August 2007

Debugging in R

August 30, 2007 | Rob J Hyndman

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...]

Geometric shapes

August 29, 2007 | Hadley Wickham

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...]

XCMS on Ubuntu Feisty

August 27, 2007 | Egon Willighagen

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...]

119 days of number crunching…

August 23, 2007 | Mario Pineda-Krch

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...]

Cow chewing on GillespieSSA

August 22, 2007 | Mario Pineda-Krch

Sorry blog for the long silence. Lately I have been juggling several time critical projects and there hardly seems to be time for such mundane activities such as sleeping, eating, never mind shaving (someone pointed out that I am starting … Continue reading →
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GGobi 2.1.6

August 20, 2007 | Hadley Wickham

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...]

GillespieSSA 0.1-0 is released

August 19, 2007 | Mario Pineda-Krch

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...]

Offset in glm ()

August 17, 2007 | Forester

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...]

Including arguments in R CMD BATCH mode

August 16, 2007 | Forester

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...]

Programing as a higher craft

August 11, 2007 | Mario Pineda-Krch

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...]

rgl: R and OpenGL

August 11, 2007 | Mario Pineda-Krch

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...]

Things overheard at the useR! meeting

August 11, 2007 | Mario Pineda-Krch

Here are a few things I overheard at the useR! meeting. These comments and quotes do not necessarily represent my opinions (although many do) and since many of them were overheard in informal discussions and rants I will not name … Continue reading → [Read more...]
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