EpiLPS (version 1.3.0)

plot.Rt: Plot the estimated reproduction number

Description

This routine can be used to plot the estimated reproduction number based on an object of class Rt.

Usage

# S3 method for Rt
plot(x, datelab = "7d", cilevel = 0.95, col = "black", cicol = "gray",
 xtickangle = 0, legendpos = "right", title = "Estimated R",
 addfit = c("none","Cori","WT"), theme = "gray", timecut = 0,...)

Value

A plot of the fitted time-varying reproduction number.

Arguments

x

An object of class Rt.

datelab

Spacing for the ticks on the x-axis.

cilevel

Level of the credible interval.

col

Color of the fitted \(R_t\) curve for LPS.

cicol

Color for shading the credible envelope.

xtickangle

Angle of the x-ticks. Default is 0 (horizontal).

legendpos

Position of the legend.

title

Title of the plot.

addfit

Should an additional \(R_t\) fit be added?

theme

Theme, either "gray", "classic", "light", "dark"

timecut

Cut time points on plot.

...

Further arguments to be passed to plot.

Author

Oswaldo Gressani

Examples

si <- c(0.05, 0.05, 0.1, 0.1, 0.1, 0.1, 0.1, 0.05, 0.05, 0.1, 0.1, 0.1)
epidemic <- episim(si = si, Rpattern = 2, endepi = 30)
epifit <- estimR(incidence = epidemic$y, K = 30, si = si)
plot(epifit)