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Information about the Tree of Life

Source: R/tol.R
tol_about.Rd

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.

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.

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.

See also

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

Examples

if (FALSE) { # \dontrun{
res <- tol_about()
tax_sources(res)
ott_id(res)
studies <- source_list(tol_about(include_source_list=TRUE))} # }