rotl - 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).

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau almost 2 years ago

rotl - rotl 3.0.12

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.

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau over 3 years ago

rotl - rotl 3.0.11

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)

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau over 4 years ago

rotl - rotl 3.0.10

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().

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau over 5 years ago

rotl - rotl 3.0.9

rotl 3.0.9

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

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau almost 6 years ago

rotl - rotl 3.0.7

rotl 3.0.7

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

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau about 6 years ago

rotl - rotl 3.0.6

rotl 3.0.6

• Minor update to address warnings seen on CRAN.

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau over 6 years ago

rotl - rotl 3.0.5

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.

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau over 6 years ago

rotl - rotl 3.0.4

rotl 3.0.4

New features

• To improve the 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.

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau about 7 years ago

rotl - 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 indiicating 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)

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau about 8 years ago

rotl - rotl 3.0.1

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)

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau over 8 years ago

rotl - rotl 3.0.0

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() (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.

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.

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau about 9 years ago

rotl - Prelease to accompany the manuscript describing the package (resubmission)

Version of the package used to generate the manuscript sent for submission after the first round of reviews

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau about 9 years ago

rotl - rotl 0.5.0

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

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau about 9 years ago

rotl - Prelease to accompany the manuscript describing the package

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau over 9 years ago

rotl - rncl v0.4.1

Initial CRAN release

Biosphere - Biodiversity Data Access and Management - R
Published by fmichonneau almost 10 years ago