OpenTreeChronograms (version 2022.1.28)

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

Description

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

Usage

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

Arguments

tnrs

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

invalid

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

remove_nonmatches

Boolean, whether to remove unsuccessfully matched names or not.

Value

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

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".