Renames and rescales output from python_focal_run() as needed to match
expected inputs for species distribution models (SDMs). Includes options to
mask by another raster and fill missing values with zero.
Usage
python_focal_finalize(
pathin,
landscape_name,
SDM,
scale,
pathout,
overwrite = FALSE,
mask = NULL,
cover = FALSE
)Arguments
- pathin, SDM, landscape_name, scale
Character strings defining the filepath (
pathin/SDM/landscape_name,scale) containing input rasters to be processed, such as those created from runningpython_focal_run()- pathout
Character string defining the filepath (
pathout/SDM/landscape_name) where output rasters should be written- overwrite
Logical; passed to
terra::writeRaster()- mask
Optional
SpatRasteror character string giving the filepath to a raster that should be used to mask the output, e.g. a study area boundary- cover
Logical; default is
FALSE. IfTRUE,maskmust not be NULL; See Details.
Details
Function expects source files to be in a directory structure created
by python_focal_run(), which is also used to inform the final processing
steps: pathin/SDM/landscape_name/scale. All .tif files in this source
directory will be read in, and optionally masked by the raster at mask.
If cover = TRUE, pixels in mask with a value of 1 will also be replaced
with a value of 0, and passed to terra::cover() to fill in missing values
in source data with zero.
If SDM = "riparian", pixel counts are converted to a proportion of the
total number of cells expected within the buffer distance represented by
scale, and the scale is appended to the predictor name in the format
"_50" or "_2000", as expected by the riparian SDMs.
If SDM = "waterbird_fall" or SDM = "waterbird_win", the scale is
appended to the predictor name in the format "_2k", "_5k", or "_10k", as
expected by the waterbird SDMs.
The final rasters are then written to the directory
pathout/SDM/landscape_name, which will be created if it doesn't yet exist.