createSpeciesRaster: Create speciesRaster

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

Create speciesRaster

Description

This function takes a rasterStack and generates both a richness raster and an associated list of species per cell, creating an object of class speciesRaster.

Usage

createSpeciesRaster(ranges, rasterTemplate = NULL, verbose = FALSE)

Arguments

ranges	Either a RasterStack, RasterBrick, or species by cell matrix. Any non-NA values in rasters are considered presences.
rasterTemplate	If input is a species x cell matrix, then a rasterTemplate must be provided, where the number of cells = the number of columns in the matrix. Cells with a value of 1 will be processed, cells with a value of 0 will be . Therefore, all cells must have a value of 0/1.
verbose	Primarily intended for debugging, print progress to the console.

Details

This function generates an object of class speciesRaster, which is a list containing the following elements:

• raster: A raster representing counts of species per cell.

• speciesList: A list of species found in each cell.

• geogSpecies: a vector of unique species in all cells.

• cellCount: a vector of counts of presence cells for each species.

• data: An empty spot that morphological data can be added to.

• phylo: An empty spot that a phylogeny can be added to.

If input is a RasterStack, then all parameters are taken from that, such as resolution, extent and projection. Any non-NA and non-zero cell is considered a presence. This function expects that all input rasters in the rasterStack have presence values (i.e., at least 1 non-NA value). If any rasters have exclusively NA cells, then the function will stop with a warning, and the output will be the index in the rasterStack of those rasters.

Value

an object of class speciesRaster.

Author(s)

Pascal Title

Examples

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

# convert polygon ranges to raster
ranges <- rasterStackFromPolyList(tamiasPolyList, resolution = 20000)

spRas <- createSpeciesRaster(ranges = ranges)

spRas

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