Reproducible Data Science with R and git

Woods Hole Oceanographic Institution

Online

Oct 5, 6, 13, 2021

9:00 am - 12:30 pm

Instructors: Brett Longworth, Maggi Brisbin, Arianna Krinos, Joe Futrelle

Helpers: Stace Beaulieu, Cory Berger, Sarah Glancy, Kali Horn, Kate Morkeski, Jane Weinstock

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. We will be learning R, a high-level programming language with great tools for data science and a vibrant community of users and developers. We will introduce git and github, a system for version control and collaboration.

We seek to provide a fun and accesible learning environment. Participants will be encouraged to help one another and to appply what they have learned to their own research problems. These workshops are sponsored by a WHOI Technical Staff Training Award from the office of the DDVP-SE.

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

Who: This course is aimed at WHOI technical staff and others interested in an introduction to reproducible data science. Registration is required. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: Oct 5, 6, 13, 2021. Add to your Google Calendar.

Requirements: Participants must have access to a computer 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).

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Registration: This workshop requires preregistration. Please register here.

Contact: Please email blongworth@whoi.edu or sbeaulieu@whoi.edu for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.

Who can attend?: This workshop is open to WHOI staff and students.

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.

Collaborative Notes

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

Surveys

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

Post-workshop Survey

Schedule

October 5th: Introduction to R

09:00	Welcome and intro to reproducible data science
09:15	Getting started with R and RStudio
09:45	Project organization
10:00	Seeking help and the R community
10:20	break
10:30	Data structures
11:20	break
11:30	Working with data frames
11:50	Subsetting data
12:30	END

October 6th: Conditions and Loops in R and Version Control with Git

09:00	Control flow
10:00	break
10:30	Version control with git and github
12:30	END

October 13th: The Tidyverse and Beyond

09:00	Functions
09:30	Transforming data with dplyr
10:20	break
10:30	Tidy data
11:20	break
11:30	Writing ~~reports~~ everything with RMarkdown
12:15	Course wrap up
12:30	END

Setup

To participate in a Software Carpentry workshop, you will need access to software as 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.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

Two monitors: If you have two monitors, plan to have the tool you are learning up on one monitor and the video conferencing software on the other.
Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.

This blog post includes detailed information on how to set up your screen to follow along during the 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.

Install Git for Windows. This will install the git executables and a UNIX-like command line environment called a shell. We will sometimes use the shell when interacting with git.

For macOS, 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.

Video Tutorial

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.

R

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

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.

Video Tutorial

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

Video Tutorial

Instructions for R installation on various Linux platforms (debian, fedora, redhat, and ubuntu) can be found at <https://cran.r-project.org/bin/linux/>. These will instruct you to use your package manager (e.g. for Fedora run sudo dnf install R and for Debian/Ubuntu, add a ppa repository and then run sudo apt-get install r-base). Also, please install the RStudio IDE.