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Monthly Archives: August 2007
Debugging in R
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 execution of a function, line by line. At any point, you can...
Debugging in R
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...
Geometric shapes
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...
XCMS on Ubuntu Feisty
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...
Execute system commands within an R Script
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)
119 days of number crunching…
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 →
Cow chewing on GillespieSSA
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 →
GGobi 2.1.6
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 ...
GillespieSSA 0.1-0 is released
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 →
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
