Extract grid cells from different layers in a raster stack in R.

extractCellsFromLayers.R

extractCellsFromLayers <- function(stack, index) {
  # --------------------------------------------------------------------------------
  # Purpose:
  #   Extract grid cells from different layers in a raster stack.
  #
  # Arguments:
  #   stack       A RasterStack object; the stack from which to extract cell values.
  #   index       A RasterLayer object; the index used to extract cells from the
  #               stack. Cell values in the index raster indicate from which layer 
  #               in the raster stack to extract the corresponding cell values.
  #
  # Author:
  #   Seth Gorelik - October 2018
  # --------------------------------------------------------------------------------
  require(raster)
  if (class(stack) != 'RasterStack') stop(paste0('object "', deparse(substitute(stack)), '" must be a RasterStack.'))
  if (class(index) != 'RasterLayer') stop(paste0('object "', deparse(substitute(index)), '" must be a RasterLayer.'))
  if (cellStats(index, 'max') > nlayers(stack)) stop('index references layer(s) not found in stack.')
  new.raster <- index * 0
  tmp.df <- as.data.frame(stack)
  new.raster[] <- tmp.df[cbind(1:ncell(index), getValues(index))]
  return(new.raster)
}

Conceptual Diagram