Reproducible Research with R Packages

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General Information

The eScience Center offers a range of free workshops and training courses, open to all researchers affiliated with Dutch research organizations. We organize workshops covering digital skills needed to put reproducible research into practice. These include online collaboration, reproducible code and good programming practices. We also offer more advanced workshops such as GPU Programming, Parallel Programming and Deep Learning.

This workshop will help you make your research reproducible, by taking your R script and turning it into a shareable package.

R packages are no more and no less than a standard way of structuring your work. The standardization makes packages easily installable and shareable, and allows others to reuse your code in a painless way, making your research more reproducible.

But by turning your script into a package you achieve more than reusability: in doing so, you become a better programmer. In the structure of a package, best software development practices are implemented. You will learn to write tests and documentation, and help your users get started with a vignette. At the end of this workshop, we aim to have made your code more robust, and your programming experience more enjoyable.

Note: This workshop is scheduled as four weekly sessions, giving you time in between meetings to apply the things you learn to your own code.

Where: This training will take place online. The instructors will provide you with the information you will need to connect to this meeting.

When: September 14 - October 05, 2022 (weekly, on Wednesdays), 9:00 - 13:00 CEST.

Requirements: Participants must have access to a computer 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 dedicated to providing a positive and accessible learning environment for all. Please notify the instructors in advance of the workshop if you require any accommodations or if there is anything we can do to make this workshop more accessible to you.

Contact: Please email or training@esciencecenter.nl for more information.

Code of Conduct

Participants are expected to follow those guidelines:

• Use welcoming and inclusive language
• Be respectful of different viewpoints and experiences
• Gracefully accept constructive criticism
• Focus on what is best for the community
• Show courtesy and respect towards other community members

Syllabus

• Introduction to packages and reproducible research with R
• How to turn your script into a package
• Writing tests
• Writing documentation and vignettes
• Sharing your R package

Schedule

This workshop is scheduled on four separate days. This allows you to work on your package in between the sessions, implementing the lessons you learned during our meetings together. Please schedule dedicated work time in your calendar, so you can take full advantage of the workshop.

All times in the schedule are in the CET timezone (Amsterdam time).

Setup

To participate in this workshop, you will need access to software as 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.

Software setup

This lesson assumes you have current versions of the following installed on your computer:

1. the R software itself, and
2. RStudio Desktop.

In addition, you will need an account on GitHub. Create one here.

You will also need to install the following packages:

• devtools
• rmarkdown
• roxygen2

They can be installed by typing the code below in the R console:

$ install.packages(c("devtools", "rmarkdown", "roxygen2"))

If the installation went right, the code below should throw no errors:

$ library(devtools)
$ library(rmarkdown)
$ library(roxygen2)

Please contact us in advance if you are experiencing problems.

During the workshop, we will take an R script, and transform it into a shareable R package. You are encouraged to bring your own project, though we will have a toy project to use if you are unable to. Packages are based around functions, so it is important that you know how to write functions, and that at least a single function is present in your script.

Install the videoconferencing client

If you haven't used Zoom before, go to the official website to download and install the Zoom client for your computer.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, RStudio, your web browser, etc..) and the window for the Zoom video conference client open. In order to see both at once, we recommend using one of the following set up options:

• Two monitors: If you have two monitors, plan to have the tool you are learing up on one monitor and the video conferencing software on the other.
• Two devices: If you don't have two monitors, do you have another device (tablet, smartphone) with a medium to large sized screen? If so, try using the smaller device as your video conference connection and your larger device (laptop or desktop) to follow along with the tool you will be learning about.
• Divide your screen: If you only have one device and one screen, practice having two windows (the video conference program and one of the tools you will be using at the workshop) open together. How can you best fit both on your screen? Will it work better for you to toggle between them using a keyboard shortcut? Try it out in advance to decide what will work best for you.