From 251d6e3d8c01245a2d147165c483ec52c48fb2aa Mon Sep 17 00:00:00 2001
From: Andrea-Havron-NOAA <andrea.havron@noaa.gov>
Date: Fri, 31 May 2024 16:14:33 -0700
Subject: [PATCH] fix bugs

---
 .../distributions/functors/density_components_base.hpp      | 3 ---
 inst/include/distributions/functors/lognormal_lpdf.hpp      | 5 ++++-
 inst/include/distributions/functors/multinomial_lpmf.hpp    | 6 +++++-
 inst/include/distributions/functors/normal_lpdf.hpp         | 6 ++++++
 4 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/inst/include/distributions/functors/density_components_base.hpp b/inst/include/distributions/functors/density_components_base.hpp
index d52946922..c441c4497 100644
--- 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
index f19bd4882..dc8f7904b 100644
--- 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
index e20f4a366..641965adb 100644
--- 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
index a527514b3..17b048274 100644
--- 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