Phylogenetics

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 data from contast results when only two traits are input. You could easily change the code to do N traits. Note that the p-value calculated for the chi-square statistic is not output from contrast, but is calculated within the function ‘PhylipWithinSpContr’. In the code below there are two functions that make a lot of busy work easier: ‘WritePhylip’ and ‘PhylipWithinSpContr’. The first function is nice because the formatting required for data input to Phylip programs is so, well, awkward - and this function does it for you. The second function runs contrast and retrieves the output data. The example data set I produce in the code below has multiple individuals per species, so that contrasts are calculated taking into account within species variation. Get Phylip’s contrast documentation here. ...

—UPDATE: I am now using code formatting from gist.github, so I replaced the old prettyR code (sorry guys). The github way is much easier and prettier. I hope readers like the change. 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 Phylometa, and Q increases with tree size. ...

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 (tree and node ages) at https://gist.github.com/938313 Get phylocom at http://www.phylodiversity.net/phylocom/ Gene Hunt’s method has many options you can mess with, including setting tip ages (not available in bladj), setting node ages, and minimum branch length imposed. You will notice that Gene’s method may be not the appropriate if you only have extant taxa. ...

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 data sets and phylogenies so it should work. I fixed errors when parentheses came up against numbers in the output, and other things. You can use the code for up to 4 levels of your grouping variable. In addition, there are some lines of code to plot the effect sizes with confidence intervals, comparing random and fixed effects models and phylogenetic and traditional models. ...

They have online seminars that you can join in on live, and watch later as recorded videos. Check it out at phyloseminar.org

The phangorn package is a relatively new package in R for the analysis and comparison of phylogenies. See here for the Bioinformatics paper and here for the package. Here is an example of using phangorn from getting sequences to making phylogenies and visualizing them:Getting sequences from GenbankMultiple alignmentMaximum likelihood tree reconstructionVisualizing treesVisualizing trees and traitsMake fake traits:Visualize them on trees: ...

Anthony Ives, of University of Wisconsin-Madison, and Matthew Helmus of the Xishuangbanna Tropical Botanical Garden, present a new statistical method for analyzing phylogenetic community structure in an early view paper in Ecological Monographs. See the abstract here. Up to now, most phylogenetic community structure papers have calculated metrics and used randomization tests to determine if observed metrics are different from random. The approach of Ives and Helmus fits models to observed data, instead of calculating single metrics. ...

Here is some code to run Phylometa from R. Phylometa is a program that conducts phylogenetic meta-analyses. The great advantage of the approach below is that you can easily run Phylometa from R, and manipulate the output from Phylometa in R. Phylometa was created by Marc Lajeunesse at University of South Florida, and is described in his 2009 AmNat paper. Phylometa can be downloaded free here. Save phylometa_fxn.R (get here) to your working directory. Then use the block of code below to call the functions within phylometa_fxn.R. ...