plot_import_export_local_transmission: plot_import_export_local_transmission

In magnusnosnes/GeoLineages: Transmission Lineages From Maximum Likelihood Mappings

plot_import_export_local_transmission

Description

This function plots the estimates of import, export and local transmission events that are obtained from running the import_export_local_transmission function. It takes the tree for which the geographical estimation has been done, the results from running import_local_transmission, the size of the time intervals used in import_local_transmission, the date of the root of the phylogeny, and the interval between dates plotted on the x-axis as input arguments.

Usage

plot_import_export_local_transmission(
  tree,
  result_import_export_local_transmission,
  time_interval_size = 1/52,
  start_time,
  date_breaks = 2,
  time_interval = c("2000-05-01", "2016-05-01"),
  main_title = "",
  text_size = 10
)

Arguments

tree	A tree object for which the geographical estimation has been done.
result_import_export_local_transmission	A list object containing the results from running the import_local_transmission function.
time_interval_size	A numeric value representing the size of the time intervals used in import_local_transmission.
start_time	A date object representing the root of the phylogeny.
date_breaks	A string representing the interval between dates plotted on the x-axis. Acceptable arguments include "1 week", "2 months","1 year" etc.
importation_or_local	A string argument that specifies whether to plot importation, local transmission or both. Acceptable arguments are: "importation","local" or "both". Note: For plotting both importation and local transmission, the grid r-package is required.

Value

This function returns a plot of importation and/or local transmission events over time.

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