Save function
Description
Section titled “Description”Saves the specified traits of a metaRangeSpecies object.
save_species(x, traits = NULL, prefix = NULL, path, overwrite = FALSE, ...)
Arguments
Section titled “Arguments”x
:<metaRangeSpecies>
metaRangeSpecies object.traits
:<character>
NULL
or a character vector specifying the trait to save. IfNULL
, all traits are saved.prefix
:<string>
prefix for the file names orNULL
.path
:<string>
path to the directory where the files are saved.overwrite
:<boolean>
overwrite existing files....
: additional arguments passed to terra::writeRaster.
Details
Section titled “Details”The generated file names are of the form
file.path(path, paste0(prefix, species_name, "_", trait_name, ".file_extension"))
.
If the trait is in a matrix or raster form, the file extension is .tif
. Otherwise it is .csv
.
The prefix is optional and mainly useful to add a time step to the file name, in case the trait
is saved multiple times during a simulation.
<invisible character>
the paths to the saved files.
Examples
Section titled “Examples”sim_env <- terra::sds(terra::rast(vals = 1, nrow = 2, ncol = 2))names(sim_env) <- "env_01"test_sim <- metaRangeSimulation$new(source_environment = sim_env)test_sim$add_species("species_01")test_sim$add_traits( "species_01", trait_01 = matrix(1, nrow = 2, ncol = 2), trait_02 = matrix(2, nrow = 2, ncol = 2))
file_prefix <- "This_could_be_a_time_step"directory_name <- tempdir()
res_path <- save_species( test_sim$species_01, traits = "trait_01", prefix = file_prefix, path = directory_name)# the following should be TRUE# but might fail due to floating point errors (that's why we round the values)identical( round(terra::as.matrix(terra::rast(res_path), wide = TRUE)), round(test_sim$species_01$traits[["trait_01"]]))
# test overwriteres_path2 <- save_species( test_sim$species_01, traits = "trait_01", prefix = file_prefix, path = directory_name, overwrite = TRUE)stopifnot(identical(res_path, res_path2))
# Saving all traitsres_path3 <- save_species( test_sim$species_01, prefix = basename(tempfile()), path = directory_name)# cleanupunlink(c(res_path, res_path3))stopifnot(all(!file.exists(res_path, res_path3)))