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

In algaeClassify: Tools to Query the 'Algaebase' Online Database, Standardize Phytoplankton Taxonomic Data, and Perform Functional Group Classifications

Wrapper function to apply gnr_simple across a data.frame or list of species names. Modified on 11/18/2025 by Vijay Patil ([e-mail]) for algaeClassify v2.0.5 (pending approval on CRAN).

Description

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

Usage

gnr_df(
  df,
  name.column,
  sourceid = NULL,
  fuzzy_uninomial = TRUE,
  name_type = "canonical_full",
  higher = FALSE
)

Arguments

df	data.frame containing names to check
name.column	integer or character string with column name containing species names
sourceid	integer vector with data source ids. see https://resolver.globalnames.org/sources/
fuzzy_uninomial	boolean. Use fuzzy matching for uninomial names?
name_type	Specify format of matched names. Options are 'canonical_simple' (canonical binomial name), 'canonical_full' (with subspecies or subgenera), or 'with_context' (with author and year appended).
higher	boolean: Return higher taxonomic classifications?

Value

new data.frame original names (input_name), information about match type,the best match (match_name), taxonomic status, and other output from gnr_simple(). Will contain a row of NAs if no matches were found for a name.

Examples

data(lakegeneva)
#example dataset with 50 rows

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

#checking for matches from all GNRS sources, first 5 rows:
lakegeneva.namematches <- gnr_df(lakegeneva,"genus_species")
lakegeneva.namematches

algaeClassify documentation built on Dec. 2, 2025, 1:06 a.m.