This post shows how to print a prettier nested pivot table, created using the {reshape} package (similar to what you would get with Microsoft Excel), so you could print it either in the R terminal or as a LaTeX table. This task is done by bridging between the cast_df object produced by the {reshape}...
useR! 2012 has issued a call for abstracts! I've extended the WebSweave concept to offer a tool to create simple abstracts online, including those with \LaTeX markup, which may then be submitted at the conference website. Use the following link for the...
I am about to start writing up the manuscript of my recent biomath seminar (Act 3: Pineda-Krch. 2011. Cycles at the edge of existence: Emergence of quasi-cycles in strongly destabilizedecosystems.). While the slides for the talk were put together using Sweave … Continue reading →
The world has changed. You can feel it on GitHub. You can smell it on Google+. For those who have been struggling with Sweave, here comes the knitr package. It has features that you have been longing for, and features that you might have never imagined. Thumb through the PDF manual to see some...
I do reports for clients with LyX and Sweave. It took me an extremely long time to get them working, but now that they’re working I can do more in an hour and thus charge more per hour. If you’re not familiar, here’s a rundown: LaTeX is the stand...
Just because it’s caturday Images by Mario Pineda-Krch (CC BY-NC-SA 3.0) This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta. Filed under: cats, computing, humour, R, Sweave
For this years Halloween I presented the mathematical biology seminar at the Centre for Mathematical Biology. Here is the title and the abstract… Cycles in finite populations: a reproducible seminar in three acts Many natural populations exhibit cyclic fluctuations. Explaining the underlying … Continue reading →
Using R with LaTeX via Sweave is a great way to create reproducible output. However, using specific fonts, e.g. your corporate fonts, can be painful with pdflatex. Over the last few weeks I have fallen in love with the TeX formatXeLaTeX and its XeTeX e...
I gave a talk at the Interface Symposium on reproducible research in practice. I went first in the session, so the slides have a bit more background and philosophy. It was a great session; one of Jon Claerbout's colleagues spoke, Sergey Fomel, a founding author of Madagascar; Sorin Mitran from UNC Chapel Hill talked...
I recently read Ewan Birney's blog post, which I found echoed a lot of my own thoughts about the use of statistical in computational biology. I thought I would compile my own similar list but for bioinformatics / computational biology in general....
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
