taxize v0.8.4

taxize 0.8.4

NEW FEATURES

• Added WoRMS integration via the new worrms package on CRAN.
  Adds functions as.wormsid(), get_wormsid(), get_wormsid_(),
  children.wormsid(), classification.wormsid(), sci2comm.wormsid(),
  comm2sci.wormsid(), and synonyms.wormsid() (#574) (#579)
• New functions for NatureServe data, including as.natservid,
  get_natservid, get_natservid_, and classification.natservid
  (#126)

BUG FIXES

• EOL API keys were not passed on to internal functions. fixed now.
  thanks @dschlaep ! (#576)
• Fix in rankagg() with respect to vegan package to work with
  older and new version of vegan - thank @jarioksa (#580) (#581)

taxize v0.8.0

NEW FEATURES

• New data source added: Open Tree of Life. New functions for the data source
  added: get_tolid(), get_tolid_(), and as.tolid() (#517)
• related to above classification() gains new method for TOL data
• related to above lowest_common() gains new method for TOL data
• Now using ritis package, an external dependency for ITIS taxonomy
  data. Note that a large number of ITIS functions were removed, and are
  now available via the package ritis. However, there are still many
  high level functions for working with ITIS data (see functions prefixed
  with itis_), and get_tsn(), classification.tsn(), and similar
  high level functions remain unchanged. (#525)
• EUBON has a new API (v1.2). We now interact with that new API version.
  In addition, eubon() fxn is now eubon_search(), although either still
  work - though eubon() will be made defunct in the next version of
  this package. Additional new functions were added: eubon_capabilities(),
  eubon_children(), and eubon_hierarchy() (#567)
• lowest_common() function gains two new data source options: COL (Catalogue
  of Life) and TOL (Tree of Life) (#505)
• Addded new function synonyms_df() as a slim wrapper around
  data.table::rbindlist() to make it easy to combine many outputs
  from synonyms() for a single data source - there is a lot of heterogeneity
  among data sources in how they report synonyms data, so we don't attempt
  to combine data across sources (#533)

MINOR IMPROVEMENTS

• Change NCBI URLs to https from http (#571)

BUG FIXES

• Fixed bug in tax_name() in which when an invalid taxon was searched
  for then classification() returned no data and caused an error.
  Fixed now. (#560) thanks @ljvillanueva for reporting it!
• Fixed bug in gnr_resolve() in which order of input names to the function
  was not retained. fixed now. (#561) thanks @bomeara for reporting it!
• Fixed bug in gbif_parse() - data format changed coming back from
  GBIF - needed to replace NULL with NA (#568) thanks @ChrKoenig for
  reporting it!

taxize v0.7.9

NEW FEATURES

• New vignette: "Strategies for programmatic name cleaning" (#549)

MINOR IMPROVEMENTS

• get_*() functions now have new attributes to further help the user:
  multiple_matches (logical) indicating whether there were multiple
  matches or not, and pattern_match (logical) indicating whether a
  pattern match was made, or not. (#550) from (#547) discussion,
  thanks @ahhurlbert ! see also (#551)
• Change all xml2::xml_find_one() to xml2::xml_find_first()
  for new xml2 version (#546)
• gnr_resolve() now retains user supplied taxa that had no matches -
  this could affect your code, make sure to check your existing code (#558)
• gnr_resolve() - stop sorting output data.frame, so order of rows
  in output data.frame now same as user input vector/list (#559)

BUG FIXES

• Fixed internal fxn sub_rows() inside of most get_*() functions
  to not fail when the data.frame rows were less than that requested by
  the user in rows parameter (#556)
• Fixed get_gbifid(), as sometimes calls failed because we now
  return numberic IDs but used to return character IDs (#555)
• Fix to all get_() functions to call the internal sub_rows()
  function later in the function flow so as not to interfere with
  taxonomic based filtering (e.g., user filtering by a taxonomic rank)
  (#555)
• Fix to gnr_resolve(), to not fail on parsing when no data
  returned when a preferred data source specified (#557)

taxize v0.7.8

MINOR IMPROVEMENTS

• Fix to iucn_summary() (#543) thanks @mcsiple
• Added message for when too many Ids passed in to ncbi_get_taxon_summary()
  suggesting to break up the ids into chunks (#541) thanks @daattali
• Fix to itis_acceptname() to accept multiple names (#534) and now
  gives back same output regardless of whether match found or not (#531)

BUG FIXES

• Fix to tax_name() for some queries that return no classification data
  via internal call to classification() (#542) thanks @daattali
• Another fix for tax_name() (#530) thanks @ibartomeus
• Fixed docs for rankagg() function, use requireNamespace() in examples
  to make sure user has vegan installed (#529)

taxize v0.7.6

MINOR IMPROVEMENTS

• Changed defunct messages in eol_invasive() and gisd_invasive()
  to point to new location in the originr
  package. Also, cleaned out code in those functions as not avail.
  anymore (#494)
• Access to IUCN taxonomy information is now provided through the newish
  rredlist package. (Two issues
  dealing with IUCN problems (#475) (#492))

BUG FIXES

• Fix to get_gbifid() to use new internal code to provide two
  ways to search GBIF taxonomy API, either via /species/match or via
  /species/search, instead of /species/suggest, which we used previously.
  The suggest route was too coarse. get_gbifid() also gains a parameter
  method to toggle whether you search for names using /species/match or
  /species/search. (#528)
• Fix for col_search() to handle when COL can return a value of
  missapplied name, which a switch() statement didn't handle yet (#511)
  thanks @jostaerk !
• Fixes for get_colid() and col_search() (#523) thanks @zachary-foster !

taxize v0.7.5

BUG FIXES

• Fixed bug in the package dependency bold, which fixes
  taxize::bold_search(), so no actual changes in taxize for
  this, but take note (#521)
• Fixed problem in gnr_resolve() where we indexed to data
  incorrectly. And added tests to account for this problem.
  Thanks @raredd ! (#519) (#520)
• Fixed bug in iucn_summary() introduced in last version.
  iucn_summary() now uses the package rredlist, which requires
  an API key, and I didn't document how to use the key. Function
  now allows user to pass the key in as a parameter, and documents
  how to get a key and save it in either .Renviron or in
  .Rprofile (#522)

taxize v0.7.4

NEW FEATURES

• New function lowest_common() for obtaining the lowest common taxon and
  rank for a given taxon name or ID. Methods so far for ITIS, NCBI, and GBIF (#505)
• New contributor James O'Donnell (@jimmyodonnell) (via #505)
• Now importing rredlist rredlist
• New function iucn_summary_id() - same as iucn_summary(), except takes
  IUCN IDs as input instead of taxonomic names (#493)

MINOR IMPROVEMENTS

• iucn_summary() fixes, long story short: a number of bug fixes, and uses
  the new IUCN API via the newish package rredlist when IDs are given as input,
  but uses the old IUCN API when taxonomic names given. Also: gains new parameter distr_details
  (#174) (#472) (#487) (#488)
• Replaced XML with xml2 for XML parsing (#499)
• Fixes to internal use of httr::content to explicitly state encoding="UTF-8" (#498)
• gnr_resolve() now outputs a column (user_supplied_name) for the exact input taxon
  name - facilitates merging data back to original data inputs (#486) thanks @Alectoria
• eol_dataobjects() gains new parameter taxonomy to toggle whether to return
  any taxonomy details from different data providers (#497)
• Catalogue of Life URLs changed - updated all appropriate COL functions to use
  the new URLs (#501)
• classification() was giving back rank values in mixed case from different data
  providers (e.g., class vs. Class). All rank values are now all lowercase (#504)
• Changed number of results returned from internal GBIF search in get_gbfid to
  50 from 20. Gives back more results, so more likely to get the thing searched for (#513)
• Fix to gni_search() to make all output columns character class
• iucn_id(), tpl_families(), and tpl_get() all gain a new parameter ... to
  pass on curl options to httr::GET()

BUG FIXES

• Fixes to get_eolid(): URI returned now always has the pageid, and goes to the
  right place; API key if passed in now actually used, woopsy (#484)
• Fixes to get_uid(): when a taxon not found, the "match" attribute was saying
  found sometimes anyway - that is now fixed; additionally, fixed docs to correctly
  state that we give back 'NA due to ask=FALSE' when ask = FALSE (#489) Additionally,
  made this doc fix in other get_*() function docs
• Fix to apgOrders() function (#490)
• Fixes to tp_search() which fixes get_tpsid(): Tropicos doesn't allow periods (.) in
  query strings, so those are URL encoded now; Tropicos doesn't like sub-specific rank names
  in name query strings, so we warn when those are found, but don't alter user inputs; and
  improved docs to be more clear about how the function fails (#491) thanks @scelmendorf !
• Fix to classification(db = "itis") to fail better when no taxa found (#495) thanks @ashenkin !
• eol_pages() fixes: the EOL API route for this method gained a new parameter taxonomy,
  this function gains that parameter. That change caused this fxn to fail. Now fixed. Also,
  parameter subject changed to subjects (#500)
• Fix to col_search() due to when misapplied name come back as a data slot. There
  was previously no parser for that type. Now there is, and it works (#512)

taxize v0.7.0

NEW FEATURES

• Now requires R >= 3.2.1. Good idea to update your R installation anyway (#476)
• New function ion() for obtaining data from Index of Organism Names (#345)
• New function eubon() for obtaining data from EU (European Union) BON
  taxonomy (#466) Note that you may onloy get partial results for some requests
  as paging isn't implemented yet in the EU BON API (#481)
• New suite of functions, with prefix fg_*() for obtaining data from Index
  Fungorum. More work has to be done yet on this data source, but these initial
  functions allow some Index Fungorum data access (#471)
• New function gbif_downstream() for obtaining downstream names from
  GBIF's backbone taxonomy. Also available in downstream(), where you can
  request downstream names from GBIF, along with other data sources (#414)

MINOR IMPROVEMENTS

• Note added in docs for all db parameters to warn users that if they
  provide the wrong db value for the given taxon ID, they can get data
  back, but it would be wrong. That is, all taxonomic data sources available
  in taxize use their own unique IDs, so a single ID value can be in multiple
  data sources, even though the ID refers to different taxa in each data source.
  There is no way we can think of to prevent this from happening, so be cautious.
  (#465)
• A note added to all IUCN functions to warn users that sometimes incorrect
  data is returned. This is beyond our control, as sometimes IUCN itself gives
  back incorrect data, and sometimes EOL/Global Names (which we use in some of
  the IUCN functions) give back incorrect data. (#468) (#473) (#174) (472) (#475)

BUG FIXES

• Fix to gnr_resolve() to by default capitalize first name of a name string
  passed to the function. GNR is case sensitive, so case matters (#469)

DEFUNCT

• phylomatic_tree() and phylomatic_format() are defunct. They were deprecated
  in recent versions, but are now gone. See the new package brranching for
  Phylomatic data (#479)

taxize v0.6.6

MINOR IMPROVEMENTS

• stripauthority argument in gnr_resolve() has been renamed to canonical
  to better match what it actually does (#451)
• gnr_resolve() now returns a single data.frame in output, or NULL
  when no data found. The input taxa that have no match at all are returned in
  an attribute with name not_known (#448)
• updated some functions to work with to R >3.2.x
• In vascan_search() changed callopts parameter to ... to pass in curl
  options to the request.
• In ipni_search() changed callopts parameter to ... to pass in curl
  options to the request. In addition, better http error handling, and
  added a test suite for this function. (#458)
• stringsAsFactors=FALSE now used for gibf_parse() (c0c4175)
• Made nearly all column headers and list names lowercase to simplify
  indexing to elements, as well as combining outputs. (#462)
• Plantminer API updated to use a new API. Option to search ThePlantList or
  the Brazilian Flora Checklist (#464)
• Added more details to the documentation for get_uid() to make more clear
  how to use the varoious parameters to get the desired result, and how to
  avoid certain pitfalls (#436)
• Removed the parameter asdf from the function eol_dataobjects() - now
  returning data.frame's only.
• Added some error catching to get_eolid() via tryCatch() to fail better
  when names not found.
• Dropped openssl as a package dependency. Not needed anymore because uBio
  dropped.

BUG FIXES

• gnr_resolve() failed when no canonical form was found.
• Fixed gnr_resolve() when no results found when best_match_only=TRUE (#432)
• Fixed bug in internal function itisdf() to give back an empty data.frame
  when no results found, often with subspecific taxa. Helps solve errors reported
  in use of downstream(), itis_downstream(), and gethierarchydownfromtsn() (#459)

NEW FEATURES

• gnr_resolve() gains new parameter with_canonical_ranks (logical) to choose
  whether infraspecific ranks are returned or not.
• New function iucn_id() to get the IUCN ID for a taxon from it's name. (#431)

DEFUNCT

• All functions that interacted with the taxonomy service uBio are now
  defunct. Of course we would deprecate first, then make defunct later, to
  make transition easier, but that is out of our hands. The functions
  that are defunct are: ubio_classification(), ubio_classification_search(),
  ubio_id(), ubio_search(), ubio_synonyms(), get_ubioid(), ubio_ping().
  In addition, ubio has been removed as an option in the synonyms() function,
  and references for uBio have been removed from the taxize_cite() utility
  function. (#449)

taxize 0.6.2

MINOR IMPROVEMENTS

• rankagg() doesn't depend on data.table anymore (fixes issue with CRAN checks)
• Replaced RCurl::base64Decode() with openssl::base64_decode(), needed for
  ubio_*() functions (#447)
• Importing only functions (via importFrom) used across all imports now (#446).
  In addition, importFrom for all non-base R pkgs, including graphics, methods,
  stats and utils packages (#441)
• Fixes to prevent problems with httr v1, where you can't pass a zero length
  list to the query parameter in GET(), but can pass NULL (#445)
• Fixes to all of the gni_*() functions, including code tidying, some
  DRYing out, and ability to pass in curl options (#444)

BUG FIXES

• Fixed typo in taxize_cite()
• Fixed a bug in classification() where numeric IDs as input got
  converted to itis ids just because they were numeric. Fixed now. (#434)
• Catalogue of Life (COL) changed from using short numeric codes for taxa to
  long alphanumeric UUID type ids. This required fixing functions using COL
  web services (#435)