Phylogenetics

Is your phylogeny informative?

January 19, 2012 | Carl

Yesterday my paper appeared in early view in Evolution (author’s preprint),1 so I’d like to take this chance to share the back-story and highlight my own view on some of our findings, and the associated package on CRAN.2 I didn’t set out to write this paper. I ... [Read more...]

My talk on doing phylogenetics in R

November 18, 2011 | Scott Chamberlain

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. ...

[Read more...]

R-TreeBASE Tutorial

October 28, 2011 | cboettig

My treebase package is now up on the CRAN repository. (Source code is up, the binaries should appear soon). Here’s a few introductory examples to illustrate some of the functionality of the package. Thanks in part to new data deposition … Continue reading → [Read more...]

treebase package on cran

October 25, 2011 | Carl

My treebase package is now up on the CRAN repository. (Source code is up, the binaries should appear soon). Here’s a few introductory examples to illustrate some of the functionality of the package. Thanks in part to new data deposition requirements at journals such as Evolution, Am Nat, and ... [Read more...]

Tenure track position in systematics at the University of Vermont

August 22, 2011 | Scott Chamberlain

There is an awesome position opening up for an assistant professor in systematics at the University of Vermont. Below is the announcement, and see the original post at the Distributed Ecology blog. Why is this related to R? One can do a lot of systemat...

[Read more...]

Showcasing the latest phylogenetic methods: AUTEUR

July 20, 2011 | Carl

While high-speed fish feeding videos may be the signature of the lab, dig a bit deeper and you’ll find a wealth of comparative phylogenetic methods sneaking in. It’s a natural union — expert functional morphology is the key to good comparative methods, just as phylogenies hold the key to ... [Read more...]

iEvoBio 2011 Synopsis

June 22, 2011 | Scott Chamberlain

We just wrapped up the 2011 iEvoBio meeting. It was awesome! If you didn't go this year or last year, definitely think about going next year.Here is a list of the cool projects that were discussed at the meeting (apologies if I left some out):Vistrails...

[Read more...]

searching ITIS and fetching Phylomatic trees

June 3, 2011 | Scott Chamberlain

I am writing a set of functions to search ITIS for taxonomic information (more databases to come) and functions to fetch plant phylogenetic trees from Phylomatic. Code at github.Also, see the examples in the demos folder on the Github site above.

[Read more...]

A simple function for plotting phylogenies in ggplot2

May 17, 2011 | Scott Chamberlain

I wrote a simple function for plotting a phylogeny in ggplot2. However, it only handles a 3 species tree right now, as I haven't figured out how to generalize the approach to N species.Any ideas on how to improve this?

[Read more...]

TreeBASE in R: a first tutorial

May 16, 2011 | Carl

My TreeBASE R package is essentially functional now. Here’s a quick tutorial on the kinds of things it can do. Grab the treebase package here, install and load the library into R. TreeBASE provides two APIs to query the database, one which searches by the metadata associated with different ... [Read more...]

Comparison of functions for comparative phylogenetics

May 11, 2011 | Scott Chamberlain

With all the packages (and beta stage groups of functions) for comparative phylogenetics in R (tested here: picante, geiger, ape, motmot, Liam Revell's functions), I was simply interested in which functions to use in cases where multiple functions exis...

[Read more...]

Treebase trees from R

May 3, 2011 | Scott Chamberlain

Treebase is a great resource for phylogenetic trees, and has a nice interface for searching for certain types of trees. However, if you want to simply download a lot of trees for analyses (like that in Davies et al.), then you want to be able to access...

[Read more...]

Running Phylip’s contrast application for trait pairs from R

April 26, 2011 | Scott Chamberlain

Here is some code to run Phylip's contrast application from R and get the output within R to easily manipulate yourself. Importantly, the code is written specifically for trait pairs only as the regular expression work in the code specifically grabs da...

[Read more...]

Phylometa from R: Randomization via Tip Shuffle

April 16, 2011 | Scott Chamberlain

I wrote earlier about some code I wrote for running Phylometa (software to do phylogenetic meta-analysis) from R.I have been concerned about what exactly is the right penalty for including phylogeny in a meta-analysis. E.g.: AIC is calculated from Q in...

[Read more...]

Adjust branch lengths with node ages: comparison of two methods

April 10, 2011 | Scott Chamberlain

Here is an approach for comparing two methods of adjusting branch lengths on trees: bladj in the program Phylocom and a fxn written by Gene Hunt at the Smithsonian.Get the code and example files here: http://wp.me/PRT1F-2vGet phylocom here: http:/...

[Read more...]

Phylometa from R – UDPATE

April 1, 2011 | Scott Chamberlain

A while back I posted some messy code to run Phylometa from R, especially useful for processing the output data from Phylometa which is not easily done. The code is still quite messy, but it should work now. I have run the code with tens of different d...

[Read more...]

Never miss an update! Subscribe to R-bloggers to receive e-mails with the latest R posts. (You will not see this message again.)

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)