Publications by Mario Pineda-Krch
Programing as a higher craft
In his keynote speech at the useR! meeting John Chambers of Statistics research at Bell Labs (one of the founders of the S System, which subsequently gave rise to the R project) asked the question what is programing? As it turns out it is surprisingly difficult to answer this seemingly simple question. He went on asking, Is it science, art, engi...
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Open Source/Science – drilling down to unknown depths in unexpected places
Yet another point John Chambers addressed in his key note speech (see previous post Programing as a higher craft) was the virtue of Open Source software. According to John there are two principles for programing (with R) Enable effective and rapid exploration of data, in particular when dealing with large scale dynamic data sets. Provide trustwo...
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GillespieSSA 0.1-0 is released
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 release is versioned as GillespieSSA 0.1-0. At this point the package is only available as a tar ...
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Cow chewing on GillespieSSA
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 to resemble a real Canadian, which of course is rather fitting since I recently became one). After a brief ...
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119 days of number crunching…
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 SSA methods). In this batch of runs I am utilizing Gillespie’s Direct method, which is the exact imp...
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Implementing the stochastic simulation algorithm in R
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 feels like an eternity I am almost there, i.e. getting close to submitting it. I just send a draft out for an in-lab review, so hopefu...
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GillespieSSA 0.2-0 is released
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 package list. What’s new in this release? Lots of bug fixes. The Binomial tau-leap method has been completely rewritten (resulting in a more ...
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GillespieSSA on CRAN
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 polishing my stochastic simulation algorithm manuscript. I am aiming to send it off to some eminent (and hopefully interested) ...
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Special Volume of JSS on Ecology and Ecological Modelling in R
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 print”. I am looking forward to many joyful moment thumbing through the papers in this issue. Here’s a run down of the contribution...
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GillespieSSA 0.3-1 released
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 on the official R package list. The release consists of a number of bug fixes (among others typos in the package URL and demo models). The ...
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