feat(ParameterVector): vectors for the remaining parameters

* [1] added to tests so they pass
* Updated Namespace
* setMethods updated for R 1-based indexing
* exit(1) calls are commented out
* json output is updated for vectors creating better cohesion
* uses fims_math::dnorm, fims_math::dmultinom
* creates new methods in ParameterVector
* Initializes values to zero

NAMESPACE

@@ -3,6 +3,8 @@
 export(AgeComp)
 export(BevertonHoltRecruitment)
 export(CreateTMBModel)
+export(SetFIMSFunctions)
+export(Finalize)
 export(DoubleLogisticSelectivity)
 export(EWAAgrowth)
 export(FIMSFrame)
@@ -16,7 +18,9 @@ export(Population)
 export(TMBDlnormDistribution)
 export(TMBDmultinomDistribution)
 export(TMBDnormDistribution)
+export(ToJSON)
 export(clear)
+export(get_log)
 export(clear_logs)
 export(get_fixed)
 export(get_random)

R/zzz.R

@@ -4,15 +4,15 @@ Rcpp::loadModule(module = "fims", what = TRUE)
   library.dynam.unload("FIMS", libpath)
 }
 
-setMethod("[<-", signature(x = "Rcpp_ParameterVector", i = "numeric"),
-          function(x, i) {
-            (x$at(i))
-             return(x)
-          })
+
+setMethod("[<-", signature(x = "Rcpp_ParameterVector"), function(x, i, j, value) {
+  x$set(i - 1, value)  # R uses 1-based indexing, C++ uses 0-based indexing
+  x  # Return the modified object
+})
 
 setMethod("[", signature(x = "Rcpp_ParameterVector", i = "numeric"),
           function(x, i) {
-            return(x$at(i))
+            return(x$get(i-1))
           })
 
 # setMethod("lapply", signature(X = "Rcpp_ParameterVector", FUN = "sum"),

inst/include/common/def.hpp

@@ -1,6 +1,6 @@
 /** \file def.hpp
  */
-
+#define TMB_MODEL
 /*
  * File:   def.hpp
  *
@@ -50,31 +50,6 @@ std::ofstream DEBUG_LOG(
 
 namespace fims {
 
-/**
- * A static class for FIMS logging.
- */
-
-class fims_log {
- public:
-  static std::map<std::string, std::ofstream>
-      FIMS_LOGS; /**< Map Log of files */
-  /**
-   * Static getter for retrieving a specific log file.
-   */
-  static std::ofstream& get(const std::string& l) {
-    typename std::map<std::string, std::ofstream>::iterator it;
-    it = fims_log::FIMS_LOGS.find(l);
-    if (it == fims_log::FIMS_LOGS.end()) {
-      std::ofstream& of = fims_log::FIMS_LOGS[l];
-      of.open(l.c_str());
-    }
-
-    return fims_log::FIMS_LOGS[l];
-  }
-};
-
-std::map<std::string, std::ofstream> fims_log::FIMS_LOGS;
-
 }  // namespace fims
 
 #endif /* TRAITS_HPP */