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 https://github.com/OpenTreeOfLife/feedback/issues/528)/fulltext was removed following its archival from CRAN.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.tol_node_info().tnrs_match_names are consistent, and remain the same even after using update().get_study_subtree gains the argument tip_label to control the formatting of the tip labels, #90, reported by @bomearais_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).get_study_subtree ignored the argument subtree_id, #89 reported by @bomearacitation("rotl") now includes the reference to the Open Tree of Life publication.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 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 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.
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).
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.
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