Articles by Shige

Ask R not to create a local directory tree

March 12, 2011 | Shige

I don't like R to create a local directory tree in my home directory because new packages will automatically be installed into that directory. The way to do this is to modify the "/usr/local/lib64/R/etc/Renviron" and mark the line "R_LIBS_USER=${R_LIBS... [Read more...]

Post-estimation results manipulation: Stata vs. R

January 26, 2011 | Shige

Stata's new "margins" command is as powerful as "Zelig" package for R for the purpose of conducting post-estimation manipulation of the results (e.g. producing predicted probabilities, confidence intervals, etc.). While "margins" uses delta method, "Ze... [Read more...]

Comparison of results

December 4, 2010 | Shige

I am doing a simple comparison of different estimation procedures in dealing with a simple binomial model. Here is where I got started:---------------------------------------------library(INLA)library(npmlreg)library(MCMCglmm)library(DPpackage)data(See... [Read more...]

Computational tools for Bayesian analysis

November 26, 2010 | Shige

The increasing number of R-oriented Bayesian computational tools such as MCMCpack, MCMCglmm, DPpackage, R-INLA, spBayes, have made BUGS less and less crucial for day to day Bayesian computation. Honestly, I cannot figure out a single analysis that BUGS... [Read more...]

Lattice vs. ggplot2

October 28, 2010 | Shige

Both lattice and ggplot2 seem really interesting and worthy of learning. But I only have time to learn one of them, and the choice is not an easy one.Here is an awesome reference; this blog is generally very interesting; and here is something... [Read more...]

For a wider use of R

October 22, 2010 | Shige

Two things that are crucial for a wider use of R among applied researchers. The first one is data manipulation/reshaping tool. I think the package "reshape" and "reshape2" have done good job and have largely removed the barrier. The second one is ... [Read more...]

The "tikzDevice" package

October 20, 2010 | Shige

The tikzDevice package is quite amazing. Here are two graphs I just made, with (lower) and without (upper) using the tikzDevice package. The difference in quality is huge.Since the LaTeX source file for the figure is quite large in size and may take si... [Read more...]


September 25, 2010 | Shige

Here are some tips to speedup matrix computation in R. The author did not provide any benchmark though. [Read more...]

Revolution R Enterprise, some thoughts

September 9, 2010 | Shige

I requested an academic copy of the Revolution R Enterprise today. Since they only have Windows or Redhat version, I installed it on an old spare machine dual-booting Linux and Windows. I like what they did with the IDE (the debugger is nice) and ... [Read more...]

Integrating R with Geany

August 4, 2010 | Shige

According to landroni, R can also be easily integrated with Geany:Download 0.19 (non-optional), then you need to set send_selection_unsafe=true in geany.conf and assign "Send selection to terminal" to a ctrl+r keybinding or similar. As long as you... [Read more...]


August 1, 2010 | Shige

Here is a bridge between NetLogo and R, which looks very interesting. But I was not able to get it work on my Ubuntu box (running the latest R).
[Read more...]


July 29, 2010 | Shige

Red-R seems to have some interesting ideas behind it. Of course it needs some time to mature.
[Read more...]

Flexmix taks long time…

July 19, 2010 | Shige

I am running a mixture logit model on a sample of 10,000 cases. The model takes a long time (3-4 hours) to run, which makes it nearly impossible to try different specifications and such. It probably makes sense to use a subsample for exploratory analys...
[Read more...]

Npmlreg and Flexmix

July 18, 2010 | Shige

In my attempt to estimate a mixture regression model for the long-term impact of prenatal famine exposure, I compared results obtained from NPMLREG and Flexmix using the "rainfall" data set came with the package "forward" and was able to achieve identi...
[Read more...]

Latent variable analysis package for R

July 17, 2010 | Shige

This is another R package for latent variable analysis. I hope it can soon include multilevel and mixture modeling capacity. Another promising package is OpenMx, which is also under active development and very promising. At this moment, OpenMx seems to...
[Read more...]
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