Dear Vincenzo. If I understand your problem problem, you do not have any explicit calibration points -- but you have a hypothesized average clock rate?
If so, then you can obtain an ultrametric tree from/ape::chronos/ for any value of the smoothing parameter (/lambda/) and then simply re-scale it to have the desired total depth (based on your hypothesized clock rate). To choose a "correct" value of /lambda/ one can use cross-validation as described in Sanderson (2002; doi:10.1093/oxfordjournals.molbev.a003974). Others should feel welcome to weigh in if this is not right. All the best, Liam Liam J. Revell Professor of Biology, University of Massachusetts Boston Web: http://faculty.umb.edu/liam.revell/ Book: Phylogenetic Comparative Methods in R <https://press.princeton.edu/books/phylogenetic-comparative-methods-in-r> (/Princeton University Press/, 2022) On 3/4/2024 11:09 AM, Vincenzo Ellis wrote: > [You don't often get email fromvael...@udel.edu. Learn why this is important > athttps://aka.ms/LearnAboutSenderIdentification ] > > CAUTION: EXTERNAL SENDER > > Dear Emmanuel, > > Thank you very much for your response. I cannot see how to provide the > substitution rate to the phangorn::pml_bb() function, but I was looking at > the ape::node.dating() function and it appears that I could provide the > substitution rate to the "mu" argument and then set the "node.dates" > argument to NA or zero for all tips (I'm not sure if NA or zero would be > preferable to force the tips to all be from a single time point). Do you > think that would work? I'm not sure how to make ape::node.dating() accept a > substitution rate rather than try to estimate one. Maybe an option could be > added to allow mu to equal a user-specified number rather than the output > of ape::estimate.mu()? > > Another option might be to calculate an estimated age for every node > connecting sister taxa in the tree by converting the genetic distances > between sister pairs to divergence times using the substitution rate and > then use those as priors in ape::chronos(). I suppose I could also apply > that logic to date all of the nodes by using the mean pairwise distances > between taxa on either side of a node and converting that to divergence > times (although the R code for such a calculation would likely take me a > while to figure out). Would that be another option? > > Thanks again, > > Vincenzo > > On Sat, Mar 2, 2024 at 5:44 AM Emmanuel Paradis<emmanuel.para...@ird.fr> > wrote: > >> Hi Vincenzo, >> >> There's no direct way to do this with ape::chronos(). You may have a look >> at the function phangorn::pml_bb() but I'm not sure it can estimate the >> dates if the rate is provided in a model object given as main argument(?) >> >> That said, I expect that estimating so many dates to be very challenging >> (unless you have a lot of known dates for calibration). This implies that >> you are certainly right to look for an approach where you don't need to >> estimate the rates. >> >> Best, >> >> Emmanuel >> >> ----- Le 27 Fév 24, à 22:40, Vincenzo ellisvael...@udel.edu a écrit : >> >>> Dear R-sig-phylo members, >>> >>> I've made a maximum likelihood tree in Raxml for several thousand taxa >>> using a single gene that has an estimated substitution rate of 0.006 >>> substitutions/nucleotide/My. Is there a way to use chronos in ape to >> apply >>> that substitution rate as a fixed clock rate and generate an ultrametric >>> time-scaled version of the tree? >>> >>> Thank you, >>> >>> Vincenzo >>> >>> [[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/ >> > [[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 athttp://www.mail-archive.com/r-sig-phylo@r-project.org/ [[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/
