rotl 3.0.0

rotl 3.0.0

• rotl now interacts with v3.0 of the Open Tree of Life APIs. The
  documentation has been updated to reflect the associated changes. More
  information about the v3.0 of the Open Tree of Life APIs can be found
  on their wiki.

New features

• New methods: tax_sources, is_suppressed, tax_rank, unique_name, name, ott_id, for objects returned by tnrs_match_names(), taxonomy_taxon_info(), taxonomy_taxon_mrca(), tol_node_info(), tol_about(), and tol_mrca(). Each of these methods have their own class.
• New method tax_lineage() to extract the higher taxonomy from an object returned by taxonomy_taxon_info() (initally suggested by Matt Pennell, #57).
• New method tol_lineage() to extract the nodes towards the root of the tree.
• New print methods for tol_node_info() and tol_mrca().
• New functions study_external_IDs() and taxon_external_IDs() that return the external identifiers for a study and associated trees (e.g., DOI, TreeBase ID); and the identifiers of taxon names in taxonomic databases. The vignette "Data mashup" includes an example on how to use it.
• The function strip_ott_id() gains the argument remove_underscores to remove underscores from tips in trees returned by OTL.

Changes

• Rename method ott_taxon_name() to tax_name() for consistency.
• Rename method synth_sources() and study_list() to source_list().
• Refactor how result of query is checked and parsed (invisible to the user).

Bug fixes

• Fix bug in studies_find_studies(), the arguments verbose and exact were ignored.
• The argument only_current has been dropped for the methods associated with objects returned by tnrs_match_names()
• The print method for tnrs_context() duplicated some names.
• inspect(), update() and synonyms() methods for tnrs_match_names() did not work if the query included unmatched taxa.