Dear Liam, Thank you for your answer. Yes, I have a hypothesized average clock rate and no explicit calibration points.
If I use ape::chronos() with default values it gives me a depth of 1 at the root. So I suppose to rescale the branch lengths I just need to multiply all of the branch lengths by a value (i.e., tree$edge.length * value), is that right? Thanks again, Vincenzo On Mon, Mar 4, 2024 at 11:43 AM Liam J. Revell <liam.rev...@umb.edu> wrote: > 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 from vael...@udel.edu. Learn why this is important > at https://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> > <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 Ellis vael...@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.orghttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=05%7C02%7Cliam.revell%40umb.edu%7C94e522b834f94ff6aa7c08dc3c659399%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638451654193183565%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=wV2IJEHNPpbc2a7Erg%2F14jVmDcIqLshVohWaKa6vG6U%3D&reserved=0 > <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> > Searchable archive at > > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=05%7C02%7Cliam.revell%40umb.edu%7C94e522b834f94ff6aa7c08dc3c659399%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638451654193196126%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=d4fLpFetiQDBjHKTmdlDijgx%2F360Z2oPddHLdCqrrUQ%3D&reserved=0 > <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.orghttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=05%7C02%7Cliam.revell%40umb.edu%7C94e522b834f94ff6aa7c08dc3c659399%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638451654193201324%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=XV4ICgm3xswIObonT8pYZcEHsQVSImxPcKHqefo8zuk%3D&reserved=0 > <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> > Searchable archive at > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=05%7C02%7Cliam.revell%40umb.edu%7C94e522b834f94ff6aa7c08dc3c659399%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638451654193205831%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=dbdnzYPubwMiyqGLncCCl8P5bPDQ%2Bn3QPUUEAt4sQZQ%3D&reserved=0 > <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 at http://www.mail-archive.com/r-sig-phylo@r-project.org/
