R: Forecast Secondary Observations Given a Fit from...

forecast_secondary {EpiNow2}

R Documentation

Forecast Secondary Observations Given a Fit from estimate_secondary

Description

This function forecasts secondary observations using the output of estimate_secondary() and either observed primary data or a forecast of primary observations. See the examples of estimate_secondary() for one use case. It can also be combined with estimate_infections() t produce a forecast for a secondary observation from a forecast of a primary observation. See the examples of estimate_secondary() for example use cases on synthetic data. See here for an example of forecasting Covid-19 deaths from Covid-19 cases.

Usage

forecast_secondary(
  estimate,
  primary,
  primary_variable = "reported_cases",
  model = NULL,
  samples = NULL,
  all_dates = FALSE,
  CrIs = c(0.2, 0.5, 0.9)
)

Arguments

`estimate`	An object of class "estimate_secondary" as produced by `estimate_secondary()`.
`primary`	A data.frame containing at least `date` and `value` (integer) variables and optionally `sample`. Used as the primary observation used to forecast the secondary observations. Alternatively, this may be an object of class "estimate_infections" as produced by `estimate_infections()`. If `primary` is of class "estimate_infections" then the internal samples will be filtered to have a minimum date ahead of those observed in the `estimate` object.
`primary_variable`	A character string indicating the primary variable, defaulting to "reported_cases". Only used when primary is of class "estimate_infections".
`model`	A compiled stan model as returned by `rstan::stan_model`.
`samples`	Numeric, number of posterior samples to simulate from. The default is to use all samples in the `primary` input when present. If not present the default is to use 1000 samples.
`all_dates`	Logical, defaults to FALSE. Should a forecast for all dates and not just those in the forecast horizon be returned.
`CrIs`	Numeric vector of credible intervals to calculate.

Value

A list containing: predictions (a data frame ordered by date with the primary, and secondary observations, and a summary of the forecast secondary observations. For primary observations in the forecast horizon when uncertainty is present the median is used), samples a data frame of forecast secondary observation posterior samples, and forecast a summary of the forecast secondary observation posterior.

Author(s)