get_validity: Validate entries of a merged taxonomy

In MoultDB/moultdbtools: Create Custom Taxonomies Based on the NCBI Taxonomy and GBIF Backbone Taxonomy

Validate entries of a merged taxonomy

Description

Validate entries of a merged taxonomy

Usage

get_validity(x, rank = "family", valid = TRUE)

Arguments

x	A tibble created with load_taxonomies() or load_population() or load_sample().
rank	A string with GBIF rank that will be used to examine a NCBI lineage for validation purposes. Must be kingdom, phylum, class, order or family. Defaults to family. Note: If kingdom is used, the term_conversion() method should first be applied.
valid	A logical indicating whether the returned data should include valid or invalid entries (defaults to TRUE).

Details

Taxonbridge matches NCBI and GBIF data by scientific name. This method will use the GBIF rank (kingdom, phylum, class, order or family) and search for this rank name in the matched NCBI lineage. The purpose is to detect scientific names that have different lineage data in the GBIF and NCBI. If the valid parameter is set to TRUE, this method will not only check the rank names, but also ensure that the GBIF taxonRank column and NCBI ncbi_rank column matches.

Value

A validated tibble.

Examples

get_validity(load_sample(), valid = TRUE)

MoultDB/moultdbtools documentation built on Feb. 2, 2024, 5:21 p.m.