clean_tnrs: Eliminates unmatched (NAs) and invalid taxa from a...

Description Usage Arguments Details Value

View source: R/opentree_taxonomy_general.R

Description

Eliminates unmatched (NAs) and invalid taxa from a rotl::tnrs_match_names or datelife::tnrs_match output Useful to get ott ids to retrieve an otol induced subtree from. Needed because using include_suppressed = FALSE in tnrs_match_names does not drop all invalid taxa

Usage

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clean_tnrs(tnrs, invalid = c("barren", "extinct", "uncultured",
  "major_rank_conflict", "incertae", "unplaced", "conflict",
  "environmental", "not_otu"))

Arguments

tnrs

A data frame, usually an output from datelife::tnrs_match or rotl::tnrs_match_names functions, but see details.

invalid

A character string with flags to be removed from final object.

Details

Input can be any data frame or named list that relates taxa stored in an element named "unique" to a validity category stored in "flags".

Value

A data frame or named list (depending on the input) with valid taxa only.


phylotastic/datelife documentation built on Jan. 14, 2019, 9:56 p.m.