rotl 3.1.0

Breaking change

• tnrs_match_names now returns the taxon with the highest matching score
  instead of the one with the lowest OTT id (issues #127 and #143 reported by
  @ajrominger).

rotl 3.0.12

rotl 3.0.12

• The default argument context_name for the function tnrs_match_names was
  changed from NULL to All life. This changes is made to address what could
  lead to unexpected results. Previously, the context was inferred based on the
  first match when several names were provided (see #134 reported by @LunaSare,
  and OpenTreeOfLife/feedback#528
• The "Suggest" dependency fulltext was removed following its archival from
  CRAN.

rotl 3.0.11

rotl 3.0.11

Other changes

• When none of the names provided to tnrs_match_names had a match in the Open
  Tree of Life, an error was thrown and nothing was returned. To make the
  behavior of the function more consistent with other situations, when none of
  the names provided have a match, a tibble is returned and a warning is issued.

Bug Fix

• When attempting to match a name that did not exist in the tree, an error was
  thrown (bug #128, PR #129, @daijiang)

rotl 3.0.10

rotl 3.0.10

• Small fixes following updates to the Open Tree of Life API (no visible change
  for users).
• Updated documentation to reflect new value in output of tol_node_info().

rotl 3.0.9

rotl 3.0.9

• Small fixes following updates to the Open Tree of Life API.

rotl 3.0.7

rotl 3.0.7

• Minor update to vignette to address change to OTL TNRS endpoint (underscores can't
  be included in the taxon names anymore.

rotl 3.0.6

rotl 3.0.6

• Minor update to address warnings seen on CRAN.

rotl 3.0.5

rotl 3.0.5

New features

• The data types in the data frame returned by tnrs_match_names are
  consistent, and remain the same even after using update().

Other changes

• Small internal changes that reflect changes in the data structures returned by
  the API.

rotl 3.0.4

rotl 3.0.4

New features

• To improve the stability of results across releases of the Open Tree Taxonomy, the
  TNRS match with the lowest OTT id is returned instead of the first one in case
  a name is shared across multiple domains (related to #88)
• A warning is issued when users attempt to use TNRS on duplicated names.

Other changes

• Fix typos and workaround broken API to retrieve supplementary materials in
  vignette.

rotl 3.0.3

New features

• The function get_study_subtree gains the argument tip_label to control the formatting of the tip labels, #90, reported by @bomeara
• The new function is_in_tree takes a list of OTT ids (i.e., the output of ott_id()), and returns a vector of logical indiicating whether they are included in the synthetic tree (workaround #31).

Bug fixes

• The function get_study_subtree ignored the argument subtree_id, #89 reported by @bomeara

Other chaanges

• citation("rotl") now includes the reference to the Open Tree of Life publication.
• The "How to use rotl?" vignette was updated to document the behavior of v3 of the OTL API which returns an HTTP error code 400 when the request for induced subtree includes taxa that are not in the synthetic tree (fix #84)