rotl (version 0.5.0)

gol_node_info: Node info

Description

Get summary information about a node in the graph database

Usage

gol_node_info(ott_id = NULL, include_lineage = FALSE, ...)
## S3 method for class 'gol_node':
tax_rank(tax)
## S3 method for class 'gol_node':
ott_id(tax, ...)
synth_sources(tax)
## S3 method for class 'gol_node':
synth_sources(tax)

Arguments

ott_id

The OpenTree taxonomic identifier.

include_lineage

Boolean. Whether to return the lineage of the node from the synthetic tree. Optional; default = FALSE.

...

additional arguments to customize the API call (see ?rotl for more information)

tax

an object returned by gol_node_info.

Value

• gol_node_info returns a list of summary information about the queried node.
  • tree_id
  {The tree identifier for a given study.}

• num_synth_tips
• {Numeric. The number of synthetic tree tip descendants.}
• name
• {String. The taxonomic name of the queried node (if it is a named node).}
• rank
• {String. The taxonomic rank of the queried node (if it is a named node).}
• ott_id
• {Numeric. The OpenTree Taxonomy ID (ottID) of the queried node (if it is a named node).}
• num_tips
• {Numeric. The number of taxonomic tip descendants.}
• tree_sources
• {A list of supporting source trees in the graph. May differ from "synth_sources", if trees are in the graph, but were not used in constructing the synthetic tree. Each source has:}
  • study_id
  {The study identifier. Will typically include a prefix ("pg_" or "ot_").}

• tree_id
• {The tree identifier for a given study.}
• git_sha
• {The git SHA identifying a particular source version.}

item

• tax_source
• synth_sources
• tree_id
• study_id
• node_id
• in_synth_tree

itemize

• git_sha

code

ott_id

Details

Summary information about a queried node, including 1) whether it is in the graph database, 2) whether it is in the synthetic tree, 3) supporting study sources, 4) number of descendant tip taxa, 5) graph node ID, and 6) taxonomic information (if it is a named node in the graph), including: name, rank, OpenTree Taxonomy ID (ottID), and source taxonomy IDs.

Examples

birds <- gol_node_info(ott_id=81461)
synth_sources(birds)
tax_rank(birds)
ott_id(birds)