Online
September 20 - October 11, 2023
9:00 - 13:00 CEST
Instructors: Barbara Vreede, Eva Viviani, Lieke de Boer
Helpers: Dani Bodor, Flavio Hafner
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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.
The participants should:
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 20 - October 11, 2023, 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.
Participants are expected to follow these guidelines:
This workshop is scheduled on four separate days over four weeks. This allows you to work on your package in between the sessions, implementing the lessons you learned during the teaching moments. Please schedule dedicated time for homework in your calendar, so you can take full advantage of the workshop.
| 9:00 | Welcome and icebreaker |
| 9:15 | Introduction, Accessing packages, Getting started |
| 10:15 | Coffee break |
| 10:30 | Writing our own functions, Licenses |
| 11:30 | Coffee break |
| 11:45 | Data |
| 12:45 | Wrap-up |
| 13:00 | END |
| 9:00 | Welcome and icebreaker |
| 9:15 | Recap homework & Lessons learned |
| 10:15 | Coffee break |
| 10:30 | Testing |
| 11:30 | Coffee break |
| 11:45 | Testing, test coverage |
| 12:45 | Wrap-up |
| 13:00 | END |
| 9:00 | Welcome and icebreaker |
| 9:15 | Recap homework & Lessons learned |
| 10:15 | Coffee break |
| 10:30 | Dependencies, Documenting your package |
| 11:30 | Coffee break |
| 11:45 | Documenting your package, Vignettes |
| 12:45 | Wrap-up |
| 13:00 | END |
| 9:00 | Welcome and icebreaker |
| 9:15 | Recap homework & Lessons learned |
| 10:15 | Coffee break |
| 10:30 | Vignettes |
| 11:30 | Coffee break |
| 11:45 | Sharing our packages |
| 12:45 | Wrap-up |
| 13:00 | END |
All times in the schedule are in the CE(S)T timezone (Amsterdam time).
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.
For this workshop, you will need to install the following software:
You will also need to install the following packages:
devtoolsrmarkdownroxygen2They 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.
You will need an account on GitHub. Create one here.
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.
This workshop will be taught via MS Teams. You will not need to install the software to join the workshop, but it will give you the best experience. Download MS Teams here: www.microsoft.com/nl-nl/microsoft-teams/download-app.
If you want to join the meeting via your browser, Edge and Chrome are recommended. You can read more about joining a meeting with your browser here.
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 video conference client open. In order to see both at once, we recommend using one of the following set up options: