Software set up instructions for workshop

1. R set up

During R portion of the class, we will be using RStudio Cloud, a hosted version of R and RStudio in the cloud. The only thing you need to do to prepare for class is sign up for a free RStudio Cloud account at, and plan to bring your laptop with you. If you do not have a laptop you can use one of the computers in the lab.

On the day of class, I’ll provide you with an RStudio Cloud project that contains materials you need.

In the unlikely event that there are problems with the internet connection, you may want to have a local installation on your computer as a backup. As a backup, please install the following in order:

  1. A recent version of R , which is available for free at <>
  2. A recent version of RStudio IDE , available for free at <>
  3. The set of relevant R packages, which you can install by connecting to the internet, opening RStudio, and running:

install.packages(c(“babynames”, “fivethirtyeight”, “formatR”, “gapminder”, “hexbin”, “mgcv”, “maps”, “mapproj”, “nycflights13”, “rmarkdown”, “skimr”, “tidyverse”, “viridis”))

If you’re a new R user, it’s possible that installing R will be challenging. In that case, feel free to ignore the backup instructions and just count on RStudio Cloud. We can talk about local installation during the workshop, and I’ll help troubleshoot.

2. Python set up

Python is a popular language for scientific computing, and great for general-purpose programming as well. Installing all of its scientific packages individually can be a bit difficult, so we recommend an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x.

For Python we will be using the Jupyter notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

  • Download and install the Python 3 Anaconda installer.
  • Use all of the defaults for installation and if asked make sure to check Make Anaconda the default Python.


We recommend the all-in-one scientific Python installer Anaconda.

  1. Download the Python 3 Anaconda installer that matches your operating system and save it in your home folder.
  2. Open a terminal window.
  3. Type bash Anaconda- and then press tab. The name of the file you just downloaded should appear.
  4. Press enter. You will follow the text-only prompts. When there is a colon at the bottom of the screen press the down arrow to move down through the text. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).

Testing your installation

Open the Anaconda Navigator application as you would any other program in your computer (in the Apps folder on Mac, or the Start button on Windows). The Anaconda Navigator provides a graphical user interface (or GUI) to start Python in several different ways, as well as other useful Python related tasks.

Start the Jupyter Notebook application, which should open the Jupyter file navigator in your default web browser. It may take a few minutes the first time. To open a Jupyter notebook either locate an existing notebook file (.ipynb file) and click the link containing that notebook’s filename, or create a new notebook by clicking the New button in the top right corner, and select Python 3. To close Jupyter, just close your browser.

Software Carpentry maintains a list of common issues that occur during installation that may be useful for our class here: Configuration Problems and Solutions wiki page.

3. Install Git

Follow instructions in Chapter 6 Install Git available at Happy Git With R

4. Create a GitHub account at