Open Notebook Thoughts

Writing reproducibly in the open with knitr

April 7, 2012 | Carl

Sweave is something of a gold standard in reproducible research. It creates a dynamic document, written in a mix of LaTeX and R code where the results of the analysis (numbers, figures, tables) are automatically generated from the code and inserted into the resulting pdf document, making them easy to ... [Read more...]

Citations in markdown using knitr

March 24, 2012 | Carl

I am finding myself more and more drawn to markdown rather then tex/Rnw as my standard format (not least of which is the ease of displaying the files on github, particularly now that we have automatic image uploading). One thing I miss from latex is the citation commands. (I ... [Read more...]

knitr, github, and a new phase for the lab notebook

March 21, 2012 | Carl

I have recently modified the basic workflow of my lab notebook since discovering knitr. Before, I would write code files which I could track on github, push figures created by the code to flickr, and then write a notebook entry on wordpress describing what I was doing. I’d embed ... [Read more...]

Citing R packages

March 20, 2012 | Carl

I’m not always careful in citing all the R packages I use. R actually has some rather nice built-in mechanisms to support this, so I really have no excuse. Here’s some quick examples: To cite the ouch package in publications use: Aaron A. King and Marguerite A. Butler (2009), ... [Read more...]

socialR: Reproducible Research & Notebook integration with R

December 10, 2010 | Carl

I’ve created an R package that uses social media tools for reproducible research.  The goal of the package is this: whenever I run a code, output figures are automatically added to my figure repository (Flickr), linked to the timestamped version of the code that produced them in the code ... [Read more...]

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