Today's guest post comes from Yihui Xie, author of the knitr package — ed. Hi, this is Yihui Xie, and I'm guest posting on the Revolutions blog to talk about one aspect of the knitr package: how we can integrate data analysis and reporting in R with the Web. This post includes both the work that has been done...
What is the best resource to learn an R package? Many R users know the almighty question mark ? in R. For example, type ?lm and you will see the documentation of the function lm. If you know nothing about a package, you can take a look at the HTML help...
A post over on Dang, another error (show me yours and I’ll show you mine) has a method of working with R which uses an IDE called Eclipse in conjunction with a plugin called StatET. Eclipse is one of a number of IDEs that I’m aware of (Tinn-R being another, but this Sciviews pages has 
I wrote before about heatmap tables as a better way of producing frequency or other tables, with a solution which works nicely in latex. It is possible to do them much more easily in ggplot2, like this library(Hmisc) library(ggplot2) library(reshape) data(HairEyeColor) P=t(HairEyeColor) Pm=melt(P) ggfluctuation(Pm,type="heatmap")+geom_text(aes(label=Pm$value),colour="white")+ opts(axis.text.x=theme_text(size = 15),axis.text.y=theme_text(size = 15)) Note that ggfluctuation will also take
People have been telling me for a while that the latest version of RStudio, the IDE for R, is a great way to generate reports. I finally got around to trying it out and for once, the hype is justified. Start with this excellent tutorial from Jeremy Anglim. Briefly: the process is not so different 
One of the possible barriers to widespread adoption of open notebook science is knowing where to start. Video reports of lab experiments hosted on Youtube can be easily embedded in a hosted WordPress blog; a MediaWiki wiki can be used to provide one page per experiment, with change tracking/history on each page and a shadow 
People use the R language every day to create the elements of reports: tables, charts, analyses, and forecasts. But assembling all of that information into a print-ready document laid out with text can a hassle. You can cut-and-paste all of the elements into Word, but then what do you do when the data file gets updated at the last...
I wrote before about heatmap tables as a better way of producing frequency or other tables, with a solution which works nicely in latex. It is possible to do them much more easily in ggplot2, like this library(Hmisc) library(ggplot2) library(reshape) data(HairEyeColor) P=t(HairEyeColor) Pm=melt(P) ggfluctuation(Pm,type="heatmap")+geom_text(aes(label=Pm$value),colour="white")+ opts(axis.text.x=theme_text(size = 15),axis.text.y=theme_text(size = 15)) Note that ggfluctuation will also take … Continue reading...
OK, let’s do this: some statistics and visualization of the tweets for ISMB 2012. First, thanks to Stephen Turner who got things started in this post at his excellent blog, Getting Genetics Done. Subscribe to his feed if you don’t already do so. I’ve created a Github repository for this project (and future Twitter-related work). 
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
