plot_SEIQRDP: Plots for Epidemic Curves

In genSEIR: Predict Epidemic Curves with Generalized SEIR Modeling

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)

genSEIR documentation built on July 12, 2021, 5:07 p.m.