rasterStackFromOccurrences: Occurrences to rasterStack

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

Occurrences to rasterStack

Description

Takes a set of occurrences and rasterizes the coordinates for each taxon.

Usage

rasterStackFromOccurrences(
  occ,
  resolution = 50000,
  extent = "auto",
  coordHeaders = c("long", "lat"),
  taxonHeader = "taxon",
  crs = "+init=epsg:4326"
)

Arguments

occ	a table of species coordinates, a list of species-specific tables of coordinates, a spatial coordinates object, or a species-specific list of spatial coordinate objects (sf or sp). If in table form, each coordinate pair must have an associated species name. If in list form, each element of the list must be named with the name of the species.
resolution	vertical and horizontal size of raster cell, in coordinate units.
extent	if 'auto', then the maximal extent of the coordinates 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.
coordHeaders	headers for longitude and latitude columns (x and y), only necessary if occ is a table.
taxonHeader	header for taxon labels, only necessary if occ is a table.
crs	coordinate reference system, only necessary if occ is a table. Otherwise, this information is pulled from occ. EPSG:4326 indicates unprojected long/lat.

Details

If there are spaces in taxon names, those will be replaced with underscores.

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

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
# To illustrate usage, we will randomly sample some coordinates from each species polygon
# and generate a couple of alternative input formats

# list of sf spatial objects
spOccList <- lapply(tamiasPolyList, function(x) st_sample(x, size = 10, type= 'random'))
spStack <- rasterStackFromOccurrences(spOccList, resolution = 50000, crs = st_crs(tamiasPolyList[[1]]))

# list of coordinate tables
spOccList2 <- lapply(spOccList, function(x) st_coordinates(x))
spStack <- rasterStackFromOccurrences(spOccList2, resolution = 50000, crs = st_crs(tamiasPolyList[[1]]))

# single table of coordinates
spOccList3 <- spOccList2
for (i in 1:length(spOccList3)) {
	spOccList3[[i]] <- cbind.data.frame(taxon = names(spOccList3)[i], spOccList3[[i]])
	colnames(spOccList3[[i]]) <- c('taxon', 'X', 'Y')
}
spOccList3 <- do.call(rbind, spOccList3)
rownames(spOccList3) <- NULL
spOccList3[, 'taxon'] <- as.character(spOccList3[, 'taxon'])
spStack <- rasterStackFromOccurrences(spOccList3, resolution = 50000, 
	coordHeaders = c('X', 'Y'), crs = st_crs(spOccList[[1]]))

# a single labeled spatial object
spOccList4 <- st_as_sf(spOccList3[, c('taxon', 'X', 'Y')], coords = c('X','Y'), 
	crs = st_crs(spOccList[[1]])$proj4string)
spStack <- rasterStackFromOccurrences(spOccList4, resolution = 50000)
	

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