Thank you everyone for your help, I really appreciate it! On Wed, Jul 26, 2017 at 11:55 AM, Jarrod Hadfield <j.hadfi...@ed.ac.uk> wrote:
> 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: >> >> 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 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]] >>>> >>>> _______________________________________________ >>>> 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. > > [[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-phylo@r-project.org/