Category Archives: GillespieSSA

Vanilla C code for the Stochastic Simulation Algorithm

Posted on October 24, 2011 by

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 →

Posted in computer simulations, computing, cookbook, Daniel Gillespie, Gillespie algorithm, GillespieSSA, R | 1 Comment

GillespieSSA 0.5-4 is released

Posted on August 16, 2010 by

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 →

Posted in computer simulations, GillespieSSA, Git, Linus Torvalds, R | Leave a comment

Paper on GillespieSSA now published

Posted on May 2, 2008 by

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

Posted in GillespieSSA, manuscript, R | Tagged | Leave a comment

Paper on the Gillespie Stochastic Simulation Algorithm in press

Posted on February 1, 2008 by

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 →

Posted in computer simulations, Gillespie algorithm, GillespieSSA, R | 5 Comments

GillespieSSA 0.5-1 is released

Posted on January 15, 2008 by

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 →

Posted in computer simulations, GillespieSSA, programing, R | Leave a comment

GillespieSSA 0.3-1 released

Posted on October 4, 2007 by

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 →

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GillespieSSA on CRAN

Posted on September 21, 2007 by

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 →

Posted in Gillespie algorithm, GillespieSSA, manuscript, R | Leave a comment

GillespieSSA 0.2-0 is released

Posted on September 19, 2007 by

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 →

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119 days of number crunching…

Posted on August 23, 2007 by

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 →

Posted in computer cluster, computer simulations, Gillespie algorithm, GillespieSSA, R | Leave a comment

Cow chewing on GillespieSSA

Posted on August 23, 2007 by

Sorry blog for the long silence. Lately I have been juggling several time critical projects and there hardly seems to be time for such mundane activities such as sleeping, eating, never mind shaving (someone pointed out that I am starting … Continue reading →

Posted in computer simulations, computing, GillespieSSA, R | 1 Comment

GillespieSSA 0.1-0 is released

Posted on August 19, 2007 by

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 →

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Looking for a few good beta testers

Posted on August 7, 2007 by

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 →

Posted in computer simulations, GillespieSSA, R | Leave a comment

Blazing fast tau-leap methods

Posted on August 4, 2007 by

Today I added the Decaying-Dimerization reaction set as a template model to GillespieSSA. This model was used by Gillespie in the paper where he introduced the Explicit tau-leap method in 2001. The model consists of three species and four reactions … Continue reading →

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GillespieSSA poster

Posted on August 3, 2007 by

Finished my poster for the useR! 2007 meeting. It is also posted on the GillespieSSA web page as part of the package documentation. Now, all I have to do is show it off in Ames next week…, oh, and I … Continue reading →

Posted in computer simulations, Gillespie algorithm, GillespieSSA, R | Leave a comment

The perils of numerical simulations

Posted on August 2, 2007 by

Sorry blog for the lack of posts lately. As the devoted reader may have realized it is less than a week left before I am supposed to finish (i.e. release) the GillespieSSA R package. Within this time period I am … Continue reading →

Posted in computer simulations, computing, GillespieSSA | Leave a comment

Adaptive tau-leaping in SSA

Posted on July 26, 2007 by

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 →

Posted in computer simulations, Daniel Gillespie, Gillespie algorithm, GillespieSSA, R | Leave a comment

Abstract for useR! 2007 poster

Posted on July 16, 2007 by

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 →

Posted in computer simulations, Gillespie algorithm, GillespieSSA, meeting, R | Leave a comment