Hello all, The package mvMORPH can also do ancestral state reconstruction of continuous characters for some OU-related models, including OUM, but I don't believe it has all the models Bruno is after. There's an example given in one of the vignettes of using mvMORPH for reconstructing a continuous character.
John John Soghigian, Ph.D. Postdoctoral Associate Deparment of Ecology and Evolutionary Biology Yale University 21 Sachem Street New Haven, CT 06511 On Mon, Jun 11, 2018 at 11:55 PM, Brian O'Meara <[email protected]> wrote: > Prompted by Bruno's email, and similar requests by some students at the > Arnold & Felsenstein Evolutionary Quantitative Genetics course, we've > started adding ancestral state reconstruction to OUwie. It still needs > debugging and testing, but should be ready fairly soon. I do believe bayou > does ancestral state estimation, too, but I don't think all the models you > want will be in the set. Could be adequate to answering the biological > question, though. > > Best, > Brian > > _______________________________________________________________________ > Brian O'Meara, http://www.brianomeara.info, especially Calendar > <http://brianomeara.info/calendars/omeara/>, CV > <http://brianomeara.info/cv/>, and Feedback > <http://brianomeara.info/teaching/feedback/> > > Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville > Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville > Associate Director for Postdoctoral Activities, National Institute for > Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS) > > > > On Mon, Jun 11, 2018 at 6:01 PM David Bapst <[email protected]> wrote: > > > Just to follow off what Lucas said, but please note you cannot rescale > > branches of a phylogeny using an OU model when the tree is > > non-ultrametric (such as when it contains extinct, fossil taxa as > > tips). Slater (2014, MEE) discusses this more in a brief correction to > > Slater (2013). > > > > I don't know if anyone in this conversation has a non-ultrametric > > tree, but I wanted to make that clear for anyone who stumbles on this > > thread n the future using a google search. > > -Dave > > > > > > > > On Sun, Jun 10, 2018 at 12:25 PM, Lucas Jardim <[email protected] > > > > wrote: > > > Hi Bruno, > > > > > > You can transform the branches of your phylogeny using the estimated > > > parameters of OU models. Then, if those models describe the observed > data > > > adequatly, the transformed tree should model the observed data as a > > > Brownian motion model. So you can use an ancestral state reconstruction > > > based on Brownian motion model. However, I do not know if that is the > > best > > > approach as optimum values would not be included into the > reconstruction > > > process. > > > > > > Best, > > > -- > > > Lucas Jardim > > > Doutor em Ecologia e Evolução > > > Bolsista do INCT-EECBio (Ecologia, Evolução e Conservação da > > > Biodiversidade) > > > Instituto de Ciências Biológicas > > > Laboratório de Ecologia Teórica e Síntese > > > Universidade Federal de Goiás > > > http://dinizfilho.wix.com/dinizfilholab > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > R-sig-phylo mailing list - [email protected] > > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > Searchable archive at > > http://www.mail-archive.com/[email protected]/ > > > > > > > > -- > > David W. Bapst, PhD > > Asst Research Professor, Geology & Geophysics, Texas A & M University > > https://github.com/dwbapst/paleotree > > Google Calendar: https://goo.gl/EpiM4J > > > > _______________________________________________ > > R-sig-phylo mailing list - [email protected] > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive at > > http://www.mail-archive.com/[email protected]/ > > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > [email protected]/ > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
