Taxon name resolution service (tnrs) applied to tips of a phylogeny

Taxon name resolution service (tnrs) applied to tips of a phylogeny

tnrs_match.phylo(phy, tip, reference_taxonomy = "otl", ...)

Arguments

phy	A phylo object
tip	A vector of mode numeric or character specifying the tips to match. If left empty all tips will be matched.
reference_taxonomy	A character vector 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

An object of class phylo and match_names. See details.

Details

The output will preserve all elements from original input phylo object and will add

phy$mapped

A character vector indicating the state of mapping of phy$tip.labels:

phy$original.tip.label

A character vector preserving all original labels.

phy$ott_ids

A numeric vector with ott id numbers of matched tips. Unmatched and original tips will be NaN.

if tips are duplicated, tnrs will only be run once (avoiding increases in function running time) but the result will be applied to all duplicated tip labels