EES 3310/5310

Tools

Software Tools for the Lab

Web-Based Tools for Lab

Installing Tools

Installing

Installing

If you have a Mac or Linux you may already have git installed. Test it by opening up a terminal window and typing which git. If you get a response like /usr/bin/git then it’s installed. If there is no response, then you need to install git.

  • Windows:
    • Download and install git from https://git-scm.com
      • Choose the default options for the installer.
    • Optionally, you might want to also install Tortoise Git, which integrates git into the Windows explorer, so you can execute git commands from the context menu when you right-click on files or directories in the explorer. You can download Tortoise Git from https://tortoisegit.org/
  • MacOS:
    • If git is not already installed on your computer, you can download and install it from https://git-scm.com
  • Linux:
    • If git is not already installed, you can install it from your distribution’s package manager:
      • sudo apt-get install git for Debian or Ubuntu
      • sudo yum install git or sudo dnf install git for Fedora, Red Hat, and related distributions.

Introducing Youself to

Whichever operating system you’re using, after you install git you will need to introduce yourself to git (you only need to do this once). It is important for git to knows your name and email address so it can keep track of who is editing files when you are working collaboratively and so it gives you credit for the files you have authored and edited.

  1. Open a terminal prompt:

    • On Windows, open a “git bash” window (git will give you the option to do this when it finishes installing) or you can do so from the Windows Start menu, under “Git”.
    • On MacOS or Linux, open a regular terminal window (on MacOS, you can find the terminal in the “applications” with Finder)

  2. Type the following at the terminal prompt:

    git config --global user.name "Your Name"
git config --global user.email your.name@vanderbilt.edu

    using your real name and email.

You only need to introduce yourself to git one time after you install it. Then it will remember who you are every time you use it.

Getting an account on GitHUB

  • Go to https://github.com and register for a free account
  • After you have set up your account, go to https://education.github.com/students and register your account for the free extras you can get as a student.
  • Send an email to Prof. Gilligan and Mr. Belanger to let us know your GitHUB account name. You can send the email from this link

Installing RStudio

  • Go to the download page for the free desktop edition of RStudio at https://www.rstudio.com/products/rstudio/download/#download and download the installer for your operating system. Windows, MacOS, and the Debian, Ubuntu, Fedora, RedHat, and openSUSE editions of Linux are all supported.

    There are other versions of RStudio (an expensive professional edition and a server edition). You want the free desktop edition. Be sure you get versoin 1.4 (the latest version, as of January 2021). Version 1.4 has important new features that previous versions did not have.

  • Run the installer.

  • After the installer finishes running, run RStudio .

    • When RStudio starts up, the lower left part of the screen should have a window that displays the R version, saying something like this:

      R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

      The details will be different depending on your operating system, but if you see something like this, RStudio correctly found R on your computer.

    • Open the “Tools” menu, and click on the “Global Options” choice.

      • Go to the “Git/SVN” tab and click “enable version control interface for RStudio projects”. If RStudio can find the git program on your computer, it will appear in the “git executable” field. If RStudio can’t find it, you can help it by browsing to the git program.
      • If you have installed on your computer (remember that this is optional), click on the SWeave tab, and select “knitr” for weaving .Rnw files, and choose pdfLaTeX for typesetting files into PDF.

Optional Tools:

Installing the tinytex package

It is optional to install the tinytex package. You will be able to do all the work for the labs without it, but if you do install it, it will give you the option to produce nicely formatted PDF output from your RMarkdown files (for lab reports, presentations, etc.).

The R tinytex package installs a sophisticated typesetting system called LaTeX on your computer. RMarkdown uses this system to generate PDF output.

The tinytex package needs to download a lot of files from the internet, and it can take 10 minutes or more to do so, even on a fast connection. So it’s a good idea to wait until you can let your computer run for a while, and until you’re connected to a good fast internet connection, preferably one that doesn’t charge you for data.

To install tinytex, go to the RStudio console, and you type the following:

install.packages('tinytex')
tinytex::install_tinytex()

If you want to uninstall tinytex later, you can just type this command at the RStudio console:

tinytex::uninstall_tinytex()`

Installing GitAhead

It is optional to install GitAhead. You will be able to do everything you need for the lab using regular and RStudio , but you may find it useful to install the GitAhead software on your computer. GitAhead is a free graphical interface that works with git and allows you to do almost everything you might want to do using a simple point-and-click interface.

GitAhead can also make it easier to understand what git is doing and when you need to commit files and push your commits to GitHub .

GitAhead is available for Windows, MacOS, and Linux, and you can get it from https://gitahead.github.io/gitahead.com/ .

Resources for Learning More

and RStudio Resources

and GitHUB Resources

  • There is a lot of free documentation about git at the git-scm website, including a full Git reference manual and a free online book, Pro Git

  • Professor Jenny Bryan at the University of British Columbia, has written a lot of helpful tutorial material specifically about using git and GitHub with RStudio at Happy Git and GitHub for the useR .

    Professor Bryan has also posted a detailed video tutorial at the RStudio Webinars and Videos page . This tutorial walks you through all the steps of setting up git with RStudio and how to use it to keep track of your edits and revisions, and synchronize your work with GitHub (this serves three functions: backing up your data to the cloud, sharing your data with other people, and collaborating on writing code or documents with other people).

Image Credit: NASA Terra/CERES

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Copyright 2022, Jonathan Gilligan.

Based on ESPM 157, by Carl Boettiger.