R for Reproducible Research (R3)

Institut Cavanilles de Biodiversitat i Biologia Evolutiva

Oct 22-23, 2019

9:00 - 16:30

Instructors: J. Ignacio Lucas Lledó

Helpers: Cristina Llopis Belenguer, Quentin Corbel

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: Sala de Reunions, SS.6. Carrer del Catedràtic José Beltran Martínez, 2. 46980 - Paterna, Spain. Get directions with OpenStreetMap or Google Maps.

When: Oct 22-23, 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).

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.

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 joiglu@uv.es for more information.

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
10:00 Project management with RStudio
10:30 Seeking help
11:00 Morning break
11:30 Data structures
12:30 Exploring data frames
13:00 Subsetting data
14:00 Lunch break
15:00 Control flow
16:10 Vectorization
16:40 Afternoon break
17:00 Creating graphics with ggplot2
18:30 END

Day 2

09:00 Functions explained
10:00 Writing data
10:30 Morning break
11:00 Splitting and combining data frames with plyr
12:00 Dataframe manipulation with dplyr
13:00 Dataframe manipulation with tidyr
14:00 Lunch break
15:00 Producing reports with knitr
16:15 Writing good software
16:30 Post-workshop Survey
16:40 END

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

Syllabus

R for reproducible scientific analysis

  • R and RStudio
  • Data structures
  • Control flow
  • Creating graphics with ggplot2
  • Vectorization
  • Functions
  • Manipulation of data frames
  • Producing reports with knitr
  • Writing good software with R
  • 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.