get_study_subtreegains the argument
tip_labelto control the formatting of the tip labels, #90, reported by @bomeara
is_in_treetakes 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_subtreeignored the argument
subtree_id, #89 reported by @bomeara
citation("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.
CITATION file with MEE manuscript information (#82)
rotlnow 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.
ott_id, for objects returned by
tol_mrca(). Each of these methods have their own class.
tax_lineage() to extract the higher taxonomy from an object returned by
taxonomy_taxon_info() (initally suggested by Matt Pennell, #57).
tol_lineage() to extract the nodes towards the root of the tree.
New print methods for
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.
strip_ott_id() gains the argument
remove_underscores to remove underscores from tips in trees returned by OTL.
tax_name() for consistency.
Refactor how result of query is checked and parsed (invisible to the user).
Fix bug in
studies_find_studies(), the arguments
exact were ignored.
only_current has been dropped for the methods associated with objects returned by
The print method for
tnrs_context() duplicated some names.
synonyms() methods for
tnrs_match_names() did not work if the query included unmatched taxa.
Improve warning and format of the result if one of the taxa requested doesn’t match anything
In the data frame returned by
tnrs_match_names, the columns
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.
list_trees returns a list of tree ids associated with studies. The function takes the output of
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
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 (
_3, etc.). (#46, reported by @bomeara)
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