create_stan_data: Create Stan Data Required for estimate_infections

Description

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(
  reported_cases,
  generation_time,
  rt,
  gp,
  obs,
  delays,
  horizon,
  backcalc,
  shifted_cases,
  truncation
)

Value

A list of stan data

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.
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.
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().
delays: A call to delay_opts() defining delay distributions and options. See the documentation of delay_opts() and the examples below for details.
horizon: Numeric, forecast horizon.
backcalc: A list of options as generated by backcalc_opts() to define the back calculation. Defaults to backcalc_opts().
shifted_cases: A dataframe of delay shifted cases
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.

Author

Sam Abbott

Sebastian Funk