Skip to contents

Run focal statistics via Python

Source: R/python_focal_stats.R
python_focal_stats.Rd

Wrapper function to call a python script for calculating focal statistics on land cover predictors for species distribution models. On first call this function imports the arcpy module and Spatial Analyst extensions then sources the Python script "focal_stats.py".

Usage

python_focal_stats(
  SDM,
  pathin,
  dir,
  landscape_names,
  regex = NULL,
  python = NULL,
  overwrite = TRUE,
  mask = NULL
)

Arguments

pathin, SDM, landscape_names

Character strings defining the filepath (pathin/SDM/landscape_names) containing input rasters to be processed, such as those written from running python_focal_prep()

dir

Filepath for the directory where output rasters should be written (as dir/SDM/landscape_name/scale)

regex

Optional regular expression to process only a subset of the rasters in pathin/SDM/landscape_name

python

Optional filepath to the preferred version of arcpy, passed to reticulate::use_python. See details.

overwrite

logical; allow Python to overwrite existing output?

mask

currently experimental

Value

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

Details

This function is designed to be called after running python_focal_prep(), and writing the resulting rasters representing land cover predictors to pathin/SDM/landscape_names. For each raster in these directories, this function calculates focal statistics required for each species distribution model, on the appropriate spatial scales and with the required summary statistics. The regex argument provides options for processing only a subset of the rasters in the directory. If overwrite=TRUE (the default), previously-created focal statistics will be overwritten. If mask provides a filepath to a raster, the results will be masked by this file before writing to file.

These calculations can be very slow, depending on the size and resolution of the rasters, and relies on the availability of arcpy and Spatial Analyst extensions for faster processing. An attempt will be made to load these the first time this function is called in each session, and by default will look here: C:/Program Files/ArcGIS/Pro/bin/Python/envs/arcgispro-py3/python.exe; use the python argument to specify a different pathway.

See also

python_focal_prep(), fit_SDM()

Examples

# See vignette