EpiNow2 (version 1.3.4)

report_plots: Report plots

Description

Returns key summary plots for estimates. May be depreciated in later releases as current S3 methods are enhanced.

Usage

report_plots(summarised_estimates, reported, target_folder = NULL, ...)

Value

A named list of ggplot2 objects, list(infections, reports, R, growth_rate, summary), which correspond to a summary combination (last item) and for the leading items @seealso plot_estimates() of summarised_estimates[variable == "infections"], summarised_estimates[variable == "reported_cases"], summarised_estimates[variable == "R"], and summarised_estimates[variable == "growth_rate"], respectively.

Arguments

summarised_estimates

A data.table of summarised estimates containing the following variables: variable, median, bottom, and top.

It should also contain the following estimates: R, infections, reported_cases_rt, and r (rate of growth).

reported

A data.table of reported cases with the following variables: date, confirm.

target_folder

Character string specifying where to save results (will create if not present).

...

Additional arguments passed to plot_estimates().

Examples

# \donttest{
# define example cases
cases <- example_confirmed[1:40]

# set up example delays
generation_time <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
incubation_period <- get_incubation_period(disease = "SARS-CoV-2", source = "lauer")
reporting_delay <- bootstrapped_dist_fit(rlnorm(100, log(6), 1), max_value = 30)

# run model
out <- estimate_infections(cases,
  stan = stan_opts(samples = 500),
  generation_time = generation_time,
  delays = delay_opts(incubation_period, reporting_delay),
  rt = NULL
)

# plot infections
plots <- report_plots(
  summarised_estimates = out$summarised,
  reported = cases
)
plots
# }