@sckott sckott released this Dec 8, 2014 · 842 commits to master since this release

NEW FEATURES

  • New function genbank2uid() to get a NCBI taxonomic id (i.e., a uid) from a either a GenBank accession number of GI number. (#375)
  • New function get_nbnid() to get a UK National Biodiversity Network taxonomic id (i.e., a nbnid). (#332)
  • New function nbn_classification() to get a taxonomic classification for a UK National Biodiversity Network taxonomic id. Using this new function, generic method classification() gains method for nbnid. (#332)
  • New function nbn_synonyms() to get taxonomic synonyms for a UK National Biodiversity Network taxonomic id. Using this new function, generic method synonyms() gains method for nbnid. (#332)
  • New function nbn_search() to search for taxa in the UK National Biodiversity Network. (#332)
  • New function ncbi_children() to get direct taxonomic children for a NCBI taxonomic id. Using this new function, generic method children() gains method for ncbi. (#348) (#351) (#354)
  • New function upstream() to get taxa upstream of a taxon. E.g., getting families upstream from a genus gets all families within the one level higher up taxonomic class than family. (#343)
  • New suite of functions as.*() to coerce numeric/alphanumeric codes to taxonomic identifiers for various databases. There are methods on this function for each of itis, ncbi, tropicos, gbif, nbn, bold, col, eol, and ubio. By default as.*() funtions make a quick check that the identifier is a real one by making a GET request against the identifier URI - this can be toggle off by setting check=FALSE. There are methods for returning itself, character, numeric, list, and data.frame. In addition, if the as.*.data.frame() function is used, a generic method exists to coerce the data.frame back to a identifier object. (#362)
  • New suite of functions named, for example, get_tsn_() (the underscore is the only different from the previous function name). These functions don't do the normal interactive process of prompts that e.g., get_tsn() do, but instead returned a list of all ids, or a subset via the rows parameter. (#237)
  • New function ncbi_get_taxon_summary() to get taxonomic name and rank for 1 or more NCBI uid's. (#348)

MINOR IMPROVEMENTS

  • assertthat removed from package imports, replaced with stopifnot(), to reduce dependency load. (#387)
  • eol_hierarchy() now defunct (no longer available) (#228) (#381)
  • tp_classifcation() now defunct (no longer available) (#228) (#381)
  • col_classification() now defunct (no longer available) (#228) (#381)
  • New manual page listing all the low level ITIS functions for which their manual pages are not shown in the package index, but are available if you to ?fxn-name.
  • All get_*() functions gain a new parameter rows to allow selection of particular rows. For example, rows=1 to select the first row, or rows=1:3 to select rows 1 through 3. (#347)
  • classification() now by default returns taxonomic identifiers for each of the names. This can be toggled off by the return_id=FALSE. (#359) (#360)
  • Simplification of many higher level functions to use switch() on the db parameter, which helps give better error message when a db value is not possible or spelled incorrectly. (#379)

BUG FIXES

  • Lots of reduction of redundancy in internal functions. (#378)

Binaries

  • Mac: taxize_0.5.0.tgz
  • Windows: taxize_0.5.0.zip
Assets 4