R: Node info

tol_lineage {rotl} | R Documentation

## Node info

### Description

Get summary information about a node in the synthetic tree

### Usage

    tol_lineage(tax, ...)

    tol_node_info(ott_id = NULL, node_id = NULL, include_lineage = FALSE, ...)

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

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

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

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

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

    ## S3 method for class 'tol_node'
    source_list(tax, ...)

    ## S3 method for class 'tol_node'
    tax_lineage(tax, ...)

    ## S3 method for class 'tol_node'
    tol_lineage(tax, ...)

### Arguments

`tax` | an object returned by `tol_node_info`.
`...` | additional arguments to customize the API call (see ?rotl for more information)
`ott_id` | Numeric. The OpenTree taxonomic identifier.
`node_id` | Character. The OpenTree node identifier.
`include_lineage` | Logical (default = FALSE). Whether to return the lineage of the node from the synthetic tree.

### Details

Returns summary information about a node in the graph. The node of interest may be specified using either a node id or an taxon id, but not both. If the specified node or OTT id is not in the graph, an error will be returned.

If the argument `include_lineage=TRUE` is used, you can use `tax_lineage()` or `tol_lineage` to return the taxonomic information or the node information for all the ancestors to this node, down to the root of the tree.

### Value

`tol_node_info` returns an invisible list of summary information about the queried node:

- node_id String. The canonical identifier of the node.

- num_tips Numeric. The number of descendent tips.

- taxon A list of taxonomic properties. Only returned if the queried node is a taxon. Each source has:

  - ott_id Numeric. The OpenTree Taxonomy ID (ottID).

  - 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.

  The following properties list support/conflict for the node across synthesis source trees. All properties involve sourceid keys and nodeid values (see `source_id_map` below).

- partial_path_of List. The edge below this synthetic tree node is compatible with the edge below each of these input tree nodes (one per tree). Each returned element is reported as sourceid:nodeid.

- supported_by List. Input tree nodes (one per tree) that support this synthetic tree node. Each returned element is reported as sourceid:nodeid.

- terminal List. Input tree nodes (one per tree) that are equivalent to this synthetic tree node (via an exact mapping, or the input tree terminal may be the only terminal descended from this synthetic tree node. Each returned element is reported as sourceid:nodeid.

- conflicts_with Named list of lists. Names correspond to sourceid keys. Each list contains input tree node ids (one or more per tree) that conflict with this synthetic node.

- source_id_map Named list of lists. Names correspond to the sourceid keys used in the 4 properties above. Source trees will have the following properties:

  - git_sha The git SHA identifying a particular source version.

  - tree_id The tree id associated with the study id used.

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

  The only sourceid that does not correspond to a source tree is the taxonomy, which will have the name "ott"+'taxonomy_version', and the value is the ott_id of the taxon in that taxonomy version. "Taxonomy" will only ever appear in `supported_by`.

`tol_lineage` and `tax_lineage` return data frames. `tol_lineage` indicate for each ancestor its node identifier, the number of tips descending from that node, and whether it corresponds to a taxonomic level.

### Examples

    ## Not run:
    birds <- tol_node_info(ott_id=81461, include_lineage=TRUE)
    source_list(birds)
    tax_rank(birds)
    ott_id(birds)
    tax_lineage(birds)
    tol_lineage(birds)
    ## End(Not run)

[Package rotl version 3.0.3 Index]