R/readLayers.R

In LewisAJones/LBGSim: Latitudinal biodiversity gradient simulator

#' Read rasters with optional discrete and plot functionality
#' 
#' Takes any raster file compatiable with 'raster' package
#'
#' @param layers RasterLayer. Filename or path of raster objects. 
#' @param from Numeric. Lower numeric value used for converting data to binary
#' @param to Numeric. Upper numeric value used for converting data to binary
#' @param plot Logical. If TRUE, and from/to are defined, binary plot is outputted
#' @return RasterLayer or RasterStack.
#' @importFrom tools file_path_sans_ext
#' @importFrom raster stack brick
#' @importFrom rasterVis levelplot
#' @export
readLayers <- function(layers, from, to, binary, plot){
  if(is.vector(layers) == TRUE){
  nme <- list.files(layers)
  layers <- raster::stack(paste(layers, "/", nme, sep = ""))
  nme <- basename(nme)
  nme <- tools::file_path_sans_ext(nme)
  names(layers) <- nme
  stk <- sapply(1:nlayers(layers), function(x){
    r <- layers[[x]]
    r[r < from | r > to] <- NA
    if(binary == TRUE){
      r[!is.na(r)] <- 1
    }
    layers[[x]] <- r
  })
  layers <- stack(stk)
  if(plot == TRUE){
    if(binary == TRUE){
      suppressWarnings(print(rasterVis::levelplot(layers, margin=FALSE, xlab = expression(paste("Longitude (",degree,")")), ylab = expression(paste("Latitude (",degree,")")), colorkey=FALSE, par.settings = rasterVis::viridisTheme())))
    }
    else{suppressWarnings(print(rasterVis::levelplot(layers, margin=TRUE, xlab = expression(paste("Longitude (",degree,")")), ylab = expression(paste("Latitude (",degree,")")), scales.margin=list(x=c(0,0), y=NULL), par.settings = rasterVis::viridisTheme())))}
  }
  return(layers)}
  else{ 
    nme <- names(layers)
    layers[layers < from] <- NA
    layers[layers > to] <- NA
    if(plot == TRUE){
      if(binary == TRUE){
        layers[layers >= from] <- 1
        suppressWarnings(print(rasterVis::levelplot(layers, margin=FALSE, xlab = expression(paste("Longitude (",degree,")")), ylab = expression(paste("Latitude (",degree,")")), colorkey=FALSE,par.settings = rasterVis::viridisTheme())))
      }
      else{suppressWarnings(print(rasterVis::levelplot(layers, margin=TRUE, xlab = expression(paste("Longitude (",degree,")")), ylab = expression(paste("Latitude (",degree,")")), scales.margin=list(x=c(0,0), y=NULL), par.settings = rasterVis::viridisTheme())))}
    }
    return(layers)
  }
}