Sourcing R Files from Parent Directory via Shell

As a programmer, you’re accustomed to navigating through directories and files with ease. However, when working with scripting languages like R, the relative file locations can be a source of confusion. In this article, we’ll delve into how to source an R file from the parent directory using the shell.

Understanding Relative File Locations in R

In R, relative file locations are always relative to the current working directory (CWD). This means that if you’re sourcing a file in one directory, it will look for the file in the CWD. If you want to source a file from a different directory, you need to explicitly set your working directory using the setwd() function.

Setting Your Working Directory

To source an R file from a specific directory, you first need to set your working directory using the setwd() function. Here’s an example:

> setwd("~/some/location")

This sets your working directory to /Users/your_username/some/location.

Sourcing Files from Different Directories

Once your working directory is set, you can source files relative to that CWD. For instance, if you’re in the /Users/your_username/some/location directory and you want to source a file named script.R, you can do so like this:

> source("script.R")

This will source the script.R file from the current working directory.

However, what if your source file is in the parent directory but references files relative to its location? You can use the chdir=TRUE option in the source() function to temporarily change the working directory to the directory containing the source file.

Using the `chdir` Option

The chdir option allows you to specify a temporary change to your working directory for the duration of the source evaluation. Here’s an example:

> source("../another_script.R", chdir = TRUE)

This will temporarily set your working directory to the directory containing the another_script.R file.

What Happens After Sourcing?

After sourcing a file using the chdir option, your working directory is set back to what it was prior to running the source() function. This means that you need to manually reset your working directory if you want to continue working from a different location.

Resetting Your Working Directory

To reset your working directory, you can use the getwd() function:

> getwd()

This will print out the current working directory.

Tips and Best Practices

Always set your working directory explicitly when sourcing files from different directories.
Use the chdir option to temporarily change your working directory for source evaluations.
Be mindful of how relative file locations work in R, especially when referencing files in different directories.
Use the getwd() function to check your current working directory before and after sourcing files.

Common Issues and Workarounds

Error: cannot open the connection: Make sure you have entered the correct path to the source file. Double-check that the file exists at the specified location.
Warning message: cannot open file: Ensure that the file you’re trying to source actually exists in the specified directory. If it doesn’t, try using a full path or relative path.

Conclusion

Sourcing R files from different directories can be challenging, but understanding how to work with relative file locations and using the chdir option can simplify your workflow. By setting your working directory explicitly and using the chdir option, you’ll be able to source files efficiently and avoid common issues like errors and warnings.

Remember to always set your working directory before sourcing files from different directories. With practice and experience, you’ll become proficient in navigating R’s file system and sourcing files with ease.

Example Use Case

Here’s an example use case that demonstrates how to source a file from the parent directory using the chdir option:

# Set working directory to /Users/your_username/some/location
setwd("~/some/location")

# Sourcing file "script.R" from current working directory
source("script.R")

# Sourcing file "another_script.R" from parent directory with chdir=TRUE
source("../another_script.R", chdir = TRUE)

This code snippet sets the working directory to /Users/your_username/some/location and then sources two files: script.R and another_script.R. The second source call uses the chdir option to temporarily change the working directory to the parent directory.

Last modified on 2023-11-12