rotl (version 0.5.0)

tol_induced_subtree: Subtree from the Open Tree of Life

Description

Extract a subtree based on a vector of ott ids.

Usage

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

Arguments

ott_ids

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

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. Ott ids that do not correspond to any nodes found in the graph, or which are in the graph but are absent from the synthetic tree (e.g. groups included in the Open Tree Taxonomy but found to be paraphyletic in in studies contributing to the synthetic tree) , will be identified in the output (but obvisouly will be absent from the resulting induced tree). Branch lengths in the result may be arbitrary, and the tip labels of the tree may either be taxonomic names or (for nodes not corresponding directly to named taxa) node ids.

Examples

res <- tol_induced_subtree(ott_ids=c(292466, 501678, 267845, 666104, 316878, 102710, 176458))
tree_file <- tempfile(fileext=".tre")
tol_induced_subtree(ott_ids=c(292466, 501678, 267845, 666104, 316878, 102710, 176458),
                    file=tree_file)