King County

May 29-30, 2018

8:30 am - 4:30 pm

Instructors: Carolina Johnson, Yee Mey Seah

Helpers: TBD

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, 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: This workshop is for analysts, evaluators, and epidemiologists at the King County Department of Community and Human Services and Public Health - Seattle and King County You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: 220 2nd Ave. S., 3rd Floor, Seattle, WA 98104. Get directions with OpenStreetMap or Google Maps.

When: May 29-30, 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.). If possible, participants should bring the laptop they use at the County, and should speak to their supervisor or the workshop coordinator if they need a laptop for this training. Participants should have a few specific software packages installed (listed below). 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 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 cajohnson@kingcounty.gov 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
08:30 Version control with Git
10:00 Coffee
12:00 Lunch break
13:00 R for Reproducible Analysis
14:30 Coffee
16:30 END

Day 2

09:00 R for Reproducible Analysis (cont'd)
10:30 Coffee
12:00 Lunch break
13:00 Managing data with SQL
14:30 Coffee
16:20 Post-workshop Survey
16:30 END

Syllabus

Version Control with Git

  • Setting up 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
  • Reference...

R for Reproducible Scientific Analysis

  • Introduction to R and RStudio
  • Data structures
  • Exploring data frames
  • Writing data
  • Dataframe manipulation with dplyr
  • Dataframe manipulation with tidyr
  • Control flow
  • Vectorization
  • Functions explained
  • Reference...

Managing Data with SQL

  • Selecting data
  • Sorting and removing duplicates
  • Filtering
  • Calculating new values
  • Missing data
  • Aggregation
  • Combining data
  • Data hygiene
  • 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.

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 nano or Notepad++ (as you prefer - the instructor will be using nano in the workshop) as your default editor and click "Next"
    4. Select "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. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    7. Keep "Use Windows' default console window" selected and click on "Next".
    8. Click on "Install".
    9. 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.

macOS

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.

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).

macOS

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 dnf install git.

 

 

Set up for King County machines: Text editor and SQLite3 installation

We have developed a customized script that will install the text editor and SQL tools on your machines without requiring administrator privileges.

To install nano (our basic text editor) and SQLite

  1. Open a Git Bash instance from the Start menu so that it opens in your home user directory (where it should open by default)
  2. Copy and paste the following commands into the Bash terminal (depending on how you copy and paste, you may need to hit enter to run the last command line):
  3. 
    mkdir .swc	
    curl -L -O http://www.nano-editor.org/dist/v2.2/NT/nano-2.2.6.zip
    unzip nano-2.2.6.zip -d .swc/nano
    curl -L -O https://sqlite.org/2015/sqlite-shell-win32-x86-3090200.zip
    unzip sqlite-shell-win32-x86-3090200.zip -d .swc/sqlite3
    echo "alias nano='winpty `pwd`/.swc/nano/nano' 
    alias sqlite3='winpty `pwd`/.swc/sqlite3/sqlite3'" >~/.bashrc
    
    
    
  4. Close and reopen Git Bash. You should see the notification "This looks like an incorrect setup. A ~/.bash_profile that loads ~/.bashrc will be created for you." This is normal and will only appear the first time after you run the installation commands.
  5. Your installation is complete. close the Git Bash window.

Installation of R and RStudio on King County machines will require going through the KCIT Software Center.

For reference, full installation instructions for non-King County machines are provided below for people who either have administrator privileges or who would like to follow along with these lessons on their personal computers.

 

 

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. Notepad++ us a decent text editor that is available for download from the KCIT software center. For this class we will default to nano a very simple editor with shell integration (installation instructions below), but Notepad++ is another decent text editor with syntax highlighting that is available for installation from the KCIT software center.

Windows

nano is a basic editor and the default that instructors use in the workshop. Running the installation commands in the "Setup for King County machines" section above will install nano for use with Bash. You can follow those steps for your personal Windows machine.

macOS

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.

SQLite

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

Windows

Running the installation commands in the "Setup for King County machines" section above will have installed SQLite for use with Bash for the workshop. If you have already run the installation script once for nano, you do not need to run it again.

macOS

SQLite comes pre-installed on macOS.

Linux

SQLite comes pre-installed on Linux.

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

R and the RStudio IDE are both available for download from the KCIT Software Center. If you are unable to access the files via the Software Center, please notify the workshop organizer and the KCIT Help Desk. If you want to install R/RStudio on a computer on which you have administrator rights, follow the instructions below.

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.

macOS

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