itis_search_df: Wrapper function for applying genus_search_itis and...

In algaeClassify: Determine Phytoplankton Functional Groups Based on Functional Traits

Wrapper function for applying genus_search_itis and species_search_itis to a whole data.frame containing scientific names

Description

Wrapper function for applying genus_search_itis and species_search_itis to a whole data.frame containing scientific names

Usage

itis_search_df(df, namecol = NA, higher = FALSE, genus.only = FALSE)

Arguments

df	data.frame containing names to check
namecol	integer or character string with column name containing species or genus names
higher	Boolean. If TRUE, add higher taxonomic classifications to output
genus.only	boolean If TRUE, search for matches with just the genus name using genus_search_itis

Value

data.frame with submitted names (orig.name), matched names (matched.name), 1/0 flag indicating that original name is currently accepted (orig.name.accepted), 1/0 flag indicating if search was genus_only (for distinguishing genus_search_itis and species_search_itis results), synonyms if any, and higher taxonomy (if higher=TRUE)

Examples

data(lakegeneva)
#example dataset with 50 rows

new.lakegeneva <- genus_species_extract(lakegeneva,'phyto_name')[1:5,]

#checking for genus-only name matches in ITIS, and extracting higher taxonomy
#flagging names with imperfect or no matches

lakegeneva.genus.itischeck <- itis_search_df(new.lakegeneva,"genus",genus.only=TRUE)
lakegeneva.genus.itischeck

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