Create Stan Data Required for estimate_infections — create_stan

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.

Usage

create_stan_data(data, seeding_time, rt, gp, obs, backcalc, 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, data 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. If all entries of confirm are missing (NA) the returned estimates will represent the prior distributions.
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().
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.

Value

A list of stan data

Examples

if (FALSE) { # \dontrun{
create_stan_data(
  example_confirmed, 7, rt_opts(), gp_opts(), obs_opts(), 7,
  backcalc_opts(), create_shifted_cases(example_confirmed, 7, 14, 7)
)
} # }