Fit a CmdStan model using NUTS — enw_sample • epinowcast

Fit a CmdStan model using NUTS

Usage

enw_sample(data, model = epinowcast::enw_model(), diagnostics = TRUE, ...)

Arguments

data: A list of data as produced by model modules (for example enw_expectation(), enw_obs(), etc.) and as required for use the model being used.
model: A cmdstanr model object as loaded by enw_model() or as supplied by the user.
diagnostics: Logical, defaults to TRUE. Should fitting diagnostics be returned as a data.frame.
...: Additional parameters passed to the sample method of cmdstanr.

Value

A data.frame containing the cmdstanr fit, the input data, the fitting arguments, and optionally summary diagnostics.

See also

Functions used to help convert models into the format required for stan enw_formula_as_data_list(), enw_get_cache(), enw_model(), enw_pathfinder(), enw_priors_as_data_list(), enw_replace_priors(), enw_set_cache(), enw_stan_to_r(), enw_unset_cache(), remove_profiling(), write_stan_files_no_profile()

Examples

if (FALSE) { # interactive()
pobs <- enw_example("preprocessed")

nowcast <- epinowcast(pobs,
 expectation = enw_expectation(~1, data = pobs),
 fit = enw_fit_opts(enw_sample, pp = TRUE),
 obs = enw_obs(family = "poisson", data = pobs),
)

summary(nowcast)
}