Software Carpentry: R for Reproducible Scientific Analysis

San Diego State University

Mar 13-14, 2020

Times TBD

Instructors: Kelsey Montgomery, Shervin Sahba

Helpers: Karen Robinett, 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: The course is aimed at graduate students and other researchers, including post-docs and faculty. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Storm Hall, SAL and FINCH Computer Labs, 5500 Campanile Dr, San Diego, CA 92182. Get directions with OpenStreetMap or Google Maps.

When: Mar 13-14, 2020. 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 R and RStudio installed and ready to go. Additionally, installing the ggplot2 package ahead of time is useful. You can install ggplot2 by running the R command: install.packages("ggplot2"). Instructions on installing R and RStudio are listed below.

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 krobinett8114@sdsu.edu , kelsey.montgomery@sagebase.org or ssahba@uw.edu for more information.


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.

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1 (Tentative Schedule)

Before Pre-workshop survey
09:00 Introduction to R and RStudio
09:45 Project Management With RStudio
10:00 Seeking Help
10:30 Break
11:00 Data Structures
11:30 Exploring Data Frames
12:00 Lunch break
13:00 Subsetting Data
13:15 Control Flow
14:00 Creating Publication-Quality Graphics with ggplot2
15:00 END

Day 2 (Tentative Schedule)

10:00 Vectorization
10:30 Functions Explained
11:00 Writing Data
12:00 Splitting and Combining Data Frames with plyr
12:30 Lunch break
13:30 Dataframe Manipulation with dplyr
14:00 Dataframe Manipulation with tidyr
15:00 Producing Reports With knitr
15:30 Post-workshop Survey
16:00 END

Syllabus

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...

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.

R

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

Video Tutorial

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.

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.