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 get the following returned, in almost 5 seconds: Setting initial dates... Fitting in progress... get a first set of estimates Penalised log-lik = -1e+100 Optimising rates... dates... -1e+100 Done. a look at attributes (attr(t.og, "message")) gives a "relative convergence (4)." The pLL, however, is -Inf. I have tried setting chronos.control to different values, with no success. It looks like it may be an issue with the optimization function inside chronos. Are there additional constraints/code I can apply to make it optimize without (apparently) simply running to the boundary? Thanks, ~John [[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/