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
)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.
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.
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.
The number of chains to use during NUTS sampling, as passed to
sampling.
The number of iterations to run during NUTS sampling, as passed
to sampling.
An integer. The knotwidth to use for the spline of Rt.
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.
A number. The random number generator seed for use in NUTS sampling or in BFGS.
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)