clean_taxon_info_children: Identifies, extracts and cleans children names from a...

Description Usage Arguments Details Value Examples

View source: R/opentree_taxonomy.R

Description

Identifies, extracts and cleans children names from a taxonomy_taxon_info() output

Usage

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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 used by Open Tree Taxonomy to detect invalid taxon names

Details

eliminates all taxa that will give problems when trying to retrieve an induced subtree from otol.

Value

a list with valid children unique OTT names, ott_ids and ranks

Examples

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# some suppressed taxa within "Gleicheniales" family of ferns:
tt <- rotl::taxonomy_taxon_info(3866048)
rotl::taxonomy_taxon_info(5262766)

phylotastic/datelife documentation built on Jan. 22, 2019, 12:29 a.m.