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/
