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Reproducible Research with Stan, R, knitr, Docker, and Git (with free GitLab hosting)

Jon Zelner recently developed a neat Docker packaging of Stan, R, and knitr for fully reproducible research. The first in his series of posts (with links to the next parts) is here:

* Reproducibility, part 1

The post on making changes online and auto-updating results using GitLab’s continuous integration service is here:

* GitLab continuous integration

It updates via pushes to a Git repository hosted by GitLab.

Jon says, “This is very much a work-in-progress, so any feedback would be greatly appreciated!”. You can leave comments on the blog itself.

4 Comments

  1. Bob says:

    This seems like a sensible and practical approach. For those interested in Docker and containers, there’s a recent overview paper:

    https://www.deepdyve.com/lp/institute-of-electrical-and-electronics-engineers/toward-a-standard-interface-for-cloud-providers-the-container-as-the-lGHrOl3w45

    or

    https://www.computer.org/csdl/mags/ic/2016/02/mic2016020066.pdf

    Unfortunately, I cannot find an unlocked copy.

    Also, the embedded link in the referenced piece doesn’t work for me (https://.about.gitlab.com/jzelner/reproducible-stan). However,
    https://gitlab.com/jzelner/reproducible-stan does work.

    Bob

  2. Thanks for the links. I’m sure Jon will fix the broken one in his post.

  3. nah says:

    What would scientists think about a government mandate of this or similar technology? As a citizen, I find it pretty apalling that so much money is squandered on research that winds up inaccessible to the public.

    After a one-time investment on retraining, it seems researchers would also reap a huge productivity dividend based on improved work flow. As a developer, I find it inappropriate that government doesn’t enforce code and data standards on grant recipients.

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