refdb_check_tax_typo: Check for typos in taxonomic names

In refdb: A DNA Reference Library Manager

Check for typos in taxonomic names

Description

This function uses the generalized Levenshtein (edit) distance to identify possible issue with taxonomic names.

Usage

refdb_check_tax_typo(x, tol = 1)

Arguments

x	a reference database.
tol	the edit distance below which two taxonomic names are reported.

Value

A list of two-columns tibbles reporting for each taxonomic level the pairs of taxonomic names sharing the same upstream taxonomy and for which the generalized Levenshtein (edit) distance is below the tol value.

Examples

lib <- read.csv(system.file("extdata", "ephem.csv", package = "refdb"))
lib <- refdb_set_fields(lib,
                        taxonomy = c(family = "family_name",
                            genus = "genus_name",
                            species = "species_name"),
                        sequence = "DNA_seq",
                        marker = "marker")
refdb_check_tax_typo(lib)

refdb documentation built on Sept. 22, 2022, 5:07 p.m.