get_dated_otol_induced_subtree: Get a dated OpenTree induced synthetic subtree from a set of...

In phylotastic/datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

Get a dated OpenTree induced synthetic subtree from a set of given taxon names, from blackrim's FePhyFoFum service.

Description

Get a dated OpenTree induced synthetic subtree from a set of given taxon names, from blackrim's FePhyFoFum service.

Usage

get_dated_otol_induced_subtree(input = NULL, ott_ids = NULL, ...)

Arguments

input	Optional. A character vector of names or a datelifeQuery object.
ott_ids	If not NULL, it takes this argument and ignores input. A numeric vector of ott ids obtained with rotl::taxonomy_taxon_info() or rotl::tnrs_match_names() or tnrs_match().
...	Arguments passed on to check_ott_input

Details

OpenTree dated tree from Stephen Smith's OpenTree scaling service at https://github.com/FePhyFoFum/gophy if you want to make an LTT plot of a dated OpenTree tree you'll need to get rid of singleton nodes with ape::collapse.singles() and also probably do phytools::force.ultrametric().

Value

A phylo object with edge length proportional to time in Myrs. It will return NA if any ott_id is invalid.

phylotastic/datelife documentation built on Jan. 17, 2024, 11:10 p.m.