Fit model for evaluation

Usage

eval_fit(
  forecast_date,
  location,
  model,
  scenario,
  hosp_data_dir,
  ww_data_dir,
  ww_data_mapping,
  scenario_dir,
  calibration_time,
  forecast_horizon,
  params_path,
  raw_output_dir,
  seed,
  iter_sampling,
  n_chains,
  adapt_delta,
  max_treedepth,
  table_of_exclusions = NULL
)

Arguments

forecast_date: As-of date for the forecast.
location: Location to forecast.
model: Model to fit. One of "ww" and "hosp"
scenario: Wastewater data availability scenario to analyze.
hosp_data_dir: Path to a directory containing vintaged hospital admissions data in date-stamped .csv files.
ww_data_dir: Path to a directory containing vintaged wastewater data in date-stamped .csv files.
ww_data_mapping: String associating forecast dates to wastewater vintage dates. Passed to date_of_ww_data().
scenario_dir: Path to a directory containing .csv files that define wastewater data availability scenarios.
calibration_time: Days of prior admissions and wastewater data to which to fit the model relative to the forecast_date.
forecast_horizon: Days forward to forecast relative to the forecast_date.
params_path: Path to a params.toml file that gives values for prior hyperparameters.
raw_output_dir: Path to a directory in which to save raw output as serialized .rds files.
seed: Seed for Stan's pseudorandom number generator.
iter_sampling: Number of samples to draw per MCMC chain.
n_chains: Number of MCMC chains to run.
adapt_delta: Target acceptance probability for the No-U-Turn sampler adaptation phase.
max_treedepth: Maximum tree depth for the No-U-Turn sampler.
table_of_exclusions: Table of outlying hospital admissions datapoints to exclude. If NULL, exclude nothing. Default NULL.

Value

NULL, saving the pre-processed data and model fitting output to disk as side effects.