Dear Liam, Thanks very much indeed - a really nice blog post. However, the issue is that I am using discrete states, which are not ordered. (and to make things more exciting there are also polymorphisms and missing data - although they can be worked around I guess)
Is there any way to get ML to yield the same as SCP would (in Mesquite at least) for this kind of data? Best wishes Roland On Thu, Jan 31, 2019 at 8:03 PM Liam Revell <liam.rev...@umb.edu> wrote: > Dear Roland. > > I didn't really solve your problem of reading a Mesquite result into R; > however I just posted about the relationship between unweighted & > weighted square-change-parsimony & ML ancestral character estimation on > my blog: > http://blog.phytools.org/2019/01/unweighted-weighted-square-change.html. > (In summary, you should be able to do what you want within R.) > > All the best, Liam > > Liam J. Revell > Associate Professor, University of Massachusetts Boston > Profesor Asistente, Universidad Católica de la Ssma Concepción > web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org > > On 1/31/2019 12:48 PM, Roland Sookias wrote: > > Dear all, > > > > I want to get squared change parsimony ancestral state reconstructions > for > > a matrix into R. > > > > I have tried the asr_max_parsimony() function from castor, but the > results > > are not the same as in Mesquite for example. To take an example, a > > two-taxon clade with a unique state for these taxa optimized as having a > > different state (shared by near relatives) at the ancestral node. This > > doesn't happen in Mesquite and is *not* what I want. > > > > If there were some way to get the results from Mesquite into R that would > > also be OK, but I cannot figure out the node numbering system in > Mesquite, > > to match them up with nodes as numbered by ape. > > > > Any help would be *very* greatly appreciated. > > > > Best wishes, > > > > Roland > > > > [[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/ > > > [[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/
