This works on a system on which your code doesn't (ubuntu x64 / R 3.0.1 /
raster 2.1-37).

library(raster)
r <- raster(ncols=60, nrows=60, xmn=0)
r[] <- 1:(60*60)
values(r)[5]<-NA
values(r)[(30*30):(60*60)]<-NA
values(r)[round(runif(3000,1,3600))]<-NA

for (i in 1:40){
  if (i==1){
    writeRaster(focal(r,w=3, fun=mean, na.rm=F, pad=TRUE, padValue=NA,
NAonly=TRUE),'tmp.tif',overwrite=TRUE)
  }else{
  t <- raster('tmp.tif')
  writeRaster(focal(t,w=3, fun=mean, na.rm=F, pad=TRUE, padValue=NA,
NAonly=TRUE),'tmp.tif',overwrite=TRUE)
  }

} # end loop i

plot(raster('tmp.tif'))


Somehow the history of the file gets in the way of your iterative approach,
writing to file decouples the original from the new file. This is either a
safeguard, or the file structure/content isn't properly updated, Robert
Hijmans should know the details on which is which.

Cheers,
Koen



On Mon, Jun 24, 2013 at 3:00 PM, Marcia Macedo <marcia.n.macedo@gmail.com>wrote:

> Hi All,
>
> I am trying to use the focal function to iteratively fill NA's in a raster,
> but am having trouble running it on my system. A colleague who was kindly
> helping me troubleshoot my code noticed that it ran as expected with an
> earlier version of R and the 'raster' package.
>
> The following example runs well on his setup (i.e., NA's are gradually
> filled in with each iteration), but not on mine (i.e., the raster only
> changes in the first iteration).
>
> #################################################################
> # A test raster with plenty of NAs
>
> r <- raster(ncols=60, nrows=60, xmn=0)
> r[] <- 1:(60*60)
> values(r)[5]<-NA
> values(r)[(30*30):(60*60)]<-NA
> values(r)[round(runif(3000,1,3600))]<-NA
>
> for (i in 1:40){
>
> newr <- focal(r,w=3, fun=mean, na.rm=T, pad=TRUE, padValue=NA, NAonly=TRUE)
>
>  print(table(is.na(r[]),is.na(newr[])))
>
> r<-newr
>
> } # end loop i
>
> #################################################################
> *The above code works on:*
>
> (Windows 7)
> R version 2.15.0
> raster 1.9-99 (1-June-2012)
>
> *It doesn't work on:*
>
> (Windows 7)
> R version 3.0.1
> raster 2.1-38
>
> The latter setup also gives the following warning message with each
>  iteration:
>
> *In .getW(w): the computation of the weights matrix has changed in version
> 2.1-35. The sum of weights is now 1.*
>
> Is it possible that the arguments for the function have been changed in the
> most recent update, but not in the documentation? Any thoughts about what
> might be going on would much appreciated!
>
> Best,
> Marcia
>
> ---------------------------------------
> *Marcia Macedo*
> Postdoctoral Fellow
> Woods Hole Research Center
> mmacedo@whrc.org
> 508.444.1538
>
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>
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