get_inconsistencies: Detect candidate inconsistencies and ambiguity between NCBI...

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

Detect candidate inconsistencies and ambiguity between NCBI and GBIF data

Description

Detect candidate inconsistencies and ambiguity between NCBI and GBIF data

Usage

get_inconsistencies(x, uninomials = TRUE, set = "intersect")

Arguments

x	A list consisting of two tibbles of different ranks that have been passed to get_validated(..., rank = ...).
uninomials	A logical indicating whether uninomials should be included in the detection. Defaults to TRUE. Note: uninomials are single names (e.g., "Coenobitidae").
set	The type of set operation to be performed on x ("intersect", "union", or "setdiff"). Defaults to intersect. Note: the set difference ("setdiff") argument is order dependent.

Details

This method will return the intersect, union, or set difference of a list of two tibbles, and is meant to be used on lists of tibbles that have already been processed with get_validity(). A list consisting of a single tibble may be passed to this method for the purpose of retrieving a character vector containing scientific names, however, set operations do not apply to lists consisting of single tibbles.

Value

A character vector containing scientific names that exhibit inconsistency or ambiguity.

Examples

sample <- load_sample()
lineages <- get_lineages(sample)
kingdom <- get_validity(lineages, rank = "kingdom", valid = FALSE)
family <- get_validity(lineages, rank = "family", valid = FALSE)
candidates <- list(kingdom, family)
get_inconsistencies(candidates, uninomials = FALSE, set = "intersect")

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