Convert Outbreak Data to a ttree Object

Transforms an outbreak data frame into a structured ttree list suitable for transmission tree plotting.

Usage

ttree_from_transmission(outbreak, dateLastSample)

Arguments

outbreak

A data frame containing at least: removal_time, infectious_period, latent_period, parent_id, and id.

dateLastSample

Numeric. The calendar date (e.g., 2024.5) corresponding to the maximum removal time in the dataset.

Value

A list of class ttree containing:

• ttree: A matrix with columns for infection time, removal time, and parent ID.

• nam: A character vector of individual IDs.