Dear list, sorry for being late to the discussion. Thanks to the generous help of Iris Bardel-Kahr we are improving the vignettes for phangorn adding some more examples for morphological / complex / special traits. Please have a look at the vignettes on the github page https://klausvigo.github.io/phangorn/ in the articles section. The titles might change and sections still get moved around at the moment. So what you are interested in is distributed over several vignettes. And suggestions for improvement are welcome. In optim.pml() / pml_bb() you need to change the default value to optEdge=FALSE in case you only want to estimate the parameters for the rate matrix. Only time reversible models are possible at the moment. A parsimony analysis at the start might be useful. If the parsimony score divided by the number of sites is high, if you expect many state changes the ancestral reconstruction. At the root you will see a mixture of all states, which is a sign of uncertainty. This can also be an artefact if you observe transitions on short edges (so-called cherries) which will bias transition rates. However this you can catch if the number of expected substitutions is considerably higher than the parsimony score / site. Kind regards, Klaus
On Mon, Nov 14, 2022 at 8:03 AM Jonas Eberle <eberle.jo...@gmail.com> wrote: > Dear Chris, > > apart from the phangorn citation > (https://cran.r-project.org/web/packages/phangorn/citation.html) you > might be interested in this one: > Sabatinelli, G., Eberle, J., Fabrizi, S. & Ahrens, D. (2020) A molecular > phylogeny of Glaphyridae (Coleoptera: Scarabaeoidea): evolution of > pollination and association with “Poppy guild” flowers. /Systematic > Entomology/ n/a. https://doi.org/10.1111/syen.12429 > > Good luck with your study! > > Best, > Jonas > > Am 12.11.2022 um 12:00 schrieb r-sig-phylo-requ...@r-project.org: > > Send R-sig-phylo mailing list submissions to > > r-sig-phylo@r-project.org > > > > To subscribe or unsubscribe via the World Wide Web, visit > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > or, via email, send a message with subject or body 'help' to > > r-sig-phylo-requ...@r-project.org > > > > You can reach the person managing the list at > > r-sig-phylo-ow...@r-project.org > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of R-sig-phylo digest..." > > > > Today's Topics: > > > > 1. Re: R-sig-phylo Digest, Vol 178, Issue 5 (Krzysztof Kozak) > > > > _______________________________________________ > > R-sig-phylo mailing list > > R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > [[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/ > -- Klaus Schliep Senior Scientist Institute of Environmental Biotechnology TU Graz https://ubt.tugraz.at <https://icbt.tugraz.at> [[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/
