Re: [R-sig-phylo] OU for non-ultrametric trees

Danielle, Apologies for the late comment on this, but what do you mean by non-rooted? Do you mean the tree is rooted, but has a three-way split with the outgroup at the root node? You shouldn't do OU on a tree you can't assign a root to. I'm also just a bit curious what gave you the sense that

Re: [R-sig-phylo] ape chronos function returning pLL of -1E100

As an update to my question--when I try to calibrate the tree itself using the default single root calibration and default 1/1 min/max ages, the function appears to run fine. When I add in my calibration table, the function exits with the -Inf LL. The tree is rooted. There are no duplicated

Re: [R-sig-phylo] Branch lengths in phytools::plot.cophylo

I didn't see the email that this addresses, but I will add a couple of comments to Juan's suggestion: (1) phytools::cophylo does not require the input trees to have branch lengths. If they do not, arbitrary branch lengths for plotting are computed using ape::compute.brlen. (2) The code

[R-sig-phylo] ape chronos function returning pLL of -1E100

I'm trying to use chronos (ape version 5.2) to scale a tree of ~800 tips, with branch lengths derived from a RAxML analysis. I'm using 4 outgroup calibrations. When I run the analysis using t.og <- chronos(tree, lambda = 1, model = "relaxed", quiet = FALSE, calibration = dd.out) I

[R-sig-phylo] Branch lengths in phytools::plot.cophylo

You can try this: tree<- compute.brtime(tree, tree$Nnode:1) It will produce an ultrametric tree with its nodes well separated. I hope it helps All the best -- Dr. Juan A. Balbuena Cavanilles Institute of Biodiversity and Evolutionary Biology Symbiont Ecology and Evolution Lab University of