R/RichnessGrid.R

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

RichnessGrid <- function(x, ras, reso = 1, type = "spnum") {
    # Input spgeoOUT objects
    if (is.spgeoOUT(x)) {
        x <- x$samples
    }
    # Input data.frame
    if (is.data.frame(x)) {
        names(x) <- tolower(names(x))
        if (!all(c("species" %in% names(x), "decimallongitude" %in% names(x), 
            "decimallatitude" %in% names(x)))) {
            x <- x[, 1:3]
            names(x) <- c("species", "decimallongitude", "decimallatitude")
        } else {
            x <- subset(x, select = c("species", "decimallongitude", "decimallatitude"))
        }
    }
    
    # Create raster
    if (missing(ras)) {
        pts <- sp::SpatialPoints(x[, c("decimallongitude", "decimallatitude")])
        e <- raster::extent(pts)
        ras <- raster::raster(e)
        raster::res(ras) <- reso
    }
    ras <- raster::setValues(ras, 0)
    
    out <- switch(type, spnum = {
        inp <- split(x, f = as.character(x$species))
        inp <- lapply(inp, function(k) .rasterSum(k, ras, type = "div"))
        Reduce("+", inp)
    }, abu = {
        .rasterSum(x, ras, type = "abu")
    })
    
    
    out[out == 0] <- NA
    
    return(out)
}