Filter out patches smaller than a specified area

Pre-process patch rasters prior to their use with MPG().

Usage

patchFilter(x, cells = NULL, area = NULL, ...)

# S4 method for RasterLayer
patchFilter(x, cells = NULL, area = NULL, ...)

Arguments

x: A binary raster (i.e. consisting of 0, 1, or NA cells), where cells =1 represent patches
cells: The minimum number of cells that constitute a patch. Default NULL. Only one of cells or area may be specified.
area: The minimum area that constitutes a patch (where area is calculated in the coordinate reference system of the raster by multiplying the count of cells in patch by the x and y resolution of a raster cell). Default NULL. Only one of cells or area may be specified.
...: Additional arguments passed to the clump() function in the raster package. For example directions = 4 may be used to be more conservative about which cells constitute a patch.

Value

A binary raster where all patches (i.e. clumped areas =1) are greater than the specified area.

Details

It examines a binary raster to identify all patches or clumps of cells with values =1, determines their area, and returns a binary raster where only patches of area greater than or equal to the specified amount are represented.

This is helpful when analyzing habitat connectivity models where patches represent a land cover or habitat type. For example, a raster may have patches of a certain habitat type of insufficient area to support the ecological process of interest. Another use case is remote sensing classification errors that have introduced artifacts. Filtering can help in both cases.

Author

Paul Galpern and Alex Chubaty

Examples

## Load raster landscape
tiny <- raster::raster(system.file("extdata/tiny.asc", package = "grainscape"))

## Create a resistance surface from a raster using an is-becomes reclassification
tinyCost <- raster::reclassify(tiny, rcl = cbind(c(1, 2, 3, 4), c(1, 5, 10, 12)))
## Produce a patch-based MPG where patches are resistance features = 10
## and all patches are greater than or equal to 2 cells in size
filteredPatch <- patchFilter(tinyCost == 10, cells = 2)
tinyPatchMPG <- MPG(cost = tinyCost, patch = filteredPatch)
if (interactive()) plot(tinyPatchMPG)

## Compare to removal of patches greater than or equal to 40 cells in size!
filteredPatch <- patchFilter(tinyCost == 10, cells = 40)
tinyPatchMPG <- MPG(cost = tinyCost, patch = filteredPatch)
if (interactive()) plot(tinyPatchMPG)

## Use a rook/castle 4-direction case rather than the queen 8-direction case
## to identify neighbouring cells in a patch
filteredPatch <- patchFilter(tinyCost == 10, cells = 40, directions = 4)
tinyPatchMPG <- MPG(cost = tinyCost, patch = filteredPatch)
if (interactive()) plot(tinyPatchMPG)