This is so cool. Thanks Liam! J > On Jun 21, 2018, at 8:22 PM, Liam J. Revell <liam.rev...@umb.edu> wrote: > > Dear Theo. > > This can be done with the function rerootingMethod as described here > http://blog.phytools.org/2013/04/estimating-ancestral-states-when.html, > although it is *very* important to note that rerootingMethod is only valid if > the fitted transition model is symmetric (e.g., "ER", "SYM", or any custom > model in which i->j == j->i for all i & j). It can also be done with > make.simmap for both symmetric & non-symmetric transition models. If you > sample enough stochastic maps & then run summary on the set of maps the > posterior probabilities will converge on the marginal ancestral states under > the defaults for make.simmap, so long as a flat prior is used on internal > nodes. This is also on my blog here: > http://blog.phytools.org/2013/03/estimating-ancestral-states-when-tips.html. > > All the best, Liam > > Liam J. Revell, Associate Professor of Biology > University of Massachusetts Boston > & Profesor Asociado, Programa de Biología > Universidad del Rosario > web: http://faculty.umb.edu/liam.revell/ > > On 6/21/2018 5:32 PM, Théo Léger wrote: >> Hello, >> I am working on the phylogeny of a subfamily of moths and I use ace from the >> ape-package to reconstruct the ancestral state of a bunch of morphological >> characters. >> I encountered a problem with the few unknown states I have on my matrix >> (coded "?", either because material for examination was missing or the state >> could not fit in any of the categories): they are treated as other >> characters. Is there a way to ignore them? Is there a way to estimate the >> state for the species with missing information? I know it is possible to >> estimate the state at a tip with missing information in functions like >> AncTresh (using bayesian reconstruction) from the phytools package, but I am >> not sure if ML reconstruction can do it. >> Thanks in advance to those who can enlighten me! >> Cheers, >> Th�o L�ger >> [[alternative HTML version deleted]] >> _______________________________________________ >> 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/
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