An alternative that doesn't require discretization of the continuous trait would be an approach I used in http://onlinelibrary.wiley.com/doi/10.1111/evo.12792/abstract. Briefly you do standard ASR of both traits (continuous = ML brownian motion; discrete = stochastic mappings) independently. Then extract the continuous trait value distribution at inferred transition points & compare to a null generated by simulating the discrete trait. If your interested in doing this email me off list and I can give you the latest version of the code for doing this using phytools stochastic mapping results.
Cheers Heath On Monday, April 4, 2016, Alejandro Gonzalez Voyer < alejandro.gonza...@iecologia.unam.mx> wrote: > Hello Gavin, > > You could have a look at the method for evolutionary contingency, which > works only for binary traits (meaning you’d have to transform your > continuous trait into a binary one). See Pagel and Meade 2006 (Bayesian > Analysis of Correlated Evolution of Discrete Characters by Reversible-Jump > Markov Chain Monte Carlo in Am Nat) for details on the method. > Note that it will provide information on whether evolutionary transitions > in trait state for one of the traits is contingent on the state of the > second one. You can infer the probable history of transitions from the > results. However, you should be careful as the method is sensitive to > trait-state distribution. > > Cheers > > Alejandro > > > > _______________________________________________ > Dr Alejandro Gonzalez Voyer > > Laboratorio de Conducta Animal > Instituto de Ecología > Circuito Exterior S/N > Ciudad Universitaria > Universidad Nacional Autónoma de México > México, D.F. > 04510 > México > > Tel: +52 55 5622 9044 > E-mail: alejandro.gonza...@iecologia.unam.mx <javascript:;> > Web: www.alejandrogonzalezvoyer.com > > > El 04/04/2016, a las 13:37, Gavin McLean Leighton <gm...@cornell.edu > <javascript:;>> escribió: > > > > Hi all, > > > > > > I have 500 trees of 80 species downloaded from birdtree.org and am > primarily interested in two traits. I have used PGLS to determine the > traits are related but would ideally like to test if there is an order to > trait evolution. To complicate matters one trait (Trait A) is continuous > while the second (Trait B) is presence/absence. I was hoping someone could > direct me to methods (assuming they exist) that would allow me to determine > the estimated value of Trait A before a gain of Trait B evolves in a > lineage. > > > > > > Thank you, > > > > Gavin > > > > > > Gavin Leighton > > NSF Postdoctoral Fellow > > Cornell University > > Cornell Laboratory of Ornithology > > 159 Sapsucker Woods Road > > Ithaca, NY > > http://www.gavinmleighton.com/ > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-phylo mailing list - R-sig-phylo@r-project.org <javascript:;> > > 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 <javascript:;> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Sent from Gmail Mobile - typos likely Heath Blackmon, Ph.D. coleoguy.github.io University of Minnesota [[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/
