resolved issues causing warnings

inst/include/common/data_object.hpp

@@ -55,7 +55,7 @@ struct DataObject : public fims::FIMSObject<Type> {
   /**
    * Constructs a one-dimensional data object.
    */
-  DataObject(size_t imax) : imax(imax), dimensions(1) {
+  DataObject(size_t imax) : dimensions(1), imax(imax) {
     data.resize(imax);
 
     this->id = DataObject<Type>::id_g++;
@@ -64,7 +64,7 @@ struct DataObject : public fims::FIMSObject<Type> {
   /**
    * Constructs a two-dimensional data object.
    */
-  DataObject(size_t imax, size_t jmax) : imax(imax), jmax(jmax), dimensions(2) {
+  DataObject(size_t imax, size_t jmax) : dimensions(2), imax(imax), jmax(jmax) {
     data.resize(imax * jmax);
     this->id = DataObject<Type>::id_g++;
   }
@@ -73,7 +73,7 @@ struct DataObject : public fims::FIMSObject<Type> {
    *  Constructs a three-dimensional data object.
    */
   DataObject(size_t imax, size_t jmax, size_t kmax)
-      : imax(imax), jmax(jmax), kmax(kmax), dimensions(3) {
+      : dimensions(3), imax(imax), jmax(jmax), kmax(kmax) {
     data.resize(imax * jmax * kmax);
     this->id = DataObject<Type>::id_g++;
   }
@@ -82,7 +82,7 @@ struct DataObject : public fims::FIMSObject<Type> {
    * Constructs a four-dimensional data object.
    */
   DataObject(size_t imax, size_t jmax, size_t kmax, size_t lmax)
-      : imax(imax), jmax(jmax), kmax(kmax), lmax(lmax), dimensions(4) {
+      : dimensions(4), imax(imax), jmax(jmax), kmax(kmax), lmax(lmax) {
     data.resize(imax * jmax * kmax * lmax);
     this->id = DataObject<Type>::id_g++;
   }

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

@@ -125,20 +125,20 @@ class PopulationInterface : public PopulationInterfaceBase {
     b0->maturity_id = this->maturity_id;
     b0->log_M.resize(this->log_M.size());
     b0->log_init_naa.resize(this->log_init_naa.size());
-    for (size_t i = 0; i < log_M.size(); i++) {
+    for (int i = 0; i < log_M.size(); i++) {
       b0->log_M[i] = this->log_M[i];
       if (estimate_M) {
         d0->RegisterParameter(b0->log_M[i]);
       }
     }
 
-    for (size_t i = 0; i < log_init_naa.size(); i++) {
+    for (int i = 0; i < log_init_naa.size(); i++) {
       b0->log_init_naa[i] = this->log_init_naa[i];
       if (estimate_initNAA) {
         d0->RegisterParameter(b0->log_init_naa[i]);
       }
     }
-    for (size_t i = 0; i < ages.size(); i++) {
+    for (int i = 0; i < ages.size(); i++) {
       b0->ages[i] = this->ages[i];
     }
 
@@ -166,19 +166,19 @@ class PopulationInterface : public PopulationInterfaceBase {
 
     b1->log_M.resize(this->log_M.size());
     b1->log_init_naa.resize(this->log_init_naa.size());
-    for (size_t i = 0; i < log_M.size(); i++) {
+    for (int i = 0; i < log_M.size(); i++) {
       b1->log_M[i] = this->log_M[i];
       if (estimate_M) {
         d1->RegisterParameter(b1->log_M[i]);
       }
     }
-    for (size_t i = 0; i < log_init_naa.size(); i++) {
+    for (int i = 0; i < log_init_naa.size(); i++) {
       b1->log_init_naa[i] = this->log_init_naa[i];
       if (estimate_initNAA) {
         d1->RegisterParameter(b1->log_init_naa[i]);
       }
     }
-    for (size_t i = 0; i < ages.size(); i++) {
+    for (int i = 0; i < ages.size(); i++) {
       b1->ages[i] = this->ages[i];
     }
 
@@ -206,20 +206,20 @@ class PopulationInterface : public PopulationInterfaceBase {
     b2->maturity_id = this->maturity_id;
 
     b2->log_init_naa.resize(this->log_init_naa.size());
-    for (size_t i = 0; i < log_M.size(); i++) {
+    for (int i = 0; i < log_M.size(); i++) {
       b2->log_M[i] = this->log_M[i];
       if (estimate_M) {
         d2->RegisterParameter(b2->log_M[i]);
       }
     }
-    for (size_t i = 0; i < log_init_naa.size(); i++) {
+    for (int i = 0; i < log_init_naa.size(); i++) {
       b2->log_init_naa[i] = this->log_init_naa[i];
       if (estimate_initNAA) {
         d2->RegisterParameter(b2->log_init_naa[i]);
       }
     }
 
-    for (size_t i = 0; i < ages.size(); i++) {
+    for (int i = 0; i < ages.size(); i++) {
       b2->ages[i] = this->ages[i];
     }
 
@@ -247,20 +247,20 @@ class PopulationInterface : public PopulationInterfaceBase {
     b3->recruitment_id = this->recruitment_id;
     b3->maturity_id = this->maturity_id;
 
-    for (size_t i = 0; i < log_M.size(); i++) {
+    for (int i = 0; i < log_M.size(); i++) {
       b3->log_M[i] = this->log_M[i];
       if (estimate_M) {
         d3->RegisterParameter(b3->log_M[i]);
       }
     }
-    for (size_t i = 0; i < log_init_naa.size(); i++) {
+    for (int i = 0; i < log_init_naa.size(); i++) {
       b3->log_init_naa[i] = this->log_init_naa[i];
       if (estimate_initNAA) {
         d3->RegisterParameter(b3->log_init_naa[i]);
       }
     }
 
-    for (size_t i = 0; i < ages.size(); i++) {
+    for (int i = 0; i < ages.size(); i++) {
       b3->ages[i] = this->ages[i];
     }
 

inst/include/population_dynamics/population/population.hpp

@@ -665,8 +665,8 @@ struct Population : public FIMSObject<Type> {
       }
     }
     FIMS_LOG << "NAA\n";
-    for (int i = 0; i < nyears; i++) {
-      for (int j = 0; j < nages; j++) {
+    for (size_t i = 0; i < nyears; i++) {
+      for (size_t j = 0; j < nages; j++) {
         FIMS_LOG << numbers_at_age[i * nages + j] << "\t";
       }
       FIMS_LOG << "\n";
@@ -675,8 +675,8 @@ struct Population : public FIMSObject<Type> {
     FIMS_LOG << "CAA\n";
     for (size_t fleet_ = 0; fleet_ < this->nfleets; fleet_++) {
       FIMS_LOG << "Fleet " << fleet_ + 1 << "\n";
-      for (int i = 0; i < nyears; i++) {
-        for (int j = 0; j < nages; j++) {
+      for (size_t i = 0; i < nyears; i++) {
+        for (size_t j = 0; j < nages; j++) {
           FIMS_LOG << fleets[fleet_]->catch_numbers_at_age[i * nages + j]
                    << "\t";
         }

src/FIMS.cpp

@@ -28,7 +28,7 @@ Type objective_function<Type>::operator()() {
       fims::Information<Type>::GetInstance();
 
     //update the parameter values
-    for(int i =0; i < information->fixed_effects_parameters.size(); i++){
+    for(size_t i =0; i < information->fixed_effects_parameters.size(); i++){
         *information->fixed_effects_parameters[i] = p[i];
     }
     model -> of = this;