Hi,
You cannot really say that "in both ace and Mesquite, it slightly favors the
asymmetrical model": the increase in log-likelihood is less than 1 which is far
from being significant with one additional parameter. So it seems that all
three pieces of software agree well on the estimate of rate for the symmetrical
model. You should fit also this model with BayeTraits to do the full comparison.
Cheers,
Emmanuel
-----Original Message-----
From: Jingchun Li <jingc...@umich.edu>
Sender: r-sig-phylo-boun...@r-project.org
Date: Thu, 4 Apr 2013 10:15:05
To: <r-sig-phylo@r-project.org>
Subject: [R-sig-phylo] ML ancestral state reconstruction using different
softwares
Hi all,
I am exploring different methods for ancestral state reconstruction for a
small phylogeny I have (26 OTUs). I have one binary trait coded as 0s and
1s for all the taxa. And I am more interested in the transition rates
between the two states.
If I understand correctly, a maximum likelihood ancestral state
reconstruction using a MK1 model or an asymmetrical rates model should give
me the optimized estimated transition rates between the two states. The
formal will assume the two rates are the same, the later will
assume independent rates.
So I firstly did this using the ape function in ace.
ERreconstruction <- ace(traits_data, tree, type="discrete", model="ER")
ERreconstruction$rates
ERreconstruction$loglik
ARDreconstruction <- ace(traits_data, tree, type="discrete", model="ARD")
ARDreconstruction$rates
ARDreconstruction$loglik
Then I tried using Mesquite, using MK1 model and the "Asymmetrical 2-param.
Markov-k Model "
Then I tried using BayesTraits, with the MultiState -> Maximum Likelihood
option, with no restrictions on q10 and q01.
What puzzled me is that I'm getting different results from the three
softwares.
--------------------------
aceER:
transition rate: 0.0059, likelihood: -7.00
aceARD:
transition rate: 0.019 and 0.00, likelihood: -6.11
Mesquite MK1:
transition rate: 0.0059, likelihood: -7.70
Mesquite Asymmetrical:
transition rate: 0.015 and 0.005, likelihood: -7.30
BayesTraits no restriction:
transition rate: 0.0057 and 0.0057, likelihood: -14.09
--------------------------------
I can see that in both ace and Mesquite,
it slightly favors the asymmetrical model with two different rates, and the
rates and likelihoods are more of less comparable. But BayesTraits seems to
think the two rates should be equal, and it has a different likelihood.
Does this has something to do with different searching algorithms? Or am I
missing something here? I am aware that the scaled likelihoods in ace are
the scaled conditional likelihoods, not the joint or marginal
reconstructions. But this should not affect the estimated transition rates?
Thank you very much!
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