407 updating log files (#499)

.github/workflows/run-googletest.yml

@@ -14,7 +14,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+      # Use windows-2019 instead of windows-latest to avoid using Mingw-w64 
+        os: [ubuntu-latest, macos-latest, windows-2019]
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 

inst/include/common/def.hpp

@@ -15,7 +15,21 @@
 #include <memory>
 #include <vector>
 
-std::ofstream FIMS_LOG("fims.log"); /**< 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 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 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 */
 
 #ifdef TMB_MODEL
 // simplify access to singletons

inst/include/common/fims_math.hpp

@@ -132,7 +132,7 @@ inline const Type logit(const Type &a, const Type &b, const Type &x) {
  */
 template <class Type>
 inline const Type inv_logit(const Type &a, const Type &b, const Type &logit_x) {
-  return a + (b - a) / (1 + fims_math::exp(-logit_x));
+  return a + (b - a) / (1.0 + fims_math::exp(-logit_x));
 }
 
 /**
@@ -194,9 +194,10 @@ const Type ad_fabs(const Type &x, Type C = 1e-5) {
  * @param C default = 1e-5
  * @return
  */
+
 template <typename Type>
 inline const Type ad_min(const Type &a, const Type &b, Type C = 1e-5) {
-  return (a + b - fims_math::ad_fabs(a - b, C)) * .5;
+  return (a + b - fims_math::ad_fabs(a - b, C)) * 0.5;
 }
 
 /**

inst/include/common/model.hpp

@@ -90,14 +90,18 @@ class Model {  // may need singleton
 
     // Loop over populations, evaluate, and sum up the recruitment likelihood
     // component
+
+
     typename fims_info::Information<Type>::population_iterator it;
+    MODEL_LOG << "Evaluating expected values and summing recruitment nlls for " << this->fims_information->populations.size() << " populations." << std::endl;
+
     for (it = this->fims_information->populations.begin();
          it != this->fims_information->populations.end(); ++it) {
-      //(*it).second points to each individual Population module
-      FIMS_LOG << "inside pop loop" << std::endl;
+      //(*it).second points to the Population module
+      MODEL_LOG << "Setting up pointer to population " << (*it).second->id << "." << std::endl;
       // Prepare recruitment
       (*it).second->recruitment->Prepare();
-      FIMS_LOG << "recruitment prepare works" << std::endl;
+      MODEL_LOG << "Recruitment for population successfully prepared" << std::endl;
 // link to TMB objective function
 #ifdef TMB_MODEL
       (*it).second->of = this->of;
@@ -106,21 +110,28 @@ class Model {  // may need singleton
       (*it).second->Evaluate();
       // Recrtuiment negative log-likelihood
       rec_nll += (*it).second->recruitment->evaluate_nll();
-      FIMS_LOG << "rec nll: " << rec_nll << std::endl;
+      MODEL_LOG << "Recruitment negative log-likelihood is: " << rec_nll << std::endl;
     }
+    MODEL_LOG << "All populations successfully evaluated." << std::endl;
 
     // Loop over fleets/surveys, and sum up age comp and index nlls
+
     typename fims_info::Information<Type>::fleet_iterator jt;
+    MODEL_LOG << "Evaluating expected values and summing nlls for " << this->fims_information->fleets.size() << " fleets." << std::endl;
+
     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;
 #endif
+      MODEL_LOG << "Setting up pointer to fleet " << (*jt).second->id << "." << std::endl; 
       age_comp_nll += (*jt).second->evaluate_age_comp_nll();
+      MODEL_LOG << "Sum of survey and age comp negative log-likelihood is: " << age_comp_nll
+               << std::endl;
       index_nll += (*jt).second->evaluate_index_nll();
     }
-
+    MODEL_LOG << "All fleets successfully evaluated." << std::endl;
     // Loop over populations and fleets/surveys and fill in reporting
 
     // initiate population index for structuring report out objects

inst/include/distributions/functors/tmb_distributions.hpp

@@ -83,7 +83,7 @@ struct Dlnorm : public DistributionsBase<Type> {
   /**
    * @brief Probability density function of the lognormal distribution.
    *
-   * \f[ \frac{1.0}{ xsd\sqrt{2\pi} }exp(-\frac{(ln(x) - mean)^{2}}{2sd^{2}})
+   * \f[ \frac{1.0}{ xsd\sqrt{2.0\pi} }exp(-\frac{(ln(x) - mean)^{2.0}}{2.0sd^{2.0}})
    * \f]
    *
    * @param do_log Boolean; if true, log densities are returned

inst/include/interface/rcpp/rcpp_interface.hpp

@@ -82,6 +82,154 @@ Rcpp::NumericVector get_random_parameters_vector() {
   return p;
 }
 
+
+/**
+ * Clears the contents of info log file.
+ */
+void clear_info_log() {
+    //First flush the output stream to make sure nothing
+    //is left in the stream memory bufffer.
+    INFO_LOG.flush();
+
+    //Next an new stream is opened and closed to
+    //overwrite the file.
+    std::ofstream CLEAR_LOG("logs/info.log");
+    CLEAR_LOG.close();
+
+    //Finally the stream output location is reset back to the start
+    //of the file.
+    INFO_LOG.seekp(0);
+}
+
+/**
+ * Clears the contents of fims log file.
+ */
+void clear_fims_log() {
+    FIMS_LOG.flush();
+    std::ofstream CLEAR_LOG("logs/fims.log");
+    CLEAR_LOG.close();
+    FIMS_LOG.seekp(0);
+}
+
+/**
+ * Clears the contents of data log file.
+ */
+void clear_data_log() {
+    DATA_LOG.flush();
+    std::ofstream CLEAR_LOG("logs/data.log");
+    CLEAR_LOG.close();
+    DATA_LOG.seekp(0);
+}
+
+/**
+ * Clears the contents of error log file.
+ */
+void clear_error_log() {
+    ERROR_LOG.flush();
+    std::ofstream CLEAR_LOG("logs/error.log");
+    CLEAR_LOG.close();
+    ERROR_LOG.seekp(0);
+}
+
+/**
+ * Clears the contents of model log file.
+ */
+void clear_model_log() {
+    MODEL_LOG.flush();
+    std::ofstream CLEAR_LOG("logs/model.log");
+    CLEAR_LOG.close();
+    MODEL_LOG.seekp(0);
+}
+
+/**
+ * Clears the contents of fleet log file.
+ */
+void clear_fleet_log() {
+    FLEET_LOG.flush();
+    std::ofstream CLEAR_LOG("logs/fleet.log");
+    CLEAR_LOG.close();
+    FLEET_LOG.seekp(0);
+}
+
+/**
+ * Clears the contents of population log file.
+ */
+void clear_population_log() {
+    POPULATION_LOG.flush();
+    std::ofstream CLEAR_LOG("logs/population.log");
+    CLEAR_LOG.close();
+    POPULATION_LOG.seekp(0);
+}
+
+/**
+ * Clears the contents of maturity log file.
+ */
+void clear_maturity_log() {
+    MATURITY_LOG.flush();
+    std::ofstream CLEAR_LOG("logs/maturity.log");
+    CLEAR_LOG.close();
+    MATURITY_LOG.seekp(0);
+}
+
+/**
+ * Clears the contents of recruitment log file.
+ */
+void clear_recruitment_log() {
+    RECRUITMENT_LOG.flush();
+    std::ofstream CLEAR_LOG("logs/recruitment.log");
+    CLEAR_LOG.close();
+    RECRUITMENT_LOG.seekp(0);
+}
+
+/**
+ * Clears the contents of growth log file.
+ */
+void clear_growth_log() {
+    GROWTH_LOG.flush();
+    std::ofstream CLEAR_LOG("logs/growth.log");
+    CLEAR_LOG.close();
+    GROWTH_LOG.seekp(0);
+}
+
+/**
+ * Clears the contents of selectivity log file.
+ */
+void clear_selectivity_log() {
+    SELECTIVITY_LOG.flush();
+    std::ofstream CLEAR_LOG("logs/selectivity.log");
+    CLEAR_LOG.close();
+    SELECTIVITY_LOG.seekp(0);
+}
+
+/**
+ * Clears the contents of debug log file.
+ */
+void clear_debug_log() {
+    DEBUG_LOG.flush();
+    std::ofstream CLEAR_LOG("logs/debug/debug.log");
+    CLEAR_LOG.close();
+    DEBUG_LOG.seekp(0);
+}
+
+
+/**
+ * Clears the contents of log files.
+ */
+void clear_logs() {
+    clear_fims_log(); 
+    clear_info_log();
+    clear_data_log();
+    clear_error_log();
+    clear_model_log();
+    clear_fleet_log();
+    clear_population_log();
+    clear_recruitment_log();
+    clear_growth_log();
+    clear_maturity_log();
+    clear_selectivity_log();
+    clear_debug_log();
+}
+
 template <typename Type>
 void clear_internal() {
   std::shared_ptr<fims_info::Information<Type>> d0 =
@@ -176,6 +324,19 @@ RCPP_MODULE(fims) {
   Rcpp::function("get_fixed", &get_fixed_parameters_vector);
   Rcpp::function("get_random", &get_random_parameters_vector);
   Rcpp::function("clear", clear);
+  Rcpp::function("clear_logs", clear_logs);
+  Rcpp::function("clear_fims_log", clear_fims_log);
+  Rcpp::function("clear_info_log", clear_info_log);
+  Rcpp::function("clear_error_log", clear_error_log);
+  Rcpp::function("clear_data_log", clear_data_log);
+  Rcpp::function("clear_population_log", clear_population_log);
+  Rcpp::function("clear_model_log", clear_model_log);
+  Rcpp::function("clear_recruitment_log", clear_recruitment_log);
+  Rcpp::function("clear_fleet_log", clear_fleet_log);
+  Rcpp::function("clear_growth_log", clear_growth_log);
+  Rcpp::function("clear_maturity_log", clear_maturity_log);
+  Rcpp::function("clear_selectivity_log", clear_selectivity_log);
+  Rcpp::function("clear_debug_log", clear_debug_log);
 
   Rcpp::class_<Parameter>("Parameter")
       .constructor()

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

@@ -106,7 +106,7 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
     for (int i = 0; i < deviations.size(); i++) {
       NLL.recruit_deviations[i] = deviations[i];
     }
-    FIMS_LOG << "Rec devs being passed to C++ are " << deviations << std::endl;
+    RECRUITMENT_LOG << "Rec devs being passed to C++ are " << deviations << std::endl;
     NLL.estimate_recruit_deviations = this->estimate_deviations;
     return NLL.evaluate_nll();
   }

inst/include/population_dynamics/fleet/fleet.hpp

@@ -140,9 +140,11 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
               0); /*!<model expected weight at age*/
     this->q = fims_math::exp(this->log_q);
     for (size_t year = 0; year < this->nyears; year++) {
-      FIMS_LOG << "input F mort " << this->log_Fmort[year] << std::endl;
-      FIMS_LOG << "input q " << this->log_q << std::endl;
+
+      FLEET_LOG << "input F mort " << this->log_Fmort[year] << std::endl;
+      FLEET_LOG << "input q " << this->log_q << std::endl;
       this->Fmort[year] = fims_math::exp(this->log_Fmort[year]);
+
     }
   }
 
@@ -153,10 +155,12 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
     size_t dims = this->observed_agecomp_data->get_imax() *
                   this->observed_agecomp_data->get_jmax();
     if (dims != this->catch_numbers_at_age.size()) {
-      fims::fims_log::get("fleet.log")
-          << "Error: observed age comp is of size " << dims
-          << " and expected is of size " << this->age_composition.size()
-          << std::endl;
+
+      ERROR_LOG << "Error: observed age comp is of size "
+                                 << dims << " and expected is of size "
+                                 << this->age_composition.size() << std::endl;
+                                 exit(1);
+
     } else {
       for (size_t y = 0; y < this->nyears; y++) {
         // EigenVector declares a vector type from the Eigen library, which is
@@ -179,8 +183,8 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
                               sum;  // probabilities for ages
 
           observed_acomp[a] = this->observed_agecomp_data->at(y, a);
-          fims::fims_log::get("fleet.log")
-              << " age " << a << " in year " << y
+
+          FLEET_LOG << " age " << a << " in year " << y
               << "has expected: " << expected_acomp[a]
               << "  and observed: " << observed_acomp[a] << std::endl;
         }
@@ -189,7 +193,7 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
         nll -= dmultinom.evaluate(true);
       }
     }
-
+    FLEET_LOG << "Age comp negative log-likelihood for fleet," << this->id << nll << std::endl;
 #endif
     return nll;
   }
@@ -204,14 +208,17 @@ struct Fleet : public fims_model_object::FIMSObject<Type> {
       dnorm.x = fims_math::log(this->observed_index_data->at(i));
       dnorm.mean = fims_math::log(this->expected_index[i]);
       nll -= dnorm.evaluate(true);
-      fims::fims_log::get("fleet.log")
-          << "observed likelihood component: " << i << " is "
+
+      FLEET_LOG
+          << "observed index data: " << i << " is "
           << this->observed_index_data->at(i)
           << " and expected is: " << this->expected_index[i] << std::endl;
     }
-    fims::fims_log::get("fleet.log")
+    FLEET_LOG
         << " log obs error is: " << this->log_obs_error << std::endl;
-    fims::fims_log::get("fleet.log") << " sd is: " << dnorm.sd << std::endl;
+    FLEET_LOG << " sd is: " << dnorm.sd << std::endl;
+    FLEET_LOG << " index nll: " << nll << std::endl;
+
 #endif
     return nll;
   }