IDE's (Integrated Development Environments)

• RStudio: http://www.rstudio.org/
• Tinn-R: http://www.sciviews.org/Tinn-R/

Graphical User Interface's

• StatET: http://www.walware.de/goto/statet
• Eclipse: http://www.eclipse.org/
• R Commander: http://socserv.mcmaster.ca/jfox/Misc/Rcmdr/
• JGR: http://cran.r-project.org/web/packages/JGR/index.html
• Deducer: http://www.deducer.org/pmwiki/pmwiki.php?n=Main.
• DeducerManual
• Rattle: http://rattle.togaware.com/
• RedR: http://www.red-r.org/

Text Editor's

• SublimeText2 (aka ST2) http://www.sublimetext.com/ - It does cost $$, but well worth it - and get Karthik Ram's ST2 plugin to pass R code to an R console here
• TextWrangler: http://www.barebones.com/products/textwrangler/
• Notepad++: http://notepad-plus-plus.org/, with Npp2r plugin: http://sourceforge.net/projects/npptor/

• Sign up for R-help mailing list here: https://stat.ethz.ch/mailman/listinfo/r-help -remember to read the posting guide before posting to the listserve
• R-help phylogenetics: https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
• R-help ecology: https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
• R-help on mixed effects models: https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
• R-help on networks/graphs: https://stat.ethz.ch/mailman/listinfo/r-sig-networks
   [all R-help listserves: https://stat.ethz.ch/mailman/listinfo/]
• Stackoverflow: http://stackoverflow.com/, especially the R tag
• The R Journal: http://journal.r-project.org/
• Google groups, ggplot2: http://groups.google.com/group/ggplot2?pli=1
• R Graphical Manual: http://rgm2.lab.nig.ac.jp/RGM2/images.php?show=all&pageID=935
• R Bloggers: http://www.r-bloggers.com/
• R Graph Gallery: http://addictedtor.free.fr/graphiques/
• Examples of figures in both Lattice and ggplot2: http://learnr.files.wordpress.com/2009/08/latbook_time1.pdf
• Quick R: http://www.statmethods.net/index.html
• CrossValidated: http://stats.stackexchange.com/
• R Inferno (pdf document): http://www.burns-stat.com/pages/Tutor/R_inferno.pdf
• Hadley Whickam's short courses: http://courses.had.co.nz/

• Analysis of Ecological and Environmental Data
• Phylogenetics
• Cluster Analysis
• Analysis of Spatial Data
• Multivariate Statistics
• Statistical Genetics

• Noam Ross' blog http://www.noamross.net/index.html
• Carl Boettiger's Lab Notebook http://carlboettiger.info/lab-notebook.html
• rOpenSci packages and related packages

• R phylogenetics Wiki: http://www.r-phylo.org/wiki/HowTo/Table_of_Contents
• Bodega Phylogenetics Wiki: http://bodegaphylo.wikispot.org/Front_Page
• Phylogenetic signal: http://bodegaphylo.wikispot.org/IV._Testing_Phylogenetic_Signal_in_R
• Morphological Evolution: http://bodegaphylo.wikispot.org/Morphological_evolution_in_R
• Brownie (Brian O'Meara's program) tutorial: http://bodegaphylo.wikispot.org/Morphological_Diversification_and_Rates_of_Evolution
• Phyloseminar.org: http://phyloseminar.org/ sometimes has a some R related stuff
• Liam Revell's blog Phylogenetic Tools for Comparative Biology: http://phytools.blogspot.com/2011/03/creating-star-phylogeny.html
• Dechronization blog: http://treethinkers.blogspot.com/

• Nice R Code site/blog by Rich FitzJohn and Daniel Falster (http://nicercode.github.io/
• The Cerebral Mastication blog has a nice list of R resources (http://www.cerebralmastication.com/r-resources/)
• Pairach Piboonrungroj has a nice list of R tutorials (here/)
• The Ecostudies blog R tricks (http://pvanb.wordpress.com/links-2/r-tips-tricks/)