This is so cool. Thanks Liam!

> On Jun 21, 2018, at 8:22 PM, Liam J. Revell <> wrote:
> Dear Theo.
> This can be done with the function rerootingMethod as described here 
> 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: 
> All the best, Liam
> Liam J. Revell, Associate Professor of Biology
> University of Massachusetts Boston
> & Profesor Asociado, Programa de Biología
> Universidad del Rosario
> web:
> 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]]
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