Our Christmas tree has not been decorated yet, but the presents are there: the BMC Bioinformatics paper on userscripts in life sciences, Bioclipse 1.2.0, a long list of blogs to rate, and a very nice overview from Wendy Warr on workflow environments, d... [Read more...]

Several people have written in to tell me that rjags crashes if you  re-run a modelling script in the same R session.  The crash is caused by a memory management bug in the JAGS library that is triggered when you … Continue reading → [Read more...]

Rattle is a graphical interface to R. It supports basic data management tasks, as well as a number of different modeling functions. I haven’t had a chance to test it out yet since I don’t have my R installation  completely up to date, but it looks promising. For ... [Read more...]

If you have a vector of factors it is easy to get the factor level; however, I always forget how to extract the factor value. I ran into the answer here. __ x x [1] 1.61 1.12 1.26 0.09 -0.13 0.16 -0.03 -0.1 0.09 -0.47 [11] A B Levels: -0.03 0.09 -0.1 -0.13 0.16 -0.47 1.12 1.26 1.61 A B__ as.numeric(x) [1] 9 7 8 2 4 5 1 3 2 6 10 11 NA__ ... [Read more...]

The Applied Bioinformatics at PRI group where I now work in Wageningen and the group of Steffen Neumann in Halle have started the MetWare project on Sourceforge to develop opensource databases for metabolomics data.The databases design will be based on... [Read more...]

During my PhD I wrote a simple but effective genetic algorithm package for R. Because there was a bug recently found, and there is interest in extending the functionality, I have set up a SourceForge project called genalg.The package provides GA support for binary and real-value chromosomes (and integer ... [Read more...]

The plotting capabilities of R are excellent; however, when I am preparing a figure for publication, I often need to combine multiple plots or add objects (e.g., arrows or text) to an existing plot. While this can be accomplished in R, my patience for ... [Read more...]

The plm package for R lets you run a number of common panel data models, including The fixed effects (or within) estimator The random effects GLS estimator It also allows for general GLS estimation, as well as GMM estimation, and includes a feature for heteroscedasticity consistent covariance estimation. It’s ... [Read more...]

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Quick-R, by Robert Kabacoff, is a wonderful R introduction site. It covers data management, basic and advanced statistics, and graphing in R, and it is aimed at an audience that has previous experience using other packages (such as SAS or Stata) that w... [Read more...]

This function is not perfect, but it does a reasonable job estimating sunrise and sunset times for my field site. If more accurate data are required, try here. Note, the command to calculate day of year is: strptime(x, "%m/%d/%Y")$yday+1suncalc [Read more...]

When I want to calculate the coordinates of a location (e.g., a nest or burrow) based on distance and bearing from a grid point, this function helps me avoid writing down SOH-CAH-TOA every time. Just note that the bearing in this case is from the grid ... [Read more...]

David Afshartous writes, What is the difference between sim() and mcsamp(), if any? If there is a difference, what should I expect in terms of difference in results? My reply:... [Read more...]

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...]

The latest issue Journal of Statistical Software is a special volume on Ecology and Ecological Modelling in R. This has been in the woodwork for quite some time now and it is nice to finally to see this out “in … Continue reading → [Read more...]

Very often, especially when plotting data, I need to reorder the levels of a factor because the default order is alphabetical. There must be many ways of reordering the levels; however, I always forget which package to look in. A direct way of reorderi... [Read more...]

READ TEXT FILES, RUN MODELS The Decision Science News R video tutorials continue with number 2. (If you missed that last one, you will want to watch R Video Tutorial Number 1 first.) The Goldstein pedometer dataset can be downloaded from http://www.dangoldstein.com/flash/Rtutorial2/pedometer.csv Topics covered this ... [Read more...]

LEARN R BY JUST WATCHING For this week, Decision Science News has created a video tutorial on how to get started using the R Language for Statistical Computing. (The tutorial is best viewed in your browser’s full-screen mode, try pressing F11 in Windows). R is free and open source, ... [Read more...]

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 → [Read more...]

Yu-Sung writes,... [Read more...]