refactor: load fims modules

NAMESPACE

@@ -3,7 +3,10 @@
 export("%>%")
 export(FIMSFrame)
 export(FIMSFrameAge)
+export(Population)
+export(clear)
 export(create_fims_rcpp_interface)
+export(get_fixed)
 export(m_agecomp)
 export(m_index)
 export(m_landings)

R/FIMS-package.R

@@ -6,5 +6,8 @@
 #' @import methods
 #' @importFrom ggplot2 .data
 #' @importFrom usethis use_template ui_stop
+#' @export Population
+#' @export clear
+#' @export get_fixed
 ## usethis namespace: end
 NULL

R/RcppExports.R

@@ -0,0 +1,7 @@
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+clear <- function() {
+    invisible(.Call(`_FIMS_clear`))
+}
+

inst/include/interface/init.hpp

@@ -38,10 +38,12 @@ SEXP _rcpp_module_boot_fims();
  *Callback definition to load the FIMS module.
  *
  */
+/*
 static const R_CallMethodDef CallEntries[] = {
     TMB_CALLDEFS,
     {"_rcpp_module_boot_fims", (DL_FUNC)&_rcpp_module_boot_fims, 0},
     {NULL, NULL, 0}};
+*/
 
 /**
  *

src/FIMS.cpp

@@ -1,9 +1,9 @@
 
 #include <cmath>
 
-#include "../inst/include/interface/rcpp/rcpp_interface.hpp"
+#include "rcpp_interface.hpp"
 #include "../inst/include/interface/interface.hpp"
-#include "../inst/include/interface/init.hpp"
+//#include "../inst/include/interface/init.hpp"
 #include "../inst/include/common/model.hpp"
 
 /// @cond

src/RcppExports.cpp

@@ -0,0 +1,35 @@
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#include <RcppEigen.h>
+#include <Rcpp.h>
+
+using namespace Rcpp;
+
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
+// clear
+void clear();
+RcppExport SEXP _FIMS_clear() {
+BEGIN_RCPP
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    clear();
+    return R_NilValue;
+END_RCPP
+}
+
+RcppExport SEXP _rcpp_module_boot_fims();
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_FIMS_clear", (DL_FUNC) &_FIMS_clear, 0},
+    {"_rcpp_module_boot_fims", (DL_FUNC) &_rcpp_module_boot_fims, 0},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_FIMS(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}

inst/include/interface/rcpp/rcpp_interface.hpp → src/rcpp_interface.hpp

@@ -11,17 +11,17 @@
 #ifndef FIMS_INTERFACE_RCPP_INTERFACE_HPP
 #define FIMS_INTERFACE_RCPP_INTERFACE_HPP
 
-#include "rcpp_objects/rcpp_data.hpp"
-#include "rcpp_objects/rcpp_fleet.hpp"
-#include "rcpp_objects/rcpp_growth.hpp"
-#include "rcpp_objects/rcpp_maturity.hpp"
-#include "rcpp_objects/rcpp_natural_mortality.hpp"
+#include "../inst/include/interface/rcpp/rcpp_objects/rcpp_data.hpp"
+#include "../inst/include/interface/rcpp/rcpp_objects/rcpp_fleet.hpp"
+#include "../inst/include/interface/rcpp/rcpp_objects/rcpp_growth.hpp"
+#include "../inst/include/interface/rcpp/rcpp_objects/rcpp_maturity.hpp"
+#include "../inst/include/interface/rcpp/rcpp_objects/rcpp_natural_mortality.hpp"
 //#include "rcpp_objects/rcpp_nll.hpp"
-#include "../../common/model.hpp"
-#include "rcpp_objects/rcpp_population.hpp"
-#include "rcpp_objects/rcpp_recruitment.hpp"
-#include "rcpp_objects/rcpp_selectivity.hpp"
-#include "rcpp_objects/rcpp_tmb_distribution.hpp"
+#include "../inst/include/common/model.hpp"
+#include "../inst/include/interface/rcpp/rcpp_objects/rcpp_population.hpp"
+#include "../inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp"
+#include "../inst/include/interface/rcpp/rcpp_objects/rcpp_selectivity.hpp"
+#include "../inst/include/interface/rcpp/rcpp_objects/rcpp_tmb_distribution.hpp"
 /**
  * @brief Create the TMB model object and add interface objects to it.
  */
@@ -235,9 +235,10 @@ void clear_internal() {
   d0->fixed_effects_parameters.clear();
   d0->random_effects_parameters.clear();
 }
-/**
- * Clears the vector of independent variables.
+/*
+ * Clears the vector of independent variables
  */
+// [[Rcpp::export]]
 void clear() {
   // rcpp_interface_base.hpp
   FIMSRcppInterfaceBase::fims_interface_objects.clear();
@@ -321,7 +322,7 @@ RCPP_MODULE(fims) {
   Rcpp::function("CreateTMBModel", &CreateTMBModel);
   Rcpp::function("get_fixed", &get_fixed_parameters_vector);
   Rcpp::function("get_random", &get_random_parameters_vector);
-  Rcpp::function("clear", clear);
+  //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);

vignettes/fims-path-maturity.Rmd

@@ -89,7 +89,7 @@ Also restarting or closing out your R session will free up memory.
 ## The Rcpp Interface
 
 The fields specific to the maturity module that are accessible from R are defined in the 
-[rcpp_interface.hpp](https://github.com/NOAA-FIMS/FIMS/blob/main/inst/include/interface/rcpp/rcpp_interface.hpp) file in the directory [inst/include/interface/rcpp](https://github.com/NOAA-FIMS/FIMS/tree/main/inst/include/interface/rcpp):
+[rcpp_interface.hpp](https://github.com/NOAA-FIMS/FIMS/blob/main/src/rcpp_interface.hpp) file in the directory [inst/include/interface/rcpp](https://github.com/NOAA-FIMS/FIMS/tree/main/inst/include/interface/rcpp):
 
 ```{Rcpp, class.source = "rcppchunk", eval = FALSE}
 Rcpp::class_<LogisticMaturityInterface>("LogisticMaturity")
@@ -157,7 +157,7 @@ class Parameter {
   }
 ```
 The fields from the `Parameter` class that are accessible from R are defined in the 
-[rcpp_interface.hpp](https://github.com/NOAA-FIMS/FIMS/blob/main/inst/include/interface/rcpp/rcpp_interface.hpp) file in the directory [inst/include/interface/rcpp](https://github.com/NOAA-FIMS/FIMS/tree/main/inst/include/interface/rcpp):
+[rcpp_interface.hpp](https://github.com/NOAA-FIMS/FIMS/blob/main/src/rcpp_interface.hpp) file in the directory [inst/include/interface/rcpp](https://github.com/NOAA-FIMS/FIMS/tree/main/inst/include/interface/rcpp):
 
 ```{Rcpp, class.source = "rcppchunk", eval = FALSE}
  Rcpp::class_<Parameter>("Parameter")