This blog has lasted a whole year already. Thanks for reading and commenting. There are a couple of announcements: Less blogging: I hope to put in many more years blogging here, but in full disclosure I am blogging for Journal of Ecology now, so I am going to be (and already have been) blogging less here. More blogging: If anyone wants to write guest posts at Recology on the topics of using R for ecology and evolution, or open science, please contact me. Different blogging: I was going to roll out the new dynamic views for this blog, but Google doesn’t allow javascript, which is how I include code using GitHub gists. Oh well… Anywho, here is the breakdown of visits to this blog, visualized using #ggplot2, of course. There were a total of about 23,000 pageviews in the first year of this blog. ...

Sorry for the temporary loss of GitHub gists…Hopefully dynamic views will support javascript soon!!

UPDATE: code and figure updated at 647 AM CST on 19 Dec ‘11. Also, see Jarrett Byrnes (improved) fork of my gist here. The site I WORK FOR THE INTERNET is collecting pictures and first names (last name initials only) to show collective support against SOPA (the Stop Online Piracy Act). Please stop by their site and add your name/picture. I used the #rstats package twitteR, created by Jeff Gentry, to search for tweets from people signing this site with their picture, then plotted using ggplot2, and also used Hadley’s lubridate to round timestamps on tweets to be able to bin tweets in to time slots for plotting. ...

Three presentations uploaded on LondonR meetings website. I especially enjoyed the JD Long presentation on the seque package for simulations using Amazon’s EC2.

I am part of the rOpenSci development team (along with Carl Boettiger, Karthik Ram, and Nick Fabina). Our website: http://ropensci.org/. Code at Github: https://github.com/ropensci We entered two of our R packages for integrating with PLoS Journals (rplos) and Mendeley (RMendeley) in the Mendeley-PLoS Binary Battle. Get them at GitHub (rplos; RMendeley). These two packages allow users (from R! of course) to search and retrieve data from PLoS journals (including their altmetrics data), and from Mendeley. You could surely mash up data from both PLoS and Mendeley. That’s what’s cool about rOpenSci - we provide the tools, and leave it up to users vast creativity to do awesome things. 3rd place gives us a $1,000 prize, plus a Parrot AR Drone helicopter.

See http://www.surveygizmo.com/s3/722753/Mendeley-PLoS-Binary-Battle-Public-Vote

I gave a talk today on doing very basic phylogenetics in R, including getting sequence data, aligning sequence data, plotting trees, doing trait evolution stuff, etc. Please comment if you have code for doing bayesian phylogenetic inference in R. I know phyloch has function mrbayes, but can’t get it to work… Phylogenetics in R View more presentations from schamber

Okay, so this post isn’t at all about R - but I can’t resist begging my readers for some help. I’m trying to get some crowdfunding for my research on the evolution of native plants in agricultural landscapes. My campaign is part of a larger project by about 50 other scientists and me to see how well it works to go straight to the public to get funding for science research. All these projects, including mine, are hosted at a site called RocketHub - a site that hosts crowdfunding projects of all sorts – and now they have science. ...

With examples from rOpenSci R packages. p.s. I am no expert at this... Web data from R View more presentations from schamber

Carl Boettiger, a graduate student at UC Davis, just got two packages on CRAN. One is treebase, which which handshakes with the Treebase API. The other is rfishbase, which connects with the Fishbase, although I believe just scrapes XML content as there is no API. See development on GitHub for treebase here, and for rfishbase here. Carl has some tutorials on treebase and rfishbase at his website here, and we have an official rOpenSci tutorial for treebase here. Basically, these two R packages let you search and pull down data from Treebase and Fishbase - pretty awesome. This improves workflow, and puts your data search and acquisition component into your code, instead of being a bunch of mouse clicks in a browser. ...