
     else if (m_populations[Eigen::Index(0)][Eigen::Index(InfectionState::Susceptible)] > 1e-12) {
-        //take initialized value for Susceptibles if value can't be calculated via the standard formula
+        // Take initialized value for Susceptibles if value can't be calculated via the standard formula.
         m_initialization_method = 2;
-        //calculate other compartment sizes for t=0
+        // Calculate other compartment sizes for t=0.
         other_compartments_current_timestep(dt);
 
-        //R; need an initial value for R, therefore do not calculate via compute_recovered()
+        // R; need an initial value for R, therefore do not calculate via compute_recovered()
         m_populations[Eigen::Index(0)][Eigen::Index(InfectionState::Recovered)] =
             m_N - m_populations[Eigen::Index(0)][Eigen::Index(InfectionState::Susceptible)] -
             m_populations[Eigen::Index(0)][Eigen::Index(InfectionState::Exposed)] -
@@ -83,9 +83,9 @@ void Model::initialize(ScalarType dt)
             m_populations[Eigen::Index(0)][Eigen::Index(InfectionState::Dead)];
     }
     else if (m_populations[Eigen::Index(0)][Eigen::Index(InfectionState::Recovered)] > 1e-12) {
-        //if value for Recovered is initialized and standard method is not applicable, calculate Susceptibles via other compartments
-        //determining other compartment sizes is not dependent of Susceptibles(0), just of the transitions of the past.
-        //calculate other compartment sizes for t=0
+        // If value for Recovered is initialized and standard method is not applicable (i.e., no value for total infections
+        //  or suceptibles given directly), calculate Susceptibles via other compartments.
+        // The calculation of other compartments' values is not dependent on Susceptibles at time 0, i.e., S(0), but only on the transitions of the past.
         m_initialization_method = 3;
         other_compartments_current_timestep(dt);
 

cpp/models/ide_secir/model.h

@@ -94,11 +94,18 @@ class Model
     }
 
     /**
-     * @brief Calculate the number of individuals in each compartment for time 0.
-     * 
-     * Initial transitions are used to calculate the initial compartment sizes.
-     * @param[in] dt Time discretization step size.         
-     */
+    * @brief Initializes the model and sets compartment values at time zero.
+    *
+    * The initialization method is selected automatically based on the different values that need to be set beforehand.
+    * Infection compartments are always computed through historic flow.
+    * Initialization methods for susceptibles and recovered are tested in the following order:
+    * 1.) If a positive number for the total number of confirmed cases is set, recovered is set according to that value and #Susceptible%s are derived.
+    * 2.) If #Susceptible%s are set, recovered will be derived.
+    * 3.) If #Recovered are set directly, #Susceptible%s are derived.
+    * 4.) If none of the above is set with positive value, the force of infection is used as in Messina et al (2021) to set the #Susceptible%s.
+    *
+    * @param[in] dt Time discretization step size.         
+    */
     void initialize(ScalarType dt);
 
     /**
@@ -201,12 +208,12 @@ class Model
     }
 
     /**
-     * @brief Specifies a number associated with the method used for initialization.
+     * @brief Returns the number associated with the method selected automatically for initialization.
      *
-     * @returns 0 if the initialization method has not yet been selected,
+    * @returns 0 if the model has not yet been initialized and the method has not yet been selected,
      *      1 if the method using the total number of confirmed cases at time 0 is used,
-     *      2 if the initialization is calculated using a prior set value for S,
-     *      3 if the initialization is calculated using a prior set value for R,
+     *      2 if the initialization is calculated using a beforehand set value for S,
+     *      3 if the initialization is calculated using a beforehand set value for R,
      *      4 if the force of infection method is used, 
      *      -1 if the initialization was not possible using any of the methods and
      *      -2 if the initialization was possible using one of the provided methods but the result is not appropriate.