plot.backnow {linelistBayes}

Plot Estimates or Reproduction Numbers

Description

This function plots estimates of case numbers or reproduction numbers ('r(t)') based on the provided object. It can handle two types of plots: 'est' for estimated case numbers over time, and 'rt' for estimated reproduction numbers over time.

Usage

## S3 method for class 'backnow'
plot(x, plottype, ...)

Arguments

x

An object containing the necessary data for plotting. This object should have specific structure depending on the 'plottype': - For ‘plottype = ’est'', 'x' should contain 'report_date', 'report_cases', 'est_back_date', and 'est_back', where 'est_back' is expected to be a matrix with three rows representing the lower bound, estimate, and upper bound. - For ‘plottype = ’rt'', 'x' should contain 'est_rt_date' and 'est_rt', with 'est_rt' formatted similarly to 'est_back'.

plottype

A character string specifying the type of plot to generate. Valid options are 'est' for case estimates and 'rt' for reproduction numbers.

...

Additional arguments passed to the plot function.

Details

Depending on the 'plottype': - 'est': Plots the reported cases over time with a polygon representing the uncertainty interval and a line showing the central estimate. - 'rt': Plots the reproduction number over time with a similar style.

Value

a plot object for an object of class 'backnow'

Examples

data("sample_onset_dates")
data("sample_report_dates")
line_list <- create_linelist(sample_report_dates, sample_onset_dates)
sip <- si(14, 4.29, 1.18)
results <- run_backnow(
  line_list, 
  MAX_ITER = as.integer(2000), 
  norm_sigma = 0.5, 
  sip = sip,
  NB_maxdelay = as.integer(20), 
  NB_size = as.integer(6), 
  workerID = 1, 
  printProgress = 1, 
  preCalcTime = TRUE)
plot(results, 'est')
plot(results, 'rt')