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 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 to NULL to disable the Gaussian process.- obs
A list of options as generated by
obs_opts()
defining the observation model. Defaults toobs_opts()
.- horizon
Numeric, forecast horizon.
- backcalc
A list of options as generated by
backcalc_opts()
to define the back calculation. Defaults tobackcalc_opts()
.- shifted_cases
A dataframe of delay shifted cases