Software Setup

Software Requirements

This workshop assumes you have the R, RStudio and Git and Bash Shell software installed on your computer and a personal GitHub account. You will also need some geospatial system libraries installed.


R can be downloaded here.


RStudio is an environment for developing using R.

It can be downloaded here. You will need the Desktop version (> 1.0) for your computer.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.


Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on “Next”.
    2. Click on “Next”.
    3. Keep “Use Git from the Windows Command Prompt” selected and click on “Next”. If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on “Next”.
    5. Keep “Checkout Windows-style, commit Unix-style line endings” selected and click on “Next”.
    6. Keep “Use Windows’ default console window” selected and click on “Next”.
    7. Click on “Install”.
    8. Click on “Finish”.
  3. If your “HOME” environment variable is not set (or you don’t know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME “%USERPROFILE%”

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

Mac OS X

The default shell in all versions of Mac OS X is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal.


The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Geospatial Libraries

Some of the workflows require geospatial packages like sf and have additional system requirements. Follow the installation instructions in sf package documentation according to your operating system.

Git & GitHub

Required for the Version Control part of the the course

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

You will also need an account at

Basic GitHub accounts are free. We encourage you to create a GitHub account if you don’t have one already. Please consider what personal information you’d like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.


Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent “mavericks” installer from this list. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled “snow-leopard” available here.


If Git is not already available on your machine you can try to install it via your distro’s package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo yum install git.

Research Compendium Exercise

For the final practical sessions, we will need to use LaTeX. If you don’t have LaTeX installed, consider installing TinyTeX, a custom LaTeX distribution based on TeX Live that is small in size but functions well in most cases, especially for R users.


Check docs before before installing.

devtools requirements

You might also need a set of development tools to install and run devtools. On Windows, download and install Rtools, and devtools takes care of the rest. On Mac, install the Xcode command line tools. On Linux, install the R development package, usually called r-devel or r-base-dev.

Install R dependecies

To be able to run materials locally, you will also need to install all the required R packages. Run the following code:

dependencies <- c("assertr", "checkmate", "cowsay", "data.table", 
                  "dataspice", "devtools", "DT", "fs", "gapminder", "geosphere", 
                  "ggthemes", "gitcreds", "glue", "here", "janitor", "jsonlite", 
                  "knitr", "leaflet", "listviewer", "magrittr", "plotly", "raster", 
                  "reprex", "rmarkdown", "sf", "skimr", "sloop", 
                  "spData", "stringr", "testthat", "tidyr", "tidyverse", "tmap", 
                  "usethis", "vroom")

# install CRAN dependencies

# install github dependencies

Package Development section

dependencies <- c("cowsay", "devtools", "rmarkdown", "pkgdown", "testthat", 

# install CRAN dependencies

Research Compendium with rrtools section

# install rrtools

# install github dependencies
dependencies <- c("dplyr", "ggplot2", "ggthemes", "gitcreds", "rticles", "Cairo")

# install CRAN dependencies

#install github dependencies

# install tinytex


1. Are there any advantages or disadvantages to setting up a github account with our university email address? Is it possible to change emails say when we finish our PhD?

I personally prefer to use a non-institutional email for registering accounts to platforms I want smooth access to regardless of affiliation. However, there are advantages associated with affiliation with an academic institution on GitHub, namely that you get a free developer account. The most important benefit of that is that it gives you unlimited public AND private repositories.

You can however add your academic email as a secondary email which will allow you to benefit from this academic research discount. You can also just use your academic address from the start and just change it once you move on.

Find out more about claiming an academic discount here.