`covidestim`

returns a base configuration of the model with the default
set of priors, and no input data. This configuration, after adding input
data (see `input_cases`

, `input_deaths`

,
`priors_*`

), represents a valid model configuration that can be passed
to `run.covidestim`

(for NUTS) or
`runOptimizer.covidestim`

(for BFGS).

```
covidestim(
nweeks,
nweeks_before = 4,
pop_size = 1e+12,
chains = 3,
iter = 2000,
nspl_rt_knotwidth = 1,
thin = 1,
seed = 42,
adapt_delta = 0.98,
max_treedepth = 14,
window.length = 7,
region,
start_p_imm,
cum_p_inf_init
)
```

- nweeks
A positive integer. The number of weeks of input data being modeled. This should always be set to the number of weeks in your input data.

- nweeks_before
A positive integer. How many weeks before the first week of model data should be modeled? A higher number will produce estimates that go farther back in time, however, those estimates will contain more and more uncertainty.

- pop_size
A positive integer What is the population in the geography being modelled? This sets the max susceptible population and becomes important as the population ever infected approaches the population size.

- chains
The number of chains to use during NUTS sampling, as passed to

`sampling`

.- iter
The number of iterations to run during NUTS sampling, as passed to

`sampling`

.- nspl_rt_knotwidth
An integer. The knotwidth to use for the spline of Rt.

- thin
A positive integer to specify period for saving samples, as passed to

`sampling`

. Modify this only if you intend to inspect raw iterations data returned by`sampling`

.- seed
A number. The random number generator seed for use in NUTS sampling or in BFGS.

- region
A string. The FIPS code (for U.S. counties) or state name (e.g.

`New York`

) being modeled. Required.

An S3 object of type `covidestim`

. This can be passed to
`run.covidestim`

or `runOptimizer.covidestim`

to execute the model, as
long as input data has been added (using the addition operator, see
example). This object can also be saved to disk using
`saveRDS`

to enable reproducibility across platforms or
sessions. However, note that Stan runs are only reproducible under very
specific conditions due to Stan's multi-language architecture. The
`print`

method is overloaded to return to the user a summary of the
configuration, including prior values and the presence or absence of input
data.

```
cfg <- covidestim(nweeks = 32, region = 'Connecticut',
pop = get_pop("Connecticut"),
start_p_imm = get_imm_init("Connecticut")$start_p_imm,
cum_p_inf_init = get_imm_init("Connecticut")$cum_p_inf_init) +
input_cases(example_ct_data('cases')) +
input_deaths(example_ct_data('deaths')) +
input_rr(example_ct_data('RR')) +
input_hosp(example_ct_data('hosp')) +
input_boost(example_ct_data('boost'))
#> Error: Number of observations in obs_cas (31) was not equal to N_weeks (32)
```