UCSB Library Software Carpentry Workshop "R", Git and Bash

April 11-12, 2019

9:00 am to 5:00 pm

Instructors: Jon Jablonski, Ian Lessing, Greg Janee, Sharon Solis, Mary Donovan, Yuan Wu

Helpers: Noah Spahn, Kristi Liu

Registration: Please make sure that you can commit to the full two days of learning. To learn about future Carpentry workshops and to be added to our mailing list, visit our UCSB Carpentry Workshop page.

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: The course is aimed at faculty and researchers. You do not need to have any previous knowledge of the tools that will be presented at the workshop.

Where: University of California, Santa Barbara Library Classroom 1312 (Day 1) Classroom 1575 (Day 2), Santa Barbara, CA 93106. Get directions with OpenStreetMap, Google Maps, or the UCSB Map.

When: April 11-12, 2019. 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). 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 collaboratory@library.ucsb.edu for more information.


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

Pre-workshop Survey

Post-workshop Survey


Before the Workshop

Complete the Setup steps below to:
  • install the software we'll be using in the Workshop
  • download the example files we'll be using in the workshop
  • Day 1: Thursday, April 11, 2019

    Before Pre-workshop survey
    08:15 Installation help. Please arrive early if you had problems installing all of the required software.
    08:30 Coffee and light breakfast
    09:00 Introductions
    09:15 The Unix Shell
    09:20 Navigating Files & Directions
    10:00 Working with Files & Directions
    10:50 Coffee
    11:05 Pipes and Filters
    11:50 Finding files
    12:25 Lunch break(lunch will be provided)
    13:25 Automated Version control
    13:35 Setting up Git
    13:45 Creating a Repository
    13:55 Tracking Changes
    14:15 Coffee
    14:45 Exploring History
    15:10 Ignoring Things
    15:15 Remotes in Github
    15:45 Collaborating
    16:10 Conflicts
    16:20 Open Science
    16:30 END

    Day 2: Friday, April 12, 2019

    08:30 Coffee and light breakfast
    09:00 Introduction to R and Rstudio
    10:00 Project Management with Rstudio
    10:30 Coffee
    10:50 Seeking Help
    11:00 Data Structures
    11:40 Data Frames
    12:10 Lunch break(lunch will be provided)
    12:55 Subsetting Data
    13:30 ploting with ggplot2
    14:30 Vectorization
    14:40 Coffee
    14:55 Dataframe manipulating with dplyr
    15:55 Dataframe manipulating with tidyr
    16:40 Writing good software
    16:50 Post-workshop Survey
    17:00 END

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


    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...


    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.

    Bash Shell Setup Instructions
    Git Version Control Setup Instructions
    "R" Setup Instructions

    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.