taxonbridge (version 1.2.1)

get_inconsistencies: 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.

Value

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

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.

Examples

# NOT RUN {
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")
# }