Hi Jesse,

In order to account for phylogenetic uncertainty you are better just pulling trees from their posterior rather than choosing trees that are incongruent. The latter will give estimates biased toward those associated with extreme trees.


If the analysis is the binomial model you posted on R-sig-mixed you can speed up the analysis by passing the latent variables from one model as the starting values in the next model without a long burn-in. If the data are Gaussian you just need to pass the (co)varinaces as starting values.

Code is below. It is untested, and clearly you need to replace ... with the exact specifications of the model.

Note that this type of approach is still biased towards a lambda/h2 of 0. To fix that you would need to simultaneously estimate the phylogeny and the parameters of the comparative analysis. The bias is probably small if the tree is well estimated, and doing it 'properly' would be difficult - perhaps BEAST can do it.

Cheers,

Jarrod

ntree<-100  # number of trees

nsample<-100 # number of samples per tree

thin<-10 # thinning interval

model_all<-MCMCglmm(...., pl=TRUE) # initial model object to which results will be written

model_i<-model_all

model_all$Sol<-matrix(NA, nsample*ntree, ncol(model_all$Sol))

model_all$VCV<-matrix(NA, nsample*ntree, ncol(model_all$VCV))

# create empty matrices for writing results from each tree

for(i in 1:ntree){

# iterate over trees

model_i<-MCMCglmm(...., pl=TRUE, start=list(liab=model_i$Liab[nsample,]), pedigree=tree[[i]], burnin=thin, thin=thin, nitt=thin*(nsample+1))

# fit model to tree i using starting values from previous model

model_all$Sol[(i-1)*nsample+1:nsample]<-model_i$Sol

model_all$VCV[(i-1)*nsample+1:nsample]<-model_i$VCV

}

model_all$Sol<-mcmc(model_all$Sol, thin=thin)

model_all$VCV<-mcmc(model_all$VCV, thin=thin)


On 26/07/2017 16:06, Santiago Sánchez wrote:
Hi Jesse,

As Eduardo says, if in fact you want to see how different trees are from a
"consensus", something that you could try is find the
maximum-clade-credibility (MCC) tree (you can do this with treeAnnotator
from BEAST). This will be a fully bifurcating tree and is essentially the
tree in the posterior distribution that maximizes  the overall clade
posterior probabilities (e.g. sum(posterior)). Once you have the MCC tree,
you can use the Robinson-Foulds distance metric (there is a function in
phytools) to compare all the topologies in your posterior distribution. The
trees with the lowest values will be the most incongruent with respect to
the MCC tree. Just remember to exclude the burnin.

Cheers,
Santiago

On Wed, Jul 26, 2017 at 6:01 AM <r-sig-phylo-requ...@r-project.org> wrote:

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Today's Topics:

    1. selecting a set of incongruent trees from a posterior
       distribution (Jesse Delia)
    2. Re: selecting a set of incongruent trees from a posterior
       distribution (Eduardo Ascarrunz)


----------------------------------------------------------------------

Message: 1
Date: Tue, 25 Jul 2017 16:16:30 -0400
From: Jesse Delia <jdeli...@gmail.com>
To: R-sig-phylo@r-project.org
Subject: [R-sig-phylo] selecting a set of incongruent trees from a
         posterior       distribution
Message-ID:
         <
ca+lom6ehmv6c2v_lso8b2sdqqvoqwfcrl56-4jhcmicvjyv...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Dear list,

Does anyone know of a function or script that could select a set of the
most incongruent trees from a list of trees? Maybe I missed a post, but
haven't found anything.

I running mixed models, which take a lot of computational space on my lap
top. In effort to account for phylogenetic uncertainty, without having to
run 100s of chains, I figured maybe i could run models across a (much)
shorter list that accounts for more diversity in tree shape observed within
the posterior distribution. Not sure if this makes sense, and/or is
extremely complicated?

Thanks for you time!

Jesse

         [[alternative HTML version deleted]]



------------------------------

Message: 2
Date: Wed, 26 Jul 2017 11:33:12 +0200
From: Eduardo Ascarrunz <ear...@gmail.com>
To: Jesse Delia <jdeli...@gmail.com>
Cc: R Sig Phylo Listserv <R-sig-phylo@r-project.org>
Subject: Re: [R-sig-phylo] selecting a set of incongruent trees from a
         posterior distribution
Message-ID:
         <
cakxhxpxj_8ucosjt-bzpzvsn+5quet9vxnd4ssd4bqaq-fp...@mail.gmail.com>
Content-Type: text/plain; charset="UTF-8"

Hi Jesse,

Do you want to select the trees that are most incongruent with some sort of
average of the tree distribution? The `treespace`and `phytools` packages
have functions that compute average trees with different metrics, and they
also allow you to measure the distance between each tree and the average
tree.

Cheers,

Eduardo

2017-07-25 22:16 GMT+02:00 Jesse Delia <jdeli...@gmail.com>:

Dear list,

Does anyone know of a function or script that could select a set of the
most incongruent trees from a list of trees? Maybe I missed a post, but
haven't found anything.

I running mixed models, which take a lot of computational space on my lap
top. In effort to account for phylogenetic uncertainty, without having to
run 100s of chains, I figured maybe i could run models across a (much)
shorter list that accounts for more diversity in tree shape observed
within
the posterior distribution. Not sure if this makes sense, and/or is
extremely complicated?

Thanks for you time!

Jesse

         [[alternative HTML version deleted]]

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