forecast_whole.R

library(EpiNow2)
library(patchwork)
library(xlsx)

df <- read.xlsx("Wave2_Raw.xlsx", sheetIndex = 1)

# set number of cores to use
old_opts <- options()
options(mc.cores = 8)
# construct example distributions
generation_time <- get_generation_time(disease = "SARS-CoV-2", source = "ganyani")
incubation_period <- get_incubation_period(disease = "SARS-CoV-2", source = "lauer")
reporting_delay <- list(mean = convert_to_logmean(3,1),
                        mean_sd = 0.1,
                        sd = convert_to_logsd(3,1),
                        sd_sd = 0.1, max = 15)

# example case data
reported_cases <- df[1:35, ]

# estimate Rt and nowcast/forecast cases by date of infection
out1 <- epinow(
  horizon = 15,
  reported_cases = reported_cases,
  generation_time = generation_time,
  delays = delay_opts(incubation_period, reporting_delay),
  rt = rt_opts(prior = list(mean = 2, sd = 0.2), future = "project"),
  stan = stan_opts(cores = 12),
  verbose = interactive()
)

# summary of the latest estimates
summary(out1)
# plot estimates
plot(out1)