R

Links

Quick-R - Excelent manual!
Cookbook for R - Great overall, using for ggplot2 related.
R & Bioconductor Manual - Excellent manual!
Hadley Wickham's courses, ggobi & Co. From basics, covering advanced graphics. Perfect.

Google's R Style Guide - it's good to have consistent style, why not start here?

GUIs for R

gedit (syntax highlighting: View>Highlight Mode>Sientific>R) + plugin for R console
Eclipse + StatEt
Rstudio

"No-saving" R

To axiomatically run R as R --no-save, so that it doesn't ask about workspace save option before quiting do:

In terminal run: sudo gedit .bashrc
In this file uncomment the right part to get:
if [ -f ~/.bash_aliases ]; then
. ~/.bash_aliases
fi
Close and again in terminal: sudo gedit .bash_aliases
In this file add line: alias R='R --no-save'
Close, done. [Based on Allan Engelhardt note in CYBAEA]

Save R history

To automaticaly save/load commands history:

Speed up R

slow	fast
system.time( for(i in 1:1000000) { 1*(1+1) } )	system.time( for(i in 1:1000000) { 1*{1+1} } )	{} instead of ()
system.time( for(i in 1:10000000) 3^2 )	system.time( for(i in 1:10000000) 3*3 )	* instead of ^
system.time( for(i in 1:100000) { a<-NA; for(j in 1:100) a[j]<-j })	system.time( for(i in 1:100000) { a<-vector(length=100); for(j in 1:100) a[j]<-j })	allocate vectors for loops
x<- rnorm(50) system.time(for(i in 1:100000){mean(x)})	x<- rnorm(50) system.time(for(a in 1:100000) .Internal(mean(x)))	internal mean when you are sure it's numbers

Where R sit on Ubuntu (as of Oneiric):

Misc.

And don't forget to DRY KISS.

Yet more Hadley (thanks Tom):

This does not belong here, move it: Designing projects

BIO...