First saveRDS & readRDS methods (#172)

IsoriX/NAMESPACE

@@ -10,6 +10,8 @@ S3method(print,CALIBFIT)
 S3method(print,ISOFIND)
 S3method(print,ISOFIT)
 S3method(print,ISOSCAPE)
+S3method(readRDS,character)
+S3method(saveRDS,ISOSCAPE)
 S3method(summary,CALIBFIT)
 S3method(summary,ISOFIND)
 S3method(summary,ISOFIT)
@@ -45,9 +47,14 @@ export(prepcipitate)
 export(prepraster)
 export(prepsources)
 export(rast)
+export(readRDS)
+export(saveRDS)
 export(shift)
 export(values)
 export(xyplot)
+exportClasses(ISOSCAPE)
+exportMethods(readRDS)
+exportMethods(saveRDS)
 importFrom(grid,gpar)
 importFrom(grid,grid.text)
 importFrom(lattice,panel.points)

IsoriX/R/S4classes.R

@@ -0,0 +1,11 @@
+# This S4 definitions of classes are required for saveRDS to work and interact properly with the package terra.
+
+#' Class ISOSCAPE
+#'
+#' @slot isoscapes a SpatRaster storing the isoscapes. 
+#' @slot sp_points a list of spatial points. 
+#'
+#' @export
+#' @rdname ISOSCAPE-class
+#' 
+setClass("ISOSCAPE", slots = c(isoscapes = "SpatRaster", sp_points = "list"))

IsoriX/R/serialize.R

@@ -0,0 +1,172 @@
+#' Save and read objects produced by IsoriX into RDS files
+#' 
+#' Because files created with IsoriX contain [`terra::SpatRaster`] and
+#' [`terra::SpatVector`] objects, they cannot be saved using [`base::saveRDS`] or
+#' [`base::save`] functions. The reason is that objects created with [terra] point
+#' to data stored in memory which are not contained in the R objects themselves.
+#' Adapting the approach implemented in the [terra] package, we provide a
+#' wrapper for [`base::saveRDS`] and [`base::readRDS`] functions, which allows one
+#' to save and read objects produced with IsoriX by simply using `saveRDS()` and
+#' `readRDS()`.
+#' 
+#' [`base::saveRDS`] and [`base::readRDS`] are standard S3 functions. So in
+#' order to be able to have a specific behaviour for objects produced with
+#' IsoriX, we turned `saveRDS` and `readRDS` into S4 generics that dispatch both
+#' S3 and S4 methods (see [Methods_for_S3]). The S3 implementation is consistent
+#' with the rest of the package and presents all usual benefits associated with
+#' S3 methods (e.g. simple access to the code). The S4 implementation makes
+#' IsoriX methods compatible with the use of [`terra::saveRDS`] and
+#' [`terra::readRDS`].
+#'
+#' @param object R object to serialize.
+#' @param file a connection or the name of the file where the R object is saved to or read from.
+#' @param ascii a logical. If `TRUE` or `NA`, an ASCII representation is written; otherwise (default), a binary one is used. See the comments in the help for save.
+#' @param version the workspace format version to use. `NULL` specifies the current default version (3). The only other supported value is `2`, the default from R 1.4.0 to R 3.5.0.
+#' @param compress a logical specifying whether saving to a named file is to use "gzip" compression, or one of "gzip", "bzip2" or "xz" to indicate the type of compression to be used. Ignored if file is a connection.
+#' @param refhook	a hook function for handling reference objects.
+#' 
+#' @name serialize
+#' 
+#' @return 
+#' For `saveRDS`, `NULL` invisibly.
+#' 
+#' For `readRDS`, an R object.
+#'
+#' @examples
+#' if (getOption_IsoriX("example_maxtime") > 30) {
+#' 
+#' ## We prepare the data
+#' GNIPDataDEagg <- prepsources(data = GNIPDataDE)
+#' 
+#' ## We fit the models
+#' GermanFit <- isofit(data = GNIPDataDEagg,
+#'                     mean_model_fix = list(elev = TRUE, lat_abs = TRUE))
+#' 
+#' ## We build the isoscapes
+#' GermanScape <- isoscape(raster = ElevRasterDE, isofit = GermanFit)
+#' 
+#' ## Saving as RDS
+#' filename <- tempfile(fileext = ".rds") # or whatever names you want
+#' saveRDS(GermanScape, file = filename)
+#' 
+#' ## Reading RDS
+#' GermanScape2 <- readRDS(filename)
+#' GermanScape2
+#' 
+#' ## Saving data.frame object as RDS
+#' filename2 <- tempfile(fileext = ".rds") # or whatever names you want
+#' saveRDS(iris, file = filename2)
+#' 
+#' ## Reading RDS containing data.frame
+#' iris2 <- readRDS(filename2) 
+#' iris2
+#' 
+#' ## Saving terra object as RDS
+#' filename3 <- tempfile(fileext = ".rds") # or whatever names you want
+#' f <- system.file("ex/elev.tif", package="terra")
+#' r <- rast(f)
+#' saveRDS(r, file = filename3)
+#' 
+#' ## Reading RDS containing terra object
+#' r2 <- readRDS(filename3) 
+#' r2
+#' 
+#' }
+#'
+NULL
+
+
+# Defining S4 generics -----------------------------------------------------
+
+#' @describeIn serialize S4 generic function for `saveRDS`
+#' 
+#' @export
+#' 
+saveRDS <- function(object, file = "", ascii = FALSE, version = NULL, compress = TRUE, refhook = NULL) UseMethod("saveRDS")
+
+#' @describeIn serialize S4 generic function for `readRDS`
+#' 
+#' @export
+#' 
+readRDS <- function(file, refhook = NULL) UseMethod("readRDS")
+
+
+# Defining S3 methods -----------------------------------------------------
+
+#' @describeIn serialize S3 method to save an `ISOSCAPE` object into a RDS file
+#' 
+#' @method  saveRDS ISOSCAPE
+#' @exportS3Method saveRDS ISOSCAPE
+#' 
+saveRDS.ISOSCAPE <- function(object, file = "", ascii = FALSE, version = NULL, compress = TRUE, refhook = NULL) {
+  message("Saving RDS using IsoriX method")
+  if (!is.null(object$isoscapes)) {
+    if (inherits(object$isoscapes, "SpatRaster")) {
+      object$isoscapes <- terra::wrap(object$isoscapes)
+    } else {
+      stop("Saving situation not implemented yet. Please contact the package maintainer.")
+    }
+  }
+  if (!is.null(object$sp_points)) {
+    object$sp_points <- lapply(object$sp_points, \(x) {
+      if (inherits(x, "SpatVector")) {
+        terra::wrap(x)
+      } else {
+        stop("Saving situation not implemented yet. Please contact the package maintainer.")
+      }
+    })
+  }
+  # class(object) <- setdiff("ISOSCAPE", class(object)) 
+  base::saveRDS(object, file = file, ascii = ascii, version = version, compress = compress, refhook = refhook)
+}
+
+#' @describeIn serialize S3 method to read an object produced with IsoriX (or other) stored in a RDS file
+#' 
+#' @method  readRDS character
+#' @exportS3Method saveRDS ISOSCAPE
+#' @export
+#' 
+readRDS.character <- function(file, refhook = NULL) {
+  message("Reading RDS using IsoriX wrapper")
+  object <- base::readRDS(file = file, refhook = refhook)
+  if (inherits(object, "PackedSpatRaster") || inherits(object, "PackedSpatVector")) {
+    return(terra::unwrap(object))
+  }
+  if (!inherits(object, "ISOSCAPE")) {
+    return(object)
+  }
+  if (!is.null(object$isoscapes)) {
+    if (inherits(object$isoscapes, "PackedSpatRaster")) {
+      object$isoscapes <- terra::unwrap(object$isoscapes)
+    } else {
+      stop("Saving situation not implemented yet. Please contact the package maintainer.")
+    }
+  }
+  if (!is.null(object$sp_points)) {
+    object$sp_points <- lapply(object$sp_points, \(x) {
+      if (inherits(x, "PackedSpatVector")) {
+        terra::unwrap(x)
+      } else {
+        stop("Saving situation not implemented yet. Please contact the package maintainer.")
+      }
+    })
+  }
+  object
+}
+
+
+# Defining S4 methods -----------------------------------------------------
+
+#' @describeIn serialize S4 method to save an `ISOSCAPE` object into a RDS file
+#' 
+#' @method saveRDS ISOSCAPE
+#' @export
+#' 
+setMethod("saveRDS", signature(object = "ISOSCAPE"), saveRDS.ISOSCAPE)
+
+#' @describeIn serialize S4 method to read an object produced with IsoriX (or other) stored in a RDS file
+#' 
+#' @method readRDS character
+#' @export
+#' 
+setMethod("readRDS", signature(file = "character"), readRDS.character)