rotl: 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