Hi Nathan, A bit late answer due to vacation but you can also try to use my mvSLOUCH package (on CRAN). While it (still) does not allow for explicit fossil species you can a very short tip branch at the place where the fossil should be. For missing observations you write NAs, the package has no problem with handling missing data on some variables in a species. It also allows for non-ultrametric trees.
Hope this will be useful if you are still working on this! Best wishes Krzysztof _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
