Hi all, I'm trying to use Rphylopars to impute some missing data, but am having some strange results with my empirical data.
The phylopars should return a `data.frame` of the original data with the missing (NA) values calculated given the phylogenetic data and evolutionary model. However, my known values are being changed in the output. For example: > head(empirical.data) species Trait 1 Species_1 14.0 2 Species_2 12.0 > head(p_BM$anc_recon) species Trait 1 Species_1 12.0 2 Species_2 8.9 The function works fine when I use different combinations of simulated data: * simulated traits + simulated phylogeny works fine * simulated traits + empirical phylogeny works fine * empirical data + simulated phylogeny works fine The phylogeny has no 0 branch lengths, is binary, and ultrametric. I have tried log-transforming the data. I have also tried sequentially dropping one tip at a time from the tree and re-running to see if any single tip is causing the problem. Different models also have the same effect. If anyone has any thoughts i'd appreciate it. Nick -- Nick Crouch http://nickcrouch.github.io/ Postdoctoral scholar, Jablonski lab The University of Chicago [[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/