R: Information about the Tree of Life

tol_about {rotl} | R Documentation

## 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 descendent 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)

[Package rotl version 3.0.4 Index]