Phylometa from R – UDPATE

April 1, 2011
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(This article was first published on Recology, and kindly contributed to R-bloggers)

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. 
Get the code at my website:
phylometa_fxn.R
phylometa_inR_run.R
(FYI: there are emticons in the code on the website, 
but it pastes fine into a text editor for me)
-This new code works with Marc’s new version of Phylometa: http://lajeunesse.myweb.usf.edu/publications.html
Again, please let me know if it doesn’t work, if it’s worthless, what changes could make it better. 

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