Work Environment

“Data is the new oil.” — Clive Humby

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What does workspace mean?

In R, the workspace contains the objects you have created in the global environment during your session, such as vectors, data frames, and functions. RStudio shows these objects in the Environment pane.

The working directory is a folder on your computer. R uses it as the starting point for relative file paths. The files in a folder and the R objects in your workspace are different things: reading a CSV file creates an object in R, while the CSV file remains on disk.

An RStudio project organizes your work in a project folder and stores project settings in an .Rproj file. Opening the project sets the working directory to that folder. We return to projects at the end of this page.

Work Environment in RStudio from Unit 1

Little reminder from Unit 1: This is the Integrated Development Environment (IDE) of RStudio. It contains

1. the script aka text editor,
2. the console for executing code,
3. the Environment pane for R objects and the History pane for previous commands,
4. the Files pane for browsing files on disk, along with panes for plots, packages, and help.

Now let’s have a closer look at the environment after you have gotten to know the script and the console.

Project directory structure

If you have a project with many data files, analysis scripts or other it is highly recommended that you create a directory structure under your main project folder to store and organize all these files. For example, you might have a project folder under C:/geomoer/Project1, whose directory structure might look like this

Project directory structure

The key elements of a project folder include:

• a Data/ folder
• a Process/ folder and
• an Output/ folder.

The Data/ folder contains all data files which include all raw data files as well as all subsets and manipulated versions of these data files.

The Process/ folder contains sub-directories with analysis files, e.g. R scripts and figures or maps that may be produced by the analyses.

And an Output/ folder stores the final reports e.g. .docx, .pdf, .Rmd files and presentations e.g. .pptx, or .html files.

Understanding the directory structures

R resolves a relative file path from the current working directory. Saving or opening an R script in another folder does not by itself change the working directory.

In this example, user Geomoer has a project folder called Project1 containing a Data/ folder and a Process/ folder. The file data.csv is in Data/, and the R session’s working directory is C:/geomoer/Project1/Process. Running the following line produces an error:

data <- read.csv("data.csv")

Error in file(file, "rt"): cannot open the connection

R looks for data.csv in Process/, where it does not exist.

An R session’s working directory can be verified by typing the following command:

getwd()

[1] "C:/geomoer/Project1/Process"

The working directory is also the starting point for relative paths when writing files. A path such as Data/data.csv is still relative; including a folder name does not make it an absolute path.

There are two options to resolve this problem.

The first is to set the working directory to the folder that contains data.csv using the setwd() function, then read the file:

setwd("C:/geomoer/Project1/Data")
dat <- read.csv("data.csv")

The second is to specify an absolute path in the read.csv() call. This works regardless of the current working directory:

dat <- read.csv("C:/geomoer/Project1/Data/data.csv")

Hint: Pay attention to the quotation marks.

Relative and absolute paths

Hard-coded absolute paths make it difficult to share the project folder with someone else who may place it under a different folder such as D:/Uni/R/Test/Project1/.

The user would need to modify paths that refer to C:/geomoer/Project1/. A relative path can avoid this. For the following example, first reset the working directory to Process/ if you changed it above:

setwd("C:/geomoer/Project1/Process")
dat <- read.csv("../Data/data.csv")

The two dots .. tell R to move up the directory hierarchy relative to the current working directory. So in our working example, ../ tells R to move out of the Process/ folder and up into the Project1/ folder. The relative path ../Data/data.csv tells R to move out of the Process/ directory and over into the Data/ directory before attempting to read the contents of the data.csv data file.

After moving the project, the same relative path works as long as Data/ and Process/ keep the same arrangement and the working directory is again Process/. You still need to select that working directory at its new location. An RStudio project can help establish a consistent starting directory, as shown below.

Absolute and relative paths An absolute (or full) path points to the same location in a file system, regardless of the current working directory. To do that, it must include the root directory. For example: C:/geomoer/Project1/Data/data.csv

By contrast, a relative path starts from the current working directory. From C:/geomoer/Project1/Process, use ../Data/data.csv. From C:/geomoer/Project1, use Data/data.csv.

Important Note to Windows Users:
R gets confused if you use a path in your code like:

c:\mydocuments\myfile.txt

This is because R sees "\" as an escape character. Instead, use:

c:\\my documents\\myfile.txt

or

c:/mydocuments/myfile.txt

Either will work. We use the second convention throughout this platform.

RStudio projects

When you open an .Rproj file in RStudio, the working directory is set to the folder containing that file. For example, if Project1.Rproj is in C:/geomoer/Project1/, use a path relative to this project folder:

dat <- read.csv("Data/data.csv")

This also works after moving the whole project folder and opening the .Rproj file at its new location. Keep the working directory at the project folder while running these examples. If you change it with setwd(), relative paths are resolved from the new working directory. Use getwd() to check your current location.

The .Rproj file stores project settings; your scripts and data remain separate files in the project folder. See the RStudio Projects documentation for more information.

Now move to the packages…