plot_SEIQRDP {genSEIR}

Plots for Epidemic Curves

Description

This function creates plots for reported and predicted active, recovered and death cases.

Usage

plot_SEIQRDP(
  object,
  reported = TRUE,
  sep = FALSE,
  show = c("S", "E", "I", "Q", "R", "D", "P"),
  ci = FALSE,
  title = NULL,
  checkRates = FALSE,
  ...
)

Arguments

object

a predict_SEIQRDP result.

reported

a logical argument. If TRUE reported official cases will be added to the plot.

sep

a logical argument. If TRUE seperate plots will be plotted. If FALSE one plot with all desired states will be plotted.

show

select one or more desired state. S: Susceptible, E: Exposed, I: Infectious, Q: Quarantined, R: Recovered, D: Dead, P: Insusceptible

ci

a logical argument. If TRUE a bootstrap confidence intetval will be added to the plot.

title

an optional title for the plot.

checkRates

if TRUE compares the fitted and calcualted death and recovered ratios through plots

...

other plot options

Value

plots for epidemic curves: active cases, recovered and deaths

Author(s)

Selcuk Korkmaz, [e-mail]

Selcuk Korkmaz, [e-mail]

See Also

SEIQRDP fit_SEIQRDP

Examples

 alpha_guess = 0.45
 beta_guess = 1
 LT_guess = 2
 Q_guess = 0.55
 lambda_guess = c(0.01,0.01,30)
 kappa_guess = c(0.01,0.001,30)

 guess = list(alpha_guess,
              beta_guess,
              1/LT_guess,
              Q_guess,
              lambda_guess[1],
              lambda_guess[2],
              lambda_guess[3],
              kappa_guess[1],
              kappa_guess[2],
              kappa_guess[3])

 pred = predict_SEIQRDP(country = "Germany", start = "10/15/20", finish = "12/15/20",
                        dt = 1, f = 30, conf = 0.95, Npop = 80000000, guess, boot = TRUE,
                        seed = 123, repeatNumber = 10, bootSample = NULL, type = "norm")


 plot_SEIQRDP(object = pred, sep = FALSE, ci = TRUE, show = c("Q", "R", "D"), checkRates = TRUE)