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 → [Read more...]

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 [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...]

The Gillespie stochastic simulation algorithm (SSA) is the gold standard for simulating state-based stochastic models. If you are a R buff, a SSA novice and want to get quickly up and running stochastic models (in particular ecological models) that are not … Continue reading → [Read more...]

On CRAN, the official web home of all things R it says, R is a free software environment for statistical computing and graphics. Well, that sounds all hunky dory. But let’s take a close look at what this statement really … Continue reading → [Read more...]

Just wrapped up the slides for the first version of the The Joy of Sweave – A Beginner’s Guide to Reproducible Research with Sweave which I presented today in our lab. I am making the slides available under a Creative Commons … Continue reading → [Read more...]

People rave about Sweave and the literate programing paradigm and I am guilty as charged. I speak Sweave, I think Sweave, I dream Sweave. As a matter of fact my default mode of operation is Sweave and anything else is an … Continue reading → [Read more...]

An obvious omission in my previous post on Great-circle distance calculations in R was a lack of discussion on the computational efficiency of the various methods, and in particular comparing different implementations of the same method. One of the comments … Continue reading → [Read more...]

Recently I found myself needing to calculate the distance between a large number of longitude and latitude locations. As it turns out, because the earth is a three-dimensional object, you cannot simply pretend that you are in Flatland, albeit some … Continue reading → [Read more...]

Spending the day churning through large data set or doing some heavy-duty number crunching? What is one to do while the computer is running in overdrive? We’ll, for one, you could get a steaming cup of joe and write a … Continue reading → [Read more...]

I just uploaded GillespieSSA 0.5-4 to CRAN. It should be  just a matter of days before it has propagated itself across all mirrors. This release consists of minor revisions with no (intended) changes in functionality. The main change (and it is … Continue reading → [Read more...]

The useR! 2008 meeting is about to commence. Although I am not able to go this year I will be keeping a close eye on the talks and slides that (I assume) will be posted.  Last years useR! meeting (which … Continue reading → [Read more...]

My paper on the GillespieSSA package has now been published in the latest volume of Journal of Statistical Software. Check it out. [Read more...]

Just got news that my revisions to the reviewer’s comments on my paper GillespieSSA: Implementing the Gillespie Stochastic Simulation Algorithm in R were accepted. Hence, this paper is not officially in press in the Journal of Statistical Software. Here’s the … Continue reading → [Read more...]

I just uploaded GillespieSSA 0.5-1 to CRAN. Now it’s just a matter of days before it has propagated itself across all CRAN mirrors. This version consists primarily of revisions I made in response to the reviewer comments on the paper … Continue reading → [Read more...]

I recently rolled up the new version of the GillespieSSA package, version 0.3-1. The tar ball of the new version is posted on its web page (here). I also submitted it to CRAN so in (due time) it should appear … Continue reading → [Read more...]

The latest issue Journal of Statistical Software is a special volume on Ecology and Ecological Modelling in R. This has been in the woodwork for quite some time now and it is nice to finally to see this out “in … Continue reading → [Read more...]

So it’s official – my R package GillespieSSA has been posted to the official list of packages on CRAN (The Comprehensive R Archive Network). Check it out. Now back to my manuscript. Over the last few days I have been … Continue reading → [Read more...]

Just finished the new version of the GillespieSSA package. The tar ball of the new version is posted on its web page (here). I also submitted it to CRAN so in (due time) it should appear on the official R … Continue reading → [Read more...]

Dear blog, no I have not forgot you or the rest of the world. Sequestered in my humble cubicle I have been hammering away day and night for the last several weeks – hammering out a manuscript. Finally after what … Continue reading → [Read more...]