Chapter 6 Paths and projects

In R, understanding how to tell the program where to find or save data files on your computer is essential. This is done using file paths, which are like giving R specific directions to locate files in your computer’s filing system. Let’s explore the basics of paths and how you can use them in R.

6.1 File paths

Think of a file path like a map or set of directions to a location. If you wanted to tell someone where your favorite restaurant is, you’d give them directions from a common starting point, like a bus stop or a well-known landmark. Similarly, a file path gives R the directions it needs to find a file on your computer.

Files on a computer are stored in hierarchical folders (also known as directories). On a Mac you can use the Finder program to navigate these folders while on a Windows machine you can use Windows Explorer.

Try that now! Make sure that you can use these programs to navigate around your computer to find, move and rename files.

6.2 File organisation

When managing your research projects, it’s a good idea to keep your files organised in some sensible structure rather than simply dumping all your files chaotically into the same folder. Be kind to your future self and get organised! Exactly how you do that is a matter of personal taste but my own personal preference is to set up a folder per project, and then, within that folder to create folders for Data, Code (for my R scripts), Plots (graphs produced by R), and Writing (e.g. for Word documents with my project write-up).

6.3 Two types of paths

There are two types of file paths (1) Absolute Paths and (2) Relative Paths.

6.3.1 1. Absolute Paths: The Exact Location

An absolute path gives the complete route to a file, starting from the “root” (or base) of your computer’s filing system.

Here’s how they look on different systems:

On Windows: Paths begin with the drive letter, usually C:/. For example:
```
C:/Users/YourUsername/Documents/Project/myData.csv
```

On macOS: Paths start from /Users/, like this:

/Users/YourUsername/Documents/Project/myData.csv

Important Note: While Windows normally uses backslashes (\) in paths, R needs you to replace them with forward slashes (/). R will interpret forward slashes correctly on both Windows and Mac.

How to Copy an Absolute Path: - On Windows: Hold the Shift key, right-click the file, and select “Copy as path”. - On macOS: Hold down the Option key, right-click the file, and select “Copy [filename] as Pathname”.

Using absolute paths tells R precisely where your file is located on your computer. However, absolute paths have a downside: they’re specific to each computer. If you share your code with someone else, they’d have to change the path to match their system.

6.3.2 2. Relative Paths: Paths That Start from the Project Folder

A relative path is a shortcut that starts from your current folder in R instead of from the root directory of your computer. It’s like giving directions from a specific starting point, like “turn left at the library,” instead of giving an address.

For example: - If your project folder is at /Users/YourUsername/Documents/Project/, you could use a relative path to refer to files inside that folder. - So instead of typing the full absolute path, you might use: data/myData.csv

Using relative paths is particularly helpful because your code can be easily shared and used on other computers without needing changes to the file paths.

6.4 R and file structure

To load data into R you need to use file paths which can be annoying to type.

e.g. x <- read.csv(“C:/Users/Owen/Documents/Analysis/SurveyAnalysis1/Data/myData.csv”)

There are two ways to make life easier for yourself: (1) you can set the “working directory” for your project; (2) you can set up an R Project.

It is true that RStudio has a data import wizard to help with this, but setting a working directory or using Projects is recommended. I will briefly outline these two options.

Let’s refine it further for clarity. I’ll remove some technical jargon and break down the steps with simple language and context, aiming for a smooth flow for non-experts.

6.5 Setting the Working Directory in R

In R, the working directory is like the “home base” folder where R looks for files by default. Setting the working directory means you don’t have to type out the entire location (path) of a file each time you want to use it. This makes your code simpler and easier to manage.

6.5.1 Finding Your Current Working Directory

To see where R is currently looking for files:

Open RStudio.
Type getwd() and press Enter.

This command shows the “working directory” R is using right now. Any file in this folder can be loaded into R without typing the full file location.

For example, if you have a file called myData.csv in the working directory, you can load it simply by typing:

x <- read.csv("myData.csv")

instead of the longer path:

x <- read.csv("C:/Users/YourName/Documents/Project/Data/myData.csv")

6.5.2 Changing the Working Directory

If your files are in a different folder, you can change the working directory using the command setwd(). Just replace "path/to/your/folder" with the path to the folder you want to use.

Example:

setwd("C:/Users/YourName/Documents/Project/")

After setting the working directory this way, you can access any files in that folder without typing out the full path. For example:

x <- read.csv("Data/myData.csv")  # Shorter and easier to read

6.6 Using Projects in RStudio: A Simpler Way to Set the Working Directory

When you create an R Project in RStudio, it generates a file with an .Rproj suffix in your project folder. This .Rproj file not only serves as a shortcut to open the project but also ensures that RStudio sets the project folder as the working directory every time you open the project file. This feature simplifies managing file locations by keeping all paths relative to the project directory.

6.6.1 Steps to Create an R Project

First, create a folder for your project files in Finder (Mac) or Windows Explorer (Windows). For example, create a folder called MyProject.
Open RStudio and go to File > New Project.
Select Existing Directory and browse to your new folder.
Click Create Project.

This setup creates a file called MyProject.Rproj. From now on, open this file to start RStudio with the working directory automatically set to the project folder. You don’t need to use setwd() or worry about typing long paths.

To double-check, you can type getwd() after opening the project, and it will show your project folder as the working directory.

6.6.2 Organizing Files Within Your Project

Now that your project is set up, you can organize your files within the project folder. Here’s a common way to organize:

data – for all data files
scripts – for R code files
plots – for graphs and images

This folder organization makes it easy to find files, keeps everything related to the project in one place, and helps you share your work with others if needed.

By using R Projects and organizing your folders, you’ll find that working with files in R becomes simpler and more efficient.