Thank you Liam! Is there anything phytools cannot do?... Not sure if this would be the right solution though. The actual trait that I am investigating is flower petal colour, so in some cases the state may be as complex as three colours. Transitions between different colours may be very simple (e.g. orange to red), or very complicated.
On Wed, Nov 9, 2022 at 3:04 AM <r-sig-phylo-requ...@r-project.org> wrote: > 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. ancestral state reconstruction with a complex discrete trait > (Krzysztof Kozak) > 2. Re: ancestral state reconstruction with a complex discrete > trait (Liam J. Revell) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 8 Nov 2022 11:35:35 -0800 > From: Krzysztof Kozak <evoeco...@gmail.com> > To: r-sig-phylo@r-project.org > Subject: [R-sig-phylo] ancestral state reconstruction with a complex > discrete trait > Message-ID: > <CABCAdWXhvDnjFnzfe8AyG=bbiq= > smzqreqs0835nnufqh+_...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > Is there a method for ancestral state reconstruction when the character can > take on multiple values, and those values vary in complexity? > For example, some species are white (0), some gray (1), some black (2), but > then some are black and white (02). > Two solutions I can think of are (1) code each combination as a simple > state (so black and white could be coded as '3'); (2) treat each state as > binary character. > Any better solutions, please? > > - Chris Kozak > > [[alternative HTML version deleted]] > > > > > ------------------------------ > > Message: 2 > Date: Tue, 8 Nov 2022 16:10:15 -0500 > From: "Liam J. Revell" <liam.rev...@umb.edu> > To: Krzysztof Kozak <evoeco...@gmail.com>, r-sig-phylo@r-project.org > Subject: Re: [R-sig-phylo] ancestral state reconstruction with a > complex discrete trait > Message-ID: <8ec56372-c156-1f07-7b02-2697eb60d...@umb.edu> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Dear Chris. > > Does it make sense to treat {02} as an intermediate condition between > {0} and {2}? If so, perhaps you'd like to try fitpolyMk in phytools, > which can also easily combine with ancestral state estimation (e.g., > with phytools::make.simmap). Here is an example: > http://blog.phytools.org/2019/07/stochastic-character-mapping-with.html. > > All the best, Liam > > Liam J. Revell > Professor of Biology, University of Massachusetts Boston > Web: http://faculty.umb.edu/liam.revell/ > > On 11/8/2022 2:35 PM, Krzysztof Kozak wrote: > > CAUTION: EXTERNAL SENDER > > > > Hello, > > > > Is there a method for ancestral state reconstruction when the character > can > > take on multiple values, and those values vary in complexity? > > For example, some species are white (0), some gray (1), some black (2), > but > > then some are black and white (02). > > Two solutions I can think of are (1) code each combination as a simple > > state (so black and white could be coded as '3'); (2) treat each state as > > binary character. > > Any better solutions, please? > > > > - Chris Kozak > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > R-sig-phylo mailing list - R-sig-phylo@r-project.org > > > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=05%7C01%7Cliam.revell%40umb.edu%7Ce7ab8068cea844ac67a408dac1c07f18%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638035329773830976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=tgBZSH6ny135%2BjW7Y14kQcHXtmxu%2FgxDF6wEDKBgyLw%3D&reserved=0 > > Searchable archive at > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=05%7C01%7Cliam.revell%40umb.edu%7Ce7ab8068cea844ac67a408dac1c07f18%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C638035329773830976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=beFK6iTET4OYiI%2FGnZylAnaGjBytYBMejwlKa1lA2WY%3D&reserved=0 > > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > ------------------------------ > > End of R-sig-phylo Digest, Vol 178, Issue 3 > ******************************************* > [[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/
