tol_about: Information about the Tree of Life

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

Information about the Tree of Life

Description

Basic information about the Open Tree of Life (the synthetic tree)

Usage

tol_about(include_source_list = FALSE, ...)

## S3 method for class 'tol_summary'
tax_rank(tax, ...)

## S3 method for class 'tol_summary'
tax_sources(tax, ...)

## S3 method for class 'tol_summary'
unique_name(tax, ...)

## S3 method for class 'tol_summary'
tax_name(tax, ...)

## S3 method for class 'tol_summary'
ott_id(tax, ...)

Arguments

include_source_list	Logical (default = FALSE). Return an ordered list of source trees.
...	additional arguments to customize the API call (see rotl for more information).
tax	an object created with a call to tol_about.

Details

Summary information about the current draft tree of life, including information about the list of trees and the taxonomy used to build it. The object returned by tol_about can be passed to the taxonomy methods (tax_name(), tax_rank(), tax_sources(), ott_id), to extract relevant taxonomic information for the root of the synthetic tree.

Value

An invisible list of synthetic tree summary statistics:

date_created

String. The creation date of the tree.

num_source_studies

Integer. The number of studies (publications)used as sources.

num_source_trees

The number of trees used as sources (may be >1 tree per study).

taxonomy_version

The Open Tree Taxonomy version used as a source.

filtered_flags

List. Taxa with these taxonomy flags were not used in construction of the tree.

root

List. Describes the root node:

node_id

String. The canonical identifier of the node.

num_tips

Numeric. The number of descendant tips.

taxon

A list of taxonomic properties:

ott_id

Numeric. The OpenTree Taxonomy ID (ott_id).

name

String. The taxonomic name of the queried node.

unique_name

String. The string that uniquely identifies the taxon in OTT.

rank

String. The taxonomic rank of the taxon in OTT.

tax_sources

List. A list of identifiers for taxonomic sources, such as other taxonomies, that define taxa judged equivalent to this taxon.

source_list

List. Present only if include_source_list is TRUE. The sourceid ordering is the precedence order for synthesis, with relationships from earlier trees in the list having priority over those from later trees in the list. See source_id_map below for study details.

source_id_map

Named list of lists. Present only if include_source_list is TRUE. Names correspond to the ‘sourceids’ used in source_list above. Source trees will have the following properties:

git_sha

String. The git SHA identifying a particular source version.

tree_id

String. The tree id associated with the study id used.

study_id

String. The study identifier. Will typically include a prefix ("pg_" or "ot_").

synth_id

The unique string for this version of the tree.

See Also

source_list to explore the list of studies used in the synthetic tree (see example).

Examples

## Not run: 
res <- tol_about()
tax_sources(res)
ott_id(res)
studies <- source_list(tol_about(include_source_list=TRUE))
## End(Not run)

rotl documentation built on Jan. 16, 2026, 1:06 a.m.