Merge pull request #419 from NOAA-FIMS/403-refactor-remove-init_naa-f…

…rom-population remove init_naa
NOAA-FIMS · Jul 13, 2023 · 1553745 · 1553745
2 parents 64880ae + 500fe8a
commit 1553745
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Showing 2 changed files with 2 additions and 8 deletions.
diff --git a/inst/include/population_dynamics/population/population.hpp b/inst/include/population_dynamics/population/population.hpp
@@ -53,8 +53,7 @@ struct Population : public FIMSObject<Type> {
   ParameterVector log_M; /*!< estimated parameter: log Natural Mortality*/
 
   // Transformed values
-  std::vector<Type> init_naa; /*!< transformed parameter: numbers at age*/
-  std::vector<Type> M;        /*!< transformed parameter: Natural Mortality*/
+ std::vector<Type> M;        /*!< transformed parameter: Natural Mortality*/
 
   std::vector<double> ages;    /*!< vector of the ages for referencing*/
   std::vector<double> years;   /*!< vector of years for referencing*/
@@ -141,7 +140,6 @@ struct Population : public FIMSObject<Type> {
     unfished_spawning_biomass.resize((nyears + 1));
     spawning_biomass.resize((nyears + 1));
     expected_recruitment.resize((nyears + 1));
-    init_naa.resize(nages);
     M.resize(nyears * nages);
     ages.resize(nages);
     log_init_naa.resize(nages);
@@ -175,7 +173,6 @@ struct Population : public FIMSObject<Type> {
 
     // Transformation Section
     for (size_t age = 0; age < this->nages; age++) {
-      this->init_naa[age] = fims::exp(this->log_init_naa[age]);
       for (size_t year = 0; year < this->nyears; year++) {
         size_t index_ay = age * this->nyears + year;
         this->M[index_ay] = fims::exp(this->log_M[index_ay]);
@@ -198,7 +195,7 @@ struct Population : public FIMSObject<Type> {
    */
   inline void CalculateInitialNumbersAA(
       size_t index_ya, size_t a) {  // inline all function unless complicated
-    this->numbers_at_age[index_ya] = this->init_naa[a];
+    this->numbers_at_age[index_ya] = fims::exp(this->log_init_naa[a]);
   }
 
   /**

diff --git a/tests/gtest/test_population_dynamics_population_initialize_prepare.cpp b/tests/gtest/test_population_dynamics_population_initialize_prepare.cpp
@@ -37,7 +37,6 @@ namespace
         EXPECT_EQ(population.spawning_biomass.size(), nyears + 1);
         EXPECT_EQ(population.log_init_naa.size(), nages);
         EXPECT_EQ(population.log_M.size(), nyears * nages);
-        EXPECT_EQ(population.init_naa.size(), nages);
         EXPECT_EQ(population.M.size(), nyears * nages);
     }
 
@@ -81,9 +80,7 @@ namespace
         for (int i = 0; i < nages; i++)
         {
             naa[i] = fims::exp(population.log_init_naa[i]);
-            EXPECT_EQ(population.init_naa[i], naa[i]);
         }
-        EXPECT_EQ(population.init_naa.size(), nages);
 
         // Test population.M
         std::vector<double> M(nyears * nages, 0);