create_stan_data function

Create Stan Data Required for estimate_infections

Takes the output of stan_opts() and converts it into a list understood by stan. Internally calls the other create_ family of functions to construct a single list for input into stan with all data required present.

create_stan_data(
  data,
  seeding_time,
  rt,
  gp,
  obs,
  backcalc,
  shifted_cases,
  forecast
)

Arguments

• data: A <data.frame> of disease reports (confirm) by date (date). confirm must be numeric and date must be in date format. Optionally this can also have a logical accumulate column which indicates whether data should be added to the next data point. This is useful when modelling e.g. weekly incidence data. See also the fill_missing() function which helps add the accumulate column with the desired properties when dealing with non-daily data. If any accumulation is done this happens after truncation as specified by the truncation argument.
• seeding_time: Integer; seeding time, usually obtained using get_seeding_time().
• rt: A list of options as generated by rt_opts() defining Rt estimation. Defaults to rt_opts(). To generate new infections using the non-mechanistic model instead of the renewal equation model, use rt = NULL. The non-mechanistic model internally uses the setting rt = rt_opts(use_rt = FALSE, future = "project", gp_on = "R0").
• 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().
• backcalc: A list of options as generated by backcalc_opts() to define the back calculation. Defaults to backcalc_opts().
• shifted_cases: A <data.frame> of delay shifted cases
• forecast: A list of options as generated by forecast_opts() defining the forecast opitions. Defaults to forecast_opts(). If NULL then no forecasting will be done.

Returns

A list of stan data

Examples

## Not run:

create_stan_data(
  example_confirmed, 7, rt_opts(), gp_opts(), obs_opts(), 7,
  backcalc_opts(), create_shifted_cases(example_confirmed, 7, 14, 7)
)
## End(Not run)