format C++ code with clang format

inst/include/common/information.hpp

@@ -175,9 +175,11 @@ class Information {
                << std::endl;
       // set index data
       if (f->fleet_observed_index_data_id_m != -999) {
-        uint32_t observed_index_id = static_cast<uint32_t>(f->fleet_observed_index_data_id_m); 
+        uint32_t observed_index_id =
+            static_cast<uint32_t>(f->fleet_observed_index_data_id_m);
         data_iterator it = this->data_objects.find(observed_index_id);
-        FIMS_LOG << "Input fleet index id = " << observed_index_id << "." << std::endl;
+        FIMS_LOG << "Input fleet index id = " << observed_index_id << "."
+                 << std::endl;
 
         if (it != this->data_objects.end()) {
           f->observed_index_data = (*it).second;

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

@@ -51,11 +51,17 @@ 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 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*/
-  int interface_observed_agecomp_data_id_m = -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*/
+  int interface_agecomp_likelihood_id_m =
+      -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*/
+  int interface_observed_agecomp_data_id_m =
+      -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*/
 
  public:
   bool is_survey = false; /*!< whether this is a survey fleet */
@@ -139,7 +145,8 @@ class FleetInterface : public FleetInterfaceBase {
     fleet->nyears = this->nyears;
     fleet->fleet_agecomp_likelihood_id_m = interface_agecomp_likelihood_id_m;
     fleet->fleet_index_likelihood_id_m = interface_index_likelihood_id_m;
-    fleet->fleet_observed_agecomp_data_id_m = interface_observed_agecomp_data_id_m;
+    fleet->fleet_observed_agecomp_data_id_m =
+        interface_observed_agecomp_data_id_m;
     fleet->fleet_observed_index_data_id_m = interface_observed_index_data_id_m;
     fleet->fleet_selectivity_id_m = interface_selectivity_id_m;
     fleet->log_obs_error = this->log_obs_error.value_m;

inst/include/population_dynamics/fleet/fleet.hpp

@@ -32,13 +32,17 @@ struct Fleet : public FIMSObject<Type> {
 
   // 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.*/
+  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::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*/
+  int fleet_agecomp_likelihood_id_m =
+      -999; /*!< id of agecomp likelihood component*/
   std::shared_ptr<fims::DistributionsBase<Type>>
       agecomp_likelihood; /*!< agecomp likelihood component*/
 

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

@@ -21,8 +21,8 @@ namespace fims {
  */
 template <typename Type>
 struct LogisticMaturity : public MaturityBase<Type> {
-  Type median; /*!< 50% quantile of the value of the quantity of interest (x); e.g.
-               age at which 50% of the fish are mature */
+  Type median; /*!< 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
                value (x) and median */
 

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

@@ -19,18 +19,18 @@ namespace fims {
  */
 template <typename Type>
 struct DoubleLogisticSelectivity : public SelectivityBase<Type> {
-  Type median_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 interest
-               value (x) and median on the ascending limb of the double logistic
-               curve*/
-  Type median_desc; /*!< 50% quantile of the value of the quantity of interest (x)
-               on the descending limb of the double logistic curve; e.g.
+  Type median_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
+                interest   value (x) and median on the ascending limb of the double
+                logistic   curve*/
+  Type median_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 interest
-              value (x) and median on the descending limb of the double logistic
-              curve */
+  Type slope_desc;  /*!<scalar multiplier of difference between quantity of
+               interest  value (x) and median on the descending limb of the double
+               logistic  curve */
 
   DoubleLogisticSelectivity() : SelectivityBase<Type>() {}
 
@@ -48,7 +48,7 @@ struct DoubleLogisticSelectivity : public SelectivityBase<Type> {
    */
   virtual const Type evaluate(const Type &x) {
     return fims::double_logistic<Type>(median_asc, slope_asc, median_desc,
-                                    slope_desc, x);
+                                       slope_desc, x);
   }
 };
 

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

@@ -22,8 +22,8 @@ namespace fims {
  */
 template <typename Type>
 struct LogisticSelectivity : public SelectivityBase<Type> {
-  Type median; /*!< 50% quantile of the value of the quantity of interest (x); e.g.
-               age at which 50% of the fish are selected */
+  Type median; /*!< 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
                value (x) and median */