[R-sig-phylo] estimate ancestral state with OUwie models
Dear colleagues, I would like to know if anyone is aware of a way to estimate the ancestral states of a continuous character using Ornstein-Uhlenbeck models that "allow the strength of selection and stochastic motion to vary across selective regimes" (as implemented in the OUwie R package). Specifically, I would like to use the models OUM, OUMV, OUMA and OUMVA, for which I already estimated the parameter values, to indicate the most likely character value for each node of the phylogeny. Any help on this will be most welcome. Thanks in advance, Bruno Bruno Vilela, Ph.D. Postdoctoral researcher, Dept. of Biology Washington University in Saint Louis One Brookings Drive, Campus Box 1137 St. Louis, MO 63130-4899 http://bvilela.weebly.com/ [[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/
Re: [R-sig-phylo] Testing tree disagreement: SH-test disappeared in ape-package
Hi Sebastian, All the likelihood-based phylogenetic inference functions have been removed from ape since version 2.4 (released in Oct 2009) because of the (incomparably better) implementation in phangorn: library(phangorn) ?SH.test Best, Emmanuel Le 08/06/2018 à 14:50, Sebastian Y. Müller a écrit : Dear all, I'd was wondering how to best perform a test to determine test disagreement (congruence test) in R? Additional information can be found in Planet et al (DOI: 10.1016/j.jbi.2005.08.008). A common test seems the Shimodaira-Hasegawa Test (SH-test) which used to be implemented in APE: https://www.rdocumentation.org/packages/ape/versions/2.3-3/topics/sh.test However, it seem to have disappeared in recent versions (e.g. ape 5.0). Did this happen for a reason? Or maybe it has been replaced by a more appropriate test? Failing this, is anyone aware of other software to perform SH-, KH- or SOWH-tests? Thanks for any help! ___ 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/
Re: [R-sig-phylo] Testing tree disagreement: SH-test disappeared in ape-package
Hi Sebastian, there is an implementation of the SH-test and SOWH-test in phangorn. Send me an mail off list if you have problems using them. Regards, Klaus On Jun 8, 2018 8:50 AM, "Sebastian Y. Müller" wrote: Dear all, I'd was wondering how to best perform a test to determine test disagreement (congruence test) in R? Additional information can be found in Planet et al (DOI: 10.1016/j.jbi.2005.08.008). A common test seems the Shimodaira-Hasegawa Test (SH-test) which used to be implemented in APE: https://www.rdocumentation.org/packages/ape/versions/2.3-3/topics/sh.test However, it seem to have disappeared in recent versions (e.g. ape 5.0). Did this happen for a reason? Or maybe it has been replaced by a more appropriate test? Failing this, is anyone aware of other software to perform SH-, KH- or SOWH-tests? Thanks for any help! -- Dr. Sebastian Müller Department of Plant Sciences University of Cambridge Downing Street, Cambridge, CB2 3EA, UK http://www.plantsci.cam.ac.uk/directory/mueller-sebastian Phone: 0044 1223 748976 ___ 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/
[R-sig-phylo] Testing tree disagreement: SH-test disappeared in ape-package
Dear all, I'd was wondering how to best perform a test to determine test disagreement (congruence test) in R? Additional information can be found in Planet et al (DOI: 10.1016/j.jbi.2005.08.008). A common test seems the Shimodaira-Hasegawa Test (SH-test) which used to be implemented in APE: https://www.rdocumentation.org/packages/ape/versions/2.3-3/topics/sh.test However, it seem to have disappeared in recent versions (e.g. ape 5.0). Did this happen for a reason? Or maybe it has been replaced by a more appropriate test? Failing this, is anyone aware of other software to perform SH-, KH- or SOWH-tests? Thanks for any help! -- Dr. Sebastian Müller Department of Plant Sciences University of Cambridge Downing Street, Cambridge, CB2 3EA, UK http://www.plantsci.cam.ac.uk/directory/mueller-sebastian Phone: 0044 1223 748976 ___ 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/
