Dear Liam, Many thanks for your message and the clarification - that was indeed not clear to me from the ace help page! Would ancRECON in package corHMM also be OK by any chance for my purposes? I see that that one also allows one to specify the prior for the root and I am dealing with binary characters with symmetric transition rates...
Cheers & thanks again for the advice! Tom -----Original Message----- From: Liam J. Revell [mailto:liam.rev...@umb.edu] Sent: 30 July 2013 05:31 To: Tom Wenseleers Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Question on ace ML reconstruction of discrete binary character Hi Tom. This was the subject of discussion recently on this list. ace does not do marginal ancestral state reconstruction (which is probably what you want) - it computes the conditional scaled likelihoods of the subtree. These are the same as the marginal reconstructions only at the root node. If your transition matrix is symmetric, then you can get the marginal reconstructions by rerooting at all the internal nodes. This is in the phytools function rerootingMethod (http://www.phytools.org/static.help/rerootingMethod.html). If you want to use a more complicated model, you will have to use another package - such as diversitree. An alternative is to use stochastic mapping and then compute the posterior frequencies from the sample of stochastic maps. This makes it easy to put an explicit prior on the root and to integrate over uncertainty in the transition matrix. This is implemented in phytools also (http://www.phytools.org/static.help/make.simmap.html). All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 7/29/2013 5:45 PM, Tom Wenseleers wrote: > Dear all, > > @Arne: yes I think it has to do something with the priors for the root. > I'm not sure what prior ace uses - I think equal, which in my case > would not be so appropriate given that nearly all species have the > trait.Would anyone know by any chance whether in ape it is possible to > haveace use a prior for the root which would reflect the frequency at > the tips, and if so, how one could specify this? > > Cheers, > > Tom > > *From:*Arne Mooers [mailto:amoo...@sfu.ca] > *Sent:* 29 July 2013 20:10 > *To:* Tom Wenseleers > *Subject:* Question on ace ML reconstruction of discrete binary > character > > Hoi Tom, > > What is the default prior on the root in ace? Different approaches use > different priors (=observed frequency at tips, equal, equal to tested > ratio of q's, etc.) That has had a big affect on reconstructions I > have done in the past. > > Cheers, > > Arne Mooers > > Begin forwarded message: > > *From: *Tom Wenseleers <tom.wensele...@bio.kuleuven.be > <mailto:tom.wensele...@bio.kuleuven.be>> > > *Date: *29 July, 2013 9:00:28 AM PDT > > *To: *"r-sig-phylo@r-project.org <mailto:r-sig-phylo@r-project.org>" > <r-sig-phylo@r-project.org <mailto:r-sig-phylo@r-project.org>> > > *Subject: [R-sig-phylo] Question on ace ML reconstruction of discrete > binary character* > > Dear all, > > I just did some ancestral state reconstructions of binary characters > (screenshot attached) using ace (using an equal rate discrete > character > reconstruction) . Everything seems to make sense to me, except the two > basal nodes, where I end up with quite low likelihoods for my red > character being 1 (cf. the pie charts), even though I get higher > likelihoods at practically all of the more shallow nodes in the tree. > Any ideas why one can get a result like this, and what I could > potentially do about it, since it doesn't seem quite right to me? > > Cheers, > > Tom > > /_____________________________________________________________________ > __________________/ > > /Prof. Tom Wenseleers/ > > */ Lab. of Socioecology and Social Evolution/ > > / Dept. of Biology/ > > / Zoological Institute/ > > / K.U.Leuven/ > > ///Naamsestraat 59, box 2466/ > > / B-3000 Leuven/ > > / Belgium > /(/+32 (0)16 32 39 64 / +32 (0)472 40 45 96/ > > 8/tom.wensele...@bio.kuleuven.be > <mailto:tom.wensele...@bio.kuleuven.be>/ > > */http://bio.kuleuven.be/ento/wenseleers/twenseleers.htm/* > > _______________________________________________ > R-sig-phylo mailing list -R-sig-phylo@r-project.org > <mailto:R-sig-phylo@r-project.org> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive > athttp://www.mail-archive.com/r-sig-phylo@r-project.org/ > > _____________________________ > Dr. Arne Mooers > Biology, Simon Fraser University > 8888 University Drive., Burnaby BC V5A 1S6 Canada amoo...@sfu.ca > <mailto:amoo...@sfu.ca> > +1 778 782 3979 > skype: arnemooers > www.sfu.ca/~amooers <http://www.sfu.ca/~amooers> www.sfu.ca/fabstar > <http://www.sfu.ca/fabstar> www.scientists-4-species.org > <http://www.scientists-4-species.org> > hesp.irmacs.sfu.ca > 7billionandyou.org > > > > > > > > > > > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
