Re: [R-sig-phylo] selecting a set of incongruent trees from a posterior distribution

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

Re: [R-sig-phylo] selecting a set of incongruent trees from a posterior distribution

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

Re: [R-sig-phylo] Function to Extend Tips?

That's definitely helpful, Joseph, but I'll need to extend the tips to varying amounts. Basically, I performed a tip-dating analysis using constraints based on the FADs of a bunch of fossils. However, now some of the analyses I want to perform require that the tips extend to the species'

Re: [R-sig-phylo] Function to Extend Tips?

If you want to just extend all tips by a constant amount you can do this: # extend terminal edges by arbitrary amount (here: 13) idx <- which(phy$edge[,2] < (phy$Nnode + 1)); phy$edge.length[idx] <- phy$edge.length[idx] + 13; HTH. Joseph. Joseph W. Brown

Re: [R-sig-phylo] selecting a set of incongruent trees from a posterior distribution

Hi Jesse, there is a function maxCladeCred() to compute maximum-clade-credibility in phangorn, if you prefer doing it in R. In the package are several distances between trees implemented see ?RF.dist (treespace uses them internally). Klaus On Wed, Jul 26, 2017 at 11:06 AM, Santiago Sánchez <

Re: [R-sig-phylo] selecting a set of incongruent trees from a posterior distribution

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

Re: [R-sig-phylo] Function to Extend Tips?

Awesome, thanks Joseph! On Wed, Jul 26, 2017 at 9:10 AM, Joseph W. Brown wrote: > I think this'll work, depending on how you store your data. > > # assumes a tree 'phy' and a dataframe, 'df', with first column of tip > names, and second column of values > for (i in

Re: [R-sig-phylo] Function to Extend Tips?

I think this'll work, depending on how you store your data. # assumes a tree 'phy' and a dataframe, 'df', with first column of tip names, and second column of values for (i in 1:dim(df)[1]) { # find index of edge length idx <- which(phy$edge[,2] == which(phy$tip.label ==