rotl (version 3.0.0)

tol_induced_subtree: Subtree from the Open Tree of Life

Description

Return the induced subtree on the synthetic tree that relates a list of nodes.

Usage

tol_induced_subtree(ott_ids = NULL, node_ids = NULL, label_format = NULL, file, ...)

Arguments

ott_ids

Numeric vector. OTT ids indicating nodes to be used as tips in the induced tree.

node_ids

Character vector. Node ids indicating nodes to be used as tips in the induced tree.

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).

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.

Details

Return a tree with tips corresponding to the nodes identified in the input set that is consistent with the topology of the current synthetic tree. This tree is equivalent to the minimal subtree induced on the draft tree by the set of identified nodes.

Examples

## Not run: 
# res <- tol_induced_subtree(ott_ids=c(292466, 267845, 666104, 316878, 102710))
# tree_file <- tempfile(fileext=".tre")
# tol_induced_subtree(ott_ids=c(292466, 267845, 666104, 316878, 102710),
#                     file=tree_file)## End(Not run)