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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!

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    The index parameter is only valid if rst is a RasterLayerSparse class object. What's wrong with your values(r1)[index]<-values method? I suspect the index parameter for RasterLayerSparse objects exists because direct value replacement might not work for sparse rasters. They're a rare thing.... – Spacedman Dec 2 '20 at 16:48
  • Thank you, that clears it up! There's nothing wrong with values(r1)[index]<-values per se, it's just a bit cumbersome when dealing with a lot of layers and I thought I could do a one liner instead. – karpfen Dec 2 '20 at 16:59
  • It would be more efficient, and clearer, to do r1[index] <- values – Robert Hijmans Dec 3 '20 at 3:24
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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)

enter image description here

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    Do you even need values? Cant you just use the brackets rst[indexvalues] <- newvalues or for a specific layer rst[[1]][indexvalues] <- newvalues – Jeffrey Evans Dec 2 '20 at 17:09
  • I think values() is safer when you have rasters that are loaded-on-demand.... – Spacedman Dec 2 '20 at 21:42
  • FWIW: I agree with Jeffrey. rst[i] <- v is more direct, as intended, and could be memory safe. – Robert Hijmans Dec 3 '20 at 3:15

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