ropensci/RNeXML: RNeXML v2.2.0

An extensive and rapidly growing collection of richly annotated phylogenetics data is now available in the NeXML format. NeXML relies on state-of-the-art data exchange technology to provide a format that can be both validated and extended, providing a data quality assurance and adaptability to the future that is lacking in other formats. See Vos et al 2012 for further details on the NeXML format.

• Fixes various (previously broken) aspects of handling polymorphic and uncertain states for discrete (non-molecular) and continuous characters, including obtaining a character matrix (#174), ensuring proper column types (#188), and serializing to NeXML (#192).
• Adds the optional ability to, in addition to the character matrix, obtain a concordantly formatted matrix of state types (standard, polymorphic, uncertain).
• Fixes loss of certain literal-valued metadata when serializing to NeXML. #193
• Drops package phylobase as dependency. (Also removes circular dependency chain, because phylobase depends on RNeXML.)