algaeClassify (version 2.0.3)

itis_search_df: 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)

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)

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

Examples

data(lakegeneva)
#example dataset

new.lakegeneva <- genus_species_extract(lakegeneva[1,],'phyto_name')
new.lakegeneva$genus_species <- trimws(paste(new.lakegeneva$genus,
new.lakegeneva$species))
#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_species")
         lakegeneva.genus.itischeck