clean_taxon_info_children {OpenTreeChronograms}

Identify, extract and clean taxonomic children names from a taxonomy_taxon_info() output.

Description

clean_taxon_info_children eliminates all taxa that will give problems when trying to retrieve an induced subtree from Open Tree of Life.

Usage

clean_taxon_info_children(
  taxon_info,
  invalid = c("barren", "extinct", "uncultured", "major_rank_conflict",
    "incertae_sedis", "unplaced", "conflict", "environmental", "not_otu", "hidden",
    "hybrid")
)

Arguments

taxon_info

An output of rotl::taxonomy_taxon_info().

invalid

A character vector of "flags", i.e., characteristics that are used by Open Tree of Life Taxonomy to detect invalid taxon names.

Value

A list with valid children unique OTT names, OTT ids and taxonomic ranks.