Run R script in different folder than data in Ubuntu Server - r

Question

I have an R script in one directory that takes in the files in a different directory, combines them into one file, and outputs a new excel file, as shown below:
first <- read_excel("file1.xlsx")
second <- read_excel("file2.xlsx")
third <- read_excel("file3.xlsx")
df <- bind_rows(first,second,third)
openxlsx::write.xlsx(df, "newfile.xlsx")
In my code, I can set the working directory to a particular folder just putting setwd("path/to/data") but this only works in one directory. I'd like to make a shell script where I can loop through various folders.
I'd like to try something like
for i in folder1,folder2,folder3
do
# Run Rscript myRscript.R in each folder
done
Ex. Folder 1 has file1, file2, and file3. Folder 2 has file1, file2, and file3. Folder 3 has file1, file2, file3. I'd like the Rscript to be one directory up from the folders and run in each folder and generate a "newfile.xlsx" file for each folder (Each folder is a different set of data but have all the same file names within each folder)
I want to avoid copying a version of the Rscript into each folder to avoid the folder changing nature of my request. Is this possible?

Answer 1

You can loop through the folders and files with R no problem.
folders <- list.dirs()
for (folder in folders) {
files <- list.files(folder)
# extra: neglect non xlsx files
# files <- files[which(str_detect(files, ".xlsx$"))]
df <- tibble()
for (file in files) {
temp <- read_excel(file)
df <- bind_rows(df, temp)
}
# creates a newfile.xlsx in each folder
openxlsx::write.xlsx(df, file.path(folder, "newfile.xlsx"))
# alternative: creates the newfile in the main folder
# openxlsx::write.xlsx(df, paste0(folder, "_newfile.xlsx"))
}