R: Extract a subtree from the synthetic tree

tol_subtree {rotl} | R Documentation

## 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 phyogenetic 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)

[Package rotl version 3.0.3 Index]