Removes the rest of log_sigma_rec*

NOAA-FIMS · Sep 26, 2024 · aa8ed94 · aa8ed94
1 parent 24fb9df
commit aa8ed94
Show file tree

Hide file tree

Showing 2 changed files with 0 additions and 17 deletions.
diff --git a/inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp b/inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp
@@ -71,7 +71,6 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
 
     double estimated_logit_steep; /**< estimated steepness or the productivity of the stock*/
     double estimated_log_rzero; /**< estimated recruitment at unfished biomass */
-    double estimated_log_sigma_recruit; /**< estimated log of the stock recruit standard deviation */
     Rcpp::NumericVector estimated_log_devs; /**< estimated log recruitment deviations*/
 
   BevertonHoltRecruitmentInterface() : RecruitmentInterfaceBase() {}
@@ -136,15 +135,6 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
                 }
             }
 
-            for (size_t i = 0; i < this->log_sigma_recruit.size(); i++) {
-                if (log_sigma_recruit[i].estimated_m) {
-                    this->log_sigma_recruit[i].estimated_value_m = recr->log_sigma_recruit[i];
-                } else {
-                    this->log_sigma_recruit[i].estimated_value_m = this->log_sigma_recruit[i].value_m;
-                }
-
-            }
-
             for (size_t i = 0; i < this->estimated_log_devs.size(); i++) {
                 if (this->log_devs[i].estimated_m) {
                     this->log_devs[i].estimated_value_m = recr->log_recruit_devs[i];
@@ -177,12 +167,6 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
         ss << "   \"type\": \"vector\",\n";
         ss << "   \"values\":" << this->log_rzero << ",\n },\n";
 
-        ss << " \"parameter\": {\n";
-        ss << "   \"name\": \"log_sigma_recruit\",\n";
-        ss << "   \"id\":" << this->log_sigma_recruit.id_m << ",\n";
-        ss << "   \"type\": \"vector\",\n";
-        ss << "   \"values\":" << this->log_sigma_recruit << ",\n },\n";
-
         ss << " \"parameter\": {\n";
         ss << "   \"name\": \"log_devs\",\n";
         ss << "   \"id\":" << this->log_devs.id_m << ",\n";

diff --git a/tests/integration/integration_test_population_tmb_nointerface.cpp b/tests/integration/integration_test_population_tmb_nointerface.cpp
@@ -136,7 +136,6 @@ Type objective_function<Type>::operator()(){
     std::make_shared<fims_popdy::SRBevertonHolt<Type> >();
   rec->rzero = R0;
   rec->steep = h;
-  rec->log_sigma_recruit = logR_sd;
   /*the log_recruit_dev vector does not include a value for year == 0
     and is of length nyears - 1 where the first position of the vector
     corresponds to the second year of the time series.*/