Dear list,
sorry for being late to the discussion. Thanks to the generous help of Iris
Bardel-Kahr we are improving the vignettes for phangorn adding some more
examples for morphological / complex / special traits. Please have a look
at the vignettes on the github page
He/Him
Professor, Dept. of Ecology & Evolutionary Biology
University of Tenneseee, Knoxville
From: R-sig-phylo on behalf of roee maor
Date: Monday, November 14, 2022 at 6:37 AM
To: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] ancestral state reconstruction with a complex
discret
Hi Chris,
I sent this message a few days ago but can't see any sign that it was
received so trying again. Apologies if anyone ends up seeing both.
To the question- in addition to the other (good) solutions given in this
thread, both HiSSE (R package) and BayesTraits (stand alone software) can
Dear Chris,
apart from the phangorn citation
(https://cran.r-project.org/web/packages/phangorn/citation.html) you
might be interested in this one:
Sabatinelli, G., Eberle, J., Fabrizi, S. & Ahrens, D. (2020) A molecular
phylogeny of Glaphyridae (Coleoptera: Scarabaeoidea): evolution of
Dear Chris,
phangorn might provide a solution for your problem. You can define
user-specific data via a contrast matrix and use this matrix to create a
phyDat object. You can then use parsimony or maximum likelihood (maybe
also Bayesian?) in phangorn to reconstruct ancestral states. I actually
Dear Krzysztof,
I would agree with Liam that it would be most sensible to treat {02} as an
intermediate condition between {0} and {2}. I have not explored
phytools::make.simmap() in detail so I apologize in advance, if what I suggest
below can be done there (probably then in an easier way).
Dear Chris.
Does it make sense to treat {02} as an intermediate condition between
{0} and {2}? If so, perhaps you'd like to try fitpolyMk in phytools,
which can also easily combine with ancestral state estimation (e.g.,
with phytools::make.simmap). Here is an example:
