plot_importation_local_transmission: plot_importation_local_transmission

In magnusnosnes/GeoLineages: Transmission Lineages From Maximum Likelihood Mappings

plot_importation_local_transmission

Description

plot_importation_local_transmission plots the estimates of importation and local transmission events that are obtained from running the import_local_transmission function.

Usage

plot_importation_local_transmission(
  tree,
  result_import_local_transmission,
  time_interval_size = 1/52,
  start_time,
  date_breaks = "1 month",
  importation_or_local = "both"
)

Arguments

tree	tree for which the geographical estimation has been done.
result_import_local_transmission	results from running import_local_transmission
time_interval_size	size of the time intervals used in import_local_transmission
start_time	date of the root of the phylogeny
date_breaks	The interval between dates plotted on the x-axis. Takes arguments such as "1 week", "2 months","1 year" etc..
importation_or_local	Whether to plot importation, local transmission or both. The variable takes the arguments: "importation","local" or "both". For plotting both the function requires the grid r-package.

magnusnosnes/GeoLineages documentation built on April 17, 2025, 6:29 p.m.