search_gnr: Retrieve and parse full taxonomic information for a list of...

In DesiQuintans/taxizehelper: Convenience Functions For ROpenSci's 'taxize' Package

Description

search_gnr() is a wrapper for taxize::gnr_resolve() that parses its output and returns a neat dataframe of taxonomic information, with every rank in a separate column. The ICN ranks (kingdom, phylum, class, order, family, genus) are ordered so that they can be accessed with kingdom:genus. All other ranks (super-, sub-, infra- versions of ICN ranks, plus tribe) are ordered to the right. Finally, the raw path and ranks strings are retained so that you can double-check them if you want.

Usage

search_gnr(species_list,
  excluded_sources = c("Open Tree of Life Reference Taxonomy",
  "The Paleobiology Database", "Union 4", "Wikispecies"))

Arguments

species_list	(Char) A vector of taxa names.
excluded_sources	(Char) A vector of sources to exclude (see taxize::gnr_datasources(). By default, excludes Open Tree of Life Reference Taxonomy, The Paleobiology Database, Union 4, and Wikispecies because rank output from these sources is poorly structured and hard to parse.

Value

A dataframe of taxonomic information, with every rank in a separate column.

Examples

my_species <- c("Coptodactyla meridionalis", "Torymus chrysochlorus", "Anaspis rufa")
search_gnr(my_species)

DesiQuintans/taxizehelper documentation built on May 14, 2019, 3:04 a.m.