diff --git a/inst/include/common/data_object.hpp b/inst/include/common/data_object.hpp
index 491f95590..fe726fa1f 100644
--- a/inst/include/common/data_object.hpp
+++ b/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.
diff --git a/inst/include/common/def.hpp b/inst/include/common/def.hpp
index 85756b93b..315c4d542 100644
--- a/inst/include/common/def.hpp
+++ b/inst/include/common/def.hpp
@@ -1,4 +1,4 @@
-/*! \file def.hpp
+/** \file def.hpp
  */
 
 /*
diff --git a/inst/include/common/fims_math.hpp b/inst/include/common/fims_math.hpp
index 6665406bf..dcdf42d06 100644
--- a/inst/include/common/fims_math.hpp
+++ b/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
diff --git a/inst/include/common/information.hpp b/inst/include/common/information.hpp
index 9111d1219..3c3794139 100644
--- a/inst/include/common/information.hpp
+++ b/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
@@ -45,14 +45,14 @@ 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
@@ -60,7 +60,7 @@ class Information {
   /**< 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
@@ -68,7 +68,7 @@ class Information {
   /**< 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
@@ -76,7 +76,7 @@ class Information {
   /**< 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
@@ -85,7 +85,7 @@ 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,
@@ -95,7 +95,7 @@ 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
@@ -105,7 +105,7 @@ 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,
diff --git a/inst/include/common/model.hpp b/inst/include/common/model.hpp
index e1130014a..a3cb74449 100644
--- a/inst/include/common/model.hpp
+++ b/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
diff --git a/inst/include/common/model_object.hpp b/inst/include/common/model_object.hpp
index f67579327..28ef1e7c8 100644
--- a/inst/include/common/model_object.hpp
+++ b/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() {}
   /**
diff --git a/inst/include/distributions/functors/distributions_base.hpp b/inst/include/distributions/functors/distributions_base.hpp
index 5c55dc3c3..5a50d05db 100644
--- a/inst/include/distributions/functors/distributions_base.hpp
+++ b/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.
diff --git a/inst/include/distributions/functors/tmb_distributions.hpp b/inst/include/distributions/functors/tmb_distributions.hpp
index b3a0ee8c1..6d96100f3 100644
--- a/inst/include/distributions/functors/tmb_distributions.hpp
+++ b/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.
@@ -20,9 +20,9 @@ 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>() {}
@@ -48,8 +48,8 @@ template <typename Type>
 struct Dmultinom : public DistributionsBase<Type> {
   /** EigenVector defined in interface.hpp */
   using Vector = typename fims::ModelTraits<Type>::EigenVector;
-  Vector x; /*!< Vector of length K of integers */
-  Vector p; /*!< Vector of length K, specifying the probability for the K
+  Vector x; /**< Vector of length K of integers */
+  Vector p; /**< Vector of length K, specifying the probability for the K
                classes (note, unlike in R these must sum to 1). */
 
   Dmultinom() : DistributionsBase<Type>() {}
@@ -74,9 +74,9 @@ 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>() {}
 
diff --git a/inst/include/interface/rcpp/rcpp_objects/rcpp_data.hpp b/inst/include/interface/rcpp/rcpp_objects/rcpp_data.hpp
index d3cd9e955..82fa7718c 100644
--- a/inst/include/interface/rcpp/rcpp_objects/rcpp_data.hpp
+++ b/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
diff --git a/inst/include/interface/rcpp/rcpp_objects/rcpp_fleet.hpp b/inst/include/interface/rcpp/rcpp_objects/rcpp_fleet.hpp
index 2a02c813f..b0706dced 100644
--- a/inst/include/interface/rcpp/rcpp_objects/rcpp_fleet.hpp
+++ b/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() {}
 
diff --git a/inst/include/interface/rcpp/rcpp_objects/rcpp_growth.hpp b/inst/include/interface/rcpp/rcpp_objects/rcpp_growth.hpp
index 543fc7853..78ba050d5 100644
--- a/inst/include/interface/rcpp/rcpp_objects/rcpp_growth.hpp
+++ b/inst/include/interface/rcpp/rcpp_objects/rcpp_growth.hpp
@@ -11,9 +11,9 @@
 #include "../../../population_dynamics/growth/growth.hpp"
 #include "rcpp_interface_base.hpp"
 
-/****************************************************************
+/**
  * Growth Rcpp interface                                   *
- ***************************************************************/
+ */
 
 /**
  * @brief Rcpp interface that serves as the parent class for
@@ -40,10 +40,10 @@ objects */
 
   virtual ~GrowthInterfaceBase() {}
 
-  /** @brief get_id method for child growth interface objects to inherit **/
+  /** @brief get_id method for child growth interface objects to inherit */
   virtual uint32_t get_id() = 0;
 
-  /** @brief evaluate method for child growth interface objects to inherit **/
+  /** @brief evaluate method for child growth interface objects to inherit */
   virtual double evaluate(double age) = 0;
 };
 
@@ -78,7 +78,7 @@ vectors have been set */
    * @param ages Type vector of ages
    * @return std::map<T, T>
    *
-   * */
+   */
   inline std::map<double, double> make_map(std::vector<double> ages,
                                            std::vector<double> weights) {
     std::map<double, double> mymap;
@@ -91,7 +91,7 @@ vectors have been set */
   /** @brief Rcpp interface to the EWAAgrowth evaluate method
    * you can call from R using
    * ewaagrowth.evaluate(age)
-   * */
+   */
   virtual double evaluate(double age) {
     fims_popdy::EWAAgrowth<double> EWAAGrowth;
 
diff --git a/inst/include/interface/rcpp/rcpp_objects/rcpp_maturity.hpp b/inst/include/interface/rcpp/rcpp_objects/rcpp_maturity.hpp
index 83cf499bf..709d37b5b 100644
--- a/inst/include/interface/rcpp/rcpp_objects/rcpp_maturity.hpp
+++ b/inst/include/interface/rcpp/rcpp_objects/rcpp_maturity.hpp
@@ -13,14 +13,14 @@
 #include "../../../population_dynamics/maturity/maturity.hpp"
 #include "rcpp_interface_base.hpp"
 
-/****************************************************************
- * maturity Rcpp interface                                   *
- ***************************************************************/
+/**
+ * maturity Rcpp interface
+ */
 
 /**
  * @brief MaturityInterfaceBase class should be inherited to
  * define different Rcpp interfaces for each possible maturity function
- * */
+ */
 class MaturityInterfaceBase : public FIMSRcppInterfaceBase {
  public:
   static uint32_t id_g; /**< static id of the recruitment interface base*/
@@ -41,7 +41,7 @@ class MaturityInterfaceBase : public FIMSRcppInterfaceBase {
   virtual ~MaturityInterfaceBase() {}
 
   /** @brief get the ID of the interface base object
-   **/
+   */
   virtual uint32_t get_id() = 0;
 
   /**
diff --git a/inst/include/interface/rcpp/rcpp_objects/rcpp_nll.hpp b/inst/include/interface/rcpp/rcpp_objects/rcpp_nll.hpp
index 9d3250e93..405ef1631 100644
--- a/inst/include/interface/rcpp/rcpp_objects/rcpp_nll.hpp
+++ b/inst/include/interface/rcpp/rcpp_objects/rcpp_nll.hpp
@@ -16,7 +16,7 @@
  * @brief NLLInterfaceBase class should be inherited to
  * define different Rcpp interfaces for each possible negative log-likelihood
  * function
- * */
+ */
 class NLLInterfaceBase : public FIMSRcppInterfaceBase {
  public:
   static uint32_t id_g; /**< static id of the recruitment interface base*/
@@ -36,10 +36,10 @@ class NLLInterfaceBase : public FIMSRcppInterfaceBase {
   virtual ~NLLInterfaceBase() {}
 
   /** @brief get the ID of the interface base object
-   **/
+   */
   virtual uint32_t get_id() = 0;
 
-  /** @brief evaluate method for child nll interface objects to inherit **/
+  /** @brief evaluate method for child nll interface objects to inherit */
   virtual double evaluate_nll() = 0;
 };
 
diff --git a/inst/include/interface/rcpp/rcpp_objects/rcpp_population.hpp b/inst/include/interface/rcpp/rcpp_objects/rcpp_population.hpp
index 14f64d21b..b336ff572 100644
--- a/inst/include/interface/rcpp/rcpp_objects/rcpp_population.hpp
+++ b/inst/include/interface/rcpp/rcpp_objects/rcpp_population.hpp
@@ -11,14 +11,14 @@
 #include "../../../population_dynamics/population/population.hpp"
 #include "rcpp_interface_base.hpp"
 
-/****************************************************************
- * Population Rcpp interface                                   *
- ***************************************************************/
+/**
+ * Population Rcpp interface
+ */
 
 /**
  * @brief PopulationInterfaceBase class should be inherited to
  * define different Rcpp interfaces for each possible Population function
- * */
+ */
 class PopulationInterfaceBase : public FIMSRcppInterfaceBase {
  public:
   static uint32_t id_g; /**< static id of the population interface base*/
diff --git a/inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp b/inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp
index 8eb351d3e..9f74f48c4 100644
--- a/inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp
+++ b/inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp
@@ -12,14 +12,14 @@
 #include "../../../population_dynamics/recruitment/recruitment.hpp"
 #include "rcpp_interface_base.hpp"
 
-/****************************************************************
- * Recruitment Rcpp interface                                   *
- ***************************************************************/
+/**
+ * Recruitment Rcpp interface
+ */
 
 /**
  * @brief RecruitmentInterfaceBase class should be inherited to
  * define different Rcpp interfaces for each possible Recruitment function
- * */
+ */
 class RecruitmentInterfaceBase : public FIMSRcppInterfaceBase {
  public:
   static uint32_t id_g; /**< static id of the recruitment interface base*/
@@ -30,8 +30,7 @@ class RecruitmentInterfaceBase : public FIMSRcppInterfaceBase {
 
   // static std::vector<double> recruit_deviations; /**< vector of recruitment
   // deviations*/
-  /// static bool constrain_deviations; /**< whether or not the rec devs are
-  /// constrained*/
+  // static bool constrain_deviations; /**< whether or not the rec devs are constrained*/
 
   RecruitmentInterfaceBase() {
     this->id = RecruitmentInterfaceBase::id_g++;
@@ -44,11 +43,11 @@ class RecruitmentInterfaceBase : public FIMSRcppInterfaceBase {
   virtual ~RecruitmentInterfaceBase() {}
 
   /** @brief get the ID of the interface base object
-   **/
+   */
   virtual uint32_t get_id() = 0;
 
   /** @brief evaluate method for child recruitment interface objects to inherit
-   * **/
+   */
   virtual double evaluate(double spawners, double ssbzero) = 0;
 
   /**
diff --git a/inst/include/interface/rcpp/rcpp_objects/rcpp_selectivity.hpp b/inst/include/interface/rcpp/rcpp_objects/rcpp_selectivity.hpp
index 5f282cebc..9cc7c88d7 100644
--- a/inst/include/interface/rcpp/rcpp_objects/rcpp_selectivity.hpp
+++ b/inst/include/interface/rcpp/rcpp_objects/rcpp_selectivity.hpp
@@ -12,14 +12,14 @@
 #include "../../../population_dynamics/selectivity/selectivity.hpp"
 #include "rcpp_interface_base.hpp"
 
-/****************************************************************
- * Selectivity Rcpp interface                                   *
- ***************************************************************/
+/**
+ * Selectivity Rcpp interface
+ */
 
 /**
  * @brief SelectivityInterfaceBase class should be inherited to
  * define different Rcpp interfaces for each possible Selectivity function
- * */
+ */
 class SelectivityInterfaceBase : public FIMSRcppInterfaceBase {
  public:
   static uint32_t id_g; /**< static id of the recruitment interface base*/
@@ -40,7 +40,7 @@ class SelectivityInterfaceBase : public FIMSRcppInterfaceBase {
   virtual ~SelectivityInterfaceBase() {}
 
   /** @brief get the ID of the interface base object
-   **/
+   */
   virtual uint32_t get_id() = 0;
 
   /**
diff --git a/inst/include/interface/rcpp/rcpp_objects/rcpp_tmb_distribution.hpp b/inst/include/interface/rcpp/rcpp_objects/rcpp_tmb_distribution.hpp
index cfce6d1fc..c7cbf9aa1 100644
--- a/inst/include/interface/rcpp/rcpp_objects/rcpp_tmb_distribution.hpp
+++ b/inst/include/interface/rcpp/rcpp_objects/rcpp_tmb_distribution.hpp
@@ -38,11 +38,11 @@ DistributionsInterfaceBase objects */
   virtual ~DistributionsInterfaceBase() {}
 
   /** @brief get_id method for child distribution interface objects to inherit
-   * **/
+   */
   virtual uint32_t get_id() = 0;
 
   /** @brief evaluate method for child distribution interface objects to inherit
-   * **/
+   */
   virtual double evaluate(bool do_log) = 0;
 };
 
@@ -64,8 +64,8 @@ std::map<uint32_t,
 class DnormDistributionsInterface : public DistributionsInterfaceBase {
  public:
   Parameter x;    /**< observed data */
-  Parameter mean; /**< mean of x for the normal distribution **/
-  Parameter sd;   /**< sd of x for the normal distribution **/
+  Parameter mean; /**< mean of x for the normal distribution */
+  Parameter sd;   /**< sd of x for the normal distribution */
 
   DnormDistributionsInterface() : DistributionsInterfaceBase() {}
 
@@ -133,9 +133,9 @@ class DnormDistributionsInterface : public DistributionsInterfaceBase {
  */
 class DlnormDistributionsInterface : public DistributionsInterfaceBase {
  public:
-  Parameter x;       /*!< observation */
-  Parameter meanlog; /*!< mean of the distribution of log(x) */
-  Parameter sdlog;   /*!< standard deviation of the distribution of log(x) */
+  Parameter x;       /**< observation */
+  Parameter meanlog; /**< mean of the distribution of log(x) */
+  Parameter sdlog;   /**< standard deviation of the distribution of log(x) */
 
   DlnormDistributionsInterface() : DistributionsInterfaceBase() {}
 
@@ -207,8 +207,8 @@ class DlnormDistributionsInterface : public DistributionsInterfaceBase {
 
 class DmultinomDistributionsInterface : public DistributionsInterfaceBase {
  public:
-  Rcpp::NumericVector x; /*!< Vector of length K of integers */
-  Rcpp::NumericVector p; /*!< Vector of length K, specifying the probability
+  Rcpp::NumericVector x; /**< Vector of length K of integers */
+  Rcpp::NumericVector p; /**< Vector of length K, specifying the probability
  for the K classes (note, unlike in R these must sum to 1). */
 
   DmultinomDistributionsInterface() : DistributionsInterfaceBase() {}
diff --git a/inst/include/population_dynamics/fleet/fleet.hpp b/inst/include/population_dynamics/fleet/fleet.hpp
index cd452333b..69a96c665 100644
--- a/inst/include/population_dynamics/fleet/fleet.hpp
+++ b/inst/include/population_dynamics/fleet/fleet.hpp
@@ -1,4 +1,4 @@
-/*! \file fleet.hpp
+/** \file fleet.hpp
  *
  * This File is part of the NOAA, National Marine Fisheries Service
  * Fisheries Integrated Modeling System project.
@@ -20,65 +20,65 @@ namespace fims_popdy {
 /** @brief Base class for all fleets.
  *
  * @tparam Type The type of the fleet object.
- **/
+ */
 template <class Type>
 struct Fleet : public fims_model_object::FIMSObject<Type> {
-  static uint32_t id_g; /*!< reference id for fleet object*/
-  size_t nyears;        /*!< the number of years in the model*/
-  size_t nages;         /*!< the number of ages in the model*/
+  static uint32_t id_g; /**< reference id for fleet object*/
+  size_t nyears;        /**< the number of years in the model*/
+  size_t nages;         /**< the number of ages in the model*/
   using ParameterVector =
-      typename fims::ModelTraits<Type>::ParameterVector; /*!< vector of fleet
+      typename fims::ModelTraits<Type>::ParameterVector; /**< vector of fleet
                                                       parameters */
 
   // This likelihood index is not currently being used as only one likelihood
   // distribution is available. These are for a future update M2+.
   int fleet_index_likelihood_id_m =
-      -999; /*!<id of index likelihood component. The "fleet_" prefix indicates
+      -999; /**<id of index likelihood component. The "fleet_" prefix indicates
                it belongs to the Fleet struct, and the "_m" postfix signifies
                that it's a member variable.*/
   std::shared_ptr<fims_distributions::DistributionsBase<Type>>
-      index_likelihood; /*!< index likelihood component*/
+      index_likelihood; /**< index likelihood component*/
 
   // This likelihood index is not currently being used as only one likelihood
   // distribution is available. These are for a future update M2+.
   int fleet_agecomp_likelihood_id_m =
-      -999; /*!< id of agecomp likelihood component*/
+      -999; /**< id of agecomp likelihood component*/
   std::shared_ptr<fims_distributions::DistributionsBase<Type>>
-      agecomp_likelihood; /*!< agecomp likelihood component*/
+      agecomp_likelihood; /**< agecomp likelihood component*/
 
   // selectivity
-  int fleet_selectivity_id_m = -999; /*!< id of selectivity component*/
+  int fleet_selectivity_id_m = -999; /**< id of selectivity component*/
   std::shared_ptr<SelectivityBase<Type>>
-      selectivity; /*!< selectivity component*/
+      selectivity; /**< selectivity component*/
 
-  int fleet_observed_index_data_id_m = -999; /*!< id of index data */
+  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*/
+      observed_index_data; /**< observed index data*/
 
-  int fleet_observed_agecomp_data_id_m = -999; /*!< id of age comp 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*/
+      observed_agecomp_data; /**< observed agecomp data*/
 
   // Mortality and catchability
-  ParameterVector log_Fmort; /*!< estimated parameter: log Fishing mortality*/
-  Type log_q; /*!< estimated parameter: catchability of the fleet */
+  ParameterVector log_Fmort; /**< estimated parameter: log Fishing mortality*/
+  Type log_q; /**< estimated parameter: catchability of the fleet */
 
-  Type log_obs_error;    /*!< estimated parameter: observation error associated
+  Type log_obs_error;    /**< estimated parameter: observation error associated
                             with index */
-  ParameterVector Fmort; /*!< transformed parameter: Fishing mortality*/
-  Type q; /*!< transofrmed parameter: the catchability of the fleet */
+  ParameterVector Fmort; /**< transformed parameter: Fishing mortality*/
+  Type q; /**< transofrmed parameter: the catchability of the fleet */
 
   // derived quantities
-  std::vector<Type> catch_at_age;    /*!<derived quantity catch at age*/
-  std::vector<Type> catch_index;     /*!<derived quantity catch index*/
-  std::vector<Type> age_composition; /*!<derived quantity age composition*/
+  std::vector<Type> catch_at_age;    /**<derived quantity catch at age*/
+  std::vector<Type> catch_index;     /**<derived quantity catch index*/
+  std::vector<Type> age_composition; /**<derived quantity age composition*/
 
   // derived quantities
-  std::vector<Type> expected_catch; /*!<model expected total catch*/
-  std::vector<Type> expected_index; /*!<model expected index of abundance*/
-  std::vector<Type> catch_numbers_at_age; /*!<model expected catch at age*/
-  std::vector<Type> catch_weight_at_age;  /*!<model expected weight at age*/
-  bool is_survey = false;                 /*!< is this fleet object a survey*/
+  std::vector<Type> expected_catch; /**<model expected total catch*/
+  std::vector<Type> expected_index; /**<model expected index of abundance*/
+  std::vector<Type> catch_numbers_at_age; /**<model expected catch at age*/
+  std::vector<Type> catch_weight_at_age;  /**<model expected weight at age*/
+  bool is_survey = false;                 /**< is this fleet object a survey*/
 
 #ifdef TMB_MODEL
   ::objective_function<Type> *of;
@@ -126,18 +126,18 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
 
     // derived quantities
     std::fill(catch_at_age.begin(), catch_at_age.end(),
-              0); /*!<derived quantity catch at age*/
+              0); /**<derived quantity catch at age*/
     std::fill(catch_index.begin(), catch_index.end(),
-              0); /*!<derived quantity catch index*/
+              0); /**<derived quantity catch index*/
     std::fill(age_composition.begin(), age_composition.end(), 0);
     std::fill(expected_catch.begin(), expected_catch.end(),
-              0); /*!<model expected total catch*/
+              0); /**<model expected total catch*/
     std::fill(expected_index.begin(), expected_index.end(),
-              0); /*!<model expected index of abundance*/
+              0); /**<model expected index of abundance*/
     std::fill(catch_numbers_at_age.begin(), catch_numbers_at_age.end(),
-              0); /*!<model expected catch at age*/
+              0); /**<model expected catch at age*/
     std::fill(catch_weight_at_age.begin(), catch_weight_at_age.end(),
-              0); /*!<model expected weight at age*/
+              0); /**<model expected weight at age*/
     this->q = fims_math::exp(this->log_q);
     for (size_t year = 0; year < this->nyears; year++) {
       FLEET_LOG << "input F mort " << this->log_Fmort[year] << std::endl;
@@ -147,7 +147,7 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
   }
 
   virtual const Type evaluate_age_comp_nll() {
-    Type nll = 0.0; /*!< The negative log likelihood value */
+    Type nll = 0.0; /**< The negative log likelihood value */
 #ifdef TMB_MODEL
     fims_distributions::Dmultinom<Type> dmultinom;
     size_t dims = this->observed_agecomp_data->get_imax() *
@@ -197,7 +197,7 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
   }
 
   virtual const Type evaluate_index_nll() {
-    Type nll = 0.0; /*!< The negative log likelihood value */
+    Type nll = 0.0; /**< The negative log likelihood value */
 
 #ifdef TMB_MODEL
     fims_distributions::Dnorm<Type> dnorm;
diff --git a/inst/include/population_dynamics/growth/functors/ewaa.hpp b/inst/include/population_dynamics/growth/functors/ewaa.hpp
index 92454ac4e..62ff5c5d8 100644
--- a/inst/include/population_dynamics/growth/functors/ewaa.hpp
+++ b/inst/include/population_dynamics/growth/functors/ewaa.hpp
@@ -26,7 +26,7 @@ struct EWAAgrowth : public GrowthBase<Type> {
   // a map looks up values based on a reference key
   // in this case, our key is age (first double), and
   //  the value is the weight at that age (second double)
-  std::map<double, double> ewaa; /*!<map of doubles for EWAA values by age,
+  std::map<double, double> ewaa; /**<map of doubles for EWAA values by age,
           where age starts at zero > */
 
   EWAAgrowth() : GrowthBase<Type>() {}
diff --git a/inst/include/population_dynamics/growth/functors/growth_base.hpp b/inst/include/population_dynamics/growth/functors/growth_base.hpp
index a6da2de1f..0b2aaabc8 100644
--- a/inst/include/population_dynamics/growth/functors/growth_base.hpp
+++ b/inst/include/population_dynamics/growth/functors/growth_base.hpp
@@ -22,14 +22,14 @@ namespace fims_popdy {
  * @brief Base class for all growth functors.
  *
  * @tparam Type The type of the growth functor.
- * */
+ */
 template <typename Type>
 struct GrowthBase : public fims_model_object::FIMSObject<Type> {
   // id_g is the ID of the instance of the  growthBase class.
   // this is like a memory tracker.
   // Assigning each one its own ID is a way to keep track of
   // all the instances of the  growthBase class.
-  static uint32_t id_g; /*!< reference id for growth object*/
+  static uint32_t id_g; /**< reference id for growth object*/
 
   /**
    * @brief Constructor.
diff --git a/inst/include/population_dynamics/maturity/functors/logistic.hpp b/inst/include/population_dynamics/maturity/functors/logistic.hpp
index d17167dd0..619a9ee6f 100644
--- a/inst/include/population_dynamics/maturity/functors/logistic.hpp
+++ b/inst/include/population_dynamics/maturity/functors/logistic.hpp
@@ -21,9 +21,9 @@ namespace fims_popdy {
  */
 template <typename Type>
 struct LogisticMaturity : public MaturityBase<Type> {
-  Type inflection_point; /*!< 50% quantile of the value of the quantity of
+  Type inflection_point; /**< 50% quantile of the value of the quantity of
                interest (x); e.g. age at which 50% of the fish are mature */
-  Type slope; /*!<scalar multiplier of difference between quantity of interest
+  Type slope; /**<scalar multiplier of difference between quantity of interest
               value (x) and inflection_point */
 
   LogisticMaturity() : MaturityBase<Type>() {}
diff --git a/inst/include/population_dynamics/maturity/functors/maturity_base.hpp b/inst/include/population_dynamics/maturity/functors/maturity_base.hpp
index 402233dfc..f3f6aadba 100644
--- a/inst/include/population_dynamics/maturity/functors/maturity_base.hpp
+++ b/inst/include/population_dynamics/maturity/functors/maturity_base.hpp
@@ -29,7 +29,7 @@ struct MaturityBase : public fims_model_object::FIMSObject<Type> {
   // this is like a memory tracker.
   // Assigning each one its own ID is a way to keep track of
   // all the instances of the MaturityBase class.
-  static uint32_t id_g; /*!< The ID of the instance of the MaturityBase class */
+  static uint32_t id_g; /**< The ID of the instance of the MaturityBase class */
 
   /** @brief Constructor.
    */
diff --git a/inst/include/population_dynamics/population/population.hpp b/inst/include/population_dynamics/population/population.hpp
index 434dcceff..ff5465b05 100644
--- a/inst/include/population_dynamics/population/population.hpp
+++ b/inst/include/population_dynamics/population/population.hpp
@@ -35,74 +35,74 @@ directly?)
 template <typename Type>
 struct Population : public fims_model_object::FIMSObject<Type> {
   using ParameterVector =
-      typename fims::ModelTraits<Type>::ParameterVector; /*!< the vector of
+      typename fims::ModelTraits<Type>::ParameterVector; /**< the vector of
                                                       population parameters*/
-  static uint32_t id_g; /*!< reference id for population object*/
-  size_t nyears;        /*!< total number of years in the fishery*/
-  size_t nseasons;      /*!< total number of seasons in the fishery*/
-  size_t nages;         /*!< total number of ages in the population*/
-  size_t nfleets;       /*!< total number of fleets in the fishery*/
+  static uint32_t id_g; /**< reference id for population object*/
+  size_t nyears;        /**< total number of years in the fishery*/
+  size_t nseasons;      /**< total number of seasons in the fishery*/
+  size_t nages;         /**< total number of ages in the population*/
+  size_t nfleets;       /**< total number of fleets in the fishery*/
 
   // constants
   const Type proportion_female =
-      0.5; /*!< Sex proportion fixed at 50/50 for M1*/
+      0.5; /**< Sex proportion fixed at 50/50 for M1*/
 
   // parameters are estimated; after initialize in create_model, push_back to
   // parameter list - in information.hpp (same for initial F in fleet)
-  std::vector<Type> log_init_naa; /*!< estimated parameter: log numbers at age*/
-  ParameterVector log_M; /*!< estimated parameter: log Natural Mortality*/
+  std::vector<Type> log_init_naa; /**< estimated parameter: log numbers at age*/
+  ParameterVector log_M; /**< estimated parameter: log Natural Mortality*/
 
   // Transformed values
-  std::vector<Type> M; /*!< transformed parameter: Natural Mortality*/
+  std::vector<Type> M; /**< transformed parameter: Natural Mortality*/
 
-  std::vector<double> ages;    /*!< vector of the ages for referencing*/
-  std::vector<double> years;   /*!< vector of years for referencing*/
-  ParameterVector mortality_F; /*!< vector of fishing mortality summed across
+  std::vector<double> ages;    /**< vector of the ages for referencing*/
+  std::vector<double> years;   /**< vector of years for referencing*/
+  ParameterVector mortality_F; /**< vector of fishing mortality summed across
                                     fleet by year and age*/
   std::vector<Type>
-      mortality_Z; /*!< vector of total mortality by year and age*/
+      mortality_Z; /**< vector of total mortality by year and age*/
 
   // derived quantities
   std::vector<Type>
-      weight_at_age; /*!< Derived quantity: expected weight at age */
+      weight_at_age; /**< Derived quantity: expected weight at age */
   // fecundity removed because we don't need it yet
-  std::vector<Type> numbers_at_age; /*!< Derived quantity: population expected
+  std::vector<Type> numbers_at_age; /**< Derived quantity: population expected
                                  numbers at age in each year*/
   std::vector<Type>
-      unfished_numbers_at_age; /*!< Derived quantity: population expected
+      unfished_numbers_at_age; /**< Derived quantity: population expected
                                 unfished numbers at age in each year*/
   std::vector<Type>
-      biomass; /*!< Derived quantity: total population biomass in each year*/
-  std::vector<Type> spawning_biomass; /*!< Derived quantity: Spawning_biomass*/
-  std::vector<Type> unfished_biomass; /*!< Derived quanity
+      biomass; /**< Derived quantity: total population biomass in each year*/
+  std::vector<Type> spawning_biomass; /**< Derived quantity: Spawning_biomass*/
+  std::vector<Type> unfished_biomass; /**< Derived quanity
                                             biomass assuming unfished*/
-  std::vector<Type> unfished_spawning_biomass; /*!< Derived quanity Spawning
+  std::vector<Type> unfished_spawning_biomass; /**< Derived quanity Spawning
                                             biomass assuming unfished*/
-  std::vector<Type> proportion_mature_at_age;  /*!< Derived quantity: Proportion
+  std::vector<Type> proportion_mature_at_age;  /**< Derived quantity: Proportion
                                              matura at age */
-  std::vector<Type> expected_numbers_at_age;   /*!< Expected values: Numbers at
+  std::vector<Type> expected_numbers_at_age;   /**< Expected values: Numbers at
                                               age (thousands?? millions??) */
-  std::vector<Type> expected_catch;            /*!< Expected values: Catch*/
-  std::vector<Type> expected_recruitment;      /*!< Expected recruitment */
-  /// recruitment
-  int recruitment_id = -999; /*!< id of recruitment model object*/
+  std::vector<Type> expected_catch;            /**< Expected values: Catch*/
+  std::vector<Type> expected_recruitment;      /**< Expected recruitment */
+  // recruitment
+  int recruitment_id = -999; /**< id of recruitment model object*/
   std::shared_ptr<RecruitmentBase<Type>>
-      recruitment; /*!< shared pointer to recruitment module */
+      recruitment; /**< shared pointer to recruitment module */
 
   // growth
-  int growth_id = -999; /*!< id of growth model object*/
+  int growth_id = -999; /**< id of growth model object*/
   std::shared_ptr<GrowthBase<Type>>
-      growth; /*!< shared pointer to growth module */
+      growth; /**< shared pointer to growth module */
 
   // maturity
-  int maturity_id = -999; /*!< id of maturity model object*/
+  int maturity_id = -999; /**< id of maturity model object*/
   std::shared_ptr<MaturityBase<Type>>
-      maturity; /*!< shared pointer to maturity module */
+      maturity; /**< shared pointer to maturity module */
 
   // fleet
-  int fleet_id = -999; /*!< id of fleet model object*/
+  int fleet_id = -999; /**< id of fleet model object*/
   std::vector<std::shared_ptr<Fleet<Type>>>
-      fleets; /*!< shared pointer to fleet module */
+      fleets; /**< shared pointer to fleet module */
 
   // Define objective function object to be able to REPORT and ADREPORT
 #ifdef TMB_MODEL
diff --git a/inst/include/population_dynamics/recruitment/functors/recruitment_base.hpp b/inst/include/population_dynamics/recruitment/functors/recruitment_base.hpp
index 7e5f096f8..af1b01716 100644
--- a/inst/include/population_dynamics/recruitment/functors/recruitment_base.hpp
+++ b/inst/include/population_dynamics/recruitment/functors/recruitment_base.hpp
@@ -1,4 +1,4 @@
-/*! \file recruitment_base.hpp
+/** \file recruitment_base.hpp
  *
  * This File is part of the NOAA, National Marine Fisheries Service
  * Fisheries Integrated Modeling System project. See LICENSE in the
@@ -29,19 +29,19 @@ namespace fims_popdy {
  */
 template <class Type>
 struct RecruitmentBase : public fims_model_object::FIMSObject<Type> {
-  static uint32_t id_g; /*!< reference id for recruitment object*/
+  static uint32_t id_g; /**< reference id for recruitment object*/
 
   typename fims::ModelTraits<Type>::ParameterVector
-      recruit_deviations;            /*!< A vector of recruitment deviations */
-  bool constrain_deviations = false; /*!< A flag to indicate if recruitment
+      recruit_deviations;            /**< A vector of recruitment deviations */
+  bool constrain_deviations = false; /**< A flag to indicate if recruitment
                                  deviations are summing to zero or not */
 
-  Type log_sigma_recruit; /*!< Log standard deviation of log recruitment
+  Type log_sigma_recruit; /**< Log standard deviation of log recruitment
                        deviations */
-  Type log_rzero;         /*!< Log of unexploited recruitment.*/
+  Type log_rzero;         /**< Log of unexploited recruitment.*/
 
   bool estimate_recruit_deviations =
-      true; /*!< A flag to indicate if recruitment deviations are estimated or
+      true; /**< A flag to indicate if recruitment deviations are estimated or
      not */
 
   /** @brief Constructor.
@@ -70,7 +70,7 @@ struct RecruitmentBase : public fims_model_object::FIMSObject<Type> {
    *
    */
   virtual const Type evaluate_nll() {
-    Type nll = 0.0; /*!< The negative log likelihood value */
+    Type nll = 0.0; /**< The negative log likelihood value */
 
     if (!this->estimate_recruit_deviations) {
       return nll;
diff --git a/inst/include/population_dynamics/recruitment/functors/sr_beverton_holt.hpp b/inst/include/population_dynamics/recruitment/functors/sr_beverton_holt.hpp
index 781eaa20f..81c4ed8a9 100644
--- a/inst/include/population_dynamics/recruitment/functors/sr_beverton_holt.hpp
+++ b/inst/include/population_dynamics/recruitment/functors/sr_beverton_holt.hpp
@@ -28,7 +28,7 @@ struct SRBevertonHolt : public RecruitmentBase<Type> {
   // Here we define the members that will be used in the Beverton Holt SR
   // function. These members are needed by Beverton Holt but will not be common
   // to all recruitment functions like spawners is below.
-  Type logit_steep; /*!< Transformed value of recruitment relative to unfished
+  Type logit_steep; /**< Transformed value of recruitment relative to unfished
                  recruitment at 20% of unfished spawning biomass.*/
 
   SRBevertonHolt() : RecruitmentBase<Type>() {}
diff --git a/inst/include/population_dynamics/selectivity/functors/double_logistic.hpp b/inst/include/population_dynamics/selectivity/functors/double_logistic.hpp
index 51bee5e8a..66d20375a 100644
--- a/inst/include/population_dynamics/selectivity/functors/double_logistic.hpp
+++ b/inst/include/population_dynamics/selectivity/functors/double_logistic.hpp
@@ -19,16 +19,16 @@ namespace fims_popdy {
  */
 template <typename Type>
 struct DoubleLogisticSelectivity : public SelectivityBase<Type> {
-  Type inflection_point_asc; /*!< 50% quantile of the value of the quantity of
+  Type inflection_point_asc; /**< 50% quantile of the value of the quantity of
                interest (x)  on the ascending limb of the double logistic curve;
                e.g. age at  which 50% of the fish are selected */
-  Type slope_asc; /*!<scalar multiplier of difference between quantity of
+  Type slope_asc; /**<scalar multiplier of difference between quantity of
               interest   value (x) and inflection_point on the ascending limb of
               the double   logistic   curve*/
-  Type inflection_point_desc; /*!< 50% quantile of the value of the quantity of
+  Type inflection_point_desc; /**< 50% quantile of the value of the quantity of
                interest (x) on the descending limb of the double logistic curve;
                e.g. age at which 50% of the fish are selected */
-  Type slope_desc; /*!<scalar multiplier of difference between quantity of
+  Type slope_desc; /**<scalar multiplier of difference between quantity of
               interest  value (x) and inflection_point on the descending limb of
               the double  logistic  curve */
 
diff --git a/inst/include/population_dynamics/selectivity/functors/logistic.hpp b/inst/include/population_dynamics/selectivity/functors/logistic.hpp
index cd50a4fd6..67aabb8f1 100644
--- a/inst/include/population_dynamics/selectivity/functors/logistic.hpp
+++ b/inst/include/population_dynamics/selectivity/functors/logistic.hpp
@@ -22,9 +22,9 @@ namespace fims_popdy {
  */
 template <typename Type>
 struct LogisticSelectivity : public SelectivityBase<Type> {
-  Type inflection_point; /*!< 50% quantile of the value of the quantity of
+  Type inflection_point; /**< 50% quantile of the value of the quantity of
                interest (x); e.g. age at which 50% of the fish are selected */
-  Type slope; /*!<scalar multiplier of difference between quantity of interest
+  Type slope; /**<scalar multiplier of difference between quantity of interest
               value (x) and inflection_point */
 
   LogisticSelectivity() : SelectivityBase<Type>() {}
diff --git a/inst/include/population_dynamics/selectivity/functors/selectivity_base.hpp b/inst/include/population_dynamics/selectivity/functors/selectivity_base.hpp
index a67b9bd8d..2e589adb0 100644
--- a/inst/include/population_dynamics/selectivity/functors/selectivity_base.hpp
+++ b/inst/include/population_dynamics/selectivity/functors/selectivity_base.hpp
@@ -30,7 +30,7 @@ struct SelectivityBase : public fims_model_object::FIMSObject<Type> {
   // Assigning each one its own ID is a way to keep track of
   // all the instances of the SelectivityBase class.
   static uint32_t
-      id_g; /*!< The ID of the instance of the SelectivityBase class */
+      id_g; /**< The ID of the instance of the SelectivityBase class */
 
   /** @brief Constructor.
    */
diff --git a/inst/include/utilities/fims_json.hpp b/inst/include/utilities/fims_json.hpp
index 114528043..c3718928a 100644
--- a/inst/include/utilities/fims_json.hpp
+++ b/inst/include/utilities/fims_json.hpp
@@ -1,7 +1,9 @@
-/// @file fims_json.hpp
-/// @brief A simple JSON parsing and generation library.
-/// @details This library provides classes and functions for parsing JSON
-/// strings and generating JSON data structures.
+/** 
+ * @file fims_json.hpp
+ *  @brief A simple JSON parsing and generation library.
+ * @details This library provides classes and functions for parsing JSON
+ * strings and generating JSON data structures.
+ */
 #include <cctype>
 #include <iostream>
 #include <map>
@@ -11,119 +13,131 @@
 
 class JsonValue;
 
-/// Alias for a JSON object, mapping strings to JSON values.
+/** 
+ * Alias for a JSON object, mapping strings to JSON values.
+ */
 using JsonObject = std::map<std::string, JsonValue>;
 
-/// Alias for a JSON array, containing a sequence of JSON values.
+/** 
+ * Alias for a JSON array, containing a sequence of JSON values.
+ */
 using JsonArray = std::vector<JsonValue>;
 
-/// Represents different types of JSON values.
+/** 
+ * Represents different types of JSON values.
+ */
 enum JsonValueType {
-  Null = 0,  ///< Null JSON value.
-  Number,    ///< Numeric JSON value.
-  String,    ///< String JSON value.
-  Bool,      ///< Boolean JSON value.
-  Object,    ///< JSON object.
-  Array      ///< JSON array.
+  Null = 0,  /**< Null JSON value. */
+  Number,    /**< Numeric JSON value. */
+  String,    /**< String JSON value. */
+  Bool,      /**< Boolean JSON value. */
+  Object,    /**< JSON object. */
+  Array      /**< JSON array. */
 };
 
-/// Represents a JSON value.
+/** 
+ * Represents a JSON value.
+ */
 class JsonValue {
  public:
-  /// Default constructor, initializes to Null value.
+  /** Default constructor, initializes to Null value. */
   JsonValue() : type(JsonValueType::Null) {}
 
-  /// Constructor for numeric JSON value (i.e., integer).
+  /** Constructor for numeric JSON value (i.e., integer). */
   JsonValue(int num) : type(JsonValueType::Number), number(num) {}
 
-  /// Constructor for numeric JSON value (i.e., double).
+  /** Constructor for numeric JSON value (i.e., double). */
   JsonValue(double num) : type(JsonValueType::Number), number(num) {}
 
-  /// Constructor for string JSON value.
+  /** Constructor for string JSON value. */
   JsonValue(const std::string& str) : type(JsonValueType::String), str(str) {}
 
-  /// Constructor for boolean JSON value.
+  /** Constructor for boolean JSON value. */
   JsonValue(bool b) : type(JsonValueType::Bool), boolean(b) {}
 
-  /// Constructor for JSON object value.
+  /** Constructor for JSON object value. */
   JsonValue(const JsonObject& obj) : type(JsonValueType::Object), object(obj) {}
 
-  /// Constructor for JSON array value.
+  /** Constructor for JSON array value. */
   JsonValue(const JsonArray& arr) : type(JsonValueType::Array), array(arr) {}
 
-  /// Get the type of the JSON value.
+  /** Get the type of the JSON value. */
   JsonValueType GetType() const { return type; }
 
-  /// Get the numeric value as an integer.
+  /** Get the numeric value as an integer. */
   int GetInt() const { return static_cast<int>(number); }
 
-  /// Get the numeric value as a double.
+  /** Get the numeric value as a double. */
   double GetDouble() const { return number; }
 
-  /// Get the string value.
+  /** Get the string value. */
   const std::string& GetString() const { return str; }
 
-  /// Get the boolean value.
+  /** Get the boolean value. */
   bool GetBool() const { return boolean; }
 
-  /// Get the JSON object.
+  /** Get the JSON object. */
   JsonObject& GetObject() { return object; }
 
-  /// Get the JSON array.
+  /** Get the JSON array. */
   JsonArray& GetArray() { return array; }
 
  private:
-  JsonValueType type;  ///< Type of the JSON value.
-  double number;       ///< Numeric value.
-  std::string str;     ///< String value.
-  bool boolean;        ///< Boolean value.
-  JsonObject object;   ///< JSON object.
-  JsonArray array;     ///< JSON array.
+  JsonValueType type;  /**< Type of the JSON value. */
+  double number;       /**< Numeric value. */
+  std::string str;     /**< String value. */
+  bool boolean;        /**< Boolean value. */
+  JsonObject object;   /**< JSON object. */
+  JsonArray array;     /**< JSON array. */
 };
 
-/// Parses JSON strings and generates JSON values.
+/** 
+ * Parses JSON strings and generates JSON values.
+ */
 class JsonParser {
  public:
-  /// Parse a JSON string and return the corresponding JSON value.
+  /** Parse a JSON string and return the corresponding JSON value. */
   JsonValue Parse(const std::string& json);
-  /// Write a JSON value to a file.
+  /** Write a JSON value to a file. */
   void WriteToFile(const std::string& filename, JsonValue jsonValue);
-  /// Display a JSON value to the standard output.
+  /** Display a JSON value to the standard output. */
   void Show(JsonValue jsonValue);
 
  private:
-  /// Skip whitespace characters in the input string.
+  /** Skip whitespace characters in the input string. */
   void SkipWhitespace();
-  /// Parse a JSON value.
+  /** Parse a JSON value. */
   JsonValue ParseValue();
-  /// Parse a numeric JSON value.
+  /** Parse a numeric JSON value. */
   JsonValue ParseNumber();
-  /// Parse a string JSON value.
+  /** Parse a string JSON value. */
   JsonValue ParseString();
-  /// Parse a boolean JSON value.
+  /** Parse a boolean JSON value. */
   JsonValue ParseBool();
-  /// Parse a null JSON value.
+  /** Parse a null JSON value. */
   JsonValue ParseNull();
-  /// Parse a JSON object.
+  /** Parse a JSON object. */
   JsonValue ParseObject();
-  /// Parse a JSON array.
+  /** Parse a JSON array. */
   JsonValue ParseArray();
-  /// Write a JSON value to an output file stream.
+  /** Write a JSON value to an output file stream. */
   void WriteJsonValue(std::ofstream& outputFile, JsonValue jsonValue);
-  /// Display a JSON value to an output stream.
+  /** Display a JSON value to an output stream. */
   void PrintJsonValue(std::ostream& outputFile, JsonValue jsonValue);
-  /// Indentation helper for printing JSON values in an output file stream.
+  /** Indentation helper for printing JSON values in an output file stream. */
   void Indent(std::ostream& outputFile, int level);
-  /// Indentation helper for printing JSON values in an output stream.
+  /** Indentation helper for printing JSON values in an output stream. */
   void Indent(std::ofstream& outputFile, int level);
 
-  std::string data;  ///< Input JSON data.
-  size_t position;   ///< Current position in the data.
+  std::string data;  /**< Input JSON data. */
+  size_t position;   /**< Current position in the data. */
 };
 
-/// Parse a JSON string and return the corresponding JSON value.
-/// @param json The JSON string to parse.
-/// @return The parsed JSON value.
+/** 
+ * Parse a JSON string and return the corresponding JSON value.
+ * @param json The JSON string to parse.
+ * @return The parsed JSON value.
+ */
 JsonValue JsonParser::Parse(const std::string& json) {
   data = json;
   position = 0;
@@ -136,10 +150,12 @@ void JsonParser::SkipWhitespace() {
   }
 }
 
-/// Parse a JSON value.
-/// @return The parsed JSON value.
+/** 
+ * Parse a JSON value.
+ *  @return The parsed JSON value.
+ */
 JsonValue JsonParser::ParseValue() {
-  /// Skip whitespace characters in the input string.
+  /** Skip whitespace characters in the input string. */
   SkipWhitespace();
   char current = data[position];
   if (current == '{') {
@@ -157,8 +173,10 @@ JsonValue JsonParser::ParseValue() {
   }
 }
 
-/// Parse a numeric JSON value.
-/// @return The parsed JSON value.
+/** 
+ * Parse a numeric JSON value.
+ * @return The parsed JSON value.
+ */
 JsonValue JsonParser::ParseNumber() {
   size_t end_pos = position;
   bool is_float = false;
@@ -186,8 +204,10 @@ JsonValue JsonParser::ParseNumber() {
   }
 }
 
-/// Parse a string JSON value.
-/// @return The parsed JSON value.
+/** 
+ * Parse a string JSON value.
+ * @return The parsed JSON value.
+ */
 JsonValue JsonParser::ParseString() {
   position++;  // Skip the initial '"'
   size_t end_pos = data.find('"', position);
@@ -196,8 +216,10 @@ JsonValue JsonParser::ParseString() {
   return JsonValue(str);
 }
 
-/// Parse a boolean JSON value.
-/// @return The parsed JSON value.
+/**
+ * Parse a boolean JSON value.
+ * @return The parsed JSON value.
+ */
 JsonValue JsonParser::ParseBool() {
   if (data.compare(position, 4, "true") == 0) {
     position += 4;
@@ -211,8 +233,10 @@ JsonValue JsonParser::ParseBool() {
   }
 }
 
-/// Parse a null JSON value.
-/// @return The parsed JSON value.
+/**
+ * Parse a null JSON value.
+ * @return The parsed JSON value.
+ */
 JsonValue JsonParser::ParseNull() {
   if (data.compare(position, 4, "null") == 0) {
     position += 4;
@@ -223,8 +247,10 @@ JsonValue JsonParser::ParseNull() {
   }
 }
 
-/// Parse a JSON object.
-/// @return The parsed JSON value representing the object.
+/**
+ * Parse a JSON object.
+ * @return The parsed JSON value representing the object.
+ */
 JsonValue JsonParser::ParseObject() {
   JsonObject obj;
   position++;  // Skip the initial '{'
@@ -248,8 +274,10 @@ JsonValue JsonParser::ParseObject() {
   return JsonValue(obj);
 }
 
-/// Parse a JSON array.
-/// @return The parsed JSON value representing the array.
+/**
+ * Parse a JSON array.
+ * @return The parsed JSON value representing the array.
+ */
 JsonValue JsonParser::ParseArray() {
   JsonArray arr;
   position++;  // Skip the initial '['
@@ -269,9 +297,11 @@ JsonValue JsonParser::ParseArray() {
   return JsonValue(arr);
 }
 
-/// Write a JSON value to an output file.
-/// @param filename The name of the output file.
-/// @param jsonValue The JSON value to write.
+/**
+ *  Write a JSON value to an output file.
+ * @param filename The name of the output file.
+ * @param jsonValue The JSON value to write.
+ */
 void JsonParser::WriteToFile(const std::string& filename, JsonValue jsonValue) {
   std::ofstream outputFile(filename);
   if (!outputFile) {
@@ -280,14 +310,16 @@ void JsonParser::WriteToFile(const std::string& filename, JsonValue jsonValue) {
     return;
   }
 
-  // Call a private helper function to write JSON values recursively
+  /** Call a private helper function to write JSON values recursively */
   WriteJsonValue(outputFile, jsonValue);
 }
 
-/// Write a JSON value to an output file.
-// Private helper function to write JSON values recursively
-/// @param outputFile The output file stream.
-/// @param jsonValue The JSON value to write.
+/**
+ * Write a JSON value to an output file.
+ * Private helper function to write JSON values recursively
+ * @param outputFile The output file stream.
+ *  @param jsonValue The JSON value to write.
+ */
 void JsonParser::WriteJsonValue(std::ofstream& outputFile,
                                 JsonValue jsonValue) {
   switch (jsonValue.GetType()) {
@@ -333,16 +365,20 @@ void JsonParser::WriteJsonValue(std::ofstream& outputFile,
   }
 }
 
-/// Display a JSON value to the standard output.
-/// @param jsonValue The JSON value to display.
+/**
+ * Display a JSON value to the standard output.
+ * @param jsonValue The JSON value to display.
+ */
 void JsonParser::Show(JsonValue jsonValue) {
   this->PrintJsonValue(std::cout, jsonValue);
   std::cout << std::endl;
 }
 
-/// Display a JSON value to an output stream.
-/// @param output The output stream.
-/// @param jsonValue The JSON value to display.
+/**
+ * Display a JSON value to an output stream.
+ * @param output The output stream.
+ * @param jsonValue The JSON value to display.
+ */
 void JsonParser::PrintJsonValue(std::ostream& output, JsonValue jsonValue) {
   switch (jsonValue.GetType()) {
     case JsonValueType::Null:
diff --git a/inst/templates/module_base_template.hpp b/inst/templates/module_base_template.hpp
index 150ed17ba..ee83ca648 100644
--- a/inst/templates/module_base_template.hpp
+++ b/inst/templates/module_base_template.hpp
@@ -22,7 +22,7 @@ namespace fims_popdy {
 /* @brief Base class for all {{{ module_type }}} functors.
  *
  * @tparam Type The type of the {{{ module_type }}} functor.
- * */
+ */
 template<typename Type>
 // Change {{{ module_type }}} to CamelCase in the class definition below. 
 struct {{{ module_type }}}Base : public fims_model_object::FIMSObject<Type> {
diff --git a/vignettes/fims-path-maturity.Rmd b/vignettes/fims-path-maturity.Rmd
index 04e433431..2708c9a88 100644
--- a/vignettes/fims-path-maturity.Rmd
+++ b/vignettes/fims-path-maturity.Rmd
@@ -297,9 +297,9 @@ namespace fims_popdy {
  */
 template <typename Type>
 struct LogisticMaturity : public MaturityBase<Type> {
-  Type inflection_point; /*!< 50% quantile of the value of the quantity of interest (x); e.g.,
+  Type inflection_point; /**< 50% quantile of the value of the quantity of interest (x); e.g.,
                age at which 50% of the fish are mature */
-  Type slope;  /*!<scalar multiplier of difference between quantity of interest
+  Type slope;  /**<scalar multiplier of difference between quantity of interest
                value (x) and inflection_point */
 
   LogisticMaturity() : MaturityBase<Type>() {}
@@ -332,9 +332,9 @@ To evaluate maturity within the `Population` class, we first need to set up a sh
 ```{Rcpp,  class.source = "fimschunk", eval = FALSE}
 //file: inst/include/population_dynamics/population/population.hpp
 // maturity is a shared pointer to MaturityBase
-int maturity_id = -999; /*!< id of maturity model object*/
+int maturity_id = -999; /**< id of maturity model object*/
 std::shared_ptr<fims_popdy::MaturityBase<Type>>
-      maturity; /*!< shared pointer to maturity module */
+      maturity; /**< shared pointer to maturity module */
 ```
 
 The `maturity_id` was set from R using the `SetMaturity()` method from the `PopulationInterface` class:
@@ -359,7 +359,7 @@ struct MaturityBase : public fims_model_object::FIMSObject<Type> {
   // this is like a memory tracker.
   // Assigning each one its own ID is a way to keep track of
   // all the instances of the MaturityBase class.
-  static uint32_t id_g; /*!< The ID of the instance of the MaturityBase class */
+  static uint32_t id_g; /**< The ID of the instance of the MaturityBase class */
 
   /** @brief Constructor.
    */
@@ -418,7 +418,7 @@ This *information* is managed in FIMS through the `Information` class in [inform
  maturity_models, that points to fims_popdy::MaturityBase
  */
 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*/
 
 //Next we set up the iterator, which will be used to loop 
@@ -453,7 +453,7 @@ Now we need to pass this pointer to the maturity pointer in population so that `
 ```{Rcpp,  class.source = "infochunk", eval = FALSE}
 //file: inst/include/common/information.hpp
 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