Publications by Mario Pineda-Krch
What is R, really?
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 is says. “free software” – what does this mean? Free as in gratis or as in Open Source free? As it turns out, R is not...
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Vanilla C code for the Stochastic Simulation Algorithm
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 overly computationally demanding you might want to consider the GillespieSSA p...
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Cycles in finite populations: A reproducible seminar in three acts
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 mechanisms of such cycles is a centr...
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The Joy of R: A Feline Guide
Just because it’s caturday The face of feline pleasures. Long heat-generating Sweaving makes you puRR. The heat sink and me – this sort of thing is my bag baby. Putting the R in purr. Images by Mario Pineda-Krch (CC BY-NC-SA 3.0) This is from the “Mario’s Entangled Bank” blog ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoret...
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To Sweave, or not to Sweave, that is the question
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 to illustrate how the literate programming paradigm can improve reproduci...
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