fix bugs

NOAA-FIMS · May 31, 2024 · 251d6e3 · 251d6e3
1 parent d19224d
commit 251d6e3
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Showing 4 changed files with 15 additions and 5 deletions.
diff --git a/inst/include/distributions/functors/density_components_base.hpp b/inst/include/distributions/functors/density_components_base.hpp
@@ -39,9 +39,6 @@ struct DensityComponentBase : public fims_model_object::FIMSObject<Type> {
  std::string  nll_type; //prior, re, data
  bool osa_flag = false;
  bool simulate_flag = false;
-  #ifdef TMB_MODEL
-   ::objective_function<Type> *of;
-  #endif
 
   /** @brief Constructor.
    */

diff --git a/inst/include/distributions/functors/lognormal_lpdf.hpp b/inst/include/distributions/functors/lognormal_lpdf.hpp
@@ -1,4 +1,4 @@
-#ifndef LOGNORMALl_LPDF
+#ifndef LOGNORMAL_LPDF
 #define LOGNORMAL_LPDF
 
 #include "density_components_base.hpp"
@@ -55,8 +55,10 @@ namespace fims_distributions
             for (size_t i = 0; i < this->observed_values.size(); i++)
             {
               if(!is_na[i]){
+                #ifdef TMB_MODEL
                 // this->nll_vec[i] = this->keep[i] * -dnorm(this->observed_values[i], mu[i], sd[i], do_log);
                 this->nll_vec[i] = -dnorm(log(this->observed_values[i]), mu[i], sd[i], do_log) - log(this->observed_values[i]);
+
                 nll += this->nll_vec[i];
                 if (this->simulate_flag)
                 {
@@ -66,6 +68,7 @@ namespace fims_distributions
                         this->observed_values[i] = exp(rnorm(mu[i], sd[i]));
                     }
                 }
+                #endif
 
                 /* osa not working yet
                   if(osa_flag){//data observation type implements osa residuals

diff --git a/inst/include/distributions/functors/multinomial_lpmf.hpp b/inst/include/distributions/functors/multinomial_lpmf.hpp
@@ -16,6 +16,9 @@ namespace fims_distributions
         Type nll = 0.0;
         fims::Vector<size_t> dims;
         std::vector<bool> is_na;
+        #ifdef TMB_MODEL
+        ::objective_function<Type> *of;
+        #endif
         // data_indicator<tmbutils::vector<Type> , Type> keep;
 
         MultinomialLPMF() : DensityComponentBase<Type>()
@@ -42,7 +45,7 @@ namespace fims_distributions
                 }
                 #ifdef TMB_model
                 this->nll_vec[i] = -dmultinom((vector<Type>)observed_vector, (vector<Type>)expected_vector, do_log);
-                #endif
+
                 nll += this->nll_vec[i];
                 /*
                 if (this->simulate_flag)
@@ -61,6 +64,7 @@ namespace fims_distributions
                     }
                 }
                 */
+               #endif
               }
             }
             #ifdef TMB_MODEL

diff --git a/inst/include/distributions/functors/normal_lpdf.hpp b/inst/include/distributions/functors/normal_lpdf.hpp
@@ -16,6 +16,9 @@ struct NormalLPDF : public DensityComponentBase<Type> {
     fims::Vector<Type> sd;
     Type nll = 0.0;
     std::vector<bool> is_na;
+    #ifdef TMB_MODEL
+    ::objective_function<Type> *of;
+    #endif
     //data_indicator<tmbutils::vector<Type> , Type> keep;
 
     NormalLPDF() : DensityComponentBase<Type>() {
@@ -43,13 +46,16 @@ struct NormalLPDF : public DensityComponentBase<Type> {
         for(size_t i=0; i<this->observed_values.size(); i++){
           if(!is_na[i]){
             // this->nll_vec[i] = this->keep[i] * -dnorm(this->observed_values[i], mu[i], sd[i], do_log);
+            #ifdef TMB_MODEL
             this->nll_vec[i] = -dnorm(this->observed_values[i], mu[i], sd[i], do_log);
+
             nll += this->nll_vec[i];
             if(this->simulate_flag){
                 FIMS_SIMULATE_F(this->of){
                     this->observed_values[i] = rnorm(mu[i], sd[i]);
                 }
             }
+            #endif
           /* osa not working yet
             if(osa_flag){//data observation type implements osa residuals
                 //code for osa cdf method