fix(proportion_female): Removes faulty est input

proportion_female appeared to be estimable and/or specified by the user
but it was still hard coded to 0.5 for every age. This commit reverts
back part of PR #543 where the hard-coded value (not by age) was made
0.5 by age with a user interface.

Part of #638

inst/include/interface/rcpp/rcpp_interface.hpp

@@ -431,9 +431,7 @@ RCPP_MODULE(fims) {
       .field("nyears", &PopulationInterface::nyears)
       .field("log_M", &PopulationInterface::log_M)
       .field("log_init_naa", &PopulationInterface::log_init_naa)
-      .field("proportion_female", &PopulationInterface::proportion_female)
       .field("ages", &PopulationInterface::ages)
-      .field("estimate_prop_female", &PopulationInterface::estimate_prop_female)
       .method("evaluate", &PopulationInterface::evaluate)
       .method("SetMaturity", &PopulationInterface::SetMaturity)
       .method("SetGrowth", &PopulationInterface::SetGrowth)

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

@@ -64,9 +64,6 @@ class PopulationInterface : public PopulationInterfaceBase {
   ParameterVector log_init_naa; /**<log of the initial numbers at age*/
   ParameterVector numbers_at_age; /**<log of the initial numbers at age*/
   Rcpp::NumericVector ages; /**<vector of ages in the population; length nages*/
-  Rcpp::NumericVector proportion_female; /**<doule representing the proportion
-                                            of female individuals */
-  bool estimate_prop_female; /**<whether proportion female should be estimated*/
 
   PopulationInterface() : PopulationInterfaceBase() {}
 
@@ -150,12 +147,6 @@ class PopulationInterface : public PopulationInterfaceBase {
     for (int i = 0; i < ages.size(); i++) {
       population->ages[i] = this->ages[i];
     }
-    for (int i = 0; i < proportion_female.size(); i++) {
-      population->proportion_female[i] = this->proportion_female[i];
-      if (estimate_prop_female) {
-        info->RegisterParameter(population->proportion_female[i]);
-      }
-    }
 
     population->numbers_at_age.resize((nyears + 1) * nages);
     info->variable_map[this->numbers_at_age.id_m] = &(population)->numbers_at_age;

inst/include/population_dynamics/population/population.hpp

@@ -40,13 +40,14 @@ struct Population : public fims_model_object::FIMSObject<Type> {
   size_t nages;         /*!< total number of ages in the population*/
   size_t nfleets;       /*!< total number of fleets in the fishery*/
 
+  // constants
+  const Type proportion_female = 0.5; /*!< Sex proportion fixed at 50/50*/
+
   // parameters are estimated; after initialize in create_model, push_back to
   // parameter list - in information.hpp (same for initial F in fleet)
   fims::Vector<Type>
       log_init_naa;         /*!< estimated parameter: log numbers at age*/
   fims::Vector<Type> log_M; /*!< estimated parameter: log Natural Mortality*/
-  fims::Vector<Type>
-      proportion_female; /*!< estimated parameter: proportion female by age */
 
   // Transformed values
   fims::Vector<Type> M; /*!< transformed parameter: Natural Mortality*/
@@ -131,7 +132,6 @@ struct Population : public fims_model_object::FIMSObject<Type> {
     mortality_F.resize(nyears * nages);
     mortality_Z.resize(nyears * nages);
     proportion_mature_at_age.resize((nyears + 1) * nages);
-    proportion_female.resize(nages);
     weight_at_age.resize(nages);
     unfished_numbers_at_age.resize((nyears + 1) * nages);
     biomass.resize((nyears + 1));
@@ -169,7 +169,6 @@ struct Population : public fims_model_object::FIMSObject<Type> {
     std::fill(proportion_mature_at_age.begin(), proportion_mature_at_age.end(),
               0.0);
     std::fill(mortality_Z.begin(), mortality_Z.end(), 0.0);
-    std::fill(proportion_female.begin(), proportion_female.end(), 0.5);
 
     // Transformation Section
     for (size_t age = 0; age < this->nages; age++) {
@@ -315,9 +314,9 @@ struct Population : public fims_model_object::FIMSObject<Type> {
    */
   void CalculateSpawningBiomass(size_t i_age_year, size_t year, size_t age) {
     this->spawning_biomass[year] +=
-        this->proportion_female[age] * this->numbers_at_age[i_age_year] *
+        this->proportion_female * this->numbers_at_age[i_age_year] *
         this->proportion_mature_at_age[i_age_year] * this->weight_at_age[age];
-    POPULATION_LOG << " proportion female " << this->proportion_female[age]
+    POPULATION_LOG << " proportion female " << this->proportion_female
                    << " "
                    << " mature age " << age << " is "
                    << this->proportion_mature_at_age[i_age_year] << " "
@@ -340,7 +339,7 @@ struct Population : public fims_model_object::FIMSObject<Type> {
   void CalculateUnfishedSpawningBiomass(size_t i_age_year, size_t year,
                                         size_t age) {
     this->unfished_spawning_biomass[year] +=
-        this->proportion_female[age] *
+        this->proportion_female *
         this->unfished_numbers_at_age[i_age_year] *
         this->proportion_mature_at_age[i_age_year] * this->weight_at_age[age];
   }
@@ -353,12 +352,12 @@ struct Population : public fims_model_object::FIMSObject<Type> {
   Type CalculateSBPR0() {
     std::vector<Type> numbers_spr(this->nages, 1.0);
     Type phi_0 = 0.0;
-    phi_0 += numbers_spr[0] * this->proportion_female[0] *
+    phi_0 += numbers_spr[0] * this->proportion_female *
              this->proportion_mature_at_age[0] *
              this->growth->evaluate(ages[0]);
     for (size_t a = 1; a < (this->nages - 1); a++) {
       numbers_spr[a] = numbers_spr[a - 1] * fims_math::exp(-this->M[a]);
-      phi_0 += numbers_spr[a] * this->proportion_female[a] *
+      phi_0 += numbers_spr[a] * this->proportion_female *
                this->proportion_mature_at_age[a] *
                this->growth->evaluate(ages[a]);
     }
@@ -367,7 +366,7 @@ struct Population : public fims_model_object::FIMSObject<Type> {
         (numbers_spr[nages - 2] * fims_math::exp(-this->M[nages - 2])) /
         (1 - fims_math::exp(-this->M[this->nages - 1]));
     phi_0 += numbers_spr[this->nages - 1] *
-             this->proportion_female[this->nages - 1] *
+             this->proportion_female *
              this->proportion_mature_at_age[this->nages - 1] *
              this->growth->evaluate(ages[this->nages - 1]);
     return phi_0;

tests/gtest/test_population_B_and_SB.cpp

@@ -13,7 +13,7 @@ namespace
         std::vector<double> test_SB(nyears + 1, 0);
         std::vector<double> test_B(nyears + 1, 0);
 
-        test_SB[year] += population.numbers_at_age[i_age_year] * population.proportion_female[age] * population.proportion_mature_at_age[i_age_year] *
+        test_SB[year] += population.numbers_at_age[i_age_year] * 0.5 * population.proportion_mature_at_age[i_age_year] *
                          population.growth->evaluate(population.ages[age]);
         test_B[year] += population.numbers_at_age[i_age_year] *
                          population.growth->evaluate(population.ages[age]);
@@ -40,7 +40,7 @@ namespace
 
         std::vector<double> test_SSB(nyears + 1, 0);
 
-        test_SSB[nyears] += population.numbers_at_age[i_age_year] * population.proportion_female[age] * 
+        test_SSB[nyears] += population.numbers_at_age[i_age_year] * 0.5 * 
             population.proportion_mature_at_age[i_age_year] * 
             population.growth->evaluate(population.ages[age]);
 

tests/gtest/test_population_Unfished_Initial.cpp

@@ -115,7 +115,7 @@ namespace
                 population.CalculateUnfishedSpawningBiomass(i_age_year, year, age);
 
                 test_unfished_spawning_biomass[year] += population.proportion_mature_at_age[i_age_year] *
-                                                        population.proportion_female[age] *
+                                                        0.5 *
                                                         test_unfished_numbers_at_age[i_age_year] *
                                                         population.growth->evaluate(population.ages[age]);
 

tests/gtest/test_population_dynamics_population_initialize_prepare.cpp

@@ -32,7 +32,6 @@ namespace
         EXPECT_EQ(population.unfished_spawning_biomass.size(), (nyears + 1));
         EXPECT_EQ(population.spawning_biomass.size(), nyears + 1);
         EXPECT_EQ(population.log_init_naa.size(), nages);
-        EXPECT_EQ(population.proportion_female.size(), nages);
         EXPECT_EQ(population.log_M.size(), nyears * nages);
         EXPECT_EQ(population.M.size(), nyears * nages);
     }
@@ -85,13 +84,6 @@ namespace
         }
         EXPECT_EQ(population.M.size(), nyears * nages);
 
-        // Test population.proportion_female
-        fims::Vector<double> p_female(nages, 0.5);
-        for(int i = 0; i < nages; i++)
-        {
-            EXPECT_EQ(population.proportion_female[i], p_female[i]);
-        }
-
         // Test population.fleet->Fmort 
         // fmort and logfmort are vectors of length year
         fims::Vector<double> Fmort(nfleets * nyears, 0);

tests/gtest/test_population_test_fixture.hpp

@@ -116,15 +116,6 @@ class PopulationEvaluateTestFixture : public testing::Test {
       population.log_init_naa[i] = log_naa_distribution(generator);
     }
 
-    // prop_female
-    double prop_female_min = 0.1;
-    double prop_female_max = 0.9;
-    std::uniform_real_distribution<double> prop_female_distribution(
-        prop_female_min, prop_female_max);
-    for (int i = 0; i < nages; i++) {
-      population.proportion_female[i] = prop_female_distribution(generator);
-    }
-
     // log_M
     double log_M_min = fims_math::log(0.1);
     double log_M_max = fims_math::log(0.3);
@@ -277,15 +268,6 @@ class PopulationPrepareTestFixture : public testing::Test {
       population.log_init_naa[i] = log_naa_distribution(generator);
     }
 
-    // prop_female
-    double prop_female_min = 0.1;
-    double prop_female_max = 0.9;
-    std::uniform_real_distribution<double> prop_female_distribution(
-        prop_female_min, prop_female_max);
-    for (int i = 0; i < nages; i++) {
-      population.proportion_female[i] = prop_female_distribution(generator);
-    }
-
     // log_M
     double log_M_min = fims_math::log(0.1);
     double log_M_max = fims_math::log(0.3);

tests/testthat/test-rcpp-population-interface.R

@@ -11,8 +11,6 @@ test_that("Population input settings work as expected", {
   population$nfleets <- 2
   population$nseasons <- 1
   population$nyears <- nyears
-  population$proportion_female <- rep(0.5, nages)
-  population$estimate_prop_female <- FALSE
 
   expect_equal(population$get_id(), 1)
   for(i in 1:(nyears * nages)){
@@ -23,8 +21,6 @@ test_that("Population input settings work as expected", {
     expect_equal(population$log_init_naa[i]$value, 0)
     expect_true(population$log_init_naa[i]$estimated)
   }
-  expect_false(population$estimate_prop_female)
-  expect_equal(population$proportion_female, rep(0.5, nages))
 
   clear()
 })