Articles by Mario Pineda-Krch

To Sweave, or not to Sweave, that is the question

December 16, 2011 | 0 Comments

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...]

The Joy of R: A Feline Guide

November 5, 2011 | 0 Comments

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 ( ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta. Filed under: cats, computing, humour, R, Sweave [Read more...]

Cycles in finite populations: A reproducible seminar in three acts

November 1, 2011 | 0 Comments

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...]

Vanilla C code for the Stochastic Simulation Algorithm

October 24, 2011 | 0 Comments

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...]

What is R, really?

March 31, 2011 | 0 Comments

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...]

Top 10 things that suck about Sweave

December 1, 2010 | 0 Comments

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 →
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Great-circle distance calculations in R

November 23, 2010 | 0 Comments

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 →
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Making R growl

November 18, 2010 | 0 Comments

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 →
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GillespieSSA 0.5-4 is released

August 16, 2010 | 0 Comments

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 →
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High-performance computing in R at useR! 2008

August 12, 2008 | 0 Comments

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 →
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Paper on the Gillespie Stochastic Simulation Algorithm in press

February 1, 2008 | 0 Comments

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 →
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GillespieSSA 0.5-1 is released

January 15, 2008 | 0 Comments

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 →
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GillespieSSA 0.3-1 released

October 4, 2007 | 0 Comments

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...]

GillespieSSA on CRAN

September 21, 2007 | 0 Comments

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 →
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GillespieSSA 0.2-0 is released

September 19, 2007 | 0 Comments

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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Implementing the stochastic simulation algorithm in R

September 8, 2007 | 0 Comments

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 →
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