Setup
Overview
Time: 10 minObjectives
Install R
Install RStudio
Install Git for Windows (if you are a windows user)
Set up a GitHub Account
Software setup
To follow along you need to set up three things before the workshop:
- Github account (use existing or create new account)
- install Git for Windows (Windows users only)
- install R & RStudio (Two separate installations OR you may use the UIC Virtual Lab)
*NOTE You will not be able to follow along with the hands-on portion of this workshop using the UIC Virtual Lab. You must use the software detailed below through installations on your own computer or on a lab computer.
See instructions below for all three setup requirements and the UIC Virtual lab option:
GitHub Account
You will need an account at GitHub.com.
You can signup for a free Github account at https://github.com/signup.
Through the Github education program,
students get additional free services beyond the basic free account.
If you are concerned about what personal information (specifically contact information) is revealed through GitHub you may review these
instructions
for keeping your email address private provided by GitHub.
Git
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 github.com. You will need a supported web browser.
You will need an account at github.com for parts of the Git lesson. 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.
- Download the Git for Windows installer.
- Run the installer and follow the steps below:
- Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
-
From the dropdown menu, "Choosing the default editor used by Git", select "Use the Nano editor by default" (NOTE: you will need to scroll
up to find it) and click on "Next". - On the page that says "Adjusting the name of the initial branch in new repositories", ensure that "Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
- Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
- Select "Use bundled OpenSSH".
- Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
- Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
- Ensure that "Use Windows' default console window" is selected and click on "Next".
- Ensure that "Default (fast-forward or merge) is selected and click "Next"
- Ensure that "Git Credential Manager" is selected and click on "Next".
- Ensure that "Enable file system caching" is selected and click on "Next".
- Leave all options unchecked on "Configuring experimental options" and click "Next".
- Click on "Install".
- Click on "Finish" or "Next".
This will provide you with both Git and Bash in the Git Bash program.
Video Tutorial
For macOS, install Git for Mac
by downloading and running the most recent "mavericks" installer from
this list.
Because this installer is not signed by the developer, you may have to
right click (control click) on the .pkg file, click Open, and click
Open on the pop up window.
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.
Video Tutorial
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 dnf install git.
R
R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.
Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.
Video Tutorial
Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.
Video Tutorial
Instructions for R installation on various Linux platforms (debian,
fedora, redhat, and ubuntu) can be found at
<https://cran.r-project.org/bin/linux/>. These will instruct you to
use your package manager (e.g. for Fedora run
sudo dnf install R and for Debian/Ubuntu, add a ppa
repository and then run sudo apt-get install r-base).
Also, please install the
RStudio IDE.
Install the videoconferencing client
If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.
Set up your workspace
Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:
- Two monitors: If you have two monitors, plan to have the tool you are learning up on one monitor and the video conferencing software on the other.
- Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
- Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.
About the Data Used in this Workshop:
This workshop utilizes the materials found in the following GitHub repository: https://github.com/UCSBCarpentry/R-repro-pub
instructions on how to download and work with these materials will be described in the workshop pages to follow.
Key Points
Install R
Install RStudio
Install Git for Windows (if you are a windows user)
Set up a GitHub Account