how to express that a character matrix provides comparative trait data for the phylogeny?

[cboettig]

MIAPA has a clear annotation to indicate that a character matrix in a nexml file (characters element) contains an alignment that was used to generate the phylogeny. Character matrices are frequently used in a rather different context in phylogenetic comparative methods (sensu Felsenstein 1985), where the traits might be described by a Brownian motion (OU, etc) model or (discrete) Markov process model, evolving on the phylogeny.

See ropensci/RNeXML#44

[hlapp]

See also a corresponding term request for OBI.