gnr_simple_df: Wrapper function to apply gnr_simple across a data.frame or...

In algaeClassify: Determine Phytoplankton Functional Groups Based on Functional Traits

Wrapper function to apply gnr_simple across a data.frame or list of species names

Description

Provides convienent output with a row per name. To streamline merging with original data.

Usage

gnr_simple_df(
  df,
  name.column,
  sourceid = NA,
  topscore = TRUE,
  numhits = TRUE,
  canonical = TRUE,
  with_context = TRUE,
  ...
)

Arguments

df	data.frame containing names to check
name.column	integer or character string with column name containing species names
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 original names (orig.name), 1/0 flag for an exact match, the best match (matched.name), and other output from gnr_simple(). scores, and number of hits (matches) from different data sources in gnr_resolve()

Examples

data(lakegeneva)
#example dataset with 50 rows

new.lakegeneva <- genus_species_extract(lakegeneva,'phyto_name')
new.lakegeneva$genus_species <- trimws(paste(new.lakegeneva$genus,
new.lakegeneva$species))

#checking for matches from all GNRS sources:
lakegeneva.namematches <- gnr_simple_df(new.lakegeneva[1:10,],"genus_species")
lakegeneva.namematches

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