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@fmichonneau fmichonneau released this Feb 3, 2016 · 285 commits to master since this release

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
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