get_validity {taxonbridge} | R Documentation |
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 |
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)