Generating Dockerfiles for reproducible research with R

This post is the draft of the vignette for a new R package by o2r team members Matthias and Daniel. Find the original file in the package repository on GitHub.

• 1. Introduction
• 2. Creating a Dockerfile
• 3. Including resources
• 4. Image metadata
• 5. Further customization
• 6. CLI
• 7. Challenges
• 8. Conclusions and future work
• Metadata

1. Introduction

Even though R is designed for open and reproducible research, users who want to share their work with others are facing challenges. Sharing merely the R script or R Markdown document should warrant reproducibility, but many analyses rely on additional resources and specific third party software as well. An R script may…

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State of the project and next steps

Yesterday the o2r team met for the second time with a group of experts to request feedback on the state of the project.

Image is licensed under a CC BY-NC-ND 4.0 International license.

Thanks to the valuable questions and comments by our external partners, the project tasks were assessed and refocussed. On top of it, we agreed to collaborate even further and sketched first ideas for putting o2r’s prototypes into real-world settings.

This workshop…

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Opening Reproducible Research at AGILE 2017 conference in Wageningen

This week o2r participates in another conference, which is partly a repetition but also a contrast to the last one:

Again, o2r team members (Markus and Daniel) are fortunate to co-organize a workshop about reproducible research: “Reproducible Geosciences Discussion Forum” at the 20th AGILE International Conference on Geographic Information Science in Wageningen, The Netherlands, took place yesterday. Read the short recap on the workshop website.

Thx! Fun, educational & productive workshop today on #reproducible #geosciences at #agilewag2017 #agile2017nl Report soon via @o2r_project pic.twitter.com/MjrWPQyoQ2

— Daniel Nüst (@nordholmen) May 9, 2017

Daniel will also present…

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Opening Reproducible Research at EGU General Assembly 2017

Last week the largest European geosciences conference of the year took place in Vienna: the European Geophysical Union General Assembly 2017.

o2r took part by co-organising a workshop on reproducible research and co-convening the session IE2.4/ESSI3.10 Open Data, Reproducible Research, and Open Science.

o2r team member Daniel Nüst presented the abstract “Executable research compendia in geoscience research infrastructures” (download poster) and supported Marius Appel and Edzer Pebesma in their work on “Reproducible Earth observation analytics: challenges, ideas, and a study case on containerized land use change detection” (download poster) in the ESSI3.10’s poster session.

It was a great experience to…

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Reproducible Research at EGU GA - A short course recap

At last week’s EGU general assembly members of the o2r and ReproZip projects organized the short course “Reproducible computational research in the publication cycle”. This post is a recap of the course by Daniel Nüst, Vicky Steeves, and Rémi Rampin.

All materials for the course are published in an Open Science Framework repository at https://osf.io/umy6g/ and you can learn about the motivation for the course in the course page at EGU.

The short was divided into two parts:…

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