See phenoscape/rphenoscape#99, which introduces functions to drop OTUs and characters. One of the RPhenoscape user stories requires this kind of functionality; accomplishing it through subsetting a character matrix or OTU list and then creating a nexml object from scratch is fraught with too many issues, many of which come back to a loss of metadata that would help to avoid them (see #239, for example).
If there's interest, we can move this code to RNeXML in the future.
See phenoscape/rphenoscape#99, which introduces functions to drop OTUs and characters. One of the RPhenoscape user stories requires this kind of functionality; accomplishing it through subsetting a character matrix or OTU list and then creating a nexml object from scratch is fraught with too many issues, many of which come back to a loss of metadata that would help to avoid them (see #239, for example).
If there's interest, we can move this code to RNeXML in the future.