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Alaska Fisheries Science Center / National Marine Fisheries Service (R Course)

March 2-3, 2016

8:00 am - 5:00 pm

Instructors: Rachel Schwartz, John Moreau

Helpers: Ned Laman, Margaret Hughes, Russell Alleen-Willems, Stan Kotwicki, Peter Munro, Dave Somerton, Chris Rooper, Bob Foy (Kodiak), Chris Long (Kodiak)

General Information

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. 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: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Jim Traynor Conference Room; Building 4; Alaska Fisheries Science Center; 7600 Sand Point Way NE; Seattle, WA 98115. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail ned.laman@noaa.gov for more information.

Schedule

Pre-workshop Survey

Day 1

08:00 Set up / troubleshooting installation
08:30 Automating tasks with the Unix shell
10:30 Coffee & snacks
12:00 Lunch break (pack or buy on site)
13:00 Building programs with R
15:00 Coffee
17:00 Wrap-up

Day 2

09:00 Version control with Git
10:30 Coffee & snacks
12:00 Lunch break (pack or buy on site)
13:00 Managing data with SQL
14:30 Coffee & snacks
16:00 Wrap-up
Dismissal Post-workshop Survey

Etherpad: http://pad.software-carpentry.org/2016-03-02-NMFS-Seattle.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

The sql notebook can be found here

The R script to load from a database can be found here

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...

Programming in R

  • Working with vectors and data frames
  • Reading and plotting data
  • Creating and using functions
  • Loops and conditionals
  • Using R from the command line
  • Reference...

Version Control with Git

  • 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...

Managing Data with SQL

  • Reading and sorting data
  • Filtering with where
  • Calculating new values on the fly
  • Handling missing values
  • Combining values using aggregation
  • Combining information from multiple tables using join
  • Creating, modifying, and deleting data
  • Programming with databases
  • 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.

Homework for Day 2

If you have not installed these packages before day 1:

  • Open RStudio.
  • At the prompt type install.packages(c("ggplot2", "installr","plyr", "gapminder", "RSQLite", "rnoaa", "RODBC","ProjectTemplate", "swirl"))
  • and press enter.

If you have installed all packages except installr:

  • Open RStudio.
  • At the prompt type install.packages("installr")
  • and press enter.

Data Files

Due to wifi limitations within the Traynor conference room, please download these data files to your desktop before you arrive for the workshop.

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

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

Open RStudio. At the prompt type install.packages(c("ggplot2", "plyr", "gapminder", "RSQLite", "rnoaa", "RODBC","ProjectTemplate", "swirl")) and press enter.

Mac OS X

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

Open RStudio. At the prompt type install.packages(c("ggplot2", "plyr", "gapminder", "RSQLite", "rnoaa", "RODBC","ProjectTemplate", "swirl")) and press enter.

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.

Open RStudio. At the prompt type install.packages(c("ggplot2", "plyr", "gapminder", "RSQLite", "rnoaa", "RODBC","ProjectTemplate", "swirl")) and press enter.

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. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

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. 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.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

The Software Carpentry Windows Installer installs Git and Bash for Windows. If you used the installer to configure nano, you don't need to run it again. These instructions are provided as a supplement in case you cannot successfully run the Installer. Windows users only should also save the GNU Bash manual, availabe as either a PDF download or as a HTML page.

  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. Click on "Next".
    4. Click on "Next".
    5. Click on "Next".
    6. Select "Use Git from the Windows Command Prompt" 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.
    7. Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
    8. Select "Use Windows' default console window" and click on "Next".
    9. Click on "Next".
    10. Click on "Finish".

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). 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).

Windows

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

Mac OS X

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.

SQLite

SQL is a specialized programming language used with databases. We use a simple database manager called SQLite in our lessons.

Windows

The Software Carpentry Windows Installer installs SQLite for Windows. If you used the installer to configure nano, you don't need to run it again.

Mac OS X

SQLite comes pre-installed on Mac OS X.

Linux

SQLite comes pre-installed on Linux.

If you installed Anaconda, it also has a copy of SQLite without support to readline. Instructors will provide a workaround for it if needed.

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