create_stan_data {EpiNow2}

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,
  seeding_time,
  rt,
  gp,
  obs,
  horizon,
  backcalc,
  shifted_cases
)

Arguments

reported_cases

A data frame of confirmed cases (confirm) by date (date). confirm must be integer 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(). 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().

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

Value

A list of stan data

Author(s)

Sam Abbott

Sebastian Funk