R has a new platform-R-Forge-that enables developers and users to communicate with each other. More importantly, it is a version control platform that enables different developers to keep track on what others have been working on. So that ideally, if... [Read more...]

My paper on the GillespieSSA package has now been published in the latest volume of Journal of Statistical Software. Check it out. [Read more...]

In R, apply() is NOT faster than a loop!!I don't know where I pick up this perception about apply() being faster than a loop in R. For a long time, I always think that apply() runs a function (for example, mean()) on a data structure (row or column) i... [Read more...]

It’s been ages since I visited the R website, so I don’t know how long they’ve had a wiki. It’s built using DokuWiki, one of my personal favourites. This is a great leap forward for R documentation, which is somewhat notorious for being (a) difficult to ... [Read more...]

As announced earlier, Miguel, Velitchka, Christoph and I held a small CDK/Metabolomics/Chemometrics unconference. We started late, and did not have an evening program, resulting in not overly much results. However, we did do molecular chemometrics.We u... [Read more...]

If a model is estimated using the following code: lm(y~x1+x2)-__p 1. bptest(p) does the Breuch Pagan test to formally check presence of heteroscedasticity. To use bptest, you will have to call lmtest library. 2. If the test is positive (low p value), you should see if ... [Read more...]

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Plenty of packages allow you to plot contours of a "z" value; however, I wanted to be able to plot a specific density contour of a sample from a bivariate distribution over a plot that was a function of the x and y parameters. The example only plots th... [Read more...]

JAGS is a cross platform BUGS. Because it runs in a command mode, it is somewhat faster than other BUGS. However, I found it is a bit tacky to use it as a Windows/PC user. I found the manual very useful but some of the language is a bit ... [Read more...]

I have made a small “translation” of a portion of “Writing R Extensions” manual about the Rd files to a vimhelp format. You can find it on vim.org, under this link http://www.vim.org/scripts/script.php?script_id=2177. If that does not work just search for a ... [Read more...]

I coauthor a paper with Ozan, a friend who I know when I was TAing Bayesian Methods in ICPSR. The paper tries to see if the 9/11 has any effect on American's attitudes on Muslim. We have dataset from different years: 2 from pre-9/11 periods and 2 from ... [Read more...]

sapply(a,class) gives type of field (character, numeric, or factor) for each variable in the data frame a. [Read more...]

I used to fit Bayesian model using WinBUGS via R a lot. But now I am more and more prone to run models on OpenBUGS directly. I have document the reason why I like OpenBUGS and wrote a auto OpenBUGS function here. In short, I like to be able to ... [Read more...]

I’ve been asked how to do this several times, so I thought it might help to put an example online. x [Read more...]

When creating a subset of a dataframe, I often exclude rows based on the level of a factor. However, the "levels" of the factor remain intact. This is the intended behavior of R, but it can cause problems in some cases. I finally discovered how to clean up levels in ... [Read more...]

Since the release of R_2.6.0, R package developers were advised to use the ``codetools" package to check potential bugs. However, as I am not familiar with computer language, I found the warning messages a bit confusing. For example:__ checkUsage(glm.fit): no visible binding for global variable ‘n’I don't ... [Read more...]

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 → [Read more...]

The GGobi book is now available from Springer and Amazon, after quite a delay. Getting the figures printed correctly was difficult. Solutions to the exercises in the back of each chapter are available for instructors by emailing Springer.The movies on ... [Read more...]

RKN over at Epidemiology blog had a small problem he solved using simulation:I have been interested in the following question: if there are, let's say, 5 genes involved in the liability of fx risk, and each gene has two alleles with one of them conferr... [Read more...]

I was trying to plot figure in R like the one below, which is basically the veto player model of Tsebelis. Based on my knowledge of R now, I encountered 2 major problems:I don't know if there is a function that can draw archs, or at least partial curves from ... [Read more...]