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.

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)

---

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)

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?