setwd() in the current working dir

Question

I have a list of folders. In each folder there's an R identical script that have to run on files into the folder. I wrote the script one time and copied the script in each folder. The problem is that I have a list of around 100 folders so it is impossible to me to setwd() in the current working dir by hand. I would like to know if it is possible to set current working dir with for example a "." in this way:

setwd("/User/myname/./")

or in another easy way that tells R the current working dir instead of typing every time the folder name.

Answer 1

how about this?

# set the working directory to the main folder containing all the directories
setwd( "/user/yourdir/" )

# pull all files and folders (including subfolders) into a character vector
# keep ONLY the files that END with ".R" or ".r"
r.scripts <- list.files( pattern=".*\\.[rR]$" , recursive = TRUE )

# look at the contents.. now you've got just the R scripts..
# i think that's what you want?
r.scripts

# and you can loop through and source() each one
for ( i in r.scripts ) source( i )

Answer 2

As far as I understand, you want to trigger a batch of R scripts, where the scripts are distributed across a number of folders.

Personally, I would probably write a shell script (or OS equivilent) to do this, rather than doing it in R.

for dir in /directoriesLocation/*/
do
    cat $dir/scriptName.R | R --slave --args $arg1 $arg2
done

where $dir is the the location of all directories containing the R script scriptName.R

Answer 3

In addition to the other great answers the source function has a chdir argument that will temporarily change the working directory to the one that the sourced file is in.

One option would be to create a vector with the filenames (including paths) for each of your script files, using list.files and/or other tools. Then source each of those files and letting source with chdir handle setting the working directory for you.