When I am working in new institutions and I am asking: “Do you have a document management system?” I often get the answer:”Yap, we are using folders” … OKAY. Making analysis, developing applications and keeping an eye on code, data and applications make this even harder as it has to ... [Read more...]

Once again working on my slides for the AMSI Lecture 2012 tour, it took me a while to get the following LaTeX code (about the family reunion puzzle) to work: \begin{frame}[fragile,label=notleM2] \slidetitle{A family meeting} \begin{block}{Random switch of couples} \only{ \begin{itemize} \item Pick two ... [Read more...]

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I fought with my LαTεX compiler this morning as it did not want to deal with my code: looking on forums for incompatibilities between beamer and algorithmic, and adding all kinds of packages, to no avail. Until I realised one \STATE was missing: (This is connected with my ... [Read more...]

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A very useful way of keeping up with blogs in a particular area is to subscribe to a blog aggregator. These will syndicate posts from a large number of blogs and provide links back to the original sources. So you only need to subscribe once to get all the good ... [Read more...]

I spent most of the Sunday afternoon trying to understand why defining did not have the same effect as writing the line until I found there is a clash due to the comment package… The assuredly simple code produces an error message: This is quite an inconvenience as I need ... [Read more...]

Monday, April 30, 2012  14h-16h. Stewart Biology Rm w6/12 (Montreal) guRu: Denis Haine (Université de Montréal) Topics Reproducible research was first coined by Pr. Jon Claerbout, professor of geophysics at Stanford University, to describe that the results from researches can be replicated by other scientists by making available data, procedures, ... [Read more...]

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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 ... [Read more...]

On my road to eventually running all of my programs off an USB device I’ve gotten a little bit closer yesterday thanks to input from Duncan Murdoch and Yihui Xie. Eventually running the entire Windows OS off a USB drive would be nice (not talking about running it as ... [Read more...]

This post is a quick follow up from my initial article on Sweave to add a note on how to get a plot in landscape orientation to fill the whole page, plus a little example of using BibTex.Just to clarify  my … Continue reading → [Read more...]

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 ... [Read more...]

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 → [Read more...]

If you use R and haven’t discovered Sweave then go and find out about it. It enables R code and plots to be incorporated into a document so the analysis and report can be combined together in a single document. … Continue reading → [Read more...]

I am writing way too many posts in a row on Google tools. I promise I will think about something else soon. I find amusing the possibility to launch a search in Google images by just dragging a picture into … Continue reading → [Read more...]

The pgf drawing package for LaTeX provides facilities for drawing simple of complicated pictures within a LaTeX document. There are many options available within the package and in this post we consider some of the basics to get up and running. Fast Tube by Casper As with all LaTeX documents ... [Read more...]