run_region {EpiNow2}

Run epinow with Regional Processing Code

Description

Internal function that handles calling epinow(). Future work will extend this function to better handle stan logs and allow the user to modify settings between regions.

Usage

run_region(
  target_region,
  generation_time,
  delays,
  truncation,
  rt,
  backcalc,
  gp,
  obs,
  stan,
  horizon,
  CrIs,
  data,
  target_folder,
  target_date,
  return_output,
  output,
  complete_logger,
  verbose,
  progress_fn,
  ...
)

Arguments

target_region

Character string indicating the region being evaluated

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 call to trunc_opts() defining the truncation of the observed data. Defaults to trunc_opts(), i.e. no truncation. See the estimate_truncation() help file for an approach to estimating this from data where the dist list element returned by estimate_truncation() is used as the truncation argument here, thereby propagating the uncertainty in the estimate.

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.

data

A ⁠<data.frame>⁠ of confirmed cases (confirm) by date (date), and region (region).

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.

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 the individual regional estimates ("regions"), samples ("samples"), plots ("plots"), copying the individual region dated folder into a latest folder (if target_folder is not null, set using "latest"), the stan fit of the underlying model ("fit"), and an overall summary across regions ("summary"). The default is to return samples and plots alongside summarised estimates and summary statistics. If target_folder is not NULL then the default is also to copy all results into a latest folder.

complete_logger

Character string indicating the logger to output the completion of estimation to.

verbose

Logical defaults to FALSE. Outputs verbose progress messages to the console from epinow().

progress_fn

Function as returned by progressr::progressor(). Allows the use of a progress bar.

...

Pass additional arguments to epinow(). See the documentation for epinow() for details.

Value

A list of processed output as produced by process_region()

See Also

regional_epinow()