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.
Arguments
- data
A
<data.frame>
of confirmed cases (confirm) by date (date).confirm
must be numeric anddate
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 tort_opts()
. Set toNULL
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 togp_opts()
. Set toNULL
to disable the Gaussian process.- obs
A list of options as generated by
obs_opts()
defining the observation model. Defaults toobs_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 tobackcalc_opts()
.- shifted_cases
A
<data.frame>
of delay shifted cases
Examples
if (FALSE) {
create_stan_data(
example_confirmed, 7, rt_opts(), gp_opts(), obs_opts(), 7,
backcalc_opts(), create_shifted_cases(example_confirmed, 7, 14, 7)
)
}