Posts Tagged ‘ Open Notebook Thoughts ’

Writing reproducibly in the open with knitr

April 7, 2012
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Writing reproducibly in the open with knitr

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 update if the data or

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Citations in markdown using knitr

March 24, 2012
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Citations in markdown using knitr

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 understand these can be provided to

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

March 21, 2012
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knitr, github, and a new phase for the lab notebook

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 each figure I wanted into the

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Citing R packages

March 20, 2012
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Citing R packages

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), ouch: Ornstein-Uhlenbeck models for phylogenetic comparative

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socialR: Reproducible Research & Notebook integration with R

December 10, 2010
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socialR: Reproducible Research & Notebook integration with R

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 repository.  Figures should be tagged by

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