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Run focal statistics via Python

Source: R/python_focal_run.R
python_focal_run.Rd

Function to call python script for calculating focal statistics on landscape rasters via arcpy.

Usage

python_focal_run(
  pathin,
  landscape_name,
  SDM,
  regex = NULL,
  scale,
  fun = "SUM",
  pathout
)

Arguments

pathin, SDM, landscape_name

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

regex

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

scale

String representing the buffer size (in m) within which focal stats are calculated

fun

Function to summarize focal statistics: 'SUM' or 'MEAN'

pathout

Filepath for the directory where output rasters should be written

Value

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

Details

This function calls the focal_stats.py function to summarize cell values for the input raster within a buffer distance defined by scale. Summary functions may include 'SUM' or 'MEAN'. The default of fun = SUM' is intended to be called only after first running python_focal_prep(), which prepares rasters representing the presence/absence of individual land cover classes, as defined by each set of species distribution models, and allows 'SUM' to effectively count the number of pixels of each land cover class within a given distance. This function can also be used with fun = 'MEAN' to estimate the mean probability of open water for a given land cover class within a given distance (i.e. _pfld predictors for waterbird models). See vignette.

Important: This function requires the availability of arcpy and Spatial Analyst extensions. While these statistics can be entirely calculated in R, arcpy is much faster. See vignette for more details.

See also

python_focal_prep(), python_focal_finalize()

Examples

# See vignette