How to replace NA's in a raster object

Question

I need to replace the NA's in the raster object (r) from the example below.

library(raster)
filename <- system.file("external/test.grd", package="raster")
r <- raster(filename)

I also tried to remove these these (and place the result in a data.frame), but to no avail.

dfr <- as.data.frame(r, na.rm=T)
summary(dfr)
# test       
# Min.   : 128.4  
# 1st Qu.: 293.2  
# Median : 371.4  
# Mean   : 423.2  
# 3rd Qu.: 499.8  
# Max.   :1805.8  
# NA's   :6097

Yes, `summary(as.data.frame(r, na.omit=T))` says that there are 6097 `NA`'s. — ils, Aug 15 '12 at 09:29
Welcome to StackOverflow. +1 for [reproducible example](http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example). — Andrie, Aug 15 '12 at 09:37
As you can see in the answer, `na.omit` is a function not an argument of `as.data.frame`. — seancarmody, Aug 15 '12 at 10:01
Try SpatialPixelsDataFrame for sparse grids without the NAs, but this is pretty open ended, what do you really need? — mdsumner, Aug 15 '12 at 12:34

Robert Hijmans · Answer 1 · 2022-05-17T16:23:31.003

31

Here are three ways in which you can do this with terra

library(terra)
f <- system.file("ex/elev.tif", package="terra")
r <- rast(f)
x <- classify(r, cbind(NA, -99))
y <- subst(r, NA, -99)
z <- ifel(is.na(r), -99, r)

With raster, the best (memory safe approach that also works for large files) is to use reclassify:

library(raster)
filename <- system.file("external/test.grd", package="raster")
r <- raster(filename)
rna <- reclassify(r, cbind(NA, 250))

edited May 17 '22 at 16:23

answered Feb 16 '13 at 07:20

Robert Hijmans

40,301
4
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This doesn't seem to work for NaN (i.e. reclassify(r, cbind(NaN, NA))) – kennyB Mar 19 '16 at 02:28

score 17 · Accepted Answer · answered Aug 15 '12 at 09:31

I'm not sure it makes sense to remove NA values from a raster object, but you can easily replace it.

For example:

oldpar <- par(mfrow=c(1, 2))
plot(r)
r[is.na(r)] <- 250
plot(r)
par(oldpar)

enter image description here

If you really want to, you can extract the raster values into a vector and then remove the NA values. (Although, since you lose the spatial information, I can't see how this can be helpful.)

r <- raster(filename)

r <- values(r)
head(r)
[1] NA NA NA NA NA NA

head(na.omit(r))
[1] 633.686 712.545 654.162 604.442 857.256 755.506

How to replace NA's in a raster object

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