tnrs_match.phylo: Taxon name resolution service (tnrs) applied to tips of a...

Description Usage Arguments Details Value

View source: R/opentree_taxonomy_general.R

Description

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

Usage

1
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.

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:

original

Tnrs matching was not attempted. Original labeling is preserved.

ott

Matching was manually made by a curator in Open Tree of Life.

tnrs

Tnrs matching was attempted and succesful with no approximate matching. Original label is replaced by the matched name.

approximated

Tnrs matching was attempted and succesful but with approximate matching. Original labeling is preserved.

unmatched

Tnrs matching was attempted and unsuccesful. Original labeling is preserved.

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

Value

An object of class phylo and match_names. See details.


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