NEWS.md

In rotl: Interface to the 'Open Tree of Life' API

rotl 3.1.0

Breaking change

• 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).

rotl 3.0.14

• Make sure that the package fails gracefully when there is no internet connection.
• The vignettes are now pre-computed.

rotl 3.0.12

• The default argument 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)/
• The "Suggest" dependency fulltext was removed following its archival from CRAN.

rotl 3.0.11

Other changes

• When none of the names provided to 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.

Bug Fix

• When attempting to match a name that did not exist in the tree, an error was thrown (bug #128, PR #129, @daijiang)

rotl 3.0.10

• 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 tol_node_info().

rotl 3.0.9

• Small fixes following updates to the Open Tree of Life API.

rotl 3.0.7

• Minor update to vignette to address change to TNRS endpoint (underscores can't be included in the taxon names anymore).

rotl 3.0.6

• Minor update to address warnings seen on CRAN.

rotl 3.0.5

New features

• The data types in the data frame returned by tnrs_match_names are consistent, and remain the same even after using update().

Other changes

• Small internal changes that reflect changes in the data structures returned by the API.

rotl 3.0.4

New features

• 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.

Other changes

• Fix typos and workaround broken API to retrieve supplementary materials in vignette.

rotl 3.0.3

New features

• The function get_study_subtree gains the argument tip_label to control the formatting of the tip labels, #90, reported by @bomeara
• The new function is_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).

Bug fixes

• The function get_study_subtree ignored the argument subtree_id, #89 reported by @bomeara

Other chaanges

• 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)

rotl 3.0.1

• 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 3.0.0

• 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 features

• 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.

Changes

• 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).

Bug fixes

• 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.

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

rotl 0.4.1

• Initial CRAN release on July, 24th 2015

rotl documentation built on July 9, 2023, 7:37 p.m.