R/RangeRichness.R

In azizka/speciesgeocodeR: Prepare Species Distributions for the Use in Phylogenetic Analyses

RangeRichness <- function(x, ras, reso = 1, buffer = 1, terrestrial = FALSE) {
    
    # enable spgeoOUT object as input
    if (is.spgeoOUT(x)) {
        x <- CalcRange(x, method = "pseudospherical")
    }
    
    # create backround raster
    if (missing(ras)) {
        ras <- raster(extent(x) + buffer)
        res(ras) <- reso
    }
    
    # rasterize range polygons
    out <- lapply(x@polygons, function(k) {
        tt <- rasterize(SpatialPolygons(list(k)), ras, background = 0)
    })
    
    # sum up the raster values
    out <- Reduce("+", out)
    
    # crop to land surface
    if (terrestrial) {
        test <- rasterize(speciesgeocodeR::landmass, out)
        out <- mask(out, test)
    }
    
    return(out)
}