Publications by Mario Pineda-Krch
GillespieSSA 0.5-1 is released
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 where the package is introduced (submitted to the Journal of Statistical Software). There are some minor changes...
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Paper on the Gillespie Stochastic Simulation Algorithm in press
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 abstract: The deterministic dynamics of populations in continuous time are traditio...
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Paper on GillespieSSA now published
My paper on the GillespieSSA package has now been published in the latest volume of Journal of Statistical Software. Check it out. Related To leave a comment for the author, please follow the link and comment on their blog: Mario's Entangled Bank » R. R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and...
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High-performance computing in R at useR! 2008
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 I attended) was a great experience and considering the list of participants for this years meeting, it is bound to be a very interesting meeting...
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GillespieSSA 0.5-4 is released
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 also minor) is a fix for warning messages in recent versions of R. I owe a thanks to Thomas Petzoldt ...
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Making R growl
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 post telling the world how you will know when the chomping and crunching is done. Some of you may say, just keep an eye on the p...
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Great-circle distance calculations in R
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 beg to differ. Of course, earth is not a perfect sphere either (it’s slightly ellipsoidal with a...
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Computational efficiency of great-circle distance calculations in R
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 pointed out that the geosphere package implements spherical trigonometry functions for ge...
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Top 10 things that suck about Sweave
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 exception. I do all my math and stats in Sweave, I write manuscripts in Sweave, my lab notebook is in Sweave, I manage my pers...
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The Joy of Sweave – A Beginner’s Guide to Reproducible Research with Sweave
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 Attribution-NonCommercial-ShareAlike 3.0 Unported License for anyone that might find them useful. Although I do not...
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