style: run clang format (#483)

Co-authored-by: Andrea-Havron-NOAA <Andrea-Havron-NOAA@users.noreply.github.com>

inst/include/common/model.hpp

@@ -69,24 +69,24 @@ class Model {  // may need singleton
     int n_fleets = fims_information->fleets.size();
     int n_pops = fims_information->populations.size();
 
-    //Create vector lists to store output for reporting
-    #ifdef TMB_MODEL
-    //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);
-    //populations
-    vector< vector<Type> > naa(n_pops);
-    vector< vector<Type> > ssb(n_pops);
-    vector< vector<Type> > biomass(n_pops);
-    vector< vector<Type> > rec_dev(n_pops);
-    vector< vector<Type> > recruitment(n_pops);
-    vector< vector<Type> > M(n_pops);
-    #endif
+// Create vector lists to store output for reporting
+#ifdef TMB_MODEL
+    // 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);
+    // populations
+    vector<vector<Type> > naa(n_pops);
+    vector<vector<Type> > ssb(n_pops);
+    vector<vector<Type> > biomass(n_pops);
+    vector<vector<Type> > rec_dev(n_pops);
+    vector<vector<Type> > recruitment(n_pops);
+    vector<vector<Type> > M(n_pops);
+#endif
 
     // Loop over populations, evaluate, and sum up the recruitment likelihood
     // component
@@ -109,11 +109,10 @@ class Model {  // may need singleton
       FIMS_LOG << "rec nll: " << rec_nll << std::endl;
     }
 
-    //Loop over fleets/surveys, and sum up age comp and index nlls
+    // Loop over fleets/surveys, and sum up age comp and index nlls
     typename fims::Information<Type>::fleet_iterator jt;
     for (jt = this->fims_information->fleets.begin();
          jt != this->fims_information->fleets.end(); ++jt) {
-
       //(*jt).second points to each individual Fleet module
 #ifdef TMB_MODEL
       (*jt).second->of = this->of;
@@ -122,43 +121,42 @@ class Model {  // may need singleton
       index_nll += (*jt).second->evaluate_index_nll();
     }
 
-    //Loop over populations and fleets/surveys and fill in reporting
+    // Loop over populations and fleets/surveys and fill in reporting
 
-    //initiate population index for structuring report out objects
+    // initiate population index for structuring report out objects
     int pop_idx = 0;
     for (it = this->fims_information->populations.begin();
          it != this->fims_information->populations.end(); ++it) {
-      #ifdef TMB_MODEL
-        naa(pop_idx) = vector<Type>((*it).second->numbers_at_age);
-        ssb(pop_idx) = vector<Type>((*it).second->spawning_biomass);
-        rec_dev(pop_idx) = vector<Type>((*it).second->recruitment->recruit_deviations);
-        recruitment(pop_idx) = vector<Type>((*it).second->expected_recruitment);
-        biomass(pop_idx) = vector<Type>((*it).second->biomass);
-        M(pop_idx) = vector<Type>((*it).second->M);
-      #endif
+#ifdef TMB_MODEL
+      naa(pop_idx) = vector<Type>((*it).second->numbers_at_age);
+      ssb(pop_idx) = vector<Type>((*it).second->spawning_biomass);
+      rec_dev(pop_idx) =
+          vector<Type>((*it).second->recruitment->recruit_deviations);
+      recruitment(pop_idx) = vector<Type>((*it).second->expected_recruitment);
+      biomass(pop_idx) = vector<Type>((*it).second->biomass);
+      M(pop_idx) = vector<Type>((*it).second->M);
+#endif
       pop_idx += 1;
-
     }
 
-    //initiate fleet index for structuring report out objects
+    // initiate fleet index for structuring report out objects
     int fleet_idx = 0;
     for (jt = this->fims_information->fleets.begin();
          jt != this->fims_information->fleets.end(); ++jt) {
-      #ifdef TMB_MODEL
-         exp_index(fleet_idx) = vector<Type>((*jt).second->expected_index);
-         exp_catch(fleet_idx) = vector<Type>((*jt).second->expected_catch);
-         F_mort(fleet_idx) = vector<Type>((*jt).second->Fmort);
-         cnaa(fleet_idx) = vector<Type>((*jt).second->catch_numbers_at_age);
-         cwaa(fleet_idx) = vector<Type>((*jt).second->catch_weight_at_age);
-      #endif
+#ifdef TMB_MODEL
+      exp_index(fleet_idx) = vector<Type>((*jt).second->expected_index);
+      exp_catch(fleet_idx) = vector<Type>((*jt).second->expected_catch);
+      F_mort(fleet_idx) = vector<Type>((*jt).second->Fmort);
+      cnaa(fleet_idx) = vector<Type>((*jt).second->catch_numbers_at_age);
+      cwaa(fleet_idx) = vector<Type>((*jt).second->catch_weight_at_age);
+#endif
       fleet_idx += 1;
     }
 
     jnll = rec_nll + age_comp_nll + index_nll;
 
-
-    //Reporting
-    #ifdef TMB_MODEL
+// Reporting
+#ifdef TMB_MODEL
     REPORT_F(rec_nll, of);
     REPORT_F(age_comp_nll, of);
     REPORT_F(index_nll, of);
@@ -194,8 +192,7 @@ class Model {  // may need singleton
     ADREPORT_F(FMort, of);
     ADREPORT_F(ExpectedIndex, of);
     ADREPORT_F(CNAA, of);
-    #endif
-
+#endif
 
     return jnll;
   }

inst/include/interface/interface.hpp

@@ -32,17 +32,17 @@
 #define ADREPORT_F(name, F) F->reportvector.push(name, #name);
 
 template <typename Type>
-vector<Type> ADREPORTvector(vector< vector<Type> > x){
+vector<Type> ADREPORTvector(vector<vector<Type> > x) {
   int outer_dim = x.size();
   int dim = 0;
-  for(int i=0; i<outer_dim; i++){
+  for (int i = 0; i < outer_dim; i++) {
     dim += x(i).size();
   }
   vector<Type> res(dim);
   int idx = 0;
-  for(int i=0; i<outer_dim; i++){
+  for (int i = 0; i < outer_dim; i++) {
     int inner_dim = x(i).size();
-    for(int j=0; j<inner_dim; j++){
+    for (int j = 0; j < inner_dim; j++) {
       res(idx) = x(i)(j);
       idx += 1;
     }