Lineage

A Lineage is an object representing an individual pathogen lineage.

YAML template

Lineages:
  <label>:
    type: <reference to LineageType object>
    sampling.time: <sampling time of pathogen>
    location: <reference to Compartment pathogen was sampled from>
    replicates: <propagate to replicate Lineage objects>

Arguments

• label is a unique string identifier that is used to map a Lineage object to a leaf/node label of a user-specified input tree.
• type identifies the LineageType that this Lineage object is an instance of.
• sampling.time records the time at which the pathogen was sampled.
• location records the source from where the pathogen was sampled from, and is a reference to a Compartment object. The location attribute will change as Lineages are traced back in time.
• replicates is a convenience parameter that is used to generate two or more Lineage objects belonging to the same host Compartment object. If replicates is set to an integer value greater than 1, then sampling.time accepts either a single integer value to be applied to all Lineage objects, or a vector of equal length to replicates specifying individual sampling times.

Details

Examples