map_to_ott: Map taxa to open tree of life

In alexpiper/taxreturn: An R package for retrieving and curating public DNA barcode reference data

Map taxa to open tree of life

Description

Map taxa to open tree of life

Usage

map_to_ott(
  x,
  db,
  from = "ncbi",
  resolve_synonyms = TRUE,
  dir = NULL,
  filter_unplaced = TRUE,
  remove_na = FALSE,
  quiet = FALSE
)

Arguments

x	a DNAbin
db	an OTT taxonomic database
from	the existing taxonomic ID format
resolve_synonyms	Whether to resolve synonyms
dir	A directory containing the OTT taxonomy, required if resolve synonyms is true
filter_unplaced	Whether to filter 'bad' entries. These include incertae_sedis major_rank_conflict unplaced environmental inconsistent extinct hidden hybrid not_otu viral barren See: https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/doc/taxon-flags.md for more info
remove_na	Whether taxa that could not be mapped to the open tree of life should be removed
quiet	Whether progress should be printed to console

alexpiper/taxreturn documentation built on Sept. 14, 2024, 7:56 p.m.