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).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 indicating 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()
(initially 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