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,
  horizon,
  backcalc,
  shifted_cases
)

Arguments

data: A <data.frame> of confirmed cases (confirm) by date (date). confirm must be numeric and date must be in date format.
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().
horizon: Numeric, defaults to 7. Number of days into the future to forecast.
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

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)
)
} # }