gnr_simple: Wrapper function for taxize::gnr_resolve() checks species...

In algaeClassify: Determine Phytoplankton Functional Groups Based on Functional Traits

Wrapper function for taxize::gnr_resolve() checks species names against a variety of online databases supports fuzzy partial matching

Description

Provides convienent output with a single result, using a variety of criteria for the best match

Usage

gnr_simple(
  name,
  sourceid = NULL,
  topscore = TRUE,
  numhits = TRUE,
  canonical = TRUE,
  with_context = TRUE,
  ...
)

Arguments

name	character string binomial scientific name to resolve
sourceid	integer with data source id from taxize::gnr_datasources()
topscore	boolean. Should the best match be returned based on score?
numhits	boolean. Should the best match be returned based on the number of sources with a match?
canonical	If TRUE, names do not include authorship or date
with_context	If TRUE, Match scores are weighted for taxonomic consistency
...	Other parameters passed to taxize::gnr_resolve()

Value

new data.frame with name matches, column indicating an exact match, scores, and number of hits (matches) from different data sources in gnr_resolve()

Examples

#use taxize::gnr_datasources() to see all possible data sources for name checking.
name<-"Aphanazomenon flos-aquae"
#sourceid=3 for ITIS database,195 for Algaebase
gnr_simple(name,sourceid=3) #search for ITIS matches
gnr_simple(name,sourceid=NULL) #search for matches from any source

algaeClassify documentation built on Nov. 22, 2023, 1:08 a.m.