Memorial University of Newfoundland

March 12-13, 2018

9:00 am - 4:30 pm

Instructors: Danielle Quinn, Oliver Stueker, Ivo Arrey

Helpers: Oihane Cereceda, Emilie Geissinger, Ernest Awonoor-Williams

Registration

Until March 1st, registration is limited to those attending the Science Atlantic Biology and Fisheries & Aquaculture Conference. After March 1st, registration will be open to anyone!

Surveys

Upon registering, please be sure to complete the pre-workshop survey. These surveys help us choose and pace the lessons that we will present at the workshop. Software Carpentry is consistently evaluating workshops to understand the impact workshops have on learners, and how the content delivery can be improved.

Pre-workshop Survey

Post-workshop Survey

General Information

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: using the Shell for task automation, Git/GitHub for version control, and basic to intermediate R programming skills, including manipulating data with {dplyr}, generating figures with {ggplot2}, and creating dynamic R markdown documents with {knitr}. 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: The course is aimed at students and researchers from any field of study. No previous knowledge of or experience with the tools presented at the workshop is required.

Where: Room IIC-2014, Bruneau Center for Research and Innovation, Memorial University, 230 Elizabeth Avenue, St. John's, Newfoundland. Get directions with OpenStreetMap or Google Maps.

When: March 12-13, 2018. 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), which will require at least R version 3.1.2. They are also required to abide by Software Carpentry's Code of Conduct.

Accessibility: We are committed to making this workshop accessible to everybody. The workshop organisers 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 danielle.quinn@mun.ca for more information.


Schedule

If you have any problems installing the required software (see Setup, below), please arrive 30 minutes early so that we can help you solve them!

Day 1

09:00 Automating Tasks with the Shell
10:30 Coffee
12:00 Lunch break
13:00 R Part I: Introduction to R
14:30 Coffee
16:00 Wrap-up

Day 2

09:00 Version Control with Git
10:30 Coffee
12:00 Lunch break
13:00 R Part II: Doing More with R
14:30 Coffee
16:00 Wrap-up

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


Syllabus

Automating Tasks with the Unix Shell

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts

R for Reproducible Scientific Analysis

  • Introduction to R and R Studio
  • Basic programming in R
  • Data structures in R
  • Exploring data frames
  • Visualizating data using {ggplot2}
  • Data frame manipulation using {dplyr}
  • Producing reports using {knitr}

Version Control with Git

  • Creating a repository
  • Recording changes to files
  • Viewing changes
  • Ignoring files
  • Working on the web
  • Resolving conflicts


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.

Windows

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. Select "Use the Nano editor by default" and click on "Next". If you forgot to do this, you can run the following command after opening Git Bash: `git config --global core.editor nano`.
    4. 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.
    5. Click on "Next".
    6. Click on "Next".
    7. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    8. Keep "Use Windows' default console window" selected and click on "Next".
    9. Click on "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.

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. You may want to keep Terminal in your dock for this workshop.

Linux

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.

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 (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

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.

Windows

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.

Linux

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.

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 Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows

nano is a basic editor and the default that instructors use in the workshop. It is automatically installed with Git-for-Windows v2.15.1 or newer.

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.

Mac OS X

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 Text Wrangler or Sublime Text.

Linux

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.

Windows

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.

Mac OS X

Video Tutorial

Install R by downloading and running this .pkg file from CRAN. Also, please install the RStudio IDE.

Linux

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 yum install R). Also, please install the RStudio IDE.