rasterStackFromPolyList: Polygon List to rasterStack

In ptitle/speciesRaster: Generation of SpeciesRaster Object and Calculation of Morphological and Phylogenetic Metrics

Polygon List to rasterStack

Description

Takes a list of polygons and creates a rasterStack.

Usage

rasterStackFromPolyList(
  polyList,
  resolution = 50000,
  method = "midpoint",
  coverCutoff = 0.1,
  retainSmallRanges = TRUE,
  extent = "auto",
  dropEmptyRasters = TRUE
)

Arguments

polyList	a list of polygons objects (sf or sp), named with taxon names.
resolution	vertical and horizontal size of raster cell, in units of the polygons' projection.
method	approach used for rasterizing. See details below.
coverCutoff	the percent that a species range must cover a grid cell to be considered present.
retainSmallRanges	boolean; should small ranged species be dropped or preserved. See details.
extent	if 'auto', then the maximal extent of the polygons will be used. If not auto, can be a SpatialPolygon or sf object, in which case the resulting rasterStack will be cropped and masked with respect to the polygon, or a spatial coordinates object, from which an extent object will be generated, or a numeric vector of length 4 with minLong, maxLong, minLat, maxLat. If 'interactive', then an interactive plot will appear in which the user can draw the desired polygon extent.
dropEmptyRasters	if TRUE, then species that have no presence cells will be dropped. If FALSE, then rasters will remain, filled entirely with NA.

Details

In the rasterization process, two approaches are implemented. For method = 'midpoint', a range polygon registers in a cell if the polygon overlaps with the cell midpoint. For method = 'gridcell', a range polygon registers in a cell if it covers that cell by at least coverCutoff fraction of the cell. If retainSmallRanges = FALSE, then species whose ranges are so small that no cell registers as present will be dropped. If retainSmallRanges = TRUE, then the cells that the small polygon is found in will be considered as present, even if it's a small percent of the cell. retainSmallRanges only applies to method = 'gridcell'.

If dropEmptyRasters = TRUE and retainSmallRanges = TRUE, then the species that will be dropped are those that are outside of the requested extent (which in that case would be specified explicitly).

In interactive mode for defining the extent, the user can draw a bounding polygon on a map. The drawn polygon will then be printed to the console so that the user can hard-code that bounding polygon in future calls to this function.

Any SpatialPolygon or SpatialPoints objects are converted to objects of class sf.

This function uses the fasterize package for conversion from polygon to raster.

In interactive mode, the basemap is from www.naturalearthdata.com.

Value

an object of class RasterStack where all rasters contain values of either NA or 1.

Author(s)

Pascal Title

Examples

library(raster)
library(sf)
# example dataset: a list of 24 chipmunk distributions as polygons
head(tamiasPolyList)

rangeStack <- rasterStackFromPolyList(tamiasPolyList, resolution = 50000)
rangeStack

ptitle/speciesRaster documentation built on June 11, 2022, 1:35 a.m.