feat(ParameterVector): Allows for time-varying p

* ParameterVector is established
* Logging
* model output with json
* C++ 17
* rebased to dev

Edits by @msupernaw

CMakeLists.txt

@@ -7,7 +7,7 @@ project(FIMS
 ) # CXX is the language name
 
 # GoogleTest requires at least C++11
-set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD 17)
 
 include(FetchContent)
 

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"),