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.
create_stan_data(
reported_cases,
generation_time,
rt,
gp,
obs,
delays,
horizon,
backcalc,
shifted_cases,
truncation
)A data frame of confirmed cases (confirm) by date (date). confirm must be integer and date must be in date format.
A list containing the mean, standard deviation of the mean (mean_sd), standard deviation (sd), standard deviation of the standard deviation and the maximum allowed value for the generation time (assuming a gamma distribution).
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.
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.
A list of options as generated by obs_opts() defining the
observation model. Defaults to obs_opts().
A call to delay_opts() defining delay distributions and options. See the documentation of delay_opts()
and the examples below for details.
Numeric, forecast horizon.
A list of options as generated by backcalc_opts() to define the
back calculation. Defaults to backcalc_opts().
A dataframe of delay shifted cases
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.
A list of stan data