Sorry, I forgot to include the list. there we go.
> ------------------------------
> *From: * Jingchun Li <[email protected]>
> *Date: *Thu, 4 Apr 2013 21:58:56 -0400
> *To: *<[email protected]>
> *Subject: *Re: [R-sig-phylo] ML ancestral state reconstruction using
> different softwares
>
> Thank you very much, Dr.Paradis. You are right that the two parameter
> model does not fit the data significantly better. I guess I'm more puzzled
> about why the three softwares gave me different likelihoods.
>
> I did fit the symmetrical model using BayesTraits later and it gave me
> about the same transition rates as the asymmetrical model and a
> similar likelihood value (-14.08 for symmetrical and -14.00 for
> asymmetrical). However I do have biological evidence that transition from 0
> to 1 might be extremely hard. So maybe I can also try set q01 to 0 (which
> is actually what ace gave me under the asymmetrical model)?
>
> Cheers,
>
> Jingchun
>
>
> On Thu, Apr 4, 2013 at 9:21 PM, Emmanuel Paradis
> <[email protected]>wrote:
>
>> 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 <[email protected]>
>> Sender: [email protected]
>> Date: Thu, 4 Apr 2013 10:15:05
>> To: <[email protected]>
>> 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!
>>
>> [[alternative HTML version deleted]]
>>
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>
>
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