get_otol_synthetic_tree: Gets Open Tree of Life synthetic tree of a set of lineages.

Description Usage Arguments Value

View source: R/all_calibrations.R

Description

Gets Open Tree of Life synthetic tree of a set of lineages.

Usage

1
get_otol_synthetic_tree(input, otol_version = "v2", ...)

Arguments

input

Target taxa names as a character vector, a newick character string, or a phylo object.

otol_version

Version of OToL to use

...

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 phylo object


phylotastic/datelife documentation built on Jan. 14, 2019, 9:56 p.m.