How to change values in raster inside loop

Question

I have aerial images of forests where I need to compute fragmentation index. I know how to do it for any individual image, but I want to use loop because the is a bunch of them.

# required libraries
library(raster)
library(SDMTools)

The desired index value is element number 11. But before I extract this value I need to replace all values to "1" (from original range 1-100)

# Individual raster can be done like this:
x <- raster(forest_cov[1])
x[x > 0] = 1
PatchStat(x)[11]


# I have tried this loop but it is not working
rast<-numeric(41)
for (i in 1:41) {
rast[i] <- PatchStat(raster(forest_cov[i][forest_cov[i] > 0 == 1]))[11]
                }

The problem is that I do not know how to replace all values in raster to 1 (inside code). What am I doing wrong?

Answer 1

To work out why your code isn't returning the expected result, you should probably run chunks of your code from the inside out. For example, does forest_cov[i] > 0 == 1 return what you expect it to return for raster 1? (I suspect not, since according to your comments, forest_cov is a character vector and so the logical comparison of element i to 0 is not sensible.) But, if so, does forest_cov[i][forest_cov[i] > 0 == 1] return what you expect, and so on.

Here's how I would approach the problem.

Prepare some fake data:

# Write out three fake rasters to temp files
writeRaster(stack(replicate(3, raster(matrix(runif(100), nc=10)))), 
            {f <- tempfile()}, bylayer=TRUE, format='ascii')

# Filenames of these fake rasters
rasters <- paste0(f, '_', 1:3, '.asc')

Calculate the frac.dim.index (i.e. 11th element of PatchStat result) of each raster:

sapply(rasters, function(x) {
  require(SDMTools)
  PatchStat(raster(x) >= 0.1)[11]
})

Alternatively, if all the rasters referred to in your character vector have consistent extent and dimensions, then you can perform the operation on a stack as follows:

s <- stack(rasters) >= 0.1
sapply(seq_len(nlayers(s)), function(i) PatchStat(s[[i]])[11])