tnrs_match: Taxon name resolution service (tnrs) applied to query by...

Description Usage Arguments Value

View source: R/opentree_taxonomy_general.R

Description

Taxon name resolution service (tnrs) applied to query by batches

Usage

1
tnrs_match(names, reference_taxonomy = "otl", ...)

Arguments

names

A character vector of taxon names to be matched to taxonomy. There is no limit to the numer of names that can be queried.

reference_taxonomy

A character vetor specifying the reference taxonomy to use for tnrs.

...

Arguments passed on to rotl::tnrs_match_names

context_name

name of the taxonomic context to be searched (length-one character vector). Must match (case sensitive) one of the values returned by tnrs_contexts.

do_approximate_matching

A logical indicating whether or not to perform approximate string (a.k.a. “fuzzy”) matching. Using FALSE will greatly improve speed. Default, however, is TRUE.

ids

A vector of ids to use for identifying names. These will be assigned to each name in the names array. If ids is provided, then ids and names must be identical in length.

include_suppressed

Ordinarily, some quasi-taxa, such as incertae sedis buckets and other non-OTUs, are suppressed from TNRS results. If this parameter is true, these quasi-taxa are allowed as possible TNRS results.

Value

A data frame from tnrs_match_names function


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