Handling multiple-extent-problem to create raster stack in R?

Question

I am storing ~ 30 raster files in a folder and want to create a raster stack. I know that not all of these rasters have completely the same extent. They do have the same resolution and CRS.

Thus I try to set the same extent for all of my rasters in this folder with the following loop in R.

#reference raster to get the extent 
a <- raster("F:/SDM/DATA/env_tiff/e_veg_d10.tif")
# where the new rasters will be stored
 outpath <- "F:/SDM/DATA/temp/"
 dir.create(outpath)
 files <- list.files(path="F:/SDM/DATA/env_tiff", pattern=".tif$") 
 # add output directory
 outfiles <- paste0(outpath, files)
 # change extensions
 extension(outfiles) <- 'tif'
 for(i in 1:length(files)) {
 e <- extent(a)
 r <-raster(files[i])
 rc <- crop(r, e)
 rc<- mask(rc, e)
 rw <- writeRaster(rc, outfiles[i], overwrite=TRUE)
 print(outfiles[i])
 }
 #creates a raster stack with all environmental rasters in this file
 env_data <- list.files(path="F:/SDM/DATA/temp", pattern = 'tif$')
 env_data<- stack(env_data)

For my loop I get the following Error message:

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘mask’ for signature ‘"RasterLayer", "Extent"’

When I comment the mask part, the loop works, but the extents are still different.

I am also not sure if I choose the right extent, since I don't know the minimum extent. I spent a lot of time searching a way to handle this multiple-extent-problem within my data and found the crop() and mask() functions.

• Jeffrey Evans: There is a funciton "align_rasters" in the gdalUtils package that makes this a bit easier.

Answer 1

You can manage multi-extent-problem resampling your data before mask() function. This work for aligned and non-aligned pixels (for non-aligned, choose wisely method argument). Also, you can use extendto align boundaries of your data. I'd made an reproducible example for recreate our problem:

library(raster)
a <- raster(xmn=-100, xmx=100, ymn=-90, ymx=90,res=10) 
# for reproducible example
r1 <- raster(xmn=-180, xmx=180, ymn=-90, ymx=90,res=10)
r2 <- raster(xmn=-190, xmx=180, ymn=-80, ymx=10,res=10)
r3 <- raster(xmn=-50, xmx=130, ymn=-80, ymx=90,res=10)
a <- setValues(a, 1:ncell(a))
r1 <- setValues(r1, 1:ncell(r1))
r2 <- setValues(r2, 1:ncell(r2))
r3 <- setValues(r3, 1:ncell(r3))
files <- list()
files[[1]] <- r1
files[[2]] <- r2
files[[3]] <- r3
results <- list()
for(i in 1:length(files)) {
 e <- extent(a)
 r <-files[[i]] # raster(files[i])
 rc <- crop(r, e)
 if(sum(as.matrix(extent(rc))!=as.matrix(e)) == 0){ # edited
 rc <- mask(rc, a) # You can't mask with extent, only with a Raster layer, RStack or RBrick
 }else{
 rc <- extend(rc,a)
 rc<- mask(rc, a)
 }
 # commented for reproducible example 
 results[[i]] <- rc # rw <- writeRaster(rc, outfiles[i], overwrite=TRUE)
 # print(outfiles[i])
}
env_data<- stack(results)

The result will depends of the nature of you data, in this case I exaggerated the problem. After this code, we got this:

plot(env_data)

enter image description here

---

Edit:

Test your layers

library(raster)
a <- raster(xmn=-100, xmx=100, ymn=-90, ymx=90,res=10) 
# for reproducible example
r1 <- raster(xmn=-180, xmx=180, ymn=-90, ymx=90,res=10)
r2 <- raster(xmn=-190, xmx=180, ymn=-80, ymx=10,res=10)
r3 <- raster(xmn=-50, xmx=130, ymn=-80, ymx=90,res=10)
# Other posibilities
r4 <- raster(xmn=-200, xmx=-150, ymn=-80, ymx=90,res=10)
r5 <- raster(xmn=-100, xmx=100, ymn=-90, ymx=90,res=5)
r6 <- a
files <- list()
files[[1]] <- r1
files[[2]] <- r2
files[[3]] <- r3
files[[4]] <- r4
files[[5]] <- r5
files[[6]] <- r6
library(testthat)
test <- list()
for(i in 1:length(files)){
 test[[i]] <- capture_warnings(compareRaster(a,files[[i]], res=T, orig=T, stopiffalse=F, showwarning=T))
}
test
[[1]]
[1] "different extent" "different number or columns"
[[2]]
[1] "different extent" "different number or columns"
[3] "different number or rows" 
[[3]]
[1] "different extent" "different number or columns"
[3] "different number or rows" 
[[4]]
[1] "different extent" "different number or columns"
[3] "different number or rows" 
[[5]]
[1] "different number or columns" "different number or rows" 
[3] "different resolution" 
[[6]]
character(0)

• Jeffrey Evans: Raster stacks not working with different extents is not entirely true, it depends on what you want to do. You can create a stack with mismatched extents by using the "quick=TRUE" argument.
• parallax: Thank you for ansering! The raster cells are aligned but don't match at the borders. What I plan to do is to extract values to points.
• aldo_tapia: Actually, this code apply to your purposes. I use it in Landsat 8 time series, especially in subsets near to borders.
• parallax: I'll try this code and give a feedback soon, Thank you aldo_tapia!
• parallax: I tried the code but I am not sure how to integrate it in my code above. I am a newbie in R and coding in general, so could you make some more comments?

Answer 2

Crop can write straight to file; I don't think the mask step is necessary? you should make sure your extent aligns with pixel edges though - see here Improving Clip Raster workflow in QGIS?