Refactor remaining interface scalar config fields to plain C++ types

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

@@ -33,12 +33,12 @@ class DistributionsInterfaceBase : public FIMSRcppInterfaceBase {
   /**
    * @brief The type of density input. The options are prior, re, or data.
    */
-  SharedString input_type_m;
+  std::string input_type_m;
   /**
    * @brief Control flag indicating whether to use the expected mean in the
    * distribution calculations.
    *
-   * This shared string member serves as a boolean flag (i.e., "yes" or "no")
+   * This string member serves as a boolean flag (i.e., "yes" or "no")
    * that determines whether the distribution should use the `expected_mean`
    * vector or other expected values (e.g., from data or random effects) when
    * computing the expected value in the likelihood calculations.
@@ -57,7 +57,7 @@ class DistributionsInterfaceBase : public FIMSRcppInterfaceBase {
    * @see DensityComponentBase::get_expected() in density_components_base.hpp
    * for the implementation that checks this flag.
    */
-  SharedString use_mean_m = fims::to_string("no");
+  std::string use_mean_m = "no";
   /**
    * @brief The map associating the ID of the DistributionsInterfaceBase to the
      DistributionsInterfaceBase objects. This is a live object, which is an
@@ -68,7 +68,7 @@ class DistributionsInterfaceBase : public FIMSRcppInterfaceBase {
   /**
    * @brief The ID of the observed data object, which is set to -999.
    */
-  SharedInt interface_observed_data_id_m = -999;
+  int interface_observed_data_id_m = -999;
 
   /**
    * @brief The log probability density function value.
@@ -230,7 +230,7 @@ class DnormDistributionsInterface : public DistributionsInterfaceBase {
    * @param observed_data_id Unique ID for the observed data object.
    */
   virtual bool set_observed_data(int observed_data_id) {
-    this->interface_observed_data_id_m.set(observed_data_id);
+    this->interface_observed_data_id_m = observed_data_id;
     return true;
   }
 
@@ -240,7 +240,7 @@ class DnormDistributionsInterface : public DistributionsInterfaceBase {
   virtual bool set_distribution_mean(double input_value) {
     this->expected_mean[0].initial_value_m = input_value;
     this->expected_mean[0].estimation_type_m.set("fixed_effects");
-    this->use_mean_m.set(fims::to_string("yes"));
+    this->use_mean_m = "yes";
     return true;
   }
 
@@ -249,7 +249,7 @@ class DnormDistributionsInterface : public DistributionsInterfaceBase {
    */
   virtual bool set_distribution_links(std::string input_type,
                                       Rcpp::IntegerVector ids) {
-    this->input_type_m.set(input_type);
+    this->input_type_m = input_type;
     this->key_m->resize(ids.size());
     for (R_xlen_t i = 0; i < ids.size(); i++) {
       this->key_m->at(i) = ids[i];
@@ -486,7 +486,7 @@ class DnormDistributionsInterface : public DistributionsInterfaceBase {
     }
     info->variable_map[this->log_sd.id_m] = &(distribution)->log_sd;
 
-    distribution->use_mean = this->use_mean_m.get();
+    distribution->use_mean = this->use_mean_m;
     distribution->expected_mean.resize(this->expected_mean.size());
     for (size_t i = 0; i < this->expected_mean.size(); i++) {
       distribution->expected_mean[i] = this->expected_mean[i].initial_value_m;
@@ -590,7 +590,7 @@ class DlnormDistributionsInterface : public DistributionsInterfaceBase {
    * @param observed_data_id Unique ID for the observed data object.
    */
   virtual bool set_observed_data(int observed_data_id) {
-    this->interface_observed_data_id_m.set(observed_data_id);
+    this->interface_observed_data_id_m = observed_data_id;
     return true;
   }
 
@@ -604,7 +604,7 @@ class DlnormDistributionsInterface : public DistributionsInterfaceBase {
    */
   virtual bool set_distribution_links(std::string input_type,
                                       Rcpp::IntegerVector ids) {
-    this->input_type_m.set(input_type);
+    this->input_type_m = input_type;
     this->key_m->resize(ids.size());
     for (R_xlen_t i = 0; i < ids.size(); i++) {
       this->key_m->at(i) = ids[i];
@@ -875,7 +875,7 @@ class DmultinomDistributionsInterface : public DistributionsInterfaceBase {
    * @brief TODO: document this.
    *
    */
-  SharedString notes;
+  std::string notes;
 
   /**
    * @brief The constructor.
@@ -915,7 +915,7 @@ class DmultinomDistributionsInterface : public DistributionsInterfaceBase {
    * @param observed_data_id Unique ID for the observed data object.
    */
   virtual bool set_observed_data(int observed_data_id) {
-    this->interface_observed_data_id_m.set(observed_data_id);
+    this->interface_observed_data_id_m = observed_data_id;
     return true;
   }
 
@@ -929,7 +929,7 @@ class DmultinomDistributionsInterface : public DistributionsInterfaceBase {
    */
   virtual bool set_distribution_links(std::string input_type,
                                       Rcpp::IntegerVector ids) {
-    this->input_type_m.set(input_type);
+    this->input_type_m = input_type;
     this->key_m->resize(ids.size());
     for (R_xlen_t i = 0; i < ids.size(); i++) {
       this->key_m->at(i) = ids[i];
@@ -942,7 +942,7 @@ class DmultinomDistributionsInterface : public DistributionsInterfaceBase {
    *
    * @param note
    */
-  void set_note(std::string note) { this->notes.set(note); }
+  void set_note(std::string note) { this->notes = note; }
 
   /**
    * @brief

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

@@ -69,51 +69,51 @@ class FleetInterface : public FleetInterfaceBase {
   /**
    * @brief The ID of the observed age-composition data object.
    */
-  SharedInt interface_observed_agecomp_data_id_m = -999;
+  int interface_observed_agecomp_data_id_m = -999;
   /**
    * @brief The ID of the observed length-composition data object.
    */
-  SharedInt interface_observed_lengthcomp_data_id_m = -999;
+  int interface_observed_lengthcomp_data_id_m = -999;
   /**
    * @brief The ID of the observed index data object.
    */
-  SharedInt interface_observed_index_data_id_m = -999;
+  int interface_observed_index_data_id_m = -999;
   /**
    * @brief The ID of the observed landings data object.
    */
-  SharedInt interface_observed_landings_data_id_m = -999;
+  int interface_observed_landings_data_id_m = -999;
   /**
    * @brief The ID of the selectivity object.
    */
-  SharedInt interface_selectivity_id_m = -999;
+  int interface_selectivity_id_m = -999;
 
  public:
   /**
    * @brief The name of the fleet.
    */
-  SharedString name = fims::to_string("NA");
+  std::string name = "NA";
   /**
    * @brief The number of age bins in the fleet data.
    */
-  SharedInt n_ages = 0;
+  int n_ages = 0;
   /**
    * @brief The number of length bins in the fleet data.
    */
-  SharedInt n_lengths = 0;
+  int n_lengths = 0;
   /**
    * @brief The number of years in the fleet data.
    */
-  SharedInt n_years = 0;
+  int n_years = 0;
   /**
    * @brief What units are the observed landings for this fleet measured in.
    * Options are weight or numbers, default is weight.
    */
-  SharedString observed_landings_units = fims::to_string("weight");
+  std::string observed_landings_units = "weight";
   /**
    * @brief What units is the observed index of abundance for this fleet
    * measured in. Options are weight or numbers, default is weight.
    */
-  SharedString observed_index_units = fims::to_string("weight");
+  std::string observed_index_units = "weight";
   /**
    * @brief The natural log of the index of abundance scaling parameter
    * for this fleet.
@@ -282,87 +282,87 @@ class FleetInterface : public FleetInterfaceBase {
    * @brief Sets the name of the fleet.
    * @param name The name to set.
    */
-  void SetName(const std::string &name) { this->name.set(name); }
+  void SetName(const std::string &name) { this->name = name; }
 
   /**
    * @brief Gets the name of the fleet.
    * @return The name.
    */
-  std::string GetName() const { return this->name.get(); }
+  std::string GetName() const { return this->name; }
 
   /**
    * @brief Set the unique ID for the observed age-composition data object.
    * @param observed_agecomp_data_id Unique ID for the observed data object.
    */
   void SetObservedAgeCompDataID(int observed_agecomp_data_id) {
-    interface_observed_agecomp_data_id_m.set(observed_agecomp_data_id);
+    interface_observed_agecomp_data_id_m = observed_agecomp_data_id;
   }
 
   /**
    * @brief Set the unique ID for the observed length-composition data object.
    * @param observed_lengthcomp_data_id Unique ID for the observed data object.
    */
   void SetObservedLengthCompDataID(int observed_lengthcomp_data_id) {
-    interface_observed_lengthcomp_data_id_m.set(observed_lengthcomp_data_id);
+    interface_observed_lengthcomp_data_id_m = observed_lengthcomp_data_id;
   }
 
   /**
    * @brief Set the unique ID for the observed index data object.
    * @param observed_index_data_id Unique ID for the observed data object.
    */
   void SetObservedIndexDataID(int observed_index_data_id) {
-    interface_observed_index_data_id_m.set(observed_index_data_id);
+    interface_observed_index_data_id_m = observed_index_data_id;
   }
 
   /**
    * @brief Set the unique ID for the observed landings data object.
    * @param observed_landings_data_id Unique ID for the observed data object.
    */
   void SetObservedLandingsDataID(int observed_landings_data_id) {
-    interface_observed_landings_data_id_m.set(observed_landings_data_id);
+    interface_observed_landings_data_id_m = observed_landings_data_id;
   }
   /**
    * @brief Set the unique ID for the selectivity object.
    * @param selectivity_id Unique ID for the observed object.
    */
   void SetSelectivityID(int selectivity_id) {
-    interface_selectivity_id_m.set(selectivity_id);
+    interface_selectivity_id_m = selectivity_id;
   }
 
   /**
    * @brief Get the unique ID for the selectivity object.
    *
    * @return uint32_t
    */
-  uint32_t GetSelectivityID() { return interface_selectivity_id_m.get(); }
+  int GetSelectivityID() { return interface_selectivity_id_m; }
 
   /**
    * @brief Get the unique ID for the observed age-composition data object.
    */
   int GetObservedAgeCompDataID() {
-    return interface_observed_agecomp_data_id_m.get();
+    return interface_observed_agecomp_data_id_m;
   }
 
   /**
    * @brief Get the unique ID for the observed length-composition data
    * object.
    */
   int GetObservedLengthCompDataID() {
-    return interface_observed_lengthcomp_data_id_m.get();
+    return interface_observed_lengthcomp_data_id_m;
   }
 
   /**
    * @brief Get the unique id for the observed index data object.
    */
   int GetObservedIndexDataID() {
-    return interface_observed_index_data_id_m.get();
+    return interface_observed_index_data_id_m;
   }
 
   /**
    * @brief Get the unique id for the observed landings data object.
    */
   int GetObservedLandingsDataID() {
-    return interface_observed_landings_data_id_m.get();
+    return interface_observed_landings_data_id_m;
   }
   /**
    * @brief Extracts the derived quantities from `Information` to the Rcpp
@@ -435,24 +435,24 @@ class FleetInterface : public FleetInterfaceBase {
 
     // set relative info
     fleet->id = this->id;
-    fleet->n_ages = this->n_ages.get();
-    fleet->n_lengths = this->n_lengths.get();
-    fleet->n_years = this->n_years.get();
+    fleet->n_ages = this->n_ages;
+    fleet->n_lengths = this->n_lengths;
+    fleet->n_years = this->n_years;
     fleet->observed_landings_units = this->observed_landings_units;
     fleet->observed_index_units = this->observed_index_units;
 
     fleet->fleet_observed_agecomp_data_id_m =
-        interface_observed_agecomp_data_id_m.get();
+        interface_observed_agecomp_data_id_m;
 
     fleet->fleet_observed_lengthcomp_data_id_m =
-        interface_observed_lengthcomp_data_id_m.get();
+        interface_observed_lengthcomp_data_id_m;
 
     fleet->fleet_observed_index_data_id_m =
-        interface_observed_index_data_id_m.get();
+        interface_observed_index_data_id_m;
     fleet->fleet_observed_landings_data_id_m =
-        interface_observed_landings_data_id_m.get();
+        interface_observed_landings_data_id_m;
 
-    fleet->fleet_selectivity_id_m = interface_selectivity_id_m.get();
+    fleet->fleet_selectivity_id_m = interface_selectivity_id_m;
 
     fleet->log_q.resize(this->log_q.size());
     for (size_t i = 0; i < this->log_q.size(); i++) {
@@ -472,16 +472,16 @@ class FleetInterface : public FleetInterfaceBase {
       }
     }
 
-    if (this->log_Fmort.size() != static_cast<size_t>(this->n_years.get())) {
+    if (this->log_Fmort.size() != static_cast<size_t>(this->n_years)) {
       FIMS_ERROR_LOG("The size of `log_Fmort` does not match `n_years`: " +
                      fims::to_string(this->log_Fmort.size()) +
-                     " != " + fims::to_string(this->n_years.get()));
+                     " != " + fims::to_string(this->n_years));
       throw std::invalid_argument(
           "Fleet log_Fmort size mismatch."
           "Fleet log_Fmort is of size " +
           fims::to_string(this->log_Fmort.size()) +
           " and the number of years is " +
-          fims::to_string(this->n_years.get()));
+          fims::to_string(this->n_years));
     }
     fleet->log_Fmort.resize(static_cast<size_t>(this->log_Fmort.size()));
     for (size_t i = 0; i < log_Fmort.size(); i++) {
@@ -503,16 +503,16 @@ class FleetInterface : public FleetInterfaceBase {
     // add to variable_map
     info->variable_map[this->log_Fmort.id_m] = &(fleet)->log_Fmort;
 
-    if (this->n_lengths.get() > 0) {
+    if (this->n_lengths > 0) {
       fleet->age_to_length_conversion.resize(
           this->age_to_length_conversion.size());
 
       if (this->age_to_length_conversion.size() !=
-          static_cast<size_t>(this->n_ages.get() * this->n_lengths.get())) {
+          static_cast<size_t>(this->n_ages * this->n_lengths)) {
         FIMS_ERROR_LOG(
             "age_to_length_conversion don't match, " +
             fims::to_string(this->age_to_length_conversion.size()) + " != " +
-            fims::to_string((this->n_ages.get() * this->n_lengths.get())));
+            fims::to_string((this->n_ages * this->n_lengths)));
       }
 
       for (size_t i = 0; i < fleet->age_to_length_conversion.size(); i++) {