style: run clang format

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_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/population_dynamics/population/population.hpp

@@ -398,10 +398,10 @@ struct Population : public fims_model_object::FIMSObject<Type> {
         /*the log_recruit_dev vector does not include a value for year == 0
         and is of length nyears - 1 where the first position of the vector
         corresponds to the second year of the time series.*/
-        fims_math::exp(this->recruitment->log_recruit_devs[i_dev-1]);
+        fims_math::exp(this->recruitment->log_recruit_devs[i_dev - 1]);
     this->expected_recruitment[year] = this->numbers_at_age[i_age_year];
-    POPULATION_LOG << " numbers at age at index i_age_year " << i_age_year << " is "
-                   << this->numbers_at_age[i_age_year] << std::endl;
+    POPULATION_LOG << " numbers at age at index i_age_year " << i_age_year
+                   << " is " << this->numbers_at_age[i_age_year] << std::endl;
   }
 
   /**

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

@@ -32,17 +32,16 @@ struct RecruitmentBase : public fims_model_object::FIMSObject<Type> {
   static uint32_t id_g; /**< reference id for recruitment object*/
 
   typename fims::ModelTraits<Type>::ParameterVector
-      log_recruit_devs;            /*!< A vector of log recruitment deviations */
+      log_recruit_devs; /*!< A vector of log 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
                        deviations */
   Type log_rzero;         /**< Log of unexploited recruitment.*/
 
-  bool estimate_log_recruit_devs =
-      true; /*!< A flag to indicate if recruitment deviations are estimated or
-     not */
+  bool estimate_log_recruit_devs = true; /*!< A flag to indicate if recruitment
+                                  deviations are estimated or not */
 
   /** @brief Constructor.
    */

inst/include/utilities/fims_json.hpp

@@ -1,4 +1,4 @@
-/** 
+/**
  * @file fims_json.hpp
  *  @brief A simple JSON parsing and generation library.
  * @details This library provides classes and functions for parsing JSON
@@ -13,29 +13,29 @@
 
 class JsonValue;
 
-/** 
+/**
  * 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.
  */
 using JsonArray = std::vector<JsonValue>;
 
-/** 
+/**
  * 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.
  */
 class JsonValue {
@@ -83,15 +83,15 @@ class JsonValue {
   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.
  */
 class JsonParser {
@@ -129,11 +129,11 @@ class JsonParser {
   /** 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.
@@ -150,7 +150,7 @@ void JsonParser::SkipWhitespace() {
   }
 }
 
-/** 
+/**
  * Parse a JSON value.
  *  @return The parsed JSON value.
  */
@@ -173,7 +173,7 @@ JsonValue JsonParser::ParseValue() {
   }
 }
 
-/** 
+/**
  * Parse a numeric JSON value.
  * @return The parsed JSON value.
  */
@@ -204,7 +204,7 @@ JsonValue JsonParser::ParseNumber() {
   }
 }
 
-/** 
+/**
  * Parse a string JSON value.
  * @return The parsed JSON value.
  */

tests/gtest/test_population_test_fixture.hpp

@@ -144,24 +144,22 @@ class PopulationEvaluateTestFixture : public testing::Test {
     population.growth = growth;
     population.Prepare();
 
-
     auto maturity = std::make_shared<fims_popdy::LogisticMaturity<double>>();
     maturity->inflection_point = 6;
     maturity->slope = 0.15;
     population.maturity = maturity;
 
-
-      auto recruitment = std::make_shared<fims_popdy::SRBevertonHolt<double>>();
-      recruitment->logit_steep = fims_math::logit(0.2, 1.0, 0.75);
-      recruitment->log_rzero = fims_math::log(1000000.0);
-      /*the log_recruit_dev vector does not include a value for year == 0
-      and is of length nyears - 1 where the first position of the vector
-      corresponds to the second year of the time series.*/
-      recruitment->log_recruit_devs.resize(nyears-1);
-      for (int i = 0; i < recruitment->log_recruit_devs.size(); i++) {
-        recruitment->log_recruit_devs[i] = 0.0;
-      }
-      population.recruitment = recruitment;
+    auto recruitment = std::make_shared<fims_popdy::SRBevertonHolt<double>>();
+    recruitment->logit_steep = fims_math::logit(0.2, 1.0, 0.75);
+    recruitment->log_rzero = fims_math::log(1000000.0);
+    /*the log_recruit_dev vector does not include a value for year == 0
+    and is of length nyears - 1 where the first position of the vector
+    corresponds to the second year of the time series.*/
+    recruitment->log_recruit_devs.resize(nyears - 1);
+    for (int i = 0; i < recruitment->log_recruit_devs.size(); i++) {
+      recruitment->log_recruit_devs[i] = 0.0;
+    }
+    population.recruitment = recruitment;
 
     int year = 4;
     int age = 6;