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 <dwba...@tamu.edu> 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 <lucas.ljard...@gmail.com> > 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 - 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/ > > > > -- > 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 - 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 at http://www.mail-archive.com/r-sig-phylo@r-project.org/
