I have a series of species distribution rasters, separated in different folders according to the observation date. I have 1 folder for each day of 2024, named like %Y%m%d, e.g. 20240101.
I want to do 2 simple operations, using {raster}:
-
Merge all files in a given folder, producing a raster of the sum of distributions of all species observed in a given day.
-
After having the “daily sum” rasters, I want to sum them cumulatively. For example: 1st raster = day 1; 2nd raster = day 1 + day 2, …
I know I can do the first operation by creating a long script similar to this:
library(raster)
files <- list.files("D:/Fantasy Birding/Ranges/Rasters/Observados/20240101", pattern="*.tif$", full.names=TRUE)
rs <- stack(files)
soma <- calc(rs, sum)
writeRaster(soma, "D:/Fantasy Birding/Ranges/Rasters/Observados por dia/diario20240101.tif")
files <- list.files("D:/Fantasy Birding/Ranges/Rasters/Observados/20240102", pattern="*.tif$", full.names=TRUE)
rs <- stack(files)
soma <- calc(rs, sum)
writeRaster(soma, "D:/Fantasy Birding/Ranges/Rasters/Observados por dia/diario20240102.tif")
However, preparing such script is quite time consuming. What would be the best way to automate this process?
To achieve this without having to do it step by step, use:
- a helper function with
lapply()to sum rasters for each day and write them to the “Observados por dia” directory - a
for()loop to cumulatively sum the diario rasters
Some regular expression (regex) magic will help with the file naming. You didn’t specify where to write the cumulative results, or what to name them. In this reprex, they are written to a new folder called “cumulative” and each file has the mmdd of the most recent date appended to the start date e.g. cumu20240101_0102.tif, cumu20240101_0103.tif etc.
Step 1: Sum rasters by day
library(raster)
# Create list of tif files from every subdirectory in Observados
files <- list.files("D:/Fantasy Birding/Ranges/Rasters/Observados/",
pattern="*.tif$",
full.names = TRUE,
recursive = TRUE)
# Create a list of tif files grouped by subdirectory
sub_files <- split(files, sub(".*/([^/]+)/.*", "\1", files))
# Helper function to process each group in sub_files
r_sum <- function(files) {
output_path <- paste0("D:/Fantasy Birding/Ranges/Rasters/Observados por dia/diario",
sub(".*/([^/]+)/.*", "\1", files[1]), ".tif")
writeRaster(calc(stack(files), sum), output_path, overwrite = TRUE)
}
# Sum each sub_files group and write result to Observados por dia directory
invisible(do.call(c, lapply(sub_files, r_sum)))
Step 2: Cumulatively sum rasters
# Create list of summed tif files from previous step
files <- list.files("D:/Fantasy Birding/Ranges/Rasters/Observados por dia/",
pattern="*.tif$",
full.names = TRUE)
# Create directory for cumulative sum results
dir.create(file.path("D:/Fantasy Birding/Ranges/Rasters/cumulative/"), showWarnings = FALSE)
# Create raster object for start of loop (if you run the loop again,
# be sure to run this every time also)
x <- raster(files[1])
# Cumulatively sum diario rasters
for(i in 2:length(files)) {
output_path <- paste0("D:/Fantasy Birding/Ranges/Rasters/cumulative/cumu20240101_",
sub(".*([0-9]{4})\.tif$", "\1", files[i]), ".tif")
x <- calc(stack(x, files[i]), sum)
writeRaster(x, output_path, overwrite = TRUE)
}