R/SpGeoCod.R

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

SpGeoCod <- function(x, y, areanames = "", occ.thresh = 0, elevation = FALSE, threshold, cleaning = FALSE, ...) {
    if (elevation == TRUE){
      ini <- ReadPoints(x, y, cleaning = cleaning, ...)
      coords <- data.frame(identifier = ini$identifier, 
                           ini$species_coordinates)
      coords$ele <- GetElevation(coords)
      
      if (max(threshold) > max(coords$ele, na.rm = T))
      {
        threshold2 <- threshold[which(threshold < max(coords$ele, na.rm = T))]
        warning(sprintf("maximum threshold (%s meter) is higher than maximum elevation in the dataset (%s meter); maximum threshold set to %s meter", 
                        max(threshold), max(coords$ele, na.rm = T), max(threshold2)))
        threshold <- threshold2
      }
            
      threshold <- unique(c(0, threshold, max(coords$ele, na.rm = T) + 1))
      coords$cuts <- cut(coords$ele, breaks = threshold, labels = paste(">", threshold[-length(threshold)], sep = ""))
      tt <- split(coords, coords$cuts)
  
      tt <- lapply(tt, function(x) .adjFormat(x))
      ini <- lapply(tt, function(x) ReadPoints(x, y, cleaning = cleaning, ...))
      outo <- lapply(ini, function(x) SpGeoCodH(x, areanames, occ.thresh = occ.thresh))
      names(outo) <- gsub(">", "over_", names(outo))
      names(outo) <- paste(names(outo), "_meters", sep = "")
      return(outo)
    }else{    
      ini <- ReadPoints(x, y, cleaning = cleaning, ...)
      outo <- SpGeoCodH(ini, areanames, occ.thresh = occ.thresh)
    return(outo)
    }
}