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 → [Read more...]

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 → [Read more...]

Many R users seem to get themselves in a bit of a mess with R files and workspaces scattered across different directories. The R files themselves also get messy and hard to follow. So here is some advice on keeping organized with R: Try to keep code ... [Read more...]

When using Rmpi to send processes to many nodes, it is convenient to create a list of tasks that are assigned to nodes as they become available. In my case, I was working through a large factorial set of simulations and needed to use a unique set of va... [Read more...]

Samantha Ross writes:... [Read more...]

Anyone who starts writing serious R code (i.e., code that involves user-written functions) soon finds the need to use debugging tools. There are a few basic tools in R that are worth knowing about. The function debug() allows one to step through the ex... [Read more...]

If you haven't seen them already, be sure to check out Barret Schloerke's geometric shapes. He's an undergrad student who's been working with us over summer to generate a variety of high-dimensional geometric shapes to explore with GGobi.The data incl... [Read more...]

I just installed XCMS 1.9.2 on my Ubuntu system. XCMS is a GPL-ed R package for metabolomics data analysis. Just for the record, you need to install the Feisty packages for NetCDF:sudo aptitude install netcdfg-dev libnetcdf3R CMD INSTALL --library=/usr... [Read more...]

To execute a system command from within an R script, just use system(). This is handy for zipping large output files on the fly.write.csv(mydat, "mydat.csv")system("gzip mydat.csv", wait=FALSE) [Read more...]

Just checked on the 70000+ simulations I submitted to the Cow last night. The purpose of these runs is to explore a given system (the logistic growth model in this case) using different implementations of the stochastic simulation algorithm (aka … Continue reading → [Read more...]

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Just a quick note to let you know that GGobi 2.1.6 has been releasedand is available from Windows, Mac (with easy installer) and Linuxfrom http://www.ggobi.org/downloads. The changes are largely internalwith a few more bugs being fixed.We are working ... [Read more...]

I just submitted the first release of the GillespieSSA package to CRAN. After much debating I finally decided to adhere to the unwritten R version numbering policy of starting really really low (and asymptotically approaching 1.0-0) . Thus, the first … Continue reading → [Read more...]

To add an offset to the linear predictor of a generalized linear model (or models from the survival package such as coxph and clogit), use offset(x) in the formula. This will add an offset to the linear predictor with known coefficient 1. [Read more...]

When you have multiple computers or processors at your disposal and wish to run the same script with different arguments, use the following at the command line (here described for Linux; remove the linebreak, it is just there for display purposes):$ R CMD BATCH --no-save --no-restore '--args a=1 b=c(2,5,6)... [Read more...]

When I first read Andrew Gelman's quick off-the-cuff review of the book Bayesian Computation with R, I thought it was a bit harsh. So did Gelman.I thumbed through the book at the joint statistical meetings, and decided to buy it along with Bayesian Cor... [Read more...]

This (by Aleks, Grazia, Yu-Sung, and myself) is really cool. Here's the abstract: We propose a new prior distribution for classical (non-hierarchical) logistic regression models, constructed by first scaling all nonbinary variables to have mea... [Read more...]

Yet another point John Chambers addressed in his key note speech (see previous post Programing as a higher craft) was the virtue of Open Source software. According to John there are two principles for programing (with R) Enable effective and … Continue reading → [Read more...]

In his keynote speech at the useR! meeting John Chambers of Statistics research at Bell Labs (one of the founders of the S System, which subsequently gave rise to the R project) asked the question what is programing? As it … Continue reading → [Read more...]

There were many presentations at the useR! meeting showing off amazing graphics that I had no idea R was capable of. It is clear to me that graphically speaking I have been living in the dark ages until now. One … Continue reading → [Read more...]