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.

Why did you copy an identical script in each folder and why do you need to set the working directory? What do you want to achieve? — Roland, Feb 22 '13 at 14:42
Why not just have one script and perform its contents for each folder? Say through a loop? — sebastian-c, Feb 22 '13 at 14:49
Hi Roland and sebastian! It is just because I start from a very big matrix (around 2.8G) so I divided it in subfolders and in each folder I run the same script because I have to do the same operations on the files. — Fuv8, Feb 22 '13 at 21:18

score 8 · Accepted Answer · answered Feb 22 '13 at 14:46

8

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 )

answered Feb 22 '13 at 14:46

Anthony Damico

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You might be interested in the `pattern` argument to `list.files`. – Roland Feb 22 '13 at 14:47
1

If the OP wants to loop through folders and set the working directories to them, they might want to consider `list.dirs(recursive=FALSE)` if they're all one level deep. – sebastian-c Feb 22 '13 at 15:01
Hi Antony, yes it is what i want more or less. – Fuv8 Feb 22 '13 at 15:05
1

You might also want `chdir = T` in `source` – hadley Feb 23 '13 at 01:35

score 3 · Answer 2 · answered Feb 22 '13 at 14:42

3

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

answered Feb 22 '13 at 14:42

mjshaw

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Hi! Yes, I run a .sh script that call a .bash script to run all the .R script since I'm working on cluster. – Fuv8 Feb 22 '13 at 15:04

score 3 · Answer 3 · answered Feb 22 '13 at 17:17

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.

setwd() in the current working dir

3 Answers3

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