[R-sig-phylo] phangorn, parsimony, and polytomies

(z))) ptree - optim.parsimony(base, chars.ph, method=fitch, cost=NULL, trace=2) plot(ptree) -- -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/- Ross Mounce PhD Student Fossils, Phylogeny and Macroevolution Research Group University of Bath 4 South Building, Lab 1.07 http://bit.ly/rossmounce

[R-sig-phylo] anyone going to the useR! conf August 2011?

to this? Has anyone been to a useR! conference before? Are they useful? Any opinions welcome... Kind regards, Ross -- -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/- Ross Mounce PhD Student Fossils, Phylogeny and Macroevolution Research Group University of Bath 4 South Building, Lab 1.07

Re: [R-sig-phylo] Pairwise tree distance matrix

. Optimal algorithms for comparing trees with labeled leaves. J. Classification 2:7–28. -- Rob Lanfear Research Fellow, Ecology, Evolution, and Genetics, Research School of Biology, Australian National University -- -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/- Ross Mounce PhD Student (writing

Re: [R-sig-phylo] Computing the maximum agreement subtree for large non-binary trees

but >> despite a dazzling array of options I can't seem to find MAST. Non-R >> solutions also welcome. >> >> >> Thanks, >> >> Ross >> >> >> -- >> -- >> -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-

[R-sig-phylo] Computing the maximum agreement subtree for large non-binary trees

-- -- -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/- Ross Mounce, PhD Dept. of Plant Sciences, University of Cambridge www.rossmounce.co.uk ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable

Re: [R-sig-phylo] How to test stratification of sampling across tree?

numerate all possible values (which I can't do for a 1000+ tip tree). Does that make sense? Certainly interesting... Ross On 14 March 2017 at 14:53, Ross Mounce <ross.mou...@gmail.com> wrote: > Thanks Dave, > > I'll try Blomberg's K with small simulated fully-bifurcatin

Re: [R-sig-phylo] How to test stratification of sampling across tree?

Thanks Brian, I think I might have to look into that idea. Whilst picante::Kcalc() is speedy for 12 taxon trees, it's a little slow for the tree & data I actually want to test which has 11,449 tips (a pruned version of Hinchliffe & Smith, 2014 [1]). It takes nearly 3 hours to calculate a single

[R-sig-phylo] How to test stratification of sampling across tree?

ences" (which is ~33% of the tips of the tree), on the given fixed tree shape. TL;DR How can I meaningfully test the evenness of the distribution of a binary trait across a tree, with R? Any ideas? Thanks, Ross -- -- -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-