format C++ code with clang format

inst/include/common/def.hpp

@@ -15,21 +15,27 @@
 #include <memory>
 #include <vector>
 
-//The following rows initialize default log files for outputing model progress 
-//comments used to assist in diagnosing model issues and tracking progress. These
-//files will only be created if a logs folder is added to the root model directory.
-std::ofstream FIMS_LOG ("logs/fims.log"); /**< Generic log file */
-std::ofstream INFO_LOG("logs/info.log"); /**< Information.hpp log file */
+// The following rows initialize default log files for outputing model progress
+// comments used to assist in diagnosing model issues and tracking progress.
+// These files will only be created if a logs folder is added to the root model
+// directory.
+std::ofstream FIMS_LOG("logs/fims.log");   /**< Generic log file */
+std::ofstream INFO_LOG("logs/info.log");   /**< Information.hpp log file */
 std::ofstream ERROR_LOG("logs/error.log"); /**< Error tracking log file */
-std::ofstream DATA_LOG("logs/data.log"); /**< Data input tracking log file */
+std::ofstream DATA_LOG("logs/data.log");   /**< Data input tracking log file */
 std::ofstream MODEL_LOG("logs/model.log"); /**< Model.hpp log file */
 std::ofstream FLEET_LOG("logs/fleet.log"); /**< Fleet module log file */
-std::ofstream POPULATION_LOG("logs/population.log"); /**< Populations module log file */
-std::ofstream RECRUITMENT_LOG("logs/recruitment.log"); /**< Recruitment module log file */
+std::ofstream POPULATION_LOG(
+    "logs/population.log"); /**< Populations module log file */
+std::ofstream RECRUITMENT_LOG(
+    "logs/recruitment.log");                 /**< Recruitment module log file */
 std::ofstream GROWTH_LOG("logs/growth.log"); /**< Growth module log file */
-std::ofstream MATURITY_LOG("logs/maturity.log"); /**< Maturity module log file */
-std::ofstream SELECTIVITY_LOG("logs/selectivity.log"); /**< Selectivity module log file */
-std::ofstream DEBUG_LOG("logs/debug/debug.log"); /**< Development debugging log file */
+std::ofstream MATURITY_LOG(
+    "logs/maturity.log"); /**< Maturity module log file */
+std::ofstream SELECTIVITY_LOG(
+    "logs/selectivity.log"); /**< Selectivity module log file */
+std::ofstream DEBUG_LOG(
+    "logs/debug/debug.log"); /**< Development debugging log file */
 
 #ifdef TMB_MODEL
 // simplify access to singletons

inst/include/common/fims_math.hpp

@@ -100,7 +100,8 @@ inline const double log(const double &x) {
  * @return
  */
 template <class Type>
-inline const Type logistic(const Type &inflection_point, const Type &slope, const Type &x) {
+inline const Type logistic(const Type &inflection_point, const Type &slope,
+                           const Type &x) {
   return (1.0) / (1.0 + exp(-1.0 * slope * (x - inflection_point)));
 }
 
@@ -138,27 +139,30 @@ inline const Type inv_logit(const Type &a, const Type &b, const Type &logit_x) {
  * @brief The general double logistic function
  *
  * \f$ \frac{1.0}{ 1.0 + exp(-1.0 * slope_{asc} (x - inflection_point_{asc}))}
- * \left(1-\frac{1.0}{ 1.0 + exp(-1.0 * slope_{desc} (x - inflection_point_{desc}))}
- * \right)\f$
+ * \left(1-\frac{1.0}{ 1.0 + exp(-1.0 * slope_{desc} (x -
+ * inflection_point_{desc}))} \right)\f$
  *
  * @param inflection_point_asc the inflection point of the ascending limb of the
  * double logistic function
  * @param slope_asc the slope of the ascending limb of the double logistic
  * function
  * @param inflection_point_desc the inflection point of the descending limb of
- * the double logistic function, where inflection_point_desc > inflection_point_asc
+ * the double logistic function, where inflection_point_desc >
+ * inflection_point_asc
  * @param slope_desc the slope of the descending limb of the double logistic
  * function
  * @param x the index the logistic function should be evaluated at
  * @return
  */
 
 template <class Type>
-inline const Type double_logistic(const Type &inflection_point_asc, const Type &slope_asc,
-                               const Type &inflection_point_desc, const Type &slope_desc,
-                               const Type &x) {
+inline const Type double_logistic(const Type &inflection_point_asc,
+                                  const Type &slope_asc,
+                                  const Type &inflection_point_desc,
+                                  const Type &slope_desc, const Type &x) {
   return (1.0) / (1.0 + exp(-1.0 * slope_asc * (x - inflection_point_asc))) *
-         (1.0 - (1.0) / (1.0 + exp(-1.0 * slope_desc * (x - inflection_point_desc))));
+         (1.0 -
+          (1.0) / (1.0 + exp(-1.0 * slope_desc * (x - inflection_point_desc))));
 }
 
 /**