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...]

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...]

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...]

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...]

Just checked on the 70000+ simulations I submitted to the Cow last night. The purpose of these runs is to explore a given system (the logistic growth model in this case) using different implementations of the stochastic simulation algorithm (aka … Continue reading → [Read more...]

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I just submitted the first release of the GillespieSSA package to CRAN. After much debating I finally decided to adhere to the unwritten R version numbering policy of starting really really low (and asymptotically approaching 1.0-0) . Thus, the first … Continue reading → [Read more...]

Sitting in a dreary hotel room in San Jose with Interstate 101 on my left and a burger joint/truck stop on my right (see previous post Report from the meeting of the Ecological Society of America in San Jose for … Continue reading → [Read more...]

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Just a brief update on my activities 11 days before the R package GillespieSSA is to be released. I have been hacking away on the code, debugging, and running test simulations like there is no tomorrow. The last SSA implementation … Continue reading → [Read more...]

Here’s my submitted abstract for the poster I will be presenting at the useR! 2007 meeting in August. GillespieSSA: A stochastic simulation package for R Mario Pineda-Krch Center for Animal Disease Modeling and Surveillance University of California, Davis Abstract Stochastic … Continue reading → [Read more...]