Hi Krishna, > (1) I'd like to examine the links between group size (cont. outcome) and > various social network measures (cont. predictors) across 10 species of > nonhuman primates. I first tried implementing the PGLS code in Caper > package that incorporates random-sampling of intraspecific variation. > Although I am getting a seemingly meaningful output, I'm also getting the > error: > > Error in pgls(mod ~ groupsize, data = primate, lambda = "ML") : > Problem with optim:52ERROR: ABNORMAL_TERMINATION_IN_LNSRCH > > Is there some way around this?
Not easily, no. The problem is likely to be that finding the ML lambda has run into numerical problems with the model. Does it still happen with lambda = 1? That would suggest that something is more fundamentally wrong with the model. I’m not sure what you mean by random sampling of infraspecific variation though - caper doesn’t handle intraspecific variation. > (2) Is there an algorithm for running a logistic PGLS that allows for > random sampling of intraspecific variation? Does adding a link function to > the regular Caper package code do the trick? Nope, afraid not, but there are other packages that do allow it - phyloglm in the phylolm package looks good! Cheers, David > > Thank you very much... looking forward to some feedback! > > Best regards, > > Krishna > > -- > Krishna N. Balasubramaniam, Ph.D. > Postdoctoral Researcher, School of Veterinary Medicine > Department of Population Health and Reproduction > University of California-Davis > One Shields Avenue > Davis, CA 95616 > Email: krishnanatara...@ucdavis.edu > > [[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/
