Modeling sediment deformation using R & RMarkdown

by on February 17, 2017

Last summer I came home from a hike one day with way too much thesis work to do (my submission date was, I think, close to a week away). As per usual, I stopped by the K.C. Irving Centre to catch up on work, and promptly sat down and started writing what would become my latest publication in the Journal of Paleolimnology. The article used R to apply mathematical functions describing how sediment is deformed when cored, and for the first time in my short career of academic writing, I wrote the paper in RMarkdown. At a certain point in the process of finalizing the publication it was necessary to switch to Word, but for the most part, the writing and coding was written in an interleaved fashion that allowed tweaking various parameters and, in seconds, viewing the resulting publication as a PDF. I have since taken to preparing most of my draft reports (and assignments that require coding) in this way.

This figure was, by far, the most difficult to prepare, even if it was the only one that wasn’t done in R.

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