UCSD Carpentries Bootcamp: Intro. to R and Version Control w/ Git

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 used with the R programming language and version control with Git. 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 open to UCSD students, staff, and faculty.

You don't need to have any previous knowledge of programming or the tools presented in the workshop to attend. A laptop is required for each session.

Where: Event Room (G1E), Geisel Library, 9500 Gilman Drive, La Jolla, CA.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below).

Contact: Please mail kkt008@ucsd.edu or rotsuji@ucsd.edu for more information.

Assessment: A Co-Curricular of Record activity recognition will be given to the student who:

Attend and participate in all sessions
Pass all workshop quizzes

For more information on the UC San Diego Co-Curricular of Record (CCR), please visit the UCSD Engaged Learning Tools Co-Curricular Record page.

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.

Surveys

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

Pre-workshop Survey

Post-workshop Survey

Schedule

Date	Session	Topics
June 13	Introduction to R - Session 1	Intro to R & RStudio - basics, data structures, and data import/export
June 14	Introduction to R - Session 2	dplyr and tidyverse
June 15	Introduction to R - Session 3	Plotting with ggplot2 and knitr
	Quiz	Due next session; posted on Canvas
June 16	Version Control with Git	Introduction to Git, creating a repository, tracking changes, and collaborating

Curriculum

For this workshop we will be referencing the R for Reproducible Scientific Analysis and Version Control with Git Carpentries curricula.

Data

We will be using the 5 year gapminder data and feline data. You can go ahead and set up a RStudio project and download the data following these instructions. The gapminder CSV file can be downloaded from here. The feline data CSV file can be downloaded from here

HackMD: We will use HackMD for taking notes, and sharing URLs and bits of code. The link for the HackMD etherpad will be provide at the start of each workshop session.

Setup

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

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: SWC R Install Windows

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

Video Tutorial: SWC R Install Mac

Instructions for R installation on various Linux platforms (debian, fedora, redhat, and ubuntu) can be found at . 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.

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 (see the Shell installation instructions).

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: SWC Install Shell, Git, and Nano on Mac

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.