In R, set NA cells in one raster where another raster has values

This can easily be solved using the overlay function from the raster package. Objects rst1 and rst2 are replicates of the initial 'volcano' layer, and a random sample of n = 1000 cells in rst2 is set to NA. Afterwards, overlay is applied and the associated function rejects all cells in rst1 that hold a valid value, i.e. different from NA, in rst2.

library(raster)

rst <- raster::raster(volcano)
rst1 <- rst
rst2 <- rst

# artificial gaps
set.seed(123)
id <- sample(1:ncell(rst), 1000)
rst2[id] <- NA

# introduce na in rst1 for all locations that are non-na in rst2
rst1_mod <- overlay(rst1, rst2, fun = function(x, y) {
  x[!is.na(y[])] <- NA
  return(x)
})

plot(rst1_mod)

The problem is the way you are addressing the raster with newraster <- raster1[is.na(raster2)]. Try is.na(raster2) by itself to see what you get!

Trying to set values of a raster using vector terminology[] doesn't always work the way one expects. Use values() to set the actual data values of the raster:

library(raster)

# Create two small rasters and set them to random values:
r1 <- r2 <- raster(nrows=5, ncols=5)
values(r2) <- values(r1) <- rnorm(length(r1))

# Set the first row of r1 to NA:
r1[1:5] <- NA

Have a look at it:

head(r1)
           1           2          3           4           5
1         NA          NA         NA          NA          NA
2  0.1451180  0.34801689  1.0545334 -1.15284126 -0.04138286
3 -1.1370768  0.05409194 -0.7767229  0.88499661  0.34104942
4 -0.7654063 -1.03248120  1.1414939 -0.07996859 -0.34718092
5 -0.0110303 -1.70203386  0.8650742 -0.69514811 -0.31484591

Now, set the values of r2 that are not NA in r1 to NA:

values(r2)[!is.na(values(r1))] <- NA

Let's check:

head(r2)
           1         2          3        4          5
1 -0.9571857 0.4479621 -0.5601638 1.207951 -0.1459748
2         NA        NA         NA       NA         NA
3         NA        NA         NA       NA         NA
4         NA        NA         NA       NA         NA
5         NA        NA         NA       NA         NA