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Final processing of focal stats for SDMs

Source: R/python_focal_finalize.R
python_focal_finalize.Rd

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 running python_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 SpatRaster or 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. If TRUE, mask must not be NULL; See Details.

Value

Nothing returned to R environment. Writes rasters to pathout for each land cover class.

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 bird 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.

If SDM = "tima", the scale is appended to the predictor name in the format "100" or "2000", as expected by the tidal marsh bird SDMs.

The final rasters are then written to the directory pathout/SDM/landscape_name, which will be created if it doesn't yet exist.

See also

python_focal_prep(), python_focal_run()

Examples

# See vignette