The problem with function ace is that it is designed for univariate data (if I understand the help file well). Moreover I would like to take variability in branch lengths into account. So I´m looking for a function doing weighted squared-change parsimony on multivariate data, but perhaps it is something still to be done in R. Anyway, thank you for your comments. Best wishes Ondra
On 27 August 2011 17:20, Theodore Garland Jr <theodore.garl...@ucr.edu> wrote: > I have not tried this, but why should you need to set the branch lengths > equal to one? That is not a requirement of the squared-change parsimony > algorithm (or ML equivalent) per se. (With variable branch lengths, people > often refer to it as weighted squared-change parsimony.) Maybe this is just > a limitation in ACE? > > Also, how does ACE handle polytomies? I know that some algorithms have > trouble with polytomies, which may be indicated as zero-length branches. > > Cheers, > Ted > > Theodore Garland, Jr. > Professor > Department of Biology > University of California, Riverside > Riverside, CA 92521 > Office Phone: (951) 827-3524 > Wet Lab Phone: (951) 827-5724 > Dry Lab Phone: (951) 827-4026 > Home Phone: (951) 328-0820 > Facsimile: (951) 827-4286 = Dept. office (not confidential) > Email: tgarl...@ucr.edu > http://www.biology.ucr.edu/people/faculty/Garland.html > > Experimental Evolution: Concepts, Methods, and Applications of Selection > Experiments > Edited by Theodore Garland, Jr. and Michael R. Rose > http://www.ucpress.edu/book.php?isbn=9780520261808 > (PDFs of chapters are available from me or from the individual authors) > > ________________________________________ > From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] > on behalf of Sam Brown [s_d_j_br...@hotmail.com] > Sent: Friday, August 26, 2011 5:11 PM > To: r-sig-phylo@r-project.org; onmik...@gmail.com > Subject: Re: [R-sig-phylo] squared-change parsimony reconstruction > >>> Date: Thu, 25 Aug 2011 13:13:47 +0200 >>> From: Ond?ej Mikula <onmik...@gmail.com> >>> To: r-sig-phylo@r-project.org >>> Subject: [R-sig-phylo] squared-change parsimony reconstruction >>> Message-ID: >>> <CAPJtSLMXJ8y=rHguP4eqEKOqcEuxvYGSjGsg+D=jmq8w6sb...@mail.gmail.com> >>> Content-Type: text/plain >>> >>> Dear all, >>> >>> I would like to make squared-change parsimony reconstruction of ancestral >>> states for continuous multivariate data as recommended by: > > Hi Ondrej > > This can be done by setting the branch lengths of your tree to '1' and running > > ace(vector_of_states, your_tree, type = "continuous", method = "ML") > > See also the R-phylo wiki: > http://www.r-phylo.org/wiki/HowTo/Ancestral_State_Reconstruction > > Cheers! > > Samuel Brown > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
