rasterStackFromPolyList: Polygon List to rasterStack

In rangeBuilder: Occurrence Filtering, Geographic Standardization and Generation of Species Range Polygons

Polygon List to rasterStack

Description

Takes a list of polygons and creates a multi-layer SpatRaster.

Usage

rasterStackFromPolyList(
  polyList,
  resolution = 50000,
  retainSmallRanges = TRUE,
  extent = "auto"
)

Arguments

polyList	a list of spatial polygon objects, named with taxon names. It is assumed that all items in last have same crs.
resolution	vertical and horizontal size of raster cell, in units of the polygons' projection
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, must be a numeric vector of length 4 with minLong, maxLong, minLat, maxLat.

Details

In the rasterization process, all cells for which the polygon covers the midpoint are considered as present and receive a value of 1. 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.

Value

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

Author(s)

Pascal Title

Examples

## Not run: 
data(crotalus)
library(sf)
library(terra)

# get 10 species occurrence sets
uniqueSp <- split(crotalus, crotalus$genSp)
uniqueSp <- lapply(uniqueSp, function(x) 
	x[!duplicated(x[, c('decimallongitude', 'decimallatitude')]),])
uniqueSp <- names(uniqueSp[sapply(uniqueSp, nrow) > 5])
uniqueSp <- uniqueSp[1:10]

# create range polygons
ranges <- vector('list', length = length(uniqueSp))
for (i in 1:length(uniqueSp)) {
	x <- crotalus[which(crotalus$genSp == uniqueSp[i]),]

	ranges[[i]] <- getDynamicAlphaHull(x, coordHeaders = c('decimallongitude', 
		'decimallatitude'), clipToCoast = 'terrestrial')
}

# name the polygons
names(ranges) <- uniqueSp

# keep only the polygons
ranges <- lapply(ranges, function(x) x[[1]])

# Create a SpatRaster with the extent inferred from the polygons, and a cell
# resolution of 0.2 degrees.
# cells with the presence of a species get a value of 1, NA if absent. 

rangeStack <- rasterStackFromPolyList(ranges, resolution = 0.2)

# calculate species richness per cell, where cell values are counts of species
richnessRaster <- app(rangeStack, fun=sum, na.rm = TRUE)

# set values of 0 to NA
richnessRaster[richnessRaster == 0] <- NA

#plot
ramp <- colorRampPalette(c('blue','yellow','red'))
plot(richnessRaster, col=ramp(100))

# to add a basic coastline, you can use the internal map
# world <- rangeBuilder:::loadWorldMap()
# plot(world, add = TRUE, lwd = 0.5)


## End(Not run)

rangeBuilder documentation built on Oct. 31, 2024, 1:08 a.m.