epinow: Real-time Rt Estimation, Forecasting and Reporting

Description

This function wraps the functionality of estimate_infections() and forecast_infections() in order to estimate Rt and cases by date of infection, forecast into these infections into the future. It also contains additional functionality to convert forecasts to date of report and produc summary output useful for reporting results and interpreting them. See here for an example of using epinow to estimate Rt for Covid-19 in a country from the ECDC data source.

Usage

epinow(
  reported_cases,
  generation_time = NULL,
  delays = delay_opts(),
  truncation = trunc_opts(),
  rt = rt_opts(),
  backcalc = backcalc_opts(),
  gp = gp_opts(),
  obs = obs_opts(),
  stan = stan_opts(),
  horizon = 7,
  CrIs = c(0.2, 0.5, 0.9),
  filter_leading_zeros = TRUE,
  zero_threshold = Inf,
  return_output = FALSE,
  output = c("samples", "plots", "latest", "fit", "timing"),
  plot_args = list(),
  target_folder = NULL,
  target_date,
  logs = tempdir(),
  id = "epinow",
  verbose = interactive()
)

Value

A list of output from estimate_infections, forecast_infections, report_cases, and report_summary.

Arguments

reported_cases: A data frame of confirmed cases (confirm) by date (date). confirm must be integer and date must be in date format.
generation_time: A call to generation_time_opts() defining the generation time distribution used. For backwards compatibility a list of summary parameters can also be passed.
delays: A call to delay_opts() defining delay distributions and options. See the documentation of delay_opts() and the examples below for details.
truncation: A list of options as generated by trunc_opts() defining the truncation of observed data. Defaults to trunc_opts(). See estimate_truncation() for an approach to estimating truncation from data.
rt: A list of options as generated by rt_opts() defining Rt estimation. Defaults to rt_opts(). Set to NULL to switch to using back calculation rather than generating infections using Rt.
backcalc: A list of options as generated by backcalc_opts() to define the back calculation. Defaults to backcalc_opts().
gp: A list of options as generated by gp_opts() to define the Gaussian process. Defaults to gp_opts().Set to NULL to disable the Gaussian process.
obs: A list of options as generated by obs_opts() defining the observation model. Defaults to obs_opts().
stan: A list of stan options as generated by stan_opts(). Defaults to stan_opts(). Can be used to override data, init, and verbose settings if desired.
horizon: Numeric, defaults to 7. Number of days into the future to forecast.
CrIs: Numeric vector of credible intervals to calculate.
filter_leading_zeros: Logical, defaults to TRUE. Should zeros at the start of the time series be filtered out.
zero_threshold: Numeric defaults to Inf. Indicates if detected zero cases are meaningful by using a threshold number of cases based on the 7 day average. If the average is above this threshold then the zero is replaced with the backwards looking rolling average. If set to infinity then no changes are made.
return_output: Logical, defaults to FALSE. Should output be returned, this automatically updates to TRUE if no directory for saving is specified.
output: A character vector of optional output to return. Supported options are samples ("samples"), plots ("plots"), the run time ("timing"), copying the dated folder into a latest folder (if target_folder is not null, set using "latest"), and the stan fit ("fit"). The default is to return all options.
plot_args: A list of optional arguments passed to plot.epinow().
target_folder: Character string specifying where to save results (will create if not present).
target_date: Date, defaults to maximum found in the data if not specified.
logs: Character path indicating the target folder in which to store log information. Defaults to the temporary directory if not specified. Default logging can be disabled if logs is set to NULL. If specifying a custom logging setup then the code for setup_default_logging and the setup_logging function are a sensible place to start.
id: A character string used to assign logging information on error. Used by regional_epinow to assign errors to regions. Alter the default to run with error catching.
verbose: Logical, defaults to TRUE when used interactively and otherwise FALSE. Should verbose debug progress messages be printed. Corresponds to the "DEBUG" level from futile.logger. See setup_logging for more detailed logging options.

Author

Sam Abbott

Examples

Run this code

# \donttest{
# set number of cores to use
old_opts <- options()
options(mc.cores = ifelse(interactive(), 4, 1))
# 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(2, 1),
  mean_sd = 0.1,
  sd = convert_to_logsd(2, 1),
  sd_sd = 0.1,
  max = 10
)

# example case data
reported_cases <- example_confirmed[1:40]

# estimate Rt and nowcast/forecast cases by date of infection
out <- epinow(
  reported_cases = reported_cases, generation_time = generation_time,
  rt = rt_opts(prior = list(mean = 2, sd = 0.1)),
  delays = delay_opts(incubation_period, reporting_delay)
)
# summary of the latest estimates
summary(out)
# plot estimates
plot(out)

# summary of R estimates
summary(out, type = "parameters", params = "R")

options(old_opts)
# }