EpiNow2 (version 1.1.0)

report_plots: Report plots

Description

Report plots

Usage

report_plots(summarised_estimates, reported, target_folder, max_plot = 10)

Arguments

summarised_estimates

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

max_plot

Numeric, defaults to 10. A multiplicative upper bound on the number of cases shown on the plot. Based on the maximum number of reported cases.

Value

A ggplot2 object

Examples

# NOT RUN {
## Define example cases
cases <- EpiNow2::example_confirmed[1:40]

 
## Set up example generation time
generation_time <- list(mean = EpiNow2::covid_generation_times[1, ]$mean,
                        mean_sd = EpiNow2::covid_generation_times[1, ]$mean_sd,
                        sd = EpiNow2::covid_generation_times[1, ]$sd,
                        sd_sd = EpiNow2::covid_generation_times[1, ]$sd_sd,
                        max = 30)
## Set                   
incubation_period <- list(mean = EpiNow2::covid_incubation_period[1, ]$mean,
                          mean_sd = EpiNow2::covid_incubation_period[1, ]$mean_sd,
                          sd = EpiNow2::covid_incubation_period[1, ]$sd,
                          sd_sd = EpiNow2::covid_incubation_period[1, ]$sd_sd,
                          max = 30)
                   
reporting_delay <- list(mean = log(5),
                        mean_sd = log(2),
                        sd = log(2),
                        sd_sd = log(1.5),
                        max = 30)
                        
## Run model
out <- EpiNow2::estimate_infections(cases, family = "negbin",
                                    generation_time = generation_time,
                                    delays = list(incubation_period, reporting_delay),
                                    samples = 1000, warmup = 200, cores = 4, chains = 4,
                                    horizon = 7, estimate_rt = TRUE, verbose = TRUE)
                            
                     
## Plot infections
plots <- report_plots(summarised_estimates = out$summarised,
                      reported = cases)
                      
plots
# }