Software Carpentry - R Workshop @ George Washington University

Sep 23-24, 2019

9:00 am - 4:30pm

Instructors: Dan Kerchner, Laura Wrubel

Helpers: Jason Hurlburt, Liem Nguyen, Monica Rigucci, Marco Suarez

General Information

This workshop is full.

To be put on the waitlist, email: lwrubel@gwu.edu

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: As noted in the EventBrite information page, the course is aimed at GWU graduate students, faculty, and other researchers. Advanced undergraduates are also welcome. (Affiliates of CTSI are also invited.) You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Rooms 301/302 @ Gelman Library, 2130 H St NW, Washington, DC. Get directions with OpenStreetMap or Google Maps.

When: Sep 23-24, 2019. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email lwrubel@gwu.edu or kerchner@gwu.edu for more information.

Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey

Schedule

Day 1

Before Pre-workshop survey
09:00 Automating Tasks with the Unix Shell
10:30 Morning break
12:00 Lunch break
13:00 R for Reproducible Scientific Analysis
14:30 Afternoon break
16:00 Wrap-up
16:30 END

Day 2

09:00 Version Control with Git and RStudio
10:30 Morning break
12:00 Lunch break
13:00 R for Reproducible Scientific Analysis
14:30 Afternoon break
16:00 Wrap-up
16:30 Post-workshop Survey
16:40 END

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.

Syllabus

The Unix Shell

  • Files and Directories
  • History and Tab Completion
  • Pipes and Redirection
  • Looping Over Files
  • Creating and Running Shell Scripts
  • Finding Things
  • Reference...

R for Reproducible Scientific Analysis

  • Introduction to R and RStudio
  • Reading Data
  • Data Structures
  • Exploring and Subsetting Data
  • Data Visualization
  • Creating Functions
  • Writing Data
  • Data Frame Manipulation
  • Producing Reports with knitr
  • Reference...

Version Control with Git and RStudio

  • Creating a Repository
  • Recording Changes to Files: add, commit, ...
  • Viewing Changes: status, diff, ...
  • Ignoring Files
  • Working on the Web: clone, pull, push, ...
  • Resolving Conflicts
  • Open Licenses
  • Where to Host Work, and Why
  • Reference...

Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

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 below:
    1. 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.
    2. Select "Use the nano editor by default" and click on "Next".
    3. Keep "Git from the command line and also from 3rd-party software" 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. Select "Use the native Windows Secure Channel library", and click "Next".
    6. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    7. Select "Use Windows' default console window" and click on "Next".
    8. Leave all three items selected, and click on "Next".
    9. Do not select the experimental option. Click "Install".
    10. 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.

To connect Git with your RStudio, after having installed RStudio, follow the Setup instructions for RStudio + Git for Collaboration and Reproducibility

The default shell in all versions of macOS 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. You may want to keep Terminal in your dock for this workshop.

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.

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

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. 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.

To connect Git with your RStudio, after having installed RStudio, follow the Setup instructions for RStudio + Git for Collaboration and Reproducibility

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.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are BBEdit or Sublime Text.

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Video Tutorial

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.

You can download the binary files for your distribution from CRAN. Or you can use your package manager (e.g. for Debian/Ubuntu run sudo apt-get install r-base and for Fedora run sudo dnf install R). Also, please install the RStudio IDE.