CRAN release: 2022-10-06
- Make sure that the package fails gracefully when there is no internet connection.
- The vignettes are now pre-computed.
CRAN release: 2021-12-08
- The default argument
context_namefor the function
tnrs_match_nameswas changed from
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)/
- The “Suggest” dependency
fulltextwas removed following its archival from CRAN.
CRAN release: 2020-10-22
- When none of the names provided to
tnrs_match_nameshad 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.
CRAN release: 2019-09-28
- Small fixes following updates to the Open Tree of Life API (no visible change for users).
- Updated documentation to reflect new value in output of
CRAN release: 2019-02-15
- Minor update to vignette to address change to TNRS endpoint (underscores can’t be included in the taxon names anymore).
CRAN release: 2018-09-29
- The data types in the data frame returned by
tnrs_match_namesare consistent, and remain the same even after using
CRAN release: 2018-04-03
- To improve stability of results across releases of the Open Tree Taxonomy, the TNRS match with the lowest OTT id is returned instead of the first one in case a name is shared across multiple domains (related to #88)
- A warning is issued when users attempt to use TNRS on duplicated names.
CRAN release: 2017-03-04
- The function
get_study_subtreegains the argument
tip_labelto control the formatting of the tip labels, #90, reported by @bomeara
- The new function
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).
citation("rotl")now includes the reference to the Open Tree of Life publication.
- The “How to use rotl?” vignette was updated to document the behavior of v3 of the OTL API which returns an HTTP error code 400 when the request for induced subtree includes taxa that are not in the synthetic tree (fix #84)
CRAN release: 2016-09-20
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.
CITATIONfile with MEE manuscript information (#82)
CRAN release: 2016-04-26
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_underscoresto remove underscores from tips in trees returned by OTL.
Refactor how result of query is checked and parsed (invisible to the user).
Fix bug in
studies_find_studies(), the arguments
only_currenthas been dropped for the methods associated with objects returned by
The print method for
tnrs_context()duplicated some names.
tnrs_match_names()did not work if the query included unmatched taxa.
CRAN release: 2016-02-03
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
character) [issue #54]
New utility function
strip_ott_idsremoves OTT id information from a character vector, making it easier to match tip labels in trees returned by
tol_induced_subtreeto taxonomic names in other data sources. This function can also remove underscores from the taxon names.
list_treesreturns a list of tree ids associated with studies. The function takes the output of
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.
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_yearfor objects of class
study_metathat returns the year of publication of the study.
A more robust approach is used by
get_tree_idsto identify the tree ids in the metadata returned by the API