fix warnings

inst/include/common/information.hpp

@@ -272,7 +272,7 @@ class Information {
       INFO_LOG << "Checking for available density components data objects."
           << std::endl;
       //set data objects
-      if(d->input_type == "data" & d->observed_data_id_m != -999){
+      if((d->input_type == "data") & (d->observed_data_id_m != -999)){
         uint32_t observed_data_id = static_cast<uint32_t>(d->observed_data_id_m);
         data_iterator it = this->data_objects.find(observed_data_id);
         INFO_LOG << "Input data id = " << observed_data_id << "." << std::endl;

inst/include/distributions/functors/density_components_base.hpp

@@ -35,7 +35,7 @@ struct DensityComponentBase : public fims_model_object::FIMSObject<Type> {
   // Assigning each one its own ID is a way to keep track of
   // all the instances of the DensityComponentBase class.
  static uint32_t id_g; /**< global unique identifier for distribution modules */
- size_t observed_data_id_m = -999; /*!< id of observed data component*/
+ uint32_t observed_data_id_m = -999; /*!< id of observed data component*/
  std::shared_ptr<fims_data_object::DataObject<Type>>
       observed_values; /**< observed data*/
  fims::Vector<Type > x; /**< input value of distribution function for proirs or random effects*/

inst/include/distributions/functors/multinomial_lpmf.hpp

@@ -73,20 +73,16 @@ namespace fims_distributions
 
                     #ifdef TMB_MODEL
                     for (size_t j = 0; j < dims[1]; j++){
-                        if (this->observed_values->at(i, j) !=
+                        if (this->observed_values->at(i, j) ==
                                 this->observed_values->na_value) {
-                            size_t idx = (i * dims[1]) + j;
-                        } else {
                             containsNA = true;
                             break;
                         }
-                    }
                     if(!containsNA){
-                        for (size_t j = 0; j < dims[1]; j++){
-                            size_t idx = (i * dims[1]) + j;
-                            x_vector[j] = this->observed_values->at(i, j);
-                            prob_vector[j] = this->expected_values[idx];
-                        }
+                        size_t idx = (i * dims[1]) + j;
+                        x_vector[j] = this->observed_values->at(i, j);
+                        prob_vector[j] = this->expected_values[idx];
+
                     }
 
                     this->lpdf_vec[i] = dmultinom((vector<Type>)x_vector, (vector<Type>)prob_vector, true);

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

@@ -108,7 +108,7 @@ class FleetInterface : public FleetInterfaceBase {
     }
 
     fleet->log_Fmort.resize(this->log_Fmort.size());
-    for (int i = 0; i < log_Fmort.size(); i++) {
+    for (size_t i = 0; i < log_Fmort.size(); i++) {
       fleet->log_Fmort[i] = this->log_Fmort[i].value_m;
 
       if (this->log_Fmort[i].estimated_m) {

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

@@ -212,7 +212,7 @@ class ParameterVector{
      * @param value The value to be assigned
      */
     void fill_min(double value){
-        for(size_t i = 0; i < this->storage_m.size(); i++){
+        for(int i = 0; i < this->storage_m.size(); i++){
             Parameter p = Rcpp::as<Parameter>(this->storage_m[i]);
             p.min_m = value;
             this->storage_m[i] = Rcpp::wrap(p);
@@ -225,7 +225,7 @@ class ParameterVector{
      * @param value The value to be assigned
      */
     void fill_max(double value){
-        for(size_t i = 0; i < this->storage_m.size(); i++){
+        for(int i = 0; i < this->storage_m.size(); i++){
             Parameter p = Rcpp::as<Parameter>(this->storage_m[i]);
             p.max_m = value;
             this->storage_m[i] = Rcpp::wrap(p);

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

@@ -130,15 +130,15 @@ class PopulationInterface : public PopulationInterfaceBase {
     population->maturity_id = this->maturity_id;
     population->log_M.resize(this->log_M.size());
     population->log_init_naa.resize(this->log_init_naa.size());
-    for (int i = 0; i < log_M.size(); i++) {
+    for (size_t i = 0; i < log_M.size(); i++) {
       population->log_M[i] = this->log_M[i].value_m;
       if (this->log_M[i].estimated_m) {
         info->RegisterParameter(population->log_M[i]);
       }
     }
     info->variable_map[this->log_M.id_m] = &(population)->log_M;
 
-    for (int i = 0; i < log_init_naa.size(); i++) {
+    for (size_t i = 0; i < log_init_naa.size(); i++) {
       population->log_init_naa[i] = this->log_init_naa[i].value_m;
       if (this->log_init_naa[i].estimated_m) {
         info->RegisterParameter(population->log_init_naa[i]);

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

@@ -113,7 +113,7 @@ class DnormDistributionsInterface : public DistributionsInterfaceBase {
   virtual void set_distribution_links(std::string input_type, Rcpp::IntegerVector ids){
     this->input_type_m = input_type;
     this->key_m.resize(ids.size());
-    for(size_t i; i<ids.size(); i++){
+    for(int i; i<ids.size(); i++){
       this->key_m[i] = ids[i];
     }
   }
@@ -130,13 +130,13 @@ class DnormDistributionsInterface : public DistributionsInterfaceBase {
     dnorm.x.resize(this->x.size());
     dnorm.expected_values.resize(this->expected_values.size());
     dnorm.log_sd.resize(this->log_sd.size());
-    for(int i=0; i<x.size(); i++){
+    for(size_t i=0; i<x.size(); i++){
       dnorm.x[i] = this->x[i].value_m;
     }
-    for(int i=0; i<expected_values.size(); i++){
+    for(size_t i=0; i<expected_values.size(); i++){
       dnorm.expected_values[i] = this->expected_values[i].value_m;
     }
-    for(int i=0; i<log_sd.size(); i++){
+    for(size_t i=0; i<log_sd.size(); i++){
       dnorm.log_sd[i] = this->log_sd[i].value_m;
     }
     return dnorm.evaluate();
@@ -161,16 +161,16 @@ class DnormDistributionsInterface : public DistributionsInterfaceBase {
 
     distribution->id = this->id_m;
     distribution->x.resize(this->x.size());
-    for(int i=0; i<this->x.size(); i++){
+    for(size_t i=0; i<this->x.size(); i++){
       distribution->x[i] = this->x[i].value_m;
     }
     // set relative info
     distribution->expected_values.resize(this->expected_values.size());
-    for(int i=0; i<this->expected_values.size(); i++){
+    for(size_t i=0; i<this->expected_values.size(); i++){
       distribution->expected_values[i] = this->expected_values[i].value_m;
     }
     distribution->log_sd.resize(this->log_sd.size());
-    for(int i=0; i<this->log_sd.size(); i++){
+    for(size_t i=0; i<this->log_sd.size(); i++){
       distribution->log_sd[i] = this->log_sd[i].value_m;
     }
 
@@ -235,7 +235,7 @@ class DlnormDistributionsInterface : public DistributionsInterfaceBase {
   virtual void set_distribution_links(std::string input_type, Rcpp::IntegerVector ids){
     this->input_type_m = input_type;
     this->key_m.resize(ids.size());
-    for(size_t i; i<ids.size(); i++){
+    for(int i; i<ids.size(); i++){
       this->key_m[i] = ids[i];
     }
   }   
@@ -253,13 +253,13 @@ class DlnormDistributionsInterface : public DistributionsInterfaceBase {
     dlnorm.x.resize(this->x.size());
     dlnorm.expected_values.resize(this->expected_values.size());
     dlnorm.log_logsd.resize(this->log_logsd.size());
-    for(int i=0; i<x.size(); i++){
+    for(size_t i=0; i<x.size(); i++){
       dlnorm.x[i] = this->x[i].value_m;
     }
-    for(int i=0; i<expected_values.size(); i++){
+    for(size_t i=0; i<expected_values.size(); i++){
       dlnorm.expected_values[i] = this->expected_values[i].value_m;
     }
-    for(int i=0; i<log_logsd.size(); i++){
+    for(size_t i=0; i<log_logsd.size(); i++){
       dlnorm.log_logsd[i] = this->log_logsd[i].value_m;
     }
     return dlnorm.evaluate();
@@ -281,16 +281,16 @@ class DlnormDistributionsInterface : public DistributionsInterfaceBase {
         interface_observed_data_id_m;
     distribution->input_type = this->input_type;
     distribution->x.resize(this->x.size());
-    for(int i=0; i<this->x.size(); i++){
+    for(size_t i=0; i<this->x.size(); i++){
       distribution->x[i] = this->x[i].value_m;
     }
     // set relative info
     distribution->expected_values.resize(this->expected_values.size());
-    for(int i=0; i<this->expected_values.size(); i++){
+    for(size_t i=0; i<this->expected_values.size(); i++){
       distribution->expected_values[i] = this->expected_values[i].value_m;
     }
     distribution->log_logsd.resize(this->log_logsd.size());
-    for(int i=0; i<this->log_logsd.size(); i++){
+    for(size_t i=0; i<this->log_logsd.size(); i++){
       distribution->log_logsd[i] = this->log_logsd[i].value_m;
     }
 
@@ -354,7 +354,7 @@ class DmultinomDistributionsInterface : public DistributionsInterfaceBase {
   virtual void set_distribution_links(std::string input_type, Rcpp::IntegerVector ids){
     this->input_type_m = input_type;
     this->key_m.resize(ids.size());
-    for(size_t i; i<ids.size(); i++){
+    for(int i; i<ids.size(); i++){
       this->key_m[i] = ids[i];
     }
   }
@@ -371,10 +371,10 @@ class DmultinomDistributionsInterface : public DistributionsInterfaceBase {
     // Declare TMBVector in this scope
     dmultinom.x.resize(this->x.size());
     dmultinom.expected_values.resize(this->expected_values.size());
-    for(int i=0; i<x.size(); i++){
+    for(size_t i=0; i<x.size(); i++){
       dmultinom.x[i] = this->x[i].value_m;
     }
-    for(int i=0; i<expected_values.size(); i++){
+    for(size_t i=0; i<expected_values.size(); i++){
       dmultinom.expected_values[i] = this->expected_values[i].value_m;
     }
     dmultinom.dims.resize(2);
@@ -397,12 +397,12 @@ class DmultinomDistributionsInterface : public DistributionsInterfaceBase {
     distribution->observed_data_id_m =
         interface_observed_data_id_m;
     distribution->x.resize(this->x.size());
-    for(int i=0; i<this->x.size(); i++){
+    for(size_t i=0; i<this->x.size(); i++){
       distribution->x[i] = this->x[i].value_m;
     }
     // set relative info
     distribution->expected_values.resize(this->expected_values.size());
-    for(int i=0; i<this->expected_values.size(); i++){
+    for(size_t i=0; i<this->expected_values.size(); i++){
       distribution->expected_values[i] = this->expected_values[i].value_m;
     }
     distribution->dims.resize(2);