R/methods_spgeoOUT.R

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

as.data.frame.spgeoOUT <- function(x, ...) {
    data.frame(x$spec_table)
}

is.spgeoOUT <- function(x) {
    inherits(x, "spgeoOUT")
}

plot.spgeoOUT <- function(x, type = "summary", mode = "percent", ...) {
    switch(type, summary = .MapAll(x), species = .BarChartSpec(x, mode = mode), 
        polygons = .BarChartPoly(x), speciesrichness = .PlotSpPoly(x), mapspecies = .MapPerSpecies(x), 
        mappolygons = .MapPerPoly(x), mapunclassified = .MapUnclassified(x), 
        mapall = .MapAll(x))
}

summary.spgeoOUT <- function(object, ...) {
    # General summary
    spnum <- length(unique(object$samples$species))
    sampnum <- nrow(object$samples)
    polnum <- length(object$polygons)
    
    suma <- c(spnum, sampnum, polnum)
    
    # Coordinate summary
    coords <- round(object$samples[, c("decimallongitude", "decimallatitude")], 
        2)
    coords <- c(min(coords$decimallongitude), max(coords$decimallongitude), 
        round(mean(coords$decimallongitude), 2), min(coords$decimallatitude), 
        max(coords$decimallatitude), round(mean(coords$decimallatitude), 2))
    
    # polygon names
    if (is.na(object$areanam)) {
        polys <- unlist(lapply(slot(object$polygons, "polygons"), function(x) slot(x, 
            "ID")))
    } else {
        polys <- unique(as.character(data.frame(object$polygons)[, object$areanam]))
    }
    
    # number of species per polygon
    sppol <- c(median(object$polygon_table), min(object$polygon_table), max(object$polygon_table))
    
    # not classified species
    nc <- c(object$polygon_table[["not_classified"]], sum(object$samples$homepolygon == 
        "not_classified"))
    
    out <- list(suma = suma, coords = coords, polys = polys, sppol = sppol, 
        nc = nc)
    
    class(out) <- c("summary.spgeoOUT", class(out))
    
    return(out)
}

print.summary.spgeoOUT <- function(x, ...) {
    # general summary
    gs <- sprintf("%s species with %s occurrences classified to %s input polygons \n\n", 
        x$suma[1], x$suma[2], x$suma[3])
    
    # Coordinate summary
    cs <- sprintf("Longitudinal range: %s to %s, mean %s\nLatitudinal range: %s to %s, mean %s \n\n", 
        x$coords[1], x$coords[2], x$coords[3], x$coords[4], x$coords[5], x$coords[6])
    
    # Number of species per polygon
    sp <- sprintf("Median number of species per polygon = %s; min = %s, max = %s\n\n", 
        x$sppol[1], x$sppol[2], x$sppol[3])
    
    # not classified records and species
    nc <- sprintf("%s species (%s records) not classified to any polygon\n", 
        x$nc[1], x$nc[2])
    
    cat(gs)
    cat(cs)
    cat(paste("Polygon names = ", paste(x$polys, collapse = " "), "\n\n"))
    cat(sp)
    cat(nc)
}