taxize v0.9.99

DEFUNCT

• tnrs() and tnrs_sources() functions are defunct. The service has been unreliable for years now, and AFAICT is down for good. Associated changes have been made throughout the package, eg. resolve() no longer has an option for tnrs, etc. (#841) (#842)

MINOR IMPROVEMENTS

• new article/vignette added on issues with taxonomic ranks, e.g., "NCBI is weird", and how rank information is maintained and used within taxize (#852)
• vignettes are no longer on cran - find them at the docs site linked in DESCRIPTION (#855)
• re-instate a tol_resolve() test following new version of rotl package on cran (#816)
• improve class2tree() function documentation regarding how the function works in more detail (#849) (#851)
• improvements for WORMS, applies to functions worms_downstream(), children(..., db="worms") and downstream(..., db="worms"): now paginate automatically for the user to get all results, and allow parameter marine_only to be passed through the high level functions children()/downstream() down to worrms::wm_children() where it toggles whether marine only results are returned (#848) thanks @oharac !

BUG FIXES

• fix to ncbi_downstream() (which cascades up to downstream(..., db="ncbi")): an unneeded line of code was removed that was also throwing an error in some cases (#850)
• fixes for WORMS ranks, applies to functions worms_downstream(), children(..., db="worms") and downstream(..., db="worms"): added ranks epifamily and infraphylum. In addition, when a rank is missing in data returned from WORMS, we'll change the missing rank to "no rank" (#847)