plot_paths: Plot epidemic paths

In pspc-data-science/branchsim: Gamma negative binomial branching process simulation of epidemics

Description

Plot epidemic paths

Usage

plot_paths(
  paths_data,
  y_var = n_infected,
  n_max = 200,
  tlim = NA,
  highlight_path_id = NA,
  show_hist = TRUE,
  show_extinct = TRUE,
  smooth_data = NULL,
  extinct_color = "red",
  n_bins = 20
)

Arguments

paths_data	A data.frame, with at least the columns id_sim, time, and a quoted variable passed as yvar.
y_var	Column in paths_data to use as y-variable.
n_max	An integer. Maximum number of paths to display. Useful to avoid graphs that are too crowded.
tlim	A scalar.
highlight_path_id	A subset of values in column id_sim of input paths_data that will be highlighted (black and thicker). If the values provided are not found in column id_sim, no path will be highlighted.
show_hist	A logical scalar. If TRUE, show the distribution of paths at the right-end of the plot. In this case, the output will be a ggarrange object, rather than a ggplot object.
show_extinct	A logical scalar. Show extinct paths along with non-extinct ones.
smooth_data	A data.frame, with at least the columns time, n_infected, and n_infectious. If given, will be superposed on top of the paths plot.
extinct_color	A color value understood by ggplot. This will be the colour of paths that went extinct before the end of the simulation.
n_bins	An integer scalar. Number of bins in the histogram panel.

Value

A plot. If show_hist = TRUE (default), the output will be a ggarrange object showing both the paths, and a histogram of the level at which they terminate. Otherwise the output will be a ggplot object showing only the paths.

pspc-data-science/branchsim documentation built on Jan. 19, 2021, 10:10 a.m.