LineageType

A LineageType is an object that represents a category of Lineage objects sharing a common set of rate parameters. While this module is in development, this object class will be a placeholder and we are going to assume that all lineages are identical and implicitly belong to the same base LineageType. However, different LineageTypes would enable the user to simulate pathogen lineages that have different non-uniform probabilities of being transmitted through a bottleneck, or that reach different effective population sizes within a host.

YAML syntax

LineageTypes:
  <label>:
    transmission.rate.modifier: <value>  # should we implement this?
    migration.rate.modifier: <value>  # ditto...
    effective.size.modifier: <value>  # allow for time-heterogeneity via R expressions?
    bottleneck.size.modifier: <value>

Description

• label is a string identifier used to associate individual Lineage objects with this LineageType.
• effective.size.modifier is a float value centred at 1.0 (no modification). A value greater than 1.0 would indicate that Lineages of this type are more likely to contribute to subsequent generations, i.e., imply a selective advantage within hosts.
• bottleneck.size.modifier is a float value centred at 1.0, where a value greater than 1.0 would indicate that Lineages of this type are more likely to survive a transmission bottleneck, i.e., imply a selective advantage at transmission.