raster - Fill the gaps using nearest neighbors

I want to fill the NA values using the average values of the nearest neighbors:

r <- raster(matrix(1:16, nrow=8, ncol=8))

r[r==12] <- NA

Answer

You can fill in the NA values using the focal function with the na.rm argument set to FALSE and pad to TRUE.

library(raster)
  r <- raster(matrix(1:16, nrow=8, ncol=8))
  r[r==12] <- NA

Function to replace the focal value with the mean of a 3x3 window if NA. If the window size increases the index value [i] needs to change as well (eg., for a 5x5 window the index would be 13).

fill.na <- function(x, i=5) {
  if( is.na(x)[i] ) {

    return( round(mean(x, na.rm=TRUE),0) )
  } else {
    return( round(x[i],0) )
  }
}  

Pass the fill.na function to raster::focal and check results. The pad argument creates virtual rows/columns of NA values to keep the vector length constant along the edges of the raster. This is why we can always expect the fifth value of the vector to be the focal value in a 3x3 window thus, the index i=5 in the fill.na function.

r2 <- focal(r, w = matrix(1,3,3), fun = fill.na, 
            pad = TRUE, na.rm = FALSE )


as.matrix(r)
as.matrix(r2)