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Generation time

Source: R/data.R
epiworld-gentime.Rd

Extraction and plotting of generation time by virus over time.

Usage

get_generation_time(x)

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

plot_generation_time(x, ...)

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.

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.

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)
#> _________________________________________________________________________
#> |Running the model...
#> |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| done.
#> |

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