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.`

## Advertising

`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:Send R-sig-phylo mailing list submissions to r-sig-phylo@r-project.org To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/r-sig-phylo or, via email, send a message with subject or body 'help' to r-sig-phylo-requ...@r-project.org You can reach the person managing the list at r-sig-phylo-ow...@r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of R-sig-phylo digest..." 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 observedwithinthe posterior distribution. Not sure if this makes sense, and/or is extremely complicated? Thanks for you time! Jesse [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r- sig-ph...@r-project.org/[[alternative HTML version deleted]] ------------------------------ Subject: Digest Footer _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ------------------------------ End of R-sig-phylo Digest, Vol 114, Issue 10 ********************************************

-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/