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
With examples from rOpenSci R packages. p.s. I am no expert at this... Web data from R View more presentations from schamber
Regular expressions are a powerful in any language to manipulate, search, etc. data. For example: > fruit <- c("apple", "banana", "pear", "pineapple") > fruit [1] "apple" "banana" "pear" "pineapple" > grep("a", fruit) # there is an "a" in each of the words [1] 1 2 3 4 > > strsplit("a string", "s") # strsplit splits the string on the "s" [[1]] [1] "a " "tring" R base has many functions for regular expressions, see slide 9 of Ed’s talk below. The package stringr, created by Hadley Wickham, is a nice alternative that wraps the base regex functions for easier use. I highly recommend stringr. ...
Rolf Lohaus, a Huxley postdoctoral fellow here in the EEB dept at Rice University, gave our R course a talk on basic visualizations in R this morning. Enjoy!
Ten Simple Rules for Open Access Publishers View more presentations from Philip Bourne
The O’Reilly Media Strata Summit has many interviews on YouTube (just search YouTube for it)Drew Conway is the author of a R packages, including infochimps, an R wrapper to the Infochimps API service. The YouTube video:
Carl Boettiger gave a talk on the topic of open science to incoming UC Davis graduate students. Here is the audio click here Here are the slides clickhere
UPDATE: I put in an R tutorial as a Github gist below. Here is a short intro R talk I gave today…for what it’s worth… R Introduction View more presentations from schamber Here’s the tutorial in a GitHub gist: https://gist.github.com/1208321
FigShare - I very much like this idea of a place to put your data online that is NOT published. Dryad is a nice place for datastes linked with published papers, but there isn’t really a place for datasets that perhaps did not make the cut for a published paper, and if known to the scientific community, could potentially help resolve the “file-drawer” effect in meta-analyses. (wow, run on sentence) ...
Stalking the Fourth Domain with Jonathan Eisen, Ph D from mendelspod on Vimeo.