R for reproducible scientific analysis

BetterLab

Oct 30-31, 2020

9:00 am - 4:30 pm

Instructors: Nelly Selem, Manuel Villalobos, Abraham Avelar

Helpers: Abel, Aaron, Vanesa

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. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Parque de Innovación AGROBIOTEG Av. Camino Real de Guanajuato S/N Ejido de Juarez, 36630 Irapuato, Gto.. Get directions with OpenStreetMap or Google Maps.

When: Oct 30-31, 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 have a few specific software packages installed (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 betterlabc@gmail.com for more information.

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


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

Day 1

Before Pre-workshop survey
09:00 Introduction to R and RStudio
10:30 Morning break
11:00 Data Structures (Continued)
12:00 Lunch break
13:00 Subsetting Data
14:30 Afternoon break
15:00 Creating Publication-Quality Graphics with ggplot2
16:00 Wrap-up
16:30 END

Day 2

09:00 Vectorization
10:30 Morning break
11:00 Splitting and Combining Data Frames with plyr
12:00 Lunch break
13:00 Dataframe Manipulation with dplyr
14:30 Afternoon break
15:00 Writing Good Software
16:00 Wrap-up
16:30 Post-workshop Survey
16:40 END

Syllabus

Programming in R


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.

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

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.