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RMarkdown & Continuous Integration


In my previous post, I wrote about writing a Makefile to render .Rmd files to pdf (or html) automatically.

I've been playing around with using continuous integration for scientific analysis using Travis-CI, RMarkdown and GitHub. This way, whenever I perform a git push to GitHub, Travis-CI will pull down the latest code and run it. Since in this case, the "code" consists of RMarkdown files containing my analyses, Travis-CI will re-run my analyses every time I update the code. This can be useful for checking that my code works but, more importantly, preserving a record of how to run the analysis code, and notifying me when something breaks.

I added continuous integration using Travis-CI to my Make + RMarkdown example. When GitHub receives a git push, Travis will clone the repository and run make which will build all RMarkdown files and notify you of any failures.

This could also be used to build RMarkdown files automatically if the output could somehow be sent elsewhere. One way to do this would be to send them to a remote machine using secure-copy or FTP.

This configuration does not handle dependency management. I added a script to install dependencies but this is less than ideal. R has really only one good solution for package management called Packrat. Packrat requires all dependencies to be tracked in Git. I'm not a fan of "vendoring" all dependencies and this could lead to licensing issues if you publish your code under MIT (many R libraries are GPL) but Packrat has at least been reliable in my experience.

See .travis.yml

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