R command for setting working directory to source file location in Rstudio

Question

I am working out some tutorials in R. Each R code is contained in a specific folder. There are data files and other files in there. I want to open the .r file and source it such that I do not have to change the working directory in Rstudio as shown below:

Is there a way to specify my working directory automatically in R.

Repine

This is probably a dupe. see ?setwd ?getwd – Nelda

https://mcmap.net/q/101731/-getting-path-of-an-r-script – Afterheat

Not a dupe, the poster wants to load .rdata-files in the same folder, not source with the working directory set to the path of the sourced file. – Selfliquidating

why is R making this so hard? – Otolith

Answer 1

To get the location of a script being sourced, you can use utils::getSrcDirectory or utils::getSrcFilename. These require a function as an input. Create a script with the following lines, and source it to see their usage:

print(utils::getSrcDirectory(function(){}))
print(utils::getSrcFilename(function(){}, full.names = TRUE))

Changing the working directory to that of the current file can be done with:

setwd(getSrcDirectory(function(){})[1])

This does not work in RStudio if you Run the code rather than Sourceing it. For that, you need to use rstudioapi::getActiveDocumentContext.

setwd(dirname(rstudioapi::getActiveDocumentContext()$path))

This second solution requires that you are using RStudio as your IDE, of course.

Boudreau

your own answer at https://mcmap.net/q/101731/-getting-path-of-an-r-script works (one must include the dirname though). I added it – Repine

Doesn't work for me. I get Error: 'getActiveDocumentContext' is not an exported object from 'namespace:rstudioapi' – Lomasi

@Lomasi are you using a recent version of RStudio? It won't work in other IDEs (including RGUI) or old versions of RStudio. Similarly, make sure you have the latest version of the rstudioapi package. – Boudreau

Note that when you run getActiveDocumentContext() in the console within RStudio, the path is reported as ''. However, if you run the line of code in the editor portion, it will execute as expected. This may address @Lomasi 's comment – Manzano

I run setwd(dirname(rstudioapi::getActiveDocumentContext()$path)) on a Mac and I got Error: 'getActiveDocumentContext' is not an exported object from 'namespace:rstudioapi' – Otolith

@giac_man It sounds like you are using a very old version of the rstudioapi package. Try updating to the latest one. – Boudreau

I get: Error in setwd(dirname(rstudioapi::getActiveDocumentContext()$path)) : cannot change working directory; Apparently because I run it in the console. It runs well in the script. – Desrosiers

@SanduUrsu Correct: the console is not an active document, so rstudioapi::getActiveDocumentContext()$path is "". – Boudreau

setwd(getSrcDirectory()[1]) didn't work for me when I sourced the file. The rstudioapi solution worked. – Towery

@RichieCotton is there a way to automatically jump to that working directory and showing it content in 'Files' tab in RStudio? – Wendling

@Wendling At the top of the console, you should see the current working directory. To the right of that is a small arrow. Click that to show the current working directory in the file browser. – Boudreau

@RichieCotton, yes, nice feature I didn't know about, thanks. But if I have multiple scripts open in the Source window its name is displayed only after I ran one (and then I still have to click on the arrow). It would be best the Files view switches automatically to that of the viewed script. – Wendling

getSrcDirectory() does not work as it needs an object or function as input. – Licentious

@Towery @SimonChemnitz-Thomsen Note that you can use the following trick in order to get the script directory using utils::getSrcDirectory(). First thing you do in the script is to define a dummy function, then call utils::getSrcDirectory() using that function as parameter. Ex: dummy = function() {}; scriptdir = utils::getSrcDirectory(dummy); rm(dummy) – Diapophysis

@RichieCotton I thought you may want to edit your answer so that using utils::getSrcDirectory() actually works to retrieve the script directory...? The trick is to define a dummy function in the script as I describe in the comment I just posted. – Diapophysis

Answer 2

I know this question is outdated, but I was searching for a solution for that as well and Google lists this at the very top:

this.dir <- dirname(parent.frame(2)$ofile)
setwd(this.dir)

put that somewhere into the file (best would be the beginning, though), so that the wd is changed according to that file.

According to the comments, this might not necessarily work on every platform (Windows seems to work, Linux/Mac for some). Keep in mind that this solution is for 'sourcing' the files, not necessarily for running chunks in that file.

see also get filename and path of `source`d file

Easel

didn't work for me either: Error in dirname(parent.frame(2)$ofile) : a character vector argument expected – Genevivegenevra

did you look in the linked thread as well? I don't know any solution by now, but there are other people with similar errors. Maybe it is OS-specific? I used it on Windows 8, but some report it didn't work on mac ... – Easel

Same problem here as @Matt O'Brien on Linux. – Compliment

running on windows, same proble here as @bisounours_tronconneuse – Enquire

Working perfectly if sourced. – Galop

Worked for me in RStudio v1.0.143 on Windows 10. If you select "Source on save", it will work just fine (you can print out the detected directory with "cat"). If you select the lines then execute them, then the result is null. – Balcer

@Easel I think this answer should be edited based on these comments: mention that this works for windows and is not tested for other OS. Thanks. – Alfaro

This works for me on a Mac when sourcing a file. However, as @Balcer pointed out above, it will not work when executing the code interactively by highlighting a chunk and pressing Command + Return. In this case, since you're not sourcing a file, there is no source file to pull the working directory from. The answer need not specify platform-specific caveats. – Know

@MrSCoder Do you have any error message or alike? Maybe the solution is already outdated. Did you try another solution here? – Easel

Answer 3

For rstudio, you can automatically set your working directory to the script directory using rstudioapi like that:

library(rstudioapi)

# Getting the path of your current open file
current_path = rstudioapi::getActiveDocumentContext()$path 
setwd(dirname(current_path ))
print( getwd() )

This works when Running or Sourceing your file.

You need to install the package rstudioapi first. Notice I print the path to be 100% sure I'm at the right place, but this is optional.

Engel

Error in setwd(dirname(current_path)) : cannot change working directory – Alfaro

@helmo check your user has write permission on the target directory. – Engel

unfortunately "rstudioapi::getActiveDocumentContext()$path" gives me an empty string – Otolith

Answer 4

dirname(rstudioapi::getActiveDocumentContext()$path)

works for me but if you don't want to use rstudioapi and you are not in a proyect, you can use the symbol ~ in your path. The symbol ~ refers to the default RStudio working directory (at least on Windows).

If your RStudio working directory is "D:/Documents", setwd("~/proyect1") is the same as setwd("D:/Documents/proyect1").

Once you set that, you can navigate to a subdirectory: read.csv("DATA/mydata.csv"). Is the same as read.csv("D:/Documents/proyect1/DATA/mydata.csv").

If you want to navigate to a parent folder, you can use "../". For example: read.csv("../olddata/DATA/mydata.csv") which is the same as read.csv("D:/Documents/oldata/DATA/mydata.csv")

This is the best way for me to code scripts, no matter what computer you are using.

Neal

Answer 5

setwd(this.path::here())

works both for sourced and "active" scripts.

Smoulder

I get "Error in loadNamespace(x) : there is no package called ‘this.path’" - what am I missing? – Otolith

You have to install the package before, you can do this by launching install.packages("this.path") – Smoulder

I confirm that this works. It is the simplest among all answers. – Preserve

Answer 6

I realize that this is an old thread, but I had a similar problem with needing to set the working directory and couldn't get any of the solutions to work for me. Here's what did work, in case anyone else stumbles across this later on:

# SET WORKING DIRECTORY TO CURRENT DIRECTORY:
system("pwd=`pwd`; $pwd 2> dummyfile.txt")
dir <- fread("dummyfile.txt")
n<- colnames(dir)[2]
n2 <- substr(n, 1, nchar(n)-1)
setwd(n2)

It's a bit convoluted, but basically this uses system commands to get the working directory and save it to dummyfile.txt, then R reads that file using data.table::fread. The rest is just cleaning up what got printed to the file so that I'm left with just the directory path.

I needed to run R on a cluster, so there was no way to know what directory I'd end up in (jobs get assigned a number and a compute node). This did the trick for me.

Docilla

Answer 7

This answer can help:

script.dir <- dirname(sys.frame(1)$ofile)

Note: script must be sourced in order to return correct path

I found it in: https://support.rstudio.com/hc/communities/public/questions/200895567-can-user-obtain-the-path-of-current-Project-s-directory-

The BumbleBee´s answer (with parent.frame instead sys.frame) didn´t work to me, I always get an error.

Cuprum

Answer 8

The here package provides the here() function, which returns your project root directory based on some heuristics.

Not the perfect solution, since it doesn't find the location of the script, but it suffices for some purposes so I thought I'd put it here.

Ibadan

Thanks for this answer. The location of the current script can be harnessed by placing a call to here::set_here() in the source. – Pasto

When run in RStudio with project setup, here::here() returns the project working directory, not the script location. this.path::here() works regardless of project setup. – Preserve

Answer 9

The solution

dirname(parent.frame(2)$ofile)

not working for me.

I'm using a brute force algorithm, but works:

File <- "filename"
Files <- list.files(path=file.path("~"),recursive=T,include.dirs=T)
Path.file <- names(unlist(sapply(Files,grep,pattern=File))[1])
Dir.wd <- dirname(Path.file)

More easy when searching a directory:

Dirname <- "subdir_name"
Dirs <- list.dirs(path=file.path("~"),recursive=T)
dir_wd <- names(unlist(sapply(Dirs,grep,pattern=Dirname))[1])

Robbins

Problem with this solution is that is very slow. Searching for all files and store in a variable also takes up a lot of memory. – Alfaro

Answer 10

If you work on Linux you can try this:

setwd(system("pwd", intern = T) )

It works for me.

Naphthol

This just gives your home directory (where your shell starts). – Awe

It gives path to directory where script you run is. – Naphthol

pwd stands for present working directory. This will set the directory to whatever the current directory of the shell is. – Kiehl

pwd also works in PowerShell (which is currently considered the default shell on Windows), where it's an alias for Get-Location. – Pasto

@Kiehl actually it stands for print working directory – Uphemia

Answer 11

I understand this is outdated, but I couldn't get the former answers to work very satisfactorily, so I wanted to contribute my method in case any one else encounters the same error mentioned in the comments to BumbleBee's answer.

Mine is based on a simple system command. All you feed the function is the name of your script:

extractRootDir <- function(x) {
    abs <- suppressWarnings(system(paste("find ./ -name",x), wait=T, intern=T, ignore.stderr=T))[1];
    path <- paste("~",substr(abs, 3, length(strsplit(abs,"")[[1]])),sep="");
    ret <- gsub(x, "", path);
    return(ret);
}

setwd(extractRootDir("myScript.R"));

The output from the function would look like "/Users/you/Path/To/Script". Hope this helps anyone else who may have gotten stuck.

Tumpline

Answer 12

I was just looking for a solution to this problem, came to this page. I know its dated but the previous solutions where unsatisfying or didn't work for me. Here is my work around if interested.

filename = "your_file.R"
filepath = file.choose()  # browse and select your_file.R in the window
dir = substr(filepath, 1, nchar(filepath)-nchar(filename))
setwd(dir)

Needham

Is there a reason why you don't just use setwd( dirname(filepath) ) ? – Bollen

Answer 13

In case you use UTF-8 encoding:

path <- rstudioapi::getActiveDocumentContext()$path
Encoding(path) <- "UTF-8"
setwd(dirname(path))

You need to install the package rstudioapi if you haven't done it yet.

Emotional

Error in setwd(dirname(path)) : cannot change working directory – Alfaro

``` Error in setwd(dirname(path)) : cannot change working directory`` your solution not working please check your answer – Thyrse

Answer 14

I feel like a mocking bird, but I'm going to say it: I know this post is old, but...

I just recently learned you cannot call the api when running the script from Task Scheduler and a .bat file. I learned this the hard way. Thought those of you who were using any of the rstudioapi:: methods might like to know that. We run lots of script this way overnight. Just recently changed our path to include the api called so we could "dynamically" set the working directory. Then, when the first one we tried with failed when triggered from Task Scheduler, investigation brought that information about.

This is the actual code that brought this issue to light:
setwd(dirname(rstudioapi::getActiveDocumentContext()$path))

Works beautifully if you're running the script though!

Just adding my two cents as I know people still pull these threads up, thought it might be helpful.

Formenti

Answer 15

Most GUIs assume that if you are in a directory and "open", double-click, or otherwise attempt to execute an .R file, that the directory in which it resides will be the working directory unless otherwise specified. The Mac GUI provides a method to change that default behavior which is changeable in the Startup panel of Preferences that you set in a running session and become effective at the next "startup". You should be also looking at:

?Startup

The RStudio documentation says:

"When launched through a file association, RStudio automatically sets the working directory to the directory of the opened file." The default setup is for RStudio to be register as a handler for .R files, although there is also mention of ability to set a default "association" with RStudio for .Rdata and .R extensions. Whether having 'handler' status and 'association' status are the same on Linux, I cannot tell.

http://www.rstudio.com/ide/docs/using/workspaces

Forcible

For sure RStudio does not make that assumption. – Afterheat

It behaves the way I described it on my machine. I have not done anything special to the RStudio Preferences. – Forcible

Does not do that on Linux :) – Afterheat

"When launched through a file association" is the key condition here. Some people might be launching Rstudio via a shortcut or a command in the terminal. You need to open the file and have the default for opening .R files be Rstudio. If you open Rstudio first (then open the file) it will not work as described. Through a file association, the above answer works in windows and mac (possibly not linux as @Afterheat points out - but I can't verify this as I don't have a linux machine). – Cousins

Answer 16

dirname(parent.frame(2)$ofile)  

doesn't work for me either, but the following (as suggested in https://mcmap.net/q/101731/-getting-path-of-an-r-script) works for me in ubuntu 14.04

dirname(rstudioapi::getActiveDocumentContext()$path)

Barouche

Error: 'getActiveDocumentContext' is not an exported object from 'namespace:rstudioapi' also in Ubuntu 14.04 – Cardiology

Maybe you can try install rstudioapi package first. – Barouche

That's strange. I'm using R-3.2.4 in a 32-bit ubuntu 14.04. I hope it is not because of operating system or different versions of R. – Barouche

Answer 17

Here is another way to do it:

set2 <- function(name=NULL) {
  wd <- rstudioapi::getSourceEditorContext()$path
  if (!is.null(name)) {
    if (substr(name, nchar(name) - 1, nchar(name)) != '.R') 
      name <- paste0(name, '.R')
  }
  else {
    name <- stringr::word(wd, -1, sep='/')
  }
  wd <- gsub(wd, pattern=paste0('/', name), replacement = '')
  no_print <- eval(expr=setwd(wd), envir = .GlobalEnv)
}
set2()

Ferro

Answer 18

Building on @Richie Cotton's, if you use RStudio, here is a snippet that will set the working directory to the current script in every of the cases of script source, run, or knitted:

# Change WD to current file
# - source and knit
srcdir <- getSrcDirectory(function(){})[1]
if (srcdir=="") {
    # - run
    srcdir <- dirname(rstudioapi::getActiveDocumentContext()$path)
}
setwd(srcdir)
rm(srcdir)

Uphemia