Run focal function on a multi-layer raster

Hi Lo?c,

Thanks for the hint - it worked like a charm!
 Greetings,
 -- Thiago V. dos Santos

PhD student
Land and Atmospheric Science
University of Minnesota

Hi Thiago,

calc is not aware of neighbouring pixels in the x,y dimensions, so 
functions like focal cannot work.

I found the function below in an old repos of mine. It still seems to 
work fine :)

#' Focal for RasterBrick or RasterStack
#'
#' @param x RasterBrick/Stack or character pointing to multilayer raster 
object written on disk
#' @param w See \code{\link{focal}}
#' @param ... Arguments to be passed to \code{\link{focal}}
#'
#' @import raster
#' @export
#'

multiFocal <- function(x, w=matrix(1, nr=3, nc=3), ...) {

   if(is.character(x)) {
     x <- brick(x)
   }
   # The function to be applied to each individual layer
   fun <- function(ind, x, w, ...){
     focal(x[[ind]], w=w, ...)
   }

   n <- seq(nlayers(x))
   list <- lapply(X=n, FUN=fun, x=x, w=w, ...)

   out <- stack(list)
   return(out)
}

I have a multi-layer raster, in this case a rasterbrick, on which I would like to apply a focal function on each layer, and get another rasterbrick as a result.

I am trying to use calc, but apparently I am not assembling my function in the proper way:

require(raster)
r <- raster(ncol=50, nrow=50)
r[]=1:ncell(r)
b <- brick(r,r,r,r,r,r)
b <- b * 1:6

multiFocal(b, w=matrix(1, 5, 5), mean)

Cheers,
Lo?c

myfocalfun <- function(x){
b.f <- focal(x, w=matrix(1, 5, 5), mean)
return(b.f)
}

b1 <- calc(b, myfocalfun)

Error in .calcTest(x[1:5], fun, na.rm, forcefun, forceapply) :
cannot use this function

What am I missing here?
  Greetings,
  -- Thiago V. dos Santos

PhD student
Land and Atmospheric Science
University of Minnesota

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