15 Dec 2016 | Daniel Nüst
This post gave the idea for the following 📢 PUBLISHED PAPER 🎉. It will not be updated anymore.
The Rockerverse: Packages and Applications
for Containerisation with R
Daniel Nüst, Dirk Eddelbuettel, Dom Bennett, Robrecht Cannoodt, Dav Clark, Gergely Daróczi, Mark Edmondson, Colin Fay, Ellis Hughes, Lars Kjeldgaard, Sean Lopp, Ben Marwick, Heather Nolis, Jacqueline Nolis, Hong Ooi, Karthik Ram, Noam Ross, Lori Shepherd, Péter Sólymos, Tyson Lee Swetnam, Nitesh Turaga, Charlotte Van Petegem, Jason Williams, Craig Willis and Nan Xiao. The R Journal (2020) 12:1, pages 437-461. doi:10.32614/RJ-2020-007
This post is regularly updated (cf. GH issue) and available under the URL http://bit.ly/docker-r. Last update: 11 Jan 2018.
Docker and R: How are they used and could they be used together?
That is the question that we regularly ask ourself.
And we try to keep up with other people’s work! In this post, we are going to share our insights with you.
Thanks to Ben Marwick for contributing to this post! You know about a project using Docker and R? Get in touch.
Several implementations of besides the one by R-core exist today, together with numerous integrations into open source and proprietary software (cf. English and German Wikipedia pages).
In the following we present the existing efforts for using open source R implementation with Docker.
The most prominent effort…
09 Nov 2016 | Daniel Nüst
We are happy to announce that a session convened by o2r team member Edzer Pebesma along with co-conveners Yolanda Gil, Kerstin Lehnert, Jens Klump, Martin Hammitzsch, and Daniel Nüst was accepted at next year’s European Geosciences Union General Assembly.
The call for abstracts is now open. The abstract submission deadline is 11 Jan 2017, 13:00 CET. So there is plenty of time to contribute, prepare an abstract and share your experience of reproducible research.
Please spread the word and find out more at https://bit.ly/rregu17.
From the session description:
This session will showcase papers that…
24 Oct 2016 | Marc Schutzeichel
The Open Access movement has improved the foundation for research reproducibility in that it has greatly advanced the accessibility of research data and text. This year’s theme for the International Open Access Week is “Open in Action”. The o2r team joins in by creating local awareness for what may come beyond Open Access.
Image by openaccessweek.org, licensed under CC BY 4.0 Int.
To transform access into action, the o2r team is working towards the implementation of a simple technical solution. A “one click reproduce” button is one of the extremes within the continuum of reproducibility.
It enables the user to recreate the original results of a study with only a mouse click. In order to realize that, a new format for the publication of research findings has to be created and integrated into the publication cycle.
In o2r we envision a container format that implements the executable research compendium (ERC) to encapsulate any information relevant to constitutating a complete set of research data, code, text and UI. This includes any necessary specification of the working and run time environments.
Towards the other end of the continuum of reproducibility we find examples of published code and data that are openly accessible and yet fail to be rebuild easily by another scholar. By being dependent on other software, vanished packages and specific versions or environments, such cases leave it to the user to reconstruct the individual computational dependency architectures.
This strongly increases the efforts to rebuild, run, or compile the code and thus effectively blocks Open Action.
With the use of ERCs such obstacles can be resolved: The orginial analysis underlying a scientific publication becomes fully reproducible for independent researchers and anyone interested.
Opening reproducibility is where we see the biggest need for Open Action in science.
23 Sep 2016 | Daniel Nüst, Markus Konkol
Just two weeks ago, o2r team members Daniel and Markus proudly presented the project’s first workshop paper “Opening the Publication Process with Executable Research Compendia” at the First International Workshop on Reproducible Open Science held in conjunction with the 20th International Conference on Theory and Practice of Digital Libraries and suppored by RDA Europe…
06 Sep 2016 | Daniel Nüst
Update: A video recoriding of the presentation is now published on the TIB AV-Portal: http://dx.doi.org/10.5446/20330
o2r team member Daniel Nüst recently participated in the worlds largest conference for geospatial open source software. The FOSS4G 2016 was hosted by the Open Source Geospatial Foundation (OSGeo) and took place close to home, namely in Bonn. Therefore Daniel was extremely happy that…