Thank you Don and Julien for your suggestions. I was able to run threshml using Rthreshml from the Rphylip package. However, now I'm not really sure what to do with the results. Can I use the output to perform ancestral state reconstruction/estimation for the continuous (3) and discrete (1) characters? I see that phytools has ancThresh, but that only seems to work with a single character.
I also believe I found Goolsby's model/software <https://github.com/nspope/epee> that Julien alluded to, but it doesn't seem to be ready for primetime yet. Thanks, Will *William Gearty* Postdoctoral Research Fellow University of Nebraska–Lincoln School of Biological Sciences williamgearty.com On Tue, Mar 3, 2020 at 11:30 AM Donald Miles <urosau...@gmail.com> wrote: > Hello William, > > You can use the threshBayes function in the package phytools to implement > Felsensteins threshold model. One can combine continuous and discrete > traits in the same analysis. > > Cheers, > > Don Miles > > On Tue, Mar 3, 2020 at 11:50 AM Julien Clavel <julien.cla...@hotmail.fr> > wrote: > >> Hi William, >> >> If you want to perform a joint reconstruction of the ancestral states for >> both continuous and discrete traits (e.g. to look at the evolutionary >> correlations) I think that you should have a look at the threshold model of >> Felsenstein (a bivariate version is available in phytools; I also remember >> an Evolution meeting where E. Goolsby was working on an efficient >> implementation of the model). The model assumes that discrete traits are >> governed by a latent process which is continuous which makes possible to >> fit a multivariate model with other continuous traits (although maybe with >> a reduced power). >> >> All the best, >> >> Julien >> >> _______________________________________________ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dphylo&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=YNd8QtTlTk3ZL6_tL7DiQw&m=GZjnKT2oArH1agTzvxdaMPurGsaOf_ZTrxSkmyVJLCU&s=v32baVgG2037LRo5VxlX2WbBVoVatPNj2YnPeE4iWkA&e=> >> Searchable archive at >> http://www.mail-archive.com/r-sig-phylo@r-project.org/ >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_r-2Dsig-2Dphylo-40r-2Dproject.org_&d=DwMFaQ&c=Cu5g146wZdoqVuKpTNsYHeFX_rg6kWhlkLF8Eft-wwo&r=YNd8QtTlTk3ZL6_tL7DiQw&m=GZjnKT2oArH1agTzvxdaMPurGsaOf_ZTrxSkmyVJLCU&s=zJqBjghYZ4ojio6DS2GgNQAwTRQKp0hi_fnR21vqJ8A&e=> >> > [[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/
