Retaining original file names when processing multiple raster files using R

Question

I have the following problem: I need to process multiple raster files using the same function in R package landscapemetrics. Basically my raster files are parts of a country map, all of the same shape and size (i.e. quadrants. I figured out a code for 1 file, but I have to do the same with more than 600 rasters. So, doing it manually is very irrational. The steps in my code are the following:

# 1. I load "raster" and "landscapemetrics" packages: 
library(raster)
library(landscapemetrics)

# 2. I read in my quadrant: 
Quadrant <- raster("C:\\Users\\customer\\Documents\\ ... \\2434-44.tif")

# 3. I process the raster to get landscape metrics tibble: 
LS_metrics <- calculate_lsm(landscape = Quadrant)

# 4. Finally, I write it into a csv: 
write.csv(LS_metrics, file = "2434-44.csv")

I need to keep the same file name for my csv files as I had for tif (e.g. results from processing quadrant "2434-44.tif", need to be stored in "2434-44.csv", possibly in a folder in wd).

I am new to R. I tried to use list.files() and then apply a for loop, but my code did not work. I need your advice. Yours faithfully, Denis

Answer 1

Your question is really about iteration and character (filename) manipulation; not about landscapemetrics etc. There are many similar questions on this site and resources elsewhere that you can consult. The basic approach can be like this:

# get input filenames
inf <- list.files("/my/path", pattern="\\.tif$", full=TRUE)

# create output filenames
outf <- gsub(".tif", ".csv", basename(inf))

# perhaps put output files in particular folder
dir.create("out", FALSE, FALSE)
outf <- file.path("out", outf)

# iterate 
for (i in 1:length(inf)) {
   # read input 
   input <- raster(inf[i])

   # do something 
   output <- data.frame(id=1)

   # write output
   write.csv(output, outf[i]) 
}

Answer 2

It's very hard to help without further information. What was the issue with your approach of looping through all files using list.files(). In general, this should work.

Furthermore, most likely you don't want to calculate all available landscape metrics, but rather specify a subselection during the calculate_lsm() function call.