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RangeShiftR/DESCRIPTION

@@ -19,6 +19,8 @@ Imports:
     Rcpp (>= 1.0.0),
     Rdpack (>= 0.7),
     methods,
+    raster
+Suggests:
     rmarkdown,
     terra
 RdMacros: Rdpack

RangeShiftR/NAMESPACE

@@ -28,4 +28,5 @@ export(readRange)
 export(validateRSparams)
 importFrom(Rcpp,sourceCpp)
 importFrom(Rdpack,reprompt)
+importFrom(methods,new)
 useDynLib(RangeShiftR)

RangeShiftR/R/RSsim.R

@@ -130,6 +130,6 @@ RSsim <- function(batchnum = 1L,
     if (!is.null(args$gene))  s <- s + gene
     if (!is.null(args$init))  s <- s + init
     # check validity
-    if(validObject(s)) return(s)
+    if(methods::validObject(s)) return(s)
     else return(NULL)
 }

RangeShiftR/R/RangeShiftR.R

@@ -92,5 +92,5 @@ RangeShiftR_license <- function ()
 #' @export
 RangeShiftR_citation <- function ()
 {
-    citation(package = "RangeShiftR", lib.loc = NULL, auto = NULL)
+    utils::citation(package = "RangeShiftR", lib.loc = NULL, auto = NULL)
 }

RangeShiftR/R/Rfunctions.R

@@ -32,13 +32,13 @@
 #----------------------
 
 #for Integer and Numerical so that 'Integer'-slots can also accept 'Numerical' input
-setClassUnion("integer_OR_numeric", c("integer", "numeric"))
+methods::setClassUnion("integer_OR_numeric", c("integer", "numeric"))
 
 #for Matrix and Numerical so that 'Matrix'-slots can also accept 'Numerical' input when 1x1-Matrix is expected
-setClassUnion("matrix_OR_numeric", c("matrix", "numeric"))
+methods::setClassUnion("matrix_OR_numeric", c("matrix", "numeric"))
 
 #for cost layer to accept habitat codes or raster map file
-setClassUnion("numeric_OR_character", c("numeric", "character"))
+methods::setClassUnion("numeric_OR_character", c("numeric", "character"))
 
 
 #-- define error and warning messages
@@ -59,4 +59,4 @@ densdep <- function(x, A0 = 1.0, alpha = 1.0, beta = 0.0) {
 #' Validate a given RS parameter object
 #'
 #' @export
-validateRSparams <- function(x){validObject(x)}
+validateRSparams <- function(x){methods::validObject(x)}

RangeShiftR/R/RunRS.R

@@ -43,7 +43,7 @@ RunRS <- function(RSparams, dirpath = getwd()){
             stop("Parameter object must be of class RSparams")
         }
         else {
-            validObject(RSparams)
+            methods::validObject(RSparams)
         }
     }
     if (is.null(dirpath)) {

RangeShiftR/R/addition.R

@@ -31,13 +31,13 @@
 setGeneric("+")
 
 setMethod("+", signature(e1 = "RSparams", e2 = "SimulationParams"), function(e1, e2) {
-    validObject(e2)
+    methods::validObject(e2)
     e1@simul <- e2
     return(e1)}
 )
 
 setMethod("+", signature(e1 = "RSparams", e2 = "LandParams"), function(e1, e2) {
-    validObject(e2)
+    methods::validObject(e2)
     if (class(e2)[1] == "ImportedLandscape") {
         if (any(e2@PatchFile=="NULL")) {
             e1@control@patchmodel = FALSE
@@ -76,7 +76,7 @@ setMethod("+", signature(e1 = "RSparams", e2 = "LandParams"), function(e1, e2) {
 )
 
 setMethod("+", signature(e1 = "RSparams", e2 = "DemogParams"), function(e1, e2) {
-    validObject(e2)
+    methods::validObject(e2)
     e1@control@reproductn = e2@ReproductionType
     if (class(e2@StageStruct)[1] == "StagesParams") {
         e1@control@repseasons = e2@StageStruct@RepSeasons
@@ -101,15 +101,15 @@ setMethod("+", signature(e1 = "RSparams", e2 = "DemogParams"), function(e1, e2)
 )
 
 setMethod("+", signature(e1 = "DemogParams", e2 = "StagesParams"), function(e1, e2) {
-    validObject(e2)
+    methods::validObject(e2)
     e1@StageStruct <- e2
     e1@Rmax <- -9L
     e1@bc <- -9L
     return(e1)}
 )
 
 setMethod("+", signature(e1 = "RSparams", e2 = "DispersalParams"), function(e1, e2) {
-    validObject(e2)
+    methods::validObject(e2)
     if (class(e2@Transfer)[1] == "DispersalKernel") {
         e1@control@transfer = 0
     }
@@ -131,34 +131,34 @@ setMethod("+", signature(e1 = "RSparams", e2 = "DispersalParams"), function(e1,
 )
 
 setMethod("+", signature(e1 = "DispersalParams", e2 = "EmigrationParams"), function(e1, e2) {
-    validObject(e2)
+    methods::validObject(e2)
     e1@Emigration <- e2
-    validObject(e1)
+    methods::validObject(e1)
     return(e1)}
 )
 
 setMethod("+", signature(e1 = "DispersalParams", e2 = "TransferParams"), function(e1, e2) {
-    validObject(e2)
+    methods::validObject(e2)
     e1@Transfer <- e2
-    validObject(e1)
+    methods::validObject(e1)
     return(e1)}
 )
 
 setMethod("+", signature(e1 = "DispersalParams", e2 = "SettlementParams"), function(e1, e2) {
-    validObject(e2)
+    methods::validObject(e2)
     e1@Settlement <- e2
-    validObject(e1)
+    methods::validObject(e1)
     return(e1)}
 )
 
 setMethod("+", signature(e1 = "RSparams", e2 = "GeneticsParams"), function(e1, e2) {
-    validObject(e2)
+    methods::validObject(e2)
     e1@gene <- e2
     return(e1)}
 )
 
 setMethod("+", signature(e1 = "RSparams", e2 = "InitialisationParams"), function(e1, e2) {
-    validObject(e2)
+    methods::validObject(e2)
     e1@init <- e2
     return(e1)}
 )

RangeShiftR/R/class_ControlParams.R

@@ -25,7 +25,7 @@
 
 # from RS 'CONTROL.txt' file
 
-ControlParams <- setClass("ControlParams", slots = c(
+ControlParams <- methods::setClass("ControlParams", slots = c(
                                    #nSimuls = "integer_OR_numeric",         # Not yet used by R version, in C++ version its read from parameterfile
                                    #nLandscapes = "integer_OR_numeric",     # Not yet used by R version, in C++ version its read from landfile
                                    batchnum = "integer_OR_numeric",         # only variable to set from RSsim(), optional