epiworldR (version 0.11.2.0)

epiworld-gentime: Generation time

Description

Extraction and plotting of generation time by virus over time.

Usage

get_generation_time(x)
# S3 method for epiworld_generation_time
plot(
  x,
  type = "b",
  xlab = "Day (step)",
  ylab = "Avg. Generation Time",
  main = "Generation Time",
  plot = TRUE,
  ...
)
plot_generation_time(x, ...)

Value

• The function get_generation_time returns a data.frame with the following columns: "agent", "virus_id", "virus", "date", and "gentime".

• The function plot_generation_time is a wrapper for plot and get_generation_time.

Arguments

x

An object of class epiworld_sir, epiworld_seir, etc. (any model), or an object of class epiworld_generation_time.

ylab, xlab, main, type

Further parameters passed to graphics::plot()

plot

Logical scalar. If TRUE (default), the function will plot the desired statistic.

...

In the case of plot methods, further arguments passed to graphics::plot.

See Also

Other Epidemiological metrics: epiworld-repnum

Examples

# SEIR Connected model
seirconn <- ModelSEIRCONN(
  name              = "Disease",
  n                 = 10000,
  prevalence        = 0.1,
  contact_rate      = 2.0,
  transmission_rate = 0.8,
  incubation_days   = 7.0,
  recovery_rate     = 0.3
)

set.seed(937)
run(seirconn, 50)

# Get and plot generation time
gent <- plot_generation_time(seirconn)