refactor data objects to be set from distributions interface

inst/include/common/information.hpp

@@ -225,82 +225,12 @@ class Information {
              << " fleets." << std::endl;
     for (fleet_iterator it = this->fleets.begin(); it != this->fleets.end();
          ++it) {
-      // Initialize fleet object
 
       std::shared_ptr<fims_popdy::Fleet<Type> > f = (*it).second;
       INFO_LOG << "Initializing fleet " << f->id << "." << std::endl;
 
       f->Initialize(f->nyears, f->nages);
 
-      INFO_LOG << "Expecting to import " << this->data_objects.size()
-               << " data objects." << std::endl;
-
-      INFO_LOG << "Checking for available fleet index data objects."
-               << std::endl;
-      // set index data
-      if (f->fleet_observed_index_data_id_m != -999) {
-        uint32_t observed_index_id =
-            static_cast<uint32_t>(f->fleet_observed_index_data_id_m);
-        data_iterator it = this->data_objects.find(observed_index_id);
-        INFO_LOG << "Input fleet index id = " << observed_index_id << "."
-                 << std::endl;
-
-        if (it != this->data_objects.end()) {
-          f->observed_index_data = (*it).second;
-          INFO_LOG << "Index data successfully set." << std::endl;
-          DATA_LOG << "" << std::endl;
-          DATA_LOG << "Observed input for fleet " << f->id << ", index "
-                   << observed_index_id << ": \n "
-                   << f->observed_index_data->at(1) << std::endl;
-        } else {
-          valid_model = false;
-          ERROR_LOG << "Error: Expected data observations not defined for fleet"
-                    << f->id << ", index " << observed_index_id << std::endl;
-          exit(1);
-        }
-
-      } else {
-        valid_model = false;
-        ERROR_LOG << "Error: No index data observed for fleet " << f->id
-                  << ". FIMS requires index data for all fleets." << std::endl;
-        exit(1);
-      }
-      // end set index data
-
-      INFO_LOG << "Checking for available fleet age comp data objects."
-               << std::endl;
-      // set age composition data
-      if (f->fleet_observed_agecomp_data_id_m != -999) {
-        uint32_t observed_agecomp_id =
-            static_cast<uint32_t>(f->fleet_observed_agecomp_data_id_m);
-        data_iterator it = this->data_objects.find(observed_agecomp_id);
-        INFO_LOG << "Input fleet age comp id = " << observed_agecomp_id << "."
-                 << std::endl;
-
-        if (it != this->data_objects.end()) {
-          f->observed_agecomp_data = (*it).second;
-          INFO_LOG << "Age comp data successfully set." << std::endl;
-          DATA_LOG << "" << std::endl;
-          DATA_LOG << "Observed input age comp for fleet " << f->id << ", comp "
-                   << observed_agecomp_id << ": \n "
-                   << f->observed_agecomp_data->at(1) << std::endl;
-        } else {
-          valid_model = false;
-          ERROR_LOG << "Error: Expected age comp data observations not defined "
-                       "for fleet "
-                    << f->id << ", index " << observed_agecomp_id << std::endl;
-          exit(1);
-        }
-
-      } else {
-        valid_model = false;
-        ERROR_LOG << "Error: No age comp data observed for fleet " << f->id
-                  << ". FIMS requires age comp data for all fleets."
-                  << std::endl;
-        exit(1);
-      }
-      // end set composition data
-
       INFO_LOG << "Checking for available fleet selectivity pattern."
                << std::endl;
       // set selectivity model
@@ -334,6 +264,37 @@ class Information {
       }
       // end set selectivity
     }
+    INFO_LOG << "Expecting to import " << this->data_objects.size()
+               << " data objects." << std::endl;
+    for(density_components_iterator it = this->density_components.begin(); 
+        it!= this->density_components.end(); ++it){
+      std::shared_ptr<fims_distributions::DensityComponentBase<Type> > d = (*it).second;
+      INFO_LOG << "Checking for available density components data objects."
+          << std::endl;
+      //set data objects
+      if(d->input_type == "data" & d->observed_data_id_m != -999){
+        uint32_t observed_data_id = static_cast<uint32_t>(d->observed_data_id_m);
+        data_iterator it = this->data_objects.find(observed_data_id);
+        INFO_LOG << "Input data id = " << observed_data_id << "." << std::endl;
+
+        if (it != this->data_objects.end()) {
+          d->observed_values = (*it).second;
+          INFO_LOG << "Data for density component, " << d->id << " successfully set." << std::endl;
+          DATA_LOG << "" << std::endl;
+        } else {
+          valid_model = false;
+          ERROR_LOG << "Error: Expected data observations not defined for density component "
+                    << d->id << ", observed data " << observed_data_id << std::endl;
+          exit(1);
+        }
+
+      } else {
+        valid_model = false;
+        ERROR_LOG << "Error: No data input for density " << d->id << std::endl;
+        exit(1);
+      }
+      // end set data
+    }
 
     INFO_LOG << "Initializing population objects for "
              << this->populations.size() << " populations." << std::endl;

inst/include/distributions/functors/density_components_base.hpp

@@ -35,6 +35,7 @@ struct DensityComponentBase : public fims_model_object::FIMSObject<Type> {
   // Assigning each one its own ID is a way to keep track of
   // all the instances of the DensityComponentBase class.
  static uint32_t id_g; /**< global unique identifier for distribution modules */
+ size_t observed_data_id_m = -999; /*!< id of observed data component*/
  std::shared_ptr<fims_data_object::DataObject<Type>>
       observed_values; /**< observed data*/
  fims::Vector<Type > x; /**< input value of distribution function for proirs or random effects*/
@@ -44,7 +45,7 @@ struct DensityComponentBase : public fims_model_object::FIMSObject<Type> {
  bool osa_flag = false; /**< Boolean; if true, osa residuals are calculated */
  bool simulate_flag = false; /**< Boolean; if true, data are simulated from the distribution */
  std::vector<uint32_t> key; /**< unique id for variable map that points to a fims::Vector */
- Type na_value = -999;   /**< specifying the NA value >*/
+  
   #ifdef TMB_MODEL
     ::objective_function<Type> *of; /**< Pointer to the TMB objective function */
   #endif

inst/include/interface/rcpp/rcpp_interface.hpp

@@ -385,8 +385,6 @@ RCPP_MODULE(fims) {
       .field("nyears", &FleetInterface::nyears)
       .field("estimate_q", &FleetInterface::estimate_q)
       .field("random_q", &FleetInterface::random_q)
-      .method("SetObservedAgeCompData", &FleetInterface::SetObservedAgeCompData)
-      .method("SetObservedIndexData", &FleetInterface::SetObservedIndexData)
       .method("SetSelectivity", &FleetInterface::SetSelectivity);
 
   Rcpp::class_<AgeCompDataInterface>("AgeComp")
@@ -421,6 +419,8 @@ RCPP_MODULE(fims) {
       .constructor()
       .method("get_id", &DnormDistributionsInterface::get_id)
       .method("evaluate", &DnormDistributionsInterface::evaluate)
+      .method("set_observed_data", &DnormDistributionsInterface::set_observed_data)
+      .method("set_distribution_links", &DnormDistributionsInterface::set_distribution_links)
       .field("x", &DnormDistributionsInterface::x)
       .field("expected_values", &DnormDistributionsInterface::expected_values)
       .field("log_sd", &DnormDistributionsInterface::log_sd);
@@ -462,6 +462,8 @@ RCPP_MODULE(fims) {
       .constructor()
       .method("get_id", &DlnormDistributionsInterface::get_id)
       .method("evaluate", &DlnormDistributionsInterface::evaluate)
+      .method("set_observed_data", &DlnormDistributionsInterface::set_observed_data)
+      .method("set_distribution_links", &DlnormDistributionsInterface::set_distribution_links)
       .field("input_type", &DlnormDistributionsInterface::input_type)
       .field("x", &DlnormDistributionsInterface::x)
       .field("expected_values", &DlnormDistributionsInterface::expected_values)
@@ -471,6 +473,8 @@ RCPP_MODULE(fims) {
       .constructor()
       .method("evaluate", &DmultinomDistributionsInterface::evaluate)
       .method("get_id", &DmultinomDistributionsInterface::get_id)
+      .method("set_observed_data", &DmultinomDistributionsInterface::set_observed_data)
+      .method("set_distribution_links", &DmultinomDistributionsInterface::set_distribution_links)
       .field("x", &DmultinomDistributionsInterface::x)
       .field("expected_values", &DmultinomDistributionsInterface::expected_values)
       .field("dims", &DmultinomDistributionsInterface::dims);

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

@@ -51,10 +51,6 @@ std::map<uint32_t, FleetInterfaceBase*> FleetInterfaceBase::live_objects;
  *
  */
 class FleetInterface : public FleetInterfaceBase {
-  int interface_observed_agecomp_data_id_m =
-      -999; /**< id of observed agecomp data object*/
-  int interface_observed_index_data_id_m =
-      -999;                              /**< id of observed index data object*/
   int interface_selectivity_id_m = -999; /**< id of selectivity component*/
 
  public:
@@ -77,25 +73,6 @@ class FleetInterface : public FleetInterfaceBase {
   /** @brief returns the id for the fleet interface */
   virtual uint32_t get_id() { return this->id; }
 
-  /**
-   * @brief Set the unique id for the Observed Age Comp Data object
-   *
-   * @param observed_agecomp_data_id Unique id for the Observed Age Comp Data
-   * object
-   */
-  void SetObservedAgeCompData(int observed_agecomp_data_id) {
-    interface_observed_agecomp_data_id_m = observed_agecomp_data_id;
-  }
-
-  /**
-   * @brief Set the unique id for the Observed Index Data object
-   *
-   * @param observed_index_data_id Unique id for the Observed Index Data object
-   */
-  void SetObservedIndexData(int observed_index_data_id) {
-    interface_observed_index_data_id_m = observed_index_data_id;
-  }
-
   /**
    * @brief Set the unique id for the Selectivity object
    *
@@ -119,11 +96,6 @@ class FleetInterface : public FleetInterfaceBase {
     fleet->is_survey = this->is_survey;
     fleet->nages = this->nages;
     fleet->nyears = this->nyears;
-    fleet->fleet_agecomp_likelihood_id_m = interface_agecomp_likelihood_id_m;
-    fleet->fleet_index_likelihood_id_m = interface_index_likelihood_id_m;
-    fleet->fleet_observed_agecomp_data_id_m =
-        interface_observed_agecomp_data_id_m;
-    fleet->fleet_observed_index_data_id_m = interface_observed_index_data_id_m;
     fleet->fleet_selectivity_id_m = interface_selectivity_id_m;
 
     fleet->log_q = this->log_q;

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

@@ -28,6 +28,8 @@ class DistributionsInterfaceBase : public FIMSRcppInterfaceBase {
   static std::map<uint32_t, DistributionsInterfaceBase *> live_objects; /**<
 map relating the ID of the DistributionsInterfaceBase to the
 DistributionsInterfaceBase objects */
+  uint32_t interface_observed_data_id_m =
+      -999; /**< id of observed data object*/
 
   DistributionsInterfaceBase() {
     this->id_m = DistributionsInterfaceBase::id_g++;
@@ -43,8 +45,11 @@ DistributionsInterfaceBase objects */
    */
   virtual uint32_t get_id() = 0;
 
-  /**
+/**
    * @brief set_distribution_links sets pointers for data observations, random effects, or priors
+   * 
+   * @param input_type String that sets whether the distribution type is: priors, random_effects, or data.
+   * @param ids Vector of unique ids for each linked parameter/s, derived value/s, or observed data vector
    */
   void set_distribution_links(std::string input_type, Rcpp::IntegerVector ids){
     this->input_type_m = input_type;
@@ -54,6 +59,17 @@ DistributionsInterfaceBase objects */
     }
   }
 
+
+  /**
+   * @brief Set the unique id for the Observed Data object
+   *
+   * @param observed_data_id Unique id for the Observed Age Comp Data
+   * object
+   */
+  void set_observed_data(int observed_data_id) {
+    interface_observed_data_id_m = observed_data_id;
+  }
+
   /** @brief evaluate method for child distribution interface objects to inherit
    */
   virtual double evaluate() = 0;
@@ -93,8 +109,6 @@ class DnormDistributionsInterface : public DistributionsInterfaceBase {
    * @tparam T
    * @return log pdf
    */
-
-
   virtual double evaluate() {
     fims_distributions::NormalLPDF<double> dnorm;
     dnorm.x.resize(this->x.size());
@@ -112,6 +126,8 @@ class DnormDistributionsInterface : public DistributionsInterfaceBase {
     return dnorm.evaluate();
   }
 
+
+
 #ifdef TMB_MODEL
 
   template <typename Type>
@@ -123,6 +139,10 @@ class DnormDistributionsInterface : public DistributionsInterfaceBase {
         std::make_shared<fims_distributions::NormalLPDF<Type>>();
 
     // interface to data/parameter value
+
+    distribution->observed_data_id_m =
+        interface_observed_data_id_m;
+
     distribution->id = this->id_m;
     distribution->x.resize(this->x.size());
     for(int i=0; i<this->x.size(); i++){
@@ -180,6 +200,7 @@ class DlnormDistributionsInterface : public DistributionsInterfaceBase {
    */
   virtual uint32_t get_id() { return this->id_m; }
 
+
   /**
    * @brief Evaluate lognormal probability density function, default returns the
    * log of the pdf
@@ -217,6 +238,8 @@ class DlnormDistributionsInterface : public DistributionsInterfaceBase {
 
     // set relative info
     distribution->id = this->id_m;
+    distribution->observed_data_id_m =
+        interface_observed_data_id_m;
     distribution->input_type = this->input_type;
     distribution->x.resize(this->x.size());
     for(int i=0; i<this->x.size(); i++){
@@ -273,6 +296,7 @@ class DmultinomDistributionsInterface : public DistributionsInterfaceBase {
 
   virtual uint32_t get_id() { return this->id_m; }
 
+
   /**
    * @brief Evaluate multinom probability density function, default returns the
    * log of the pdf
@@ -308,6 +332,8 @@ class DmultinomDistributionsInterface : public DistributionsInterfaceBase {
         std::make_shared<fims_distributions::MultinomialLPMF<Type>>();
 
     distribution->id = this->id_m;
+    distribution->observed_data_id_m =
+        interface_observed_data_id_m;
     distribution->x.resize(this->x.size());
     for(int i=0; i<this->x.size(); i++){
       distribution->x[i] = this->x[i].value_m;

inst/include/population_dynamics/fleet/fleet.hpp

@@ -33,14 +33,6 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
   std::shared_ptr<SelectivityBase<Type>>
       selectivity; /*!< selectivity component*/
 
-  int fleet_observed_index_data_id_m = -999; /*!< id of index data */
-  std::shared_ptr<fims_data_object::DataObject<Type>>
-      observed_index_data; /*!< observed index data*/
-
-  int fleet_observed_agecomp_data_id_m = -999; /*!< id of age comp data */
-  std::shared_ptr<fims_data_object::DataObject<Type>>
-      observed_agecomp_data; /*!< observed agecomp data*/
-
   // Mortality and catchability
   fims::Vector<Type>
       log_Fmort; /*!< estimated parameter: log Fishing mortality*/