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Prepare landscape rasters for focal statistics via Python

Source: R/python_focal_prep.R
python_focal_prep.Rd

Prepare for running focal statistics on a landscape raster via Python, to generate inputs for use with species distribution models.

Usage

python_focal_prep(
  landscape,
  SDM,
  pathout,
  landscape_name,
  suffix = NULL,
  mask = NULL,
  pixel_value = NULL,
  overwrite = FALSE
)

Arguments

landscape

SpatRaster created by terra::rast()

SDM

The name of intended species distribution model, for which landscape will be reclassified: "riparian", "waterbird_fall", or "waterbird_win"

pathout, landscape_name

Character strings defining the filepath (pathout/SDM/landscape_name) where output rasters should be written

suffix

Character string; custom suffix appended to layer names (optional unless mask is not NULL)

mask

Optional SpatRaster; see Details

pixel_value

Numeric value to replace cell values with (optional); default NULL

overwrite

Logical; passed to terra::writeRaster(); default FALSE

Value

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

Details

Splits landscape raster into separate layers representing the presence (1) or absence (0) of each land cover class, then regroups and renames them into the land cover classes used in by the intended species distribution model (SDM), with an optional custom suffix appended to the layer name. Cell values representing land cover presence (1) can also optionally be replaced with a different pixel_value (e.g., the area of each pixel).

By providing a mask, this function can also optionally use the land cover presence layers as a mask to extract the values of another layer (e.g., surface water data). To distinguish these layers, suffix is required to have two values. See examples.

See also

python_focal_run(), python_focal_finalize()

Examples

#f <- system.file("ex/elev.tif", package="terra")
#r <- terra::rast(f) # add an example
#python_prep(landscape = r, SDM = 'riparian', pathout = 'example')

#try(python_prep(landscape = r, SDM = 'waterbird_win', pathout = 'example',
#pixel_value = 0.09, mask = system.file('ex/elev.tif', package = 'terra')))
## suffix is required if mask is not `NULL`

#python_prep(landscape = r, SDM = 'waterbird_win', pathout = 'example',
#pixel_value = 0.09, mask = system.file('ex/elev.tif', package = 'terra'),
#suffix = c('_area', '_elev'))