This is a gem of a book. It will become the book I give PhD students when they are learning how to write good R code. That is, if I ever see it again. I had hoped to write a review of it, but I haven’t seen it since it arrived in the mail...
Posts Tagged ‘ computing ’
What you wish you knew before you started a PhD
I asked my research group recently what they wished they had learned before they started work on a PhD. Here are some of the responses. More mathematics. Particular topics they named included real analysis, functional analysis, measure theory, algebra, linear algebra. That would have been my response also. I still wish I knew more mathematics...
The Joy of R: A Feline Guide
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 ( http://pineda-krch.com ) of Mario Pineda-Krch, a theoretical biologist at the University of Alberta. Filed under: cats, computing, humour, R, Sweave
Vanilla C code for the Stochastic Simulation Algorithm
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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 →
pscl 1.04 live on CRAN
Update to my pscl package, now on CRAN. Biggest change: fixing a bug in the way MCMC draws for item parameters were being stored and summarized by ideal.
GRIMS — General R Interface for Markov Sampling
I have released a (very) preliminary version of my new MCMC software in R, which I’m calling GRIMS, for General R Interface for Markov Sampling. You can get it here. This software differs from other more-or-less general MCMC packages in several respects, all but one of which make it, I think, a much better...
Character occurrence in passwords
As everyone knows, it seems that Sony is taking a bit of a battering from hackers. Thanks to Sony, numerous account and password details are now circulating on the internet. Recently, Troy Hunt carried out a brief analysis of the password structure. Here is a summary of his post: There were around 40,000 passwords, of...
New patches to speed up R 2.13.0
I have now released a new collection of 30 patches to speed up R version 2.13.0. You can get them here Assessing how much these patches speed up R is difficult. First of all, the speedup varies tremendously with the type of program. It also varies quite a bit with the machine and compiler...
Comparing HoltWinters() and ets()
I received this email today: I have a question about the ets() function in R, which I am trying to use for Holt-Winters exponential smoothing. My problem is that I am getting very different estimates of the alpha, beta and gamma parameters using ets() compared to HoltWinters(), and I can’t figure out why. This...
Slowing down matrix multiplication in R
After I realized that some aspects of R’s implementation are rather inefficient, one of the first things I looked at was matrix multiplication. There I found a huge performance penalty for many matrix multiplies, a penalty which remains in the current version, 2.13.0. As discussed below, eliminating this penalty speeds up long vector dot...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).