serialize: Save and read objects produced by IsoriX using RDS files

In IsoriX: Isoscape Computation and Inference of Spatial Origins using Mixed Models

Save and read objects produced by IsoriX using RDS files

Description

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().

Usage

saveRDS_IsoriX(
  object,
  file = "",
  ascii = FALSE,
  version = NULL,
  compress = TRUE,
  refhook = NULL
)

## S3 method for class 'ISOSCAPE'
saveRDS(
  object,
  file = "",
  ascii = FALSE,
  version = NULL,
  compress = TRUE,
  refhook = NULL
)

## S3 method for class 'CALIBFIT'
saveRDS(
  object,
  file = "",
  ascii = FALSE,
  version = NULL,
  compress = TRUE,
  refhook = NULL
)

## S3 method for class 'ISOFIND'
saveRDS(
  object,
  file = "",
  ascii = FALSE,
  version = NULL,
  compress = TRUE,
  refhook = NULL
)

## S3 method for class 'character'
readRDS(file, refhook = NULL)

## S4 method for signature 'ISOSCAPE'
saveRDS(
  object,
  file = "",
  ascii = FALSE,
  version = NULL,
  compress = TRUE,
  refhook = NULL
)

## S4 method for signature 'CALIBFIT'
saveRDS(
  object,
  file = "",
  ascii = FALSE,
  version = NULL,
  compress = TRUE,
  refhook = NULL
)

## S4 method for signature 'ISOFIND'
saveRDS(
  object,
  file = "",
  ascii = FALSE,
  version = NULL,
  compress = TRUE,
  refhook = NULL
)

## S4 method for signature 'character'
readRDS(file, refhook = NULL)

Arguments

object	(definition copied from base::readRDS:) R object to serialize.
file	(definition copied from base::readRDS:) a connection or the name of the file where the R object is saved to or read from.
ascii	(definition copied from base::readRDS:) 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 base::save.
version	(definition copied from base::readRDS:) 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.
compress	(definition copied from base::readRDS:) 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.
refhook	(definition copied from base::readRDS:) a hook function for handling reference objects.

Details

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 imported saveRDS and readRDS S4 generics from terra to dispatch both S3 and S4 IsoriX-specific 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.

Value

For saveRDS, NULL invisibly.

For readRDS, an R object.

Functions

• saveRDS_IsoriX(): S3 function to save IsoriX objects into a RDS file

• saveRDS(ISOSCAPE): S3 method to save an ISOSCAPE object into a RDS file

• saveRDS(CALIBFIT): S3 method to save a CALIBFIT object into a RDS file

• saveRDS(ISOFIND): S3 method to save an ISOFIND object into a RDS file

• readRDS(character): S3 method to read an object produced with IsoriX (or other) stored in a RDS file

• saveRDS(ISOSCAPE): S4 method to save an ISOSCAPE object into a RDS file

• saveRDS(CALIBFIT): S4 method to save an CALIBFIT object into a RDS file

• saveRDS(ISOFIND): S4 method to save an ISOFIND object into a RDS file

• readRDS(character): S4 method to read an object produced with IsoriX (or other) stored in a RDS file

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
}

IsoriX documentation built on Nov. 14, 2023, 5:09 p.m.