clean_taxon_info_children: Identify, extract and clean taxonomic children names from a...

In phylotastic/datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

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.

phylotastic/datelife documentation built on June 9, 2024, 6:50 p.m.