Usage of index in R raster setValues function

Question

I have a RasterStack object and want to replace some values at a set of indices in all layers. That doesn't work as expected, however. setValues replaces all values even though I pass a set of indices. The following code illustrates my problem:
library (raster)

# Create sample object
r1 <- raster (nrows = 10, ncols = 10)
r2 <- raster (nrows = 10, ncols = 10)
r3 <- raster (nrows = 10, ncols = 10)
values (r1) <- runif (ncell (r1))
values (r2) <- runif (ncell (r2))
values (r3) <- runif (ncell (r3))
rst <- stack (r1, r2, r3)

# Pixel IDs to replace
indexvalues <- c (1, 2, 99)

# Values to substitute
newvalues <- c (10, -10, NA)

result <- setValues (rst, newvalues, index = indexvalues)

# All values are replaced, not just the ones at the indices
plot (result)

### This is what I would expect
values (r1) [indexvalues] <- newvalues
values (r2) [indexvalues] <- newvalues
values (r3) [indexvalues] <- newvalues
rst <- stack (r1, r2, r3)

plot (rst)

Any ideas how I can get setValues to produce my expected result or is there something else wrong? Thanks!

Spacedman · Accepted Answer

The values of a stack is a matrix, so you can directly replace rows to change all the pixels in a location in a stack without having to do each layer separately:
Test stack, using fixed values per layer to make it easier to see the changes than random numbers:
> r1 = raster(matrix(50,10,10))
> r2 = raster(matrix(60,10,10))
> r3 = raster(matrix(70,10,10))
> 
> rst <- stack (r1, r2, r3)
> 
> plot(rst)

Then replace values by row:
> values(rst)[indexvalues,] =  newvalues
> 
> plot(rst)

Usage of index in R raster setValues function

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