report_plots: Report plots

In EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters

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, ...)

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().

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.

See Also

plot_estimates() of summarised_estimates[variable == "infections"], summarised_estimates[variable == "reported_cases"], summarised_estimates[variable == "R"], and summarised_estimates[variable == "growth_rate"], respectively.

Examples

# get example output form estimate_infections
out <- readRDS(system.file(
    package = "EpiNow2", "extdata", "example_estimate_infections.rds"
))

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

EpiNow2 documentation built on Oct. 31, 2024, 5:09 p.m.