If you have multiple measurements per species (multiple individuals of a species, to represent a single tip), there is a program Rphylopars that is now available, that accounts for within-species variation.
Though maybe it’s not appropriate for your data, as Liam was saying. I like it, but I would love to hear from those individuals here that are much more qualified than I am… Chris > On Jan 27, 2017, at 12:00 PM, Liam J. Revell <liam.rev...@umb.edu> wrote: > > Hi Philip. > > Do not create very short tips. This will actually lead to very high weight > being given to any difference between these two observations! Take the > average of the different observations. Using the methods of Felsenstein > (2008) or Ives & Garland (2007) it is also possible to take into account > within-species sampling error, though this is not precisely what you have > here (you do not know how uncertain each measure is, nor how uncertain are > your estimates for other species), nor is this implemented in R. > > All the best, Liam > > Liam J. Revell, Associate Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > On 1/27/2017 11:45 AM, Philip Shirk wrote: >> I know this is a repeat question ( >> http://www.mail-archive.com/r-sig-phylo@r-project.org/msg04424.html) but I >> didn't see any reponses/answers to the first posting, so I thought I'd ask >> again: >> >> I have a pre-published tree for my species of interest that includes all >> the species in my dataset. However, my dataset contains duplicate data for >> a few species (different estimates from different authors). What is the >> best way to incorporate all the data into a PGLS analysis? When I try to >> run the analysis with gls() I get the error: >> "Error in Initialize.corPhyl(X[[i]], ...) : number of observations and >> number of tips in the tree are not equal." >> >> I imagine that I could: >> 1. toss out duplicates >> 2. average/combine duplicates >> 3. create very short branches for duplicate species and treat them as very >> closely-related but separate species (but I don't know how to actually do >> this.) >> 4. ??? >> >> Thanks, >> Philip Shirk >> >> [[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 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 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/
