Intro to Bash Scripting

Creating a simple R project set up tool.
Command line
R
Author

Brenden Smith

Published

November 15, 2023

And I thought R gave me super powers…

Introduction

Recently, I’ve been having fun with Linux. I really didn’t know much about Linux or how it was different from MacOS or Windows. All I really knew was that very smart people use it and many computers depend on it!

By recommendation of a friend, I tried loading Pop!_OS on an old Macbook Air I had laying around. I quickly learned how lightweight many distributions of Linux are, and how customizable they can be.

For anyone familiar with Linux you know that, even when you are just setting up a computer with the OS, you have to start using a bit of the command line. I had used this before learning some helpful functions with git, but nothing has exposed me to the command line and Bash more than this endeavor.

I have been inspired by this exposure and want to start learning more about the functionality of Bash. As a part of this, I wanted to try creating a Bash script of my own that I could implement into my current workflows.

The Idea

I work primarily in R. And I love a good R Project. One of my usual habits for creating a project include adding sub folders and a starting script. I realized Bash is really good for doing this! So with some basic commands, I wanted to create a single executable script that makes a new R project, default sub folders, and a starting script.

Writing the Script

For the script I wanted several tasks accomplished:

  1. Created an R project file within a contained folder
  2. Several sub-directories within that folder (data-raw, data, ref, output)
  3. A blank R script file

To start, I had the script ask for the name of the project. This was done by using echo to print the prompt, then read takes in the name of the project.

Code 
#!/bin/bash

echo "Please enter your project title: "

read name

Next, I had to make the script navigate to the folder I want my projects in (for me, this is a folder on my desktop called ‘R’). Then, I had a directory made with sub-folders using mkdir -p. Here we use $name to use the variable stored as the name of the project. Within the {} are the names of the sub-folder I most commonly use. This could be anything you like though! Lastly, touch creates the blank R script.

Code 
cd Desktop/R

mkdir -p $name/{data-raw,data,ref,output}

cd $name

touch script.R

Next, we have an extra step that allows RStudio to open our new project properly. When I first tried this script out, I created a blank file with the .Rproj extension to set up the project. This immediately gave me problems when I tried to open the project. Specifically, I recall an issue with the version being unspecified.

After a bit a research, I discovered that files with .Rproj are nothing really but a .txt file. I opened one of my existing R projects with a text editor and copied the contents exactly into the code chunk below. I wrote this text into the new R project. After some trial and error, I can confirm this method works!

Code 

echo -e 'Version: 1.0

RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default

EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8

RnwWeave: Sweave
LaTex: pdfLaTeX' >> $name.Rproj

The last few lines of code echo some responses to the terminal and launch the new R project.

Code 
echo "Project $name has been created."
echo "It is stored in the R directory."
echo "Opening project now..."

open $name.Rproj

Making it Accessible

For me, personally, I like to be able to execute my scripts without worrying where I am in the terminal. Once my script was working properly, I moved it to the /usr/local/bin folder.

Code 
mv setupr /usr/local/bin

And that’s it! You can find the full script code below. I hope this is helpful! It was certainly useful to me to learn more about bash and make a useful script to help me set up projects.

Full Script Code

Code 
#!/bin/bash

echo "Please enter your project title: "

read name

cd Desktop/R

mkdir -p $name/{data-raw,data,ref,output}

cd $name

touch script.R

echo -e 'Version: 1.0

RestoreWorkspace: Default
SaveWorkspace: Default
AlwaysSaveHistory: Default

EnableCodeIndexing: Yes
UseSpacesForTab: Yes
NumSpacesForTab: 2
Encoding: UTF-8

RnwWeave: Sweave
LaTex: pdfLaTeX' >> $name.Rproj

echo "Project $name has been created."
echo "It is stored in the R directory."
echo "Opening project now..."

open $name.Rproj