Re: [R-sig-phylo] behavior of is.monophyletic()

Hi Bret, This is fixed and will be in the next release. In the meantime, you can edit the function and change the last line to: all.equal(tips, desc) Thanks for the report. Cheers, Emmanuel -Original Message- From: Bret Larget lar...@stat.wisc.edu Sender:

Re: [R-sig-phylo] avPlots for PGLS?

Hi Jay, There isn't a function but you can get the plots directly from models. The avPlot function can be reproduced quite simply: library(car) mod1 - lm(prestige ~ income+education+type, data=Duncan) mod2 - lm(prestige ~ education+type, data=Duncan) mod3 - lm(income ~ education+type,

Re: [R-sig-phylo] Error with PGLS under OU model using corMartins

Hi Nick, You can fix the value of alpha in corMartins: corMartins(1, tree, fixed=TRUE) You can try with different values to see which one gives the best fit. Best, Emmanuel -Original Message- From: Nicholas Mason nicholas.albert.ma...@gmail.com Sender: