tol_subtree: Extract a subtree from the synthetic tree

In rotl: Interface to the 'Open Tree of Life' API

Extract a subtree from the synthetic tree

Description

Extract a subtree from the synthetic tree from an Open Tree node id.

Usage

tol_subtree(ott_id = NULL, node_id = NULL, label_format = NULL, file, ...)

Arguments

ott_id	Numeric. The ott id of the node in the tree that should serve as the root of the tree returned.
node_id	Character. The node id of the node in the tree that should serve as the root of the tree returned.
label_format	Character. Defines the label type; one of “name”, “id”, or “name_and_id” (the default).
file	If specified, the function will write the subtree to a file in newick format.
...	additional arguments to customize the API call (see rotl for more information).

Details

Given a node, return the subtree of the synthetic tree descended from that node. The start node may be specified using either a node id or an ott id, but not both. If the specified node is not in the synthetic tree an error will be returned. There is a size limit of 25000 tips for this method.

Value

If no value is specified to the file argument (default), a phylogenetic tree of class phylo. Otherwise, the function returns invisibly a logical indicating whether the file was successfully created.

Examples

## Not run: 
res <- tol_subtree(ott_id=241841)
## End(Not run)

rotl documentation built on July 9, 2023, 7:37 p.m.