Merge pull request #500 from NOAA-FIMS/format-c++-code

format C++ code with clang format

inst/include/common/fims_math.hpp

@@ -26,8 +26,8 @@ namespace fims_math {
 /**
  * @brief The exponential function.
  *
- * @param x value to exponentiate. Please use fims_math::exp<double>(x) if x is an
- * integer.
+ * @param x value to exponentiate. Please use fims_math::exp<double>(x) if x is
+ * an integer.
  * @return the exponentiated value
  */
 template <class Type>
@@ -37,8 +37,8 @@ inline const Type exp(const Type &x) {
 
 /**
  * @brief The natural log function (base e)
- * @param x the value to take the log of. Please use fims_math::log<double>(x) if x
- * is an integer.
+ * @param x the value to take the log of. Please use fims_math::log<double>(x)
+ * if x is an integer.
  * @return
  */
 template <class Type>
@@ -54,8 +54,8 @@ inline const Type log(const Type &x) {
  * @brief The exponential function.
  * The code cannot be tested using the compilation flag
  * -DTMB_MODEL through CMake and Google Test
- * @param x value to exponentiate. Please use fims_math::exp<double>(x) if x is an
- * integer.
+ * @param x value to exponentiate. Please use fims_math::exp<double>(x) if x is
+ * an integer.
  * @return the exponentiated value
  */
 template <class Type>
@@ -73,8 +73,8 @@ inline const double exp(const double &x) {
  * @brief The natural log function (base e)
  * The code cannot be tested using the compilation flag
  * -DTMB_MODEL through CMake and Google Test.
- * @param x the value to take the log of. Please use fims_math::log<double>(x) if x
- * is an integer.
+ * @param x the value to take the log of. Please use fims_math::log<double>(x)
+ * if x is an integer.
  * @return the log of the value
  */
 template <class Type>
@@ -100,7 +100,8 @@ inline const double log(const double &x) {
  * @return
  */
 template <class Type>
-inline const Type logistic(const Type &median, const Type &slope, const Type &x) {
+inline const Type logistic(const Type &median, const Type &slope,
+                           const Type &x) {
   return (1.0) / (1.0 + exp(-1.0 * slope * (x - median)));
 }
 
@@ -155,8 +156,8 @@ inline const Type inv_logit(const Type &a, const Type &b, const Type &logit_x) {
 
 template <class Type>
 inline const Type double_logistic(const Type &median_asc, const Type &slope_asc,
-                               const Type &median_desc, const Type &slope_desc,
-                               const Type &x) {
+                                  const Type &median_desc,
+                                  const Type &slope_desc, const Type &x) {
   return (1.0) / (1.0 + exp(-1.0 * slope_asc * (x - median_asc))) *
          (1.0 - (1.0) / (1.0 + exp(-1.0 * slope_desc * (x - median_desc))));
 }

inst/include/common/information.hpp

@@ -36,7 +36,7 @@ class Information {
   size_t nages;        /**< number of ages>*/
 
   static std::shared_ptr<Information<Type> >
-      fims_information;       /**< singleton instance >*/
+      fims_information;          /**< singleton instance >*/
   std::vector<Type*> parameters; /**< list of all estimated parameters >*/
   std::vector<Type*>
       random_effects_parameters; /**< list of all random effects parameters >*/
@@ -46,42 +46,40 @@ class Information {
   // data objects
   std::map<uint32_t, std::shared_ptr<fims_data_object::DataObject<Type> > >
       data_objects; /*!< map that holds data objects >*/
-  typedef typename std::map<uint32_t,
-                            std::shared_ptr<fims_data_object::DataObject<Type> > >::iterator
+  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
                              location in memory*/
-  typedef
-      typename std::map<uint32_t,
-                        std::shared_ptr<fims_popdy::RecruitmentBase<Type> > >::iterator
-          recruitment_models_iterator;
+  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
                              location in memory*/
-  typedef
-      typename std::map<uint32_t,
-                        std::shared_ptr<fims_popdy::SelectivityBase<Type> > >::iterator
-          selectivity_models_iterator;
+  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
                         memory*/
-  typedef typename std::map<uint32_t,
-                            std::shared_ptr<fims_popdy::GrowthBase<Type> > >::iterator
+  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
                           in memory*/
-  typedef typename std::map<uint32_t,
-                            std::shared_ptr<fims_popdy::MaturityBase<Type> > >::iterator
+  typedef typename std::map<
+      uint32_t, std::shared_ptr<fims_popdy::MaturityBase<Type> > >::iterator
       maturity_models_iterator;
   /**< iterator for maturity objects>*/
 
@@ -90,27 +88,29 @@ class Information {
       fleets; /*!<hash map to link each object to its shared location in
                  memory*/
   typedef
-      typename std::map<uint32_t, std::shared_ptr<fims_popdy::Fleet<Type> > >::iterator
+      typename std::map<uint32_t,
+                        std::shared_ptr<fims_popdy::Fleet<Type> > >::iterator
           fleet_iterator;
   /**< iterator for fleet objects>*/
 
   // populations
   std::map<uint32_t, std::shared_ptr<fims_popdy::Population<Type> > >
       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
+  typedef typename std::map<
+      uint32_t, std::shared_ptr<fims_popdy::Population<Type> > >::iterator
       population_iterator;
   /**< iterator for population objects>*/
 
   // distributions
-  std::map<uint32_t, std::shared_ptr<fims_distributions::DistributionsBase<Type> > >
+  std::map<uint32_t,
+           std::shared_ptr<fims_distributions::DistributionsBase<Type> > >
       distribution_models; /*!<hash map to link each object to its shared
                               location in memory*/
-  typedef
-      typename std::map<uint32_t,
-                        std::shared_ptr<fims_distributions::DistributionsBase<Type> > >::iterator
-          distribution_models_iterator;
+  typedef typename std::map<
+      uint32_t,
+      std::shared_ptr<fims_distributions::DistributionsBase<Type> > >::iterator
+      distribution_models_iterator;
   /**< iterator for distribution objects>*/
 
   Information() {}
@@ -135,7 +135,9 @@ class Information {
    *
    * @param p
    */
-  void RegisterParameter(Type& p) { this->fixed_effects_parameters.push_back(&p); }
+  void RegisterParameter(Type& p) {
+    this->fixed_effects_parameters.push_back(&p);
+  }
 
   /**
    * Register a random effect as estimable.

inst/include/distributions/functors/tmb_distributions.hpp

@@ -22,8 +22,8 @@ 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
-             positive.*/
+  Type sd; /*!< standard deviation of the normal distribution, must be strictly
+           positive.*/
 
   Dnorm() : DistributionsBase<Type>() {}
 

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

@@ -86,7 +86,8 @@ class AgeCompDataInterface : public DataInterfaceBase {
   template <typename Type>
   bool add_to_fims_tmb_internal() {
     std::shared_ptr<fims_data_object::DataObject<Type>> age_comp_data =
-        std::make_shared<fims_data_object::DataObject<Type>>(this->ymax, this->amax);
+        std::make_shared<fims_data_object::DataObject<Type>>(this->ymax,
+                                                             this->amax);
 
     age_comp_data->id = this->id;
     for (int y = 0; y < ymax; y++) {

inst/include/population_dynamics/fleet/fleet.hpp

@@ -153,9 +153,10 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
     size_t dims = this->observed_agecomp_data->get_imax() *
                   this->observed_agecomp_data->get_jmax();
     if (dims != this->catch_numbers_at_age.size()) {
-      fims::fims_log::get("fleet.log") << "Error: observed age comp is of size "
-                                 << dims << " and expected is of size "
-                                 << this->age_composition.size() << std::endl;
+      fims::fims_log::get("fleet.log")
+          << "Error: observed age comp is of size " << dims
+          << " and expected is of size " << this->age_composition.size()
+          << std::endl;
     } else {
       for (size_t y = 0; y < this->nyears; y++) {
         // EigenVector declares a vector type from the Eigen library, which is

inst/include/population_dynamics/growth/functors/ewaa.hpp

@@ -43,5 +43,5 @@ struct EWAAgrowth : public GrowthBase<Type> {
     return ret;
   }
 };
-}  // namespace fims
+}  // namespace fims_popdy
 #endif /* POPULATION_DYNAMICS_GROWTH_EWAA_HPP */

inst/include/population_dynamics/growth/functors/growth_base.hpp

@@ -48,6 +48,6 @@ struct GrowthBase : public fims_model_object::FIMSObject<Type> {
 template <typename Type>
 uint32_t GrowthBase<Type>::id_g = 0;
 
-}  // namespace fims
+}  // namespace fims_popdy
 
 #endif /* POPULATION_DYNAMICS_GROWTH_BASE_HPP */

inst/include/population_dynamics/maturity/functors/logistic.hpp

@@ -37,11 +37,11 @@ struct LogisticMaturity : public MaturityBase<Type> {
    * @param x  The independent variable in the logistic function (e.g., age or
    * size at maturity).
    */
-  virtual const Type evaluate(const Type & x) {
+  virtual const Type evaluate(const Type& x) {
     return fims_math::logistic<Type>(median, slope, x);
   }
 };
 
-}  // namespace fims
+}  // namespace fims_popdy
 
 #endif /* POPULATION_DYNAMICS_MATURITY_LOGISTIC_HPP */

inst/include/population_dynamics/maturity/functors/maturity_base.hpp

@@ -50,6 +50,6 @@ struct MaturityBase : public fims_model_object::FIMSObject<Type> {
 template <typename Type>
 uint32_t MaturityBase<Type>::id_g = 0;
 
-}  // namespace fims
+}  // namespace fims_popdy
 
 #endif /* POPULATION_DYNAMICS_MATURITY_BASE_HPP */

inst/include/population_dynamics/population/population.hpp

@@ -35,8 +35,8 @@ directly?)
 template <typename Type>
 struct Population : public fims_model_object::FIMSObject<Type> {
   using ParameterVector =
-      typename fims::ModelTraits<Type>::ParameterVector; /*!< the vector of population
-                                                      parameters*/
+      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*/
@@ -106,12 +106,14 @@ struct Population : public fims_model_object::FIMSObject<Type> {
 
   // Define objective function object to be able to REPORT and ADREPORT
 #ifdef TMB_MODEL
-  ::objective_function<Type> *of; // :: references global namespace, defined in src/FIMS.cpp, available anywhere in the R package
+  ::objective_function<Type>
+      *of;  // :: references global namespace, defined in src/FIMS.cpp,
+            // available anywhere in the R package
 #endif
 
   // this -> means you're referring to a class member (member of self)
 
-  Population() { this->id = Population::id_g++; } 
+  Population() { this->id = Population::id_g++; }
 
   /**
    * @brief Initialize values. Called once at the start of model run.
@@ -692,6 +694,6 @@ struct Population : public fims_model_object::FIMSObject<Type> {
 template <class Type>
 uint32_t Population<Type>::id_g = 0;
 
-}  // namespace fims
+}  // namespace fims_popdy
 
 #endif /* FIMS_POPULATION_DYNAMICS_POPULATION_HPP */

inst/include/population_dynamics/population/subpopulation.hpp

@@ -40,6 +40,6 @@ namespace fims_popdy {
 template <typename Type>
 class Subpopulation {};
 
-}  // namespace fims
+}  // namespace fims_popdy
 
 #endif /* FIMS_POPULATION_DYNAMICS_POPULATION_SUBPOPULATION_HPP */

inst/include/population_dynamics/recruitment/functors/recruitment_base.hpp

@@ -115,6 +115,6 @@ struct RecruitmentBase : public fims_model_object::FIMSObject<Type> {
 
 template <class Type>
 uint32_t RecruitmentBase<Type>::id_g = 0;
-}  // namespace fims
+}  // namespace fims_popdy
 
 #endif /* FIMS_POPULATION_DYNAMICS_RECRUITMENT_BASE_HPP */

inst/include/population_dynamics/recruitment/functors/sr_beverton_holt.hpp

@@ -62,6 +62,6 @@ struct SRBevertonHolt : public RecruitmentBase<Type> {
   }
 };
 
-}  // namespace fims
+}  // namespace fims_popdy
 
 #endif /* FIMS_POPULATION_DYNAMICS_RECRUITMENT_SR_BEVERTON_HOLT_HPP */

inst/include/population_dynamics/selectivity/functors/double_logistic.hpp

@@ -48,10 +48,10 @@ struct DoubleLogisticSelectivity : public SelectivityBase<Type> {
    */
   virtual const Type evaluate(const Type &x) {
     return fims_math::double_logistic<Type>(median_asc, slope_asc, median_desc,
-                                       slope_desc, x);
+                                            slope_desc, x);
   }
 };
 
-}  // namespace fims
+}  // namespace fims_popdy
 
 #endif /* POPULATION_DYNAMICS_SELECTIVITY_DOUBLE_LOGISTIC_HPP */

inst/include/population_dynamics/selectivity/functors/logistic.hpp

@@ -45,6 +45,6 @@ struct LogisticSelectivity : public SelectivityBase<Type> {
   }
 };
 
-}  // namespace fims
+}  // namespace fims_popdy
 
 #endif /* POPULATION_DYNAMICS_SELECTIVITY_LOGISTIC_HPP */

inst/include/population_dynamics/selectivity/functors/selectivity_base.hpp

@@ -53,6 +53,6 @@ struct SelectivityBase : public fims_model_object::FIMSObject<Type> {
 template <typename Type>
 uint32_t SelectivityBase<Type>::id_g = 0;
 
-}  // namespace fims
+}  // namespace fims_popdy
 
 #endif /* POPULATION_DYNAMICS_SELECTIVITY_BASE_HPP */

tests/gtest/test_population_test_fixture.hpp

@@ -77,7 +77,8 @@ class PopulationPrepareTestFixture : public testing::Test {
     // Does Fmort need to be in side of the year loop like log_q?
     for (int i = 0; i < nfleets; i++) {
       auto fleet = std::make_shared<fims_popdy::Fleet<double>>();
-      auto selectivity = std::make_shared<fims_popdy::LogisticSelectivity<double>>();
+      auto selectivity =
+          std::make_shared<fims_popdy::LogisticSelectivity<double>>();
       selectivity->median = 7;
       selectivity->slope = 0.5;