rotl 3.0.1

rotl 3.0.1

• Fix tests and vignette to reflect changes accompanying release 6.1 of the
  synthetic tree
• Add section in vignette "How to use rotl?" about how to get the higher
  taxonomy from a given taxon.
• Add CITATION file with MEE manuscript information (#82)

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.

Prelease to accompany the manuscript describing the package (resubmission)

Version of the package used to generate the manuscript sent for submission after the first round of reviews

rotl 0.5.0

rotl 0.5.0

• New vignette: meta-analysis
• Added arguments include_lineage and list_terminal_descendants to
  taxonomy_taxon()
• Improve warning and format of the result if one of the taxa requested doesn't
  match anything tnrs_match_names.
• In the data frame returned by tnrs_match_names, the columns
  approximate_match, is_synonym and is_deprecated are now logical
  (instead of character) [issue #54]
• New utility function strip_ott_ids removes OTT id information from
  a character vector, making it easier to match tip labels in trees returned by
  tol_induced_subtree to taxonomic names in other data sources. This function
  can also remove underscores from the taxon names.
• New method list_trees returns a list of tree ids associated with
  studies. The function takes the output of studies_find_studies or
  studies_find_trees.
• studies_find_studies and studies_find_trees gain argument detailed
  (default set to TRUE), that produces a data frame summarizing information
  (title of the study, year of publication, DOI, ids of associated trees, ...)
  about the studies matching the search criteria.
• get_study_tree gains argument deduplicate. When TRUE, if the tree
  returned for a given study contains duplicated tip labels, they will be made
  unique before being parsed by NCL by appending a suffix (_1, _2, _3,
  etc.). (#46, reported by @bomeara)
• New method get_study_year for objects of class study_meta that returns the
  year of publication of the study.
• A more robust approach is used by get_tree_ids to identify the tree ids in
  the metadata returned by the API

Prelease to accompany the manuscript describing the package

Break down data-matching in meta-analysis vignette

* Add a few more code blocks to demonstrate why the tips/nodes of the
  tree need to be processed
* Fixed some spelling/grammar issues

rncl v0.4.1

Initial CRAN release