R/MapRichness.R

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

MapRichness <- function(x, buffer = 1, show.occ = FALSE) {
    if (!is.spgeoOUT(x)) {
        stop("this function is only defined for class \"spgeoOUT\"")
    }
    # background map
    e <- raster::extent(x$polygons) + buffer
    bgmap <- speciesgeocodeR::landmass
    bgmap <- raster::crop(bgmap, e)
    bgmap <- ggplot2::fortify(bgmap)
    
    # link species number information with polygons
    pol.f <- ggplot2::fortify(model = x$polygons)
    pol <- merge(pol.f, x$polygons@data, by.x = "id", by.y = "row.names")
    pol$sppol <- as.integer(pol$sppol)
    
    # create plot
    plo.out <- ggplot2::ggplot() + ggplot2::geom_polygon(data = bgmap, aes_string(x = "long", 
        y = "lat", group = "group"), col = "grey60") + ggplot2::geom_polygon(data = pol, 
        aes_string(x = "long", y = "lat", group = "group", fill = "sppol")) + 
        viridis::scale_fill_viridis(option = "viridis", name = "Species") + 
        ggplot2::coord_fixed() + ggplot2::theme_bw() + ggplot2::theme(axis.title = element_blank())
    
    if (show.occ) {
        plo.out <- plo.out + ggplot2::geom_point(data = x$samples, aes_string(x = "decimallongitude", 
            y = "decimallatitude"), col = "red")
    }
    print(plo.out)
}