Fetches a list of divergence times of nodes in TimeTree from the specified taxon to the common ancestor of all cellular organisms.
Usage
getTimeline(
taxId,
divergenceTimeType = "adjusted_age",
timetreeBaseTimeline = "http://timetree.temple.edu/api/timeline/"
)Arguments
- taxId
An integer: The NCBI id of a taxon
- divergenceTimeType
Optional parameter specifying which type of divergence time to read from TimeTree. Two types are available; the default is
adjusted_age:summary_age: the median divergence time across all studies from TimeTree;adjusted_age: a time adjusted when a node is older than its parent in the global timetree reconstructed from individual timetrees.
- timetreeBaseTimeline
Optional parameter specifying the base URL for retrieving timelines from the TimeTree API.
Value
A dataframe in which each row corresponds to an ancestor.
Each row contains the divergence time (divtime), its confidence interval
(divtimeCI_low and divtimeCI_high), and additional information,
including the scientific name (name) and taxonomic rank (rank).
If the divergence time is not found in the TimeTree database, it returns NA.