get_valid_children {OpenTreeChronograms}

Extract valid children from given taxonomic name(s) or Open Tree of Life Taxonomic identifiers (OTT ids) from a taxonomic source.

Description

Extract valid children from given taxonomic name(s) or Open Tree of Life Taxonomic identifiers (OTT ids) from a taxonomic source.

Usage

get_valid_children(input = NULL, ott_ids = NULL, taxonomic_source = "ncbi")

Arguments

input

Optional. A character vector of names.

ott_ids

If not NULL, it takes this argument and ignores input. A numeric vector of ott ids obtained with rotl::taxonomy_taxon_info() or rotl::tnrs_match_names() or tnrs_match().

taxonomic_source

A character vector with the desired taxonomic sources. Options are "ncbi", "gbif" or "irmng". Any other value will retrieve data from all taxonomic sources. The function defaults to "ncbi".

Details

GBIF and other taxonomies contain deprecated taxa that are not marked as such in the Open Tree of Life Taxonomy. We are relying mainly in the NCBI taxonomy for now.

Value

A named list containing valid taxonomic children of given taxonomic name(s).

Examples

# genus Dictyophyllidites with ott id = 6003921 has only extinct children
# in cases like this the same name will be returned

tti <- rotl::taxonomy_taxon_info(6003921, include_children = TRUE)
gvc <- get_valid_children(ott_ids = 6003921)

# More examples:

get_valid_children(ott_ids = 769681) # Psilotopsida
get_valid_children(ott_ids = 56601) # Marchantiophyta