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
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2. Re: selecting a set of incongruent trees from a posterior
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----------------------------------------------------------------------
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>
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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
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