refactor: Remove code that is commented out

R/initialize_modules.R

@@ -112,14 +112,6 @@ initialize_module <- function(parameters, data, module_name) {
       "nlengths",
       "proportion_catch_numbers_at_length"
     ))
-    # else {
-    #   module_fields <- setdiff(module_fields, c(
-    #   "age_length_conversion_matrix",
-    #   # Right now we can also remove nlengths because the default is 0
-    #   "nlength",
-    #   "proportion_catch_numbers_at_length"
-    # ))
-    # }
   }
 
   # Populate fields based on common and specific settings
@@ -654,19 +646,6 @@ initialize_fims <- function(parameters, data) {
       linked_ids = fleet_module_ids
     )
 
-    # Set up fishery index data using the lognormal
-    # fleet_index_distribution[[i]] <- initialize_distribution(
-    #   module_input = parameters[["parameters"]][[fleet_names[i]]],
-    #   distribution_name = parameters[["modules"]][["fleets"]][[
-    #     fleet_names[i]
-    #   ]][["data_distribution"]]["Index"],
-    #   distribution_type = "data",
-    #   linked_ids = c(
-    #     data_link = fleet[[i]]$GetObservedIndexDataID(),
-    #     fleet_link = fleet[[i]]$log_expected_index$get_id()
-    #   )
-    # )
-
     # TODO: update argument sd to log_sd to match the Rcpp interface
     parameter_value_name <- grep(
       paste0("log_sd", ".value"),
@@ -699,21 +678,6 @@ initialize_fims <- function(parameters, data) {
       data_type = "index"
     )
 
-    # Set up fishery age-composition data using the multinomial
-    # fleet_agecomp_distribution[[i]] <- initialize_distribution(
-    #   module_input = NULL,
-    #   distribution_name = parameters[["modules"]][["fleets"]][[
-    #     fleet_names[i]
-    #   ]][["data_distribution"]]["AgeComp"],
-    #   distribution_type = "data",
-    #   linked_ids = c(
-    #     data_link = fleet[[i]]$GetObservedAgeCompDataID(),
-    #     fleet_link = fleet[[
-    #       i
-    #     ]]$proportion_catch_numbers_at_age$get_id()
-    #   )
-    # )
-
     fleet_agecomp_distribution[[i]] <- initialize_data_distribution(
       module = fleet[[i]],
       family = multinomial(link = "logit"),
@@ -740,15 +704,6 @@ initialize_fims <- function(parameters, data) {
     data = data
   )
 
-  # recruitment_distribution <- initialize_distribution(
-  #   module_input = parameters[["parameters"]][["recruitment"]],
-  #   distribution_name = parameters[["modules"]][[
-  #     "recruitment"
-  #   ]][["process_distribution"]],
-  #   distribution_type = "process",
-  #   linked_ids = recruitment$get_id()
-  # )
-
   parameter_name <- names(parameters$modules$recruitment$process_distribution)
   field_value_name <- grep(
     paste0("log_sd.value"),

inst/include/common/def.hpp

@@ -63,7 +63,6 @@
 
 #ifdef FIMS_WINDOWS
 #include <Windows.h>
-//#define __PRETTY_FUNCTION__ __FUNCSIG__
 #endif
 
 #if !defined(__PRETTY_FUNCTION__) && !defined(__GNUC__)

inst/include/common/fims_math.hpp

@@ -10,7 +10,6 @@
 
 // note: this is modeling platform specific, must be controlled by
 // preprocessing macros
-//#include "def.hpp"
 #include <cmath>
 #include <random>
 #include <sstream>
@@ -61,7 +60,6 @@ inline const Type pow(const Type &x, const Type &y) {
 #endif
 
 #ifdef TMB_MODEL
-// #include <TMB.hpp>
 
 /**
  * @brief The exponential function.

inst/include/common/model.hpp

@@ -222,8 +222,6 @@ namespace fims_model {
                 fleet_idx += 1;
             }
 
-            // jnll = rec_nll + age_comp_nll + index_nll;
-
             // Reporting
 #ifdef TMB_MODEL
             //FIMS_REPORT_F(rec_nll, of);

inst/include/distributions/functors/lognormal_lpdf.hpp

@@ -61,8 +61,6 @@ namespace fims_distributions
               // See Deroba and Miller, 2016 (https://doi.org/10.1016/j.fishres.2015.12.002) for
               // the use of lognormal constant
               if(this->observed_values->at(i) != this->observed_values->na_value){
-              // this->lpdf_vec[i] = this->keep[i] * -dnorm(log(this->observed_values->at(i)), this->expected_values.get_force_scalar(i),
-              //                                            fims_math::exp(log_sd.get_force_scalar(i)), true) - log(this->observed_values->->at(i));
                   this->lpdf_vec[i] = dnorm(log(this->observed_values->at(i)), this->expected_values.get_force_scalar(i),
                                             fims_math::exp(log_sd.get_force_scalar(i)), true) - log(this->observed_values->at(i));
                 } else {
@@ -90,13 +88,6 @@ namespace fims_distributions
                 }
             }
             #endif
-
-            /* osa not working yet
-              if(osa_flag){//data observation type implements osa residuals
-                  //code for osa cdf method
-                  this->lpdf_vec[i] = this->keep.cdf_lower[i] * log( pnorm(this->x[i], this->expected_values.get_force_scalar(i), fims_math::exp(log_sd.get_force_scalar(i))) );
-                  this->lpdf_vec[i] = this->keep.cdf_upper[i] * log( 1.0 - pnorm(this->x[i], this->expected_values.get_force_scalar(i), fims_math::exp(log_sd.get_force_scalar(i))) );
-              } */
             }
             #ifdef TMB_MODEL
             vector<Type> lognormal_x = this->x;

inst/include/distributions/functors/multinomial_lpmf.hpp

@@ -25,8 +25,6 @@ namespace fims_distributions
         Type lpdf = 0.0; /**< total negative log-likelihood contribution of the distribution */
         fims::Vector<size_t> dims; /**< Dimensions of the number of rows and columns of the multivariate dataset */
 
-        // data_indicator<tmbutils::vector<Type> , Type> keep;  /**< Indicator used in TMB one-step-ahead residual calculations */
-
         /** @brief Constructor.
          */
         MultinomialLPMF() : DensityComponentBase<Type>()
@@ -119,8 +117,6 @@ namespace fims_distributions
                 }
             }
             #ifdef TMB_MODEL
-          //   vector<Type> x = this->observed_values->data;
-          //  FIMS_REPORT_F(x, this->of);
             #endif
             return (lpdf);
         }

inst/include/distributions/functors/normal_lpdf.hpp

@@ -24,8 +24,6 @@ struct NormalLPDF : public DensityComponentBase<Type> {
     fims::Vector<Type> log_sd; /**< log of the standard deviation of the distribution; can be a vector or scalar */
     Type lpdf = 0.0; /**< total log probability density contribution of the distribution */
 
-    //data_indicator<tmbutils::vector<Type> , Type> keep; /**< Indicator used in TMB one-step-ahead residual calculations */
-
     /** @brief Constructor.
      */
     NormalLPDF() : DensityComponentBase<Type>() {
@@ -57,7 +55,6 @@ struct NormalLPDF : public DensityComponentBase<Type> {
         if(this->input_type == "data"){
           // if data, check if there are any NA values and skip lpdf calculation if there are
           if(this->observed_values->at(i) != this->observed_values->na_value){
-          // this->lpdf_vec[i] = this->keep[i] * -dnorm(this->observed_values->at(i), this->expected_values.get_force_scalar(i), sd[i], true);
             this->lpdf_vec[i] = dnorm(this->observed_values->at(i), this->expected_values.get_force_scalar(i), fims_math::exp(log_sd.get_force_scalar(i)), true);
           } else {
             this->lpdf_vec[i] = 0;
@@ -87,7 +84,6 @@ struct NormalLPDF : public DensityComponentBase<Type> {
         }
         #ifdef TMB_MODEL
         vector<Type> normal_x = this->x;
-        //FIMS_REPORT_F(normal_x, this->of);
         #endif
         return(lpdf);
     }

inst/include/interface/rcpp/rcpp_interface.hpp

@@ -644,10 +644,6 @@ void log_error(std::string log_entry) {
 
     std::string ret = ss_ret.str(); //"find error";//Rcpp::as<std::string>(result);
 
-
-    //    Rcpp::Environment base = Rcpp::Environment::global_env();
-    //    Rcpp::Function f  = base["traceback"];
-    //    std::string ret = Rcpp::as<std::string>(f());
     fims::FIMSLog::fims_log->error_message(log_entry, -1, "R_env", ret.c_str());
 }
 

inst/include/interface/rcpp/rcpp_objects/rcpp_distribution.hpp

@@ -486,7 +486,6 @@ class DlnormDistributionsInterface : public DistributionsInterfaceBase {
  * dmultinom_ <- new(DmultinomDistribution)
  *
  */
-// template <typename Type>
 
 class DmultinomDistributionsInterface : public DistributionsInterfaceBase {
  public:

inst/include/interface/rcpp/rcpp_objects/rcpp_interface_base.hpp

@@ -142,7 +142,6 @@ class ParameterVector{
     ParameterVector(){
         this->id_m = ParameterVector::id_g++;
         this->storage_m = std::make_shared<std::vector<Parameter> >();
-        //        Parameter p;
         this->storage_m->resize(1); //push_back(Rcpp::wrap(p));
     }
 

inst/include/population_dynamics/maturity/functors/logistic.hpp

@@ -10,7 +10,6 @@
 #ifndef POPULATION_DYNAMICS_MATURITY_LOGISTIC_HPP
 #define POPULATION_DYNAMICS_MATURITY_LOGISTIC_HPP
 
-//#include "../../../interface/interface.hpp"
 #include "../../../common/fims_math.hpp"
 #include "../../../common/fims_vector.hpp"
 #include "maturity_base.hpp"

inst/include/population_dynamics/population/population.hpp

@@ -12,7 +12,6 @@
 #include "../fleet/fleet.hpp"
 #include "../growth/growth.hpp"
 #include "../recruitment/recruitment.hpp"
-//#include "subpopulation.hpp"
 #include "../../interface/interface.hpp"
 #include "../maturity/maturity.hpp"
 
@@ -548,7 +547,6 @@ namespace fims_popdy {
                         CalculateInitialNumbersAA(i_age_year, a);
 
                         if (a == 0) {
-                            // this->numbers_at_age[i_age_year] = this->recruitment->rzero;
                             this->unfished_numbers_at_age[i_age_year] =
                                     fims_math::exp(this->recruitment->log_rzero[0]);
                         } else {