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:
Hello,
Is there a method for ancestral state reconstruction when the character can
take on multiple values, and those values vary in complexity?
For example, some species are white (0), some gray (1), some black (2), but
then some are black and white (02).
Two solutions I can think of are (1)
