Report case counts by date of report — report

Convolves latent infections to reported cases via an observation model. Likely to be removed/replaced in later releases by functionality drawing on the stan implementation.

Usage

report_cases(
  case_estimates,
  case_forecast = NULL,
  delays,
  type = "sample",
  reporting_effect,
  CrIs = c(0.2, 0.5, 0.9)
)

Arguments

case_estimates: A data.table of case estimates with the following variables: date, sample, cases
case_forecast: A data.table of case forecasts with the following variables: date, sample, cases. If not supplied the default is not to incorporate forecasts.
delays: A call to delay_opts() defining delay distributions and options. See the documentation of delay_opts() and the examples below for details.
type: Character string indicating the method to use to transform counts. Supports either "sample" which approximates sampling or "median" would shift by the median of the distribution.
reporting_effect: A data.table giving the weekly reporting effect with the following variables: sample (must be the same as in nowcast), effect (numeric scaling factor for each weekday),day (numeric 1 - 7 (1 = Monday and 7 = Sunday)). If not supplied then no weekly reporting effect is assumed.
CrIs: Numeric vector of credible intervals to calculate.

Value

A list of data.tables. The first entry contains the following variables sample, date and cases with the second being summarised across samples.