format C++ code with clang format

inst/include/common/information.hpp

@@ -20,9 +20,8 @@
 #include "../population_dynamics/recruitment/recruitment.hpp"
 #include "../population_dynamics/selectivity/selectivity.hpp"
 #include "def.hpp"
-#include "model_object.hpp"
 #include "fims_vector.hpp"
-
+#include "model_object.hpp"
 
 namespace fims_info {
 

inst/include/common/model.hpp

@@ -74,11 +74,11 @@ class Model {  // may need singleton
     // vector< vector<Type> > creates a nested vector structure where
     // each vector can be a different dimension. Does not work with ADREPORT
     // fleets
-      vector<vector<Type> > exp_index(n_fleets);
-      vector<vector<Type> > exp_catch(n_fleets);
-      vector<vector<Type> > cnaa(n_fleets);
-      vector<vector<Type> > cwaa(n_fleets);
-      vector<vector<Type> > F_mort(n_fleets);
+    vector<vector<Type> > exp_index(n_fleets);
+    vector<vector<Type> > exp_catch(n_fleets);
+    vector<vector<Type> > cnaa(n_fleets);
+    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);
@@ -163,11 +163,11 @@ class Model {  // may need singleton
     for (jt = this->fims_information->fleets.begin();
          jt != this->fims_information->fleets.end(); ++jt) {
 #ifdef TMB_MODEL
-        exp_index(fleet_idx) = (*jt).second->expected_index;
-        exp_catch(fleet_idx) = (*jt).second->expected_catch;
-        F_mort(fleet_idx) = (*jt).second->Fmort;
-        cnaa(fleet_idx) = (*jt).second->catch_numbers_at_age;
-        cwaa(fleet_idx) = (*jt).second->catch_weight_at_age;
+      exp_index(fleet_idx) = (*jt).second->expected_index;
+      exp_catch(fleet_idx) = (*jt).second->expected_catch;
+      F_mort(fleet_idx) = (*jt).second->Fmort;
+      cnaa(fleet_idx) = (*jt).second->catch_numbers_at_age;
+      cwaa(fleet_idx) = (*jt).second->catch_weight_at_age;
 #endif
       fleet_idx += 1;
     }
@@ -215,7 +215,6 @@ class Model {  // may need singleton
 
     return jnll;
   }
-
 };
 
 // Create singleton instance of Model class

inst/include/distributions/functors/tmb_distributions.hpp

@@ -11,8 +11,8 @@
 
 #ifdef TMB_MODEL
 
-#include "distributions_base.hpp"
 #include "../../common/fims_vector.hpp"
+#include "distributions_base.hpp"
 
 namespace fims_distributions {
 
@@ -48,8 +48,8 @@ struct Dnorm : public DistributionsBase<Type> {
 template <typename Type>
 struct Dmultinom : public DistributionsBase<Type> {
   fims::Vector<Type> x; /*!< Vector of length K of integers */
-  fims::Vector<Type> p; /*!< Vector of length K, specifying the probability for the K
-               classes (note, unlike in R these must sum to 1). */
+  fims::Vector<Type> p; /*!< Vector of length K, specifying the probability for
+               the K classes (note, unlike in R these must sum to 1). */
 
   Dmultinom() : DistributionsBase<Type>() {}
 

inst/include/interface/interface.hpp

@@ -20,6 +20,7 @@
 // use isnan macro in math.h instead of TMB's isnan for fixing the r-cmd-check
 // issue
 #include <math.h>
+
 #include <TMB.hpp>
 
 // define REPORT, ADREPORT, and SIMULATE

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

@@ -72,10 +72,10 @@ class FleetInterface : public FleetInterfaceBase {
       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 estimate_obs_error = false; /**< whether the parameter log_obs_error 
-                                        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*/
+  bool estimate_obs_error = false;   /**< whether the parameter log_obs_error
+                                          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*/
   Rcpp::NumericVector log_obs_error; /**< the log of the observation error */
 
   FleetInterface() : FleetInterfaceBase() {}

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

@@ -30,7 +30,8 @@ class RecruitmentInterfaceBase : public FIMSRcppInterfaceBase {
 
   // static std::vector<double> log_recruit_devs; /**< vector of log 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++;
@@ -69,12 +70,12 @@ std::map<uint32_t, RecruitmentInterfaceBase*>
  */
 class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
  public:
-  Parameter logit_steep;       /**< steepness or the productivity of the stock*/
-  Parameter log_rzero;         /**< recruitment at unfished biomass */
-  Parameter log_sigma_recruit; /**< the log of the stock recruit standard deviation */
-  Rcpp::NumericVector log_devs; /**< log recruitment deviations*/
-  bool estimate_log_devs =
-      false; /**< boolean describing whether to estimate */
+  Parameter logit_steep; /**< steepness or the productivity of the stock*/
+  Parameter log_rzero;   /**< recruitment at unfished biomass */
+  Parameter
+      log_sigma_recruit; /**< the log of the stock recruit standard deviation */
+  Rcpp::NumericVector log_devs;   /**< log recruitment deviations*/
+  bool estimate_log_devs = false; /**< boolean describing whether to estimate */
 
   BevertonHoltRecruitmentInterface() : RecruitmentInterfaceBase() {}
 

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

@@ -240,7 +240,6 @@ class DmultinomDistributionsInterface : public DistributionsInterfaceBase {
 
   template <typename Type>
   bool add_to_fims_tmb_internal() {
-
     std::shared_ptr<fims_info::Information<Type>> info =
         fims_info::Information<Type>::GetInstance();
 

inst/include/population_dynamics/fleet/fleet.hpp

@@ -11,10 +11,10 @@
 #define FIMS_POPULATION_DYNAMICS_FLEET_HPP
 
 #include "../../common/data_object.hpp"
+#include "../../common/fims_vector.hpp"
 #include "../../common/model_object.hpp"
 #include "../../distributions/distributions.hpp"
 #include "../selectivity/selectivity.hpp"
-#include "../../common/fims_vector.hpp"
 
 namespace fims_popdy {
 
@@ -24,62 +24,63 @@ namespace fims_popdy {
  */
 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*/
-
-    // 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
-           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*/
-
-    // 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*/
-    std::shared_ptr<fims_distributions::DistributionsBase<Type>>
-    agecomp_likelihood; /*!< agecomp likelihood component*/
-
-    // selectivity
-    int fleet_selectivity_id_m = -999; /*!< id of selectivity component*/
-    std::shared_ptr<SelectivityBase<Type>>
-    selectivity; /*!< selectivity component*/
-
-    int fleet_observed_index_data_id_m = -999; /*!< id of index data */
-    std::shared_ptr<fims_data_object::DataObject<Type>>
-    observed_index_data; /*!< observed index data*/
-
-    int fleet_observed_agecomp_data_id_m = -999; /*!< id of age comp data */
-    std::shared_ptr<fims_data_object::DataObject<Type>>
-    observed_agecomp_data; /*!< observed agecomp data*/
-
-    // Mortality and catchability
-    fims::Vector<Type> log_Fmort; /*!< estimated parameter: log Fishing mortality*/
-    Type log_q; /*!< estimated parameter: catchability of the fleet */
-
-    fims::Vector<Type> log_obs_error;    /*!< estimated parameters: observation error associated
-                            with index */
-    fims::Vector<Type> Fmort; /*!< transformed parameter: Fishing mortality*/
-    Type q; /*!< transofrmed parameter: the catchability of the fleet */
-
-    // derived quantities
-    fims::Vector<Type> catch_at_age;    /*!<derived quantity catch at age*/
-    fims::Vector<Type> catch_index;     /*!<derived quantity catch index*/
-    fims::Vector<Type> age_composition; /*!<derived quantity age composition*/
-
-    // derived quantities
-    fims::Vector<Type> expected_catch; /*!<model expected total catch*/
-    fims::Vector<Type> expected_index; /*!<model expected index of abundance*/
-    fims::Vector<Type> catch_numbers_at_age; /*!<model expected catch at age*/
-    fims::Vector<Type> catch_weight_at_age;  /*!<model expected weight at age*/
-    bool is_survey = false;                 /*!< is this fleet object a survey*/
-
+  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*/
+
+  // 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
+             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*/
+
+  // 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*/
+  std::shared_ptr<fims_distributions::DistributionsBase<Type>>
+      agecomp_likelihood; /*!< agecomp likelihood component*/
+
+  // selectivity
+  int fleet_selectivity_id_m = -999; /*!< id of selectivity component*/
+  std::shared_ptr<SelectivityBase<Type>>
+      selectivity; /*!< selectivity component*/
+
+  int fleet_observed_index_data_id_m = -999; /*!< id of index data */
+  std::shared_ptr<fims_data_object::DataObject<Type>>
+      observed_index_data; /*!< observed index data*/
+
+  int fleet_observed_agecomp_data_id_m = -999; /*!< id of age comp data */
+  std::shared_ptr<fims_data_object::DataObject<Type>>
+      observed_agecomp_data; /*!< observed agecomp data*/
+
+  // Mortality and catchability
+  fims::Vector<Type>
+      log_Fmort; /*!< estimated parameter: log Fishing mortality*/
+  Type log_q;    /*!< estimated parameter: catchability of the fleet */
+
+  fims::Vector<Type> log_obs_error; /*!< estimated parameters: observation error
+                       associated with index */
+  fims::Vector<Type> Fmort; /*!< transformed parameter: Fishing mortality*/
+  Type q; /*!< transofrmed parameter: the catchability of the fleet */
+
+  // derived quantities
+  fims::Vector<Type> catch_at_age;    /*!<derived quantity catch at age*/
+  fims::Vector<Type> catch_index;     /*!<derived quantity catch index*/
+  fims::Vector<Type> age_composition; /*!<derived quantity age composition*/
+
+  // derived quantities
+  fims::Vector<Type> expected_catch; /*!<model expected total catch*/
+  fims::Vector<Type> expected_index; /*!<model expected index of abundance*/
+  fims::Vector<Type> catch_numbers_at_age; /*!<model expected catch at age*/
+  fims::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;
+  ::objective_function<Type> *of;
 #endif
 
   /**
@@ -108,7 +109,7 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
     expected_catch.resize(nyears);
     expected_index.resize(nyears);  // assume index is for all ages.
     catch_numbers_at_age.resize(nyears * nages);
-    
+
     log_obs_error.resize(nyears);
     log_Fmort.resize(nyears);
     Fmort.resize(nyears);
@@ -141,7 +142,8 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
     for (size_t year = 0; year < this->nyears; year++) {
       FLEET_LOG << "input F mort " << this->log_Fmort[year] << std::endl;
       FLEET_LOG << "input q " << this->log_q << std::endl;
-      FLEET_LOG << "input log_obs_error " << this->log_obs_error[year] << std::endl;
+      FLEET_LOG << "input log_obs_error " << this->log_obs_error[year]
+                << std::endl;
       this->Fmort[year] = fims_math::exp(this->log_Fmort[year]);
     }
   }
@@ -160,7 +162,6 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
 
     } else {
       for (size_t y = 0; y < this->nyears; y++) {
-
         fims::Vector<Type> observed_acomp;
         fims::Vector<Type> expected_acomp;
 
@@ -191,31 +192,31 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
     FLEET_LOG << "Age comp negative log-likelihood for fleet," << this->id
               << nll << std::endl;
 #endif
-        return nll;
-    }
-    
-    virtual const Type evaluate_index_nll() {
-        Type nll = 0.0; /*!< The negative log likelihood value */
-        
+    return nll;
+  }
+
+  virtual const Type evaluate_index_nll() {
+    Type nll = 0.0; /*!< The negative log likelihood value */
+
 #ifdef TMB_MODEL
-        fims_distributions::Dnorm<Type> dnorm;
-        for (size_t i = 0; i < this->expected_index.size(); i++) {
-            dnorm.x = fims_math::log(this->observed_index_data->at(i));
-            dnorm.mean = fims_math::log(this->expected_index[i]);
-            dnorm.sd = fims_math::exp(this->log_obs_error[i]);
-            nll -= dnorm.evaluate(true);
-      
-        FLEET_LOG << "observed index data: " << i << " is "
-                  << this->observed_index_data->at(i)
-                  << " and expected is: " << this->expected_index[i] << std::endl;
-        FLEET_LOG << " log obs error is: " << this->log_obs_error[i] << std::endl;
-        }
-        FLEET_LOG << " sd is: " << dnorm.sd << std::endl;
+    fims_distributions::Dnorm<Type> dnorm;
+    for (size_t i = 0; i < this->expected_index.size(); i++) {
+      dnorm.x = fims_math::log(this->observed_index_data->at(i));
+      dnorm.mean = fims_math::log(this->expected_index[i]);
+      dnorm.sd = fims_math::exp(this->log_obs_error[i]);
+      nll -= dnorm.evaluate(true);
+
+      FLEET_LOG << "observed index data: " << i << " is "
+                << this->observed_index_data->at(i)
+                << " and expected is: " << this->expected_index[i] << std::endl;
+      FLEET_LOG << " log obs error is: " << this->log_obs_error[i] << std::endl;
+    }
+    FLEET_LOG << " sd is: " << dnorm.sd << std::endl;
     FLEET_LOG << " index nll: " << nll << std::endl;
 
 #endif
-        return nll;
-    }
+    return nll;
+  }
 };
 
 // default id of the singleton fleet class