Jingchun,
Thanks to Daniel for giving a detailed answer to your first question.
You can use ace() to fit a model with irreversible change. You need to build a
custom model like this:
> Q <- matrix(0, 2, 2)
> Q[2, 1] <- 1
> Q
[,1] [,2]
[1,] 0 0
[2,] 1 0
In this case there's one rate to be estimated and the other is fixed to zero
(the 0's on the diagonal are ignored). This can be generalized to more
complicated models (there's an example in my book). Then call ace with:
ace(traits_data, tree, type = "d", model = Q)
This time you cannot compare this model with the "ER" one with an LRT: compare
directly the log-liks since they have the same number of parameters or use
AIC(). BTW, there is an anova methods to compare nested models fitted with ace:
this avoids the pain to compute correctly df's.
Cheers,
Emmanuel
-----Original Message-----
From: Jingchun Li <[email protected]>
Date: Thu, 4 Apr 2013 22:25:09
To: <[email protected]>; <[email protected]>
Subject: Re: [R-sig-phylo] ML ancestral state reconstruction using different
softwares
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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