Merge branch 'main' into fims_vector

inst/include/common/data_object.hpp

@@ -44,13 +44,13 @@ namespace fims_data_object {
  */
 template <typename Type>
 struct DataObject : public fims_model_object::FIMSObject<Type> {
-  static uint32_t id_g;   /*!< id of the Data Object >*/
-  std::vector<Type> data; /*!< vector of the data >*/
-  size_t dimensions;      /*!< dimension of the Data object >*/
-  size_t imax;            /*!<1st dimension of data object >*/
-  size_t jmax;            /*!< 2nd dimension of data object>*/
-  size_t kmax;            /*!< 3rd dimension of data object>*/
-  size_t lmax;            /*!< 4th dimension of data object>*/
+  static uint32_t id_g;   /**< id of the Data Object >*/
+  std::vector<Type> data; /**< vector of the data >*/
+  size_t dimensions;      /**< dimension of the Data object >*/
+  size_t imax;            /**<1st dimension of data object >*/
+  size_t jmax;            /**< 2nd dimension of data object>*/
+  size_t kmax;            /**< 3rd dimension of data object>*/
+  size_t lmax;            /**< 4th dimension of data object>*/
 
   /**
    * Constructs a one-dimensional data object.

inst/include/common/def.hpp

@@ -1,4 +1,4 @@
-/*! \file def.hpp
+/** \file def.hpp
  */
 
 /*

inst/include/common/fims_math.hpp

@@ -1,4 +1,4 @@
-/*! \file fims_math.hpp
+/** \file fims_math.hpp
  */
 // note: To document a global C function, typedef, enum or preprocessor
 // definition you must first document the file that contains it

inst/include/common/information.hpp

@@ -1,4 +1,4 @@
-/*! \file information.hpp
+/** \file information.hpp
  *
  * This File is part of the NOAA, National Marine Fisheries Service
  * Fisheries Integrated Modeling System project. See LICENSE in the
@@ -47,38 +47,38 @@ class Information {
 
   // data objects
   std::map<uint32_t, std::shared_ptr<fims_data_object::DataObject<Type> > >
-      data_objects; /*!< map that holds data objects >*/
+      data_objects; /**< map that holds data objects >*/
   typedef typename std::map<
       uint32_t, std::shared_ptr<fims_data_object::DataObject<Type> > >::iterator
       data_iterator; /**< iterator for the data objects */
 
   // life history modules
   std::map<uint32_t, std::shared_ptr<fims_popdy::RecruitmentBase<Type> > >
-      recruitment_models; /*!<hash map to link each object to its shared
+      recruitment_models; /**<hash map to link each object to its shared
                              location in memory*/
   typedef typename std::map<
       uint32_t, std::shared_ptr<fims_popdy::RecruitmentBase<Type> > >::iterator
       recruitment_models_iterator;
   /**< iterator for recruitment objects>*/
 
   std::map<uint32_t, std::shared_ptr<fims_popdy::SelectivityBase<Type> > >
-      selectivity_models; /*!<hash map to link each object to its shared
+      selectivity_models; /**<hash map to link each object to its shared
                              location in memory*/
   typedef typename std::map<
       uint32_t, std::shared_ptr<fims_popdy::SelectivityBase<Type> > >::iterator
       selectivity_models_iterator;
   /**< iterator for selectivity objects>*/
 
   std::map<uint32_t, std::shared_ptr<fims_popdy::GrowthBase<Type> > >
-      growth_models; /*!<hash map to link each object to its shared location in
+      growth_models; /**<hash map to link each object to its shared location in
                         memory*/
   typedef typename std::map<
       uint32_t, std::shared_ptr<fims_popdy::GrowthBase<Type> > >::iterator
       growth_models_iterator;
   /**< iterator for growth objects>*/
 
   std::map<uint32_t, std::shared_ptr<fims_popdy::MaturityBase<Type> > >
-      maturity_models; /*!<hash map to link each object to its shared location
+      maturity_models; /**<hash map to link each object to its shared location
                           in memory*/
   typedef typename std::map<
       uint32_t, std::shared_ptr<fims_popdy::MaturityBase<Type> > >::iterator
@@ -87,7 +87,7 @@ class Information {
 
   // fleet modules
   std::map<uint32_t, std::shared_ptr<fims_popdy::Fleet<Type> > >
-      fleets; /*!<hash map to link each object to its shared location in
+      fleets; /**<hash map to link each object to its shared location in
                  memory*/
   typedef
       typename std::map<uint32_t,
@@ -97,7 +97,7 @@ class Information {
 
   // populations
   std::map<uint32_t, std::shared_ptr<fims_popdy::Population<Type> > >
-      populations; /*!<hash map to link each object to its shared location in
+      populations; /**<hash map to link each object to its shared location in
                       memory*/
   typedef typename std::map<
       uint32_t, std::shared_ptr<fims_popdy::Population<Type> > >::iterator
@@ -107,7 +107,7 @@ class Information {
   // distributions
   std::map<uint32_t,
            std::shared_ptr<fims_distributions::DistributionsBase<Type> > >
-      distribution_models; /*!<hash map to link each object to its shared
+      distribution_models; /**<hash map to link each object to its shared
                               location in memory*/
   typedef typename std::map<
       uint32_t,

inst/include/common/model.hpp

@@ -30,9 +30,9 @@ template <typename Type>
 class Model {  // may need singleton
  public:
   static std::shared_ptr<Model<Type> >
-      fims_model; /*!< Create a shared fims_model as a pointer to Model*/
+      fims_model; /**< Create a shared fims_model as a pointer to Model*/
   std::shared_ptr<fims_info::Information<Type> >
-      fims_information; /*!< Create a shared fims_information as a pointer to
+      fims_information; /**< Create a shared fims_information as a pointer to
                            Information*/
 
 #ifdef TMB_MODEL
@@ -80,12 +80,13 @@ class Model {  // may need singleton
       vector<vector<Type> > cwaa(n_fleets);
       vector<vector<Type> > F_mort(n_fleets);
     // populations
-      vector<vector<Type> > naa(n_pops);
-      vector<vector<Type> > ssb(n_pops);
-      vector<vector<Type> > biomass(n_pops);
-      vector<vector<Type> > rec_dev(n_pops);
-      vector<vector<Type> > recruitment(n_pops);
-      vector<vector<Type> > M(n_pops);
+    vector<vector<Type> > naa(n_pops);
+    vector<vector<Type> > ssb(n_pops);
+    vector<vector<Type> > biomass(n_pops);
+    vector<vector<Type> > log_recruit_dev(n_pops);
+    vector<vector<Type> > recruitment(n_pops);
+    vector<vector<Type> > M(n_pops);
+
 #endif
 
     // Loop over populations, evaluate, and sum up the recruitment likelihood
@@ -148,8 +149,8 @@ class Model {  // may need singleton
 #ifdef TMB_MODEL
       naa(pop_idx) = vector<Type>((*it).second->numbers_at_age);
       ssb(pop_idx) = vector<Type>((*it).second->spawning_biomass);
-      rec_dev(pop_idx) =
-          vector<Type>((*it).second->recruitment->recruit_deviations);
+      log_recruit_dev(pop_idx) =
+          vector<Type>((*it).second->recruitment->log_recruit_devs);
       recruitment(pop_idx) = vector<Type>((*it).second->expected_recruitment);
       biomass(pop_idx) = vector<Type>((*it).second->biomass);
       M(pop_idx) = vector<Type>((*it).second->M);
@@ -181,7 +182,7 @@ class Model {  // may need singleton
     REPORT_F(jnll, of);
     REPORT_F(naa, of);
     REPORT_F(ssb, of);
-    REPORT_F(rec_dev, of);
+    REPORT_F(log_recruit_dev, of);
     REPORT_F(recruitment, of);
     REPORT_F(biomass, of);
     REPORT_F(M, of);
@@ -198,15 +199,15 @@ class Model {  // may need singleton
     vector<Type> NAA = ADREPORTvector(naa);
     vector<Type> Biomass = ADREPORTvector(biomass);
     vector<Type> SSB = ADREPORTvector(ssb);
-    vector<Type> RecDev = ADREPORTvector(rec_dev);
+    vector<Type> LogRecDev = ADREPORTvector(log_recruit_dev);
     vector<Type> FMort = ADREPORTvector(F_mort);
     vector<Type> ExpectedIndex = ADREPORTvector(exp_index);
     vector<Type> CNAA = ADREPORTvector(cnaa);
 
     ADREPORT_F(NAA, of);
     ADREPORT_F(Biomass, of);
     ADREPORT_F(SSB, of);
-    ADREPORT_F(RecDev, of);
+    ADREPORT_F(LogRecDev, of);
     ADREPORT_F(FMort, of);
     ADREPORT_F(ExpectedIndex, of);
     ADREPORT_F(CNAA, of);

inst/include/common/model_object.hpp

@@ -23,12 +23,12 @@ namespace fims_model_object {
  */
 template <typename Type>
 struct FIMSObject {
-  uint32_t id; /*!< unique identifier assigned for all fims objects */
-  std::vector<Type*> parameters; /*!< list of estimable parameters */
+  uint32_t id; /**< unique identifier assigned for all fims objects */
+  std::vector<Type*> parameters; /**< list of estimable parameters */
   std::vector<Type*>
-      random_effects_parameters; /*!< list of all random effects parameters */
+      random_effects_parameters; /**< list of all random effects parameters */
   std::vector<Type*>
-      fixed_effects_parameters; /*!< list of fixed effects parameters */
+      fixed_effects_parameters; /**< list of fixed effects parameters */
 
   virtual ~FIMSObject() {}
   /**

inst/include/distributions/functors/distributions_base.hpp

@@ -1,4 +1,4 @@
-/*! \file distributions_base.hpp
+/** \file distributions_base.hpp
  * This File is part of the NOAA, National Marine Fisheries Service
  * Fisheries Integrated Modeling System project. See LICENSE in the
  * source folder for reuse information.

inst/include/distributions/functors/tmb_distributions.hpp

@@ -1,4 +1,4 @@
-/*! \file tmb_distributions.hpp
+/** \file tmb_distributions.hpp
  * This File is part of the NOAA, National Marine Fisheries Service
  * Fisheries Integrated Modeling System project.
  * Refer to the LICENSE file for reuse information.
@@ -21,9 +21,9 @@ namespace fims_distributions {
  */
 template <typename Type>
 struct Dnorm : public DistributionsBase<Type> {
-  Type x;    /*!< observation */
-  Type mean; /*!< mean of the normal distribution */
-  Type sd; /*!< standard deviation of the normal distribution, must be strictly
+  Type x;    /**< observation */
+  Type mean; /**< mean of the normal distribution */
+  Type sd; /**< standard deviation of the normal distribution, must be strictly
            positive.*/
 
   Dnorm() : DistributionsBase<Type>() {}
@@ -73,9 +73,9 @@ struct Dmultinom : public DistributionsBase<Type> {
  */
 template <typename Type>
 struct Dlnorm : public DistributionsBase<Type> {
-  Type x;       /*!< observation */
-  Type meanlog; /*!< mean of the distribution of log(x) */
-  Type sdlog;   /*!< standard deviation of the distribution of log(x) */
+  Type x;       /**< observation */
+  Type meanlog; /**< mean of the distribution of log(x) */
+  Type sdlog;   /**< standard deviation of the distribution of log(x) */
 
   Dlnorm() : DistributionsBase<Type>() {}
 

inst/include/interface/rcpp/rcpp_interface.hpp

@@ -350,9 +350,9 @@ RCPP_MODULE(fims) {
       .constructor()
       .field("logit_steep", &BevertonHoltRecruitmentInterface::logit_steep)
       .field("log_rzero", &BevertonHoltRecruitmentInterface::log_rzero)
-      .field("deviations", &BevertonHoltRecruitmentInterface::deviations)
-      .field("estimate_deviations",
-             &BevertonHoltRecruitmentInterface::estimate_deviations)
+      .field("log_devs", &BevertonHoltRecruitmentInterface::log_devs)
+      .field("estimate_log_devs",
+             &BevertonHoltRecruitmentInterface::estimate_log_devs)
       .method("get_id", &BevertonHoltRecruitmentInterface::get_id)
       .field("log_sigma_recruit",
              &BevertonHoltRecruitmentInterface::log_sigma_recruit)

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

@@ -19,7 +19,7 @@
  */
 class DataInterfaceBase : public FIMSRcppInterfaceBase {
  public:
-  Rcpp::NumericVector observed_data; /*!< The data */
+  Rcpp::NumericVector observed_data; /**< The data */
   static uint32_t id_g; /**< static id of the DataInterfaceBase object */
   uint32_t id;          /**< local id of the DataInterfaceBase object */
   // live objects in C++ are objects that have been created and live in memory
@@ -42,7 +42,7 @@ class DataInterfaceBase : public FIMSRcppInterfaceBase {
   virtual ~DataInterfaceBase() {}
 
   /** @brief get the ID of the interface base object
-   **/
+   */
   virtual uint32_t get_id() { return this->id; }
 
   /**@brief add_to_fims_tmb dummy method
@@ -60,9 +60,9 @@ std::map<uint32_t, DataInterfaceBase*> DataInterfaceBase::live_objects;
  */
 class AgeCompDataInterface : public DataInterfaceBase {
  public:
-  int amax;                          /*!< first dimension of the data */
-  int ymax;                          /*!< second dimension of the data */
-  Rcpp::NumericVector age_comp_data; /*!<the age composition data*/
+  int amax;                          /**< first dimension of the data */
+  int ymax;                          /**< second dimension of the data */
+  Rcpp::NumericVector age_comp_data; /**<the age composition data*/
 
   /**
    * @brief constructor
@@ -78,7 +78,7 @@ class AgeCompDataInterface : public DataInterfaceBase {
   virtual ~AgeCompDataInterface() {}
 
   /** @brief get the ID of the interface base object
-   **/
+   */
   virtual uint32_t get_id() { return this->id; }
 
 #ifdef TMB_MODEL
@@ -127,8 +127,8 @@ class AgeCompDataInterface : public DataInterfaceBase {
  */
 class IndexDataInterface : public DataInterfaceBase {
  public:
-  int ymax;                       /*!< second dimension of the data */
-  Rcpp::NumericVector index_data; /*!<the age composition data*/
+  int ymax;                       /**< second dimension of the data */
+  Rcpp::NumericVector index_data; /**<the age composition data*/
 
   /**
    * @brief constructor
@@ -141,7 +141,7 @@ class IndexDataInterface : public DataInterfaceBase {
   virtual ~IndexDataInterface() {}
 
   /** @brief get the ID of the interface base object
-   **/
+   */
   virtual uint32_t get_id() { return this->id; }
 
 #ifdef TMB_MODEL

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

@@ -37,7 +37,7 @@ objects */
 
   virtual ~FleetInterfaceBase() {}
 
-  /** @brief get_id method for child fleet interface objects to inherit **/
+  /** @brief get_id method for child fleet interface objects to inherit */
   virtual uint32_t get_id() = 0;
 };
 
@@ -52,29 +52,29 @@ std::map<uint32_t, FleetInterfaceBase*> FleetInterfaceBase::live_objects;
  */
 class FleetInterface : public FleetInterfaceBase {
   int interface_agecomp_likelihood_id_m =
-      -999; /*!< id of agecomp likelihood component. The "interface_" prefix
+      -999; /**< id of agecomp likelihood component. The "interface_" prefix
                indicates it belongs to the FleetInterface class, and the "_m"
                postfix signifies that it's a member variable. */
   int interface_index_likelihood_id_m =
-      -999; /*!< id of index likelihood component*/
+      -999; /**< id of index likelihood component*/
   int interface_observed_agecomp_data_id_m =
-      -999; /*!< id of observed agecomp data object*/
+      -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*/
+      -999;                              /**< id of observed index data object*/
+  int interface_selectivity_id_m = -999; /**< id of selectivity component*/
 
  public:
-  bool is_survey = false; /*!< whether this is a survey fleet */
-  int nages;              /*!< number of ages in the fleet data*/
-  int nyears;             /*!< number of years in the fleet data */
-  double log_q;           /*!< log of catchability for the fleet*/
+  bool is_survey = false; /**< whether this is a survey fleet */
+  int nages;              /**< number of ages in the fleet data*/
+  int nyears;             /**< number of years in the fleet data */
+  double log_q;           /**< log of catchability for the fleet*/
   Rcpp::NumericVector
-      log_Fmort;           /*!< log of fishing mortality rate for the fleet*/
-  bool estimate_F = false; /*!< whether the parameter F should be estimated*/
-  bool estimate_q = false; /*!< whether the parameter q should be estimated*/
-  bool random_q = false;   /*!< whether q should be a random effect*/
-  bool random_F = false;   /*!< whether F should be a random effect*/
-  Parameter log_obs_error; /*!< the log of the observation error */
+      log_Fmort;           /**< log of fishing mortality rate for the fleet*/
+  bool estimate_F = false; /**< whether the parameter F should be estimated*/
+  bool estimate_q = false; /**< whether the parameter q should be estimated*/
+  bool random_q = false;   /**< whether q should be a random effect*/
+  bool random_F = false;   /**< whether F should be a random effect*/
+  Parameter log_obs_error; /**< the log of the observation error */
 
   FleetInterface() : FleetInterfaceBase() {}