Alex, Thanks for the clear example. I had not considered that case. I have added an argument 'updateNA' to the mask function (version 2.2-43) such that you can do:
masked_image <- mask(img, msk, updatevalue=2, updateNA=TRUE) That is, if updateNA is TRUE, NA cells outside the mask are also updated. Robert On Fri, Jul 18, 2014 at 11:18 AM, Alex Zvoleff <azvol...@conservation.org> wrote: > I am using the mask function in the raster package (2.2-38) to mask out > areas within an image that are outside an area of interest (AOI). There are > NAs within this AOI that are meaningful - after masking the image I am > using freq to tabulate these NAs along with the other values in my AOI. For > this reason, I am using the "updatevalue" option in the mask function to > recode all areas outside of my AOI to a value (say 99) so that I can ignore > these areas in subsequent analysis, without having ignored areas share a > value (NA) with areas inside my AOI. > > However, the mask function does not operate as I expected - areas in the > image that should be masked but that are NA prior to masking are not set to > "updatevalue". Is there an way to tell the mask function to recode all > areas (regardless of their initial value) to updatevalue? The below example > shows my problem: > > library(raster) > # Setup an image with two NA values. Make one NA value inside > # the AOI, and make the other outside the AOI > img <- matrix(1, nrow=5, ncol=5) > img[3, 2] <- NA # Inside AOI > img[1, 2] <- NA # Outside AOI > img <- raster(img) > plot(img) > > # Setup a mask where only the 3x3 region in the center of img is retained > msk <- matrix(1, nrow=5, ncol=5) > msk[1,] <- NA > msk[5,] <- NA > msk[,1] <- NA > msk[,5] <- NA > msk <- raster(msk) > plot(msk) > > # Apply mask > masked_image <- mask(img, msk, updatevalue=2) > > # Notice that cell (1, 2) of masked_image is NA, instead of the updatevalue > (2). > # This cell was not affected by the mask because it was NA prior to calling > mask. > # Is there a way to tell the mask function to set all masked areas to > updatevalue, > # regardless of whether a cell is NA prior to masking? > plot(masked_image) > > Thanks, > Alex > > -- > Alex Zvoleff > Postdoctoral Associate > Tropical Ecology Assessment and Monitoring (TEAM) Network > Conservation International > 2011 Crystal Dr. Suite 500, Arlington, Virginia 22202, USA > Tel: +1-703-341-2749, Fax: +1-703-979-0953, Skype: azvoleff > http://www.teamnetwork.org | http://www.conservation.org > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-Geo mailing list > R-sig-Geo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-geo _______________________________________________ R-sig-Geo mailing list R-sig-Geo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-geo
