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Reproductive number (Rt)

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

Extraction and plotting of the reproductive number (Rt) by virus over time.

Usage

get_reproductive_number(x)

# S3 method for class 'epiworld_repnum'
plot(
  x,
  y = NULL,
  ylab = "Average Rep. Number",
  xlab = "Day (step)",
  main = "Reproductive Number",
  type = "b",
  plot = TRUE,
  ...
)

plot_reproductive_number(x, ...)

Arguments

x

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

y

Ignored.

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 get_reproductive_number function returns an object of class epiworld_repnum.

  • The plot method for epiworld_repnum returns a plot of the reproductive number over time.

Details

The plot_reproductive_number function is a wrapper around get_reproductive_number that plots the result.

See also

Other Epidemiological metrics: epiworld-gentime

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.
#> |

# Retrieving (and plotting) the reproductive number
rp <- get_reproductive_number(seirconn)
plot(rp) # Also equivalent to plot_reproductive_number(seirconn)