Estimate epidemiological parameters from wastewater measurements

EpiSewer estimates the effective reproduction number Rt and other parameters of interest from wastewater measurements over time. This function combines data, assumptions and modeling details to fit a Bayesian hierarchical model to the measurements. The resulting posterior estimates of Rt and other parameters can be plotted and further analyzed.

The inputs to this function can be specified using various helper functions (see below). It is best to define the inputs in advance as separate variables and then pass them to EpiSewer.

Usage

EpiSewer(
  data = sewer_data(),
  assumptions = sewer_assumptions(),
  measurements = model_measurements(),
  sampling = model_sampling(),
  sewage = model_sewage(),
  shedding = model_shedding(),
  infections = model_infections(),
  forecast = model_forecast(),
  fit_opts = set_fit_opts(),
  results_opts = set_results_opts(),
  run_fit = TRUE
)

Arguments

data: Observations such as concentration measurements and flows, specified via sewer_data(). The data can also be directly supplied to the relevant model components, in which case data can be left empty.
assumptions: Assumptions about infections, shedding, or the sewage system, specified via sewer_assumptions(). The assumptions can also be directly supplied to the relevant model components, in which case assumptions can be left empty.
measurements: The measurements module, see model_measurements().
sampling: The sampling module, see model_sampling().
sewage: The sewage module, see model_sewage().
shedding: The shedding module, see model_shedding().
infections: The infections module, see model_infections().
fit_opts: Settings for model fitting, see set_fit_opts().
results_opts: Settings for results to be returned, see set_results_opts().
run_fit: If TRUE (the default), the model is fitted immediately. If FALSE, the EpiSewerJob object is returned without fitting the model (it can be fitted later or even on a different machine).

Value

If the model fitting was successful, a list with the following elements is returned:

job: the EpiSewerJob that was run
summary: a summary of parameter estimates of interest
fitted: the fitted model (if results_opts(fitted = TRUE))

If the model fitting fails, a list with the following elements is returned:

error: information about the errors and warnings that were thrown
sampler_output: potential outputs printed by the sampler