resolve_names: Resolve canonical names against GNA

In taxotools: Taxonomic List Processing

Resolve canonical names against GNA

Description

Resolve names against Global Names Architecture (GNA) to make sure the name exists

Usage

resolve_names(
  taxolist,
  sciname = "canonical",
  score_threshold = 0.98,
  best_match_only = TRUE,
  add_fields = NA,
  verbose = TRUE
)

Arguments

taxolist	(data frame) taxonomic list
sciname	() column name for scientific names
score_threshold	(numeric) to make sure names match as desired. Default (0.98) Higher value indicates best match, lower values would return matches at genus level
best_match_only	(logical) If TRUE, best match only returned else return all records returned by GNA. Default: TRUE
add_fields	(character) One of NA (default) , minimal or all. NA adds a logical column 'resolved', Minimal gives back just four fields, whereas all gives all fields back.
verbose	(logical) verbose output, Default: FALSE

Value

(data frame) names list resolves

See Also

Other Name functions: build_gen_syn(), cast_canonical(), cast_scientificname(), check_scientific(), expand_name(), get_accepted_names(), guess_taxo_rank(), list_higher_taxo(), melt_canonical(), melt_scientificname(), taxo_fuzzy_match()

Examples

mylist <- data.frame("canonical" = c("Abrothrix longipilis",
                                     "Acodon hirtus",
                                     "Akodon longipilis apta",
                                     "AKODON LONGIPILIS CASTANEUS",
                                     "Chroeomys jelskii",
                                     "Acodon jelskii pyrrhotis"),
                     stringsAsFactors = FALSE)
test <- resolve_names(mylist)
test1 <- resolve_names(mylist,add_fields = "minimal")
test2 <- resolve_names(mylist,best_match_only = FALSE,add_fields = "minimal")
test3 <- resolve_names(mylist,best_match_only = FALSE,add_fields = "all")

taxotools documentation built on Jan. 23, 2023, 5:24 p.m.