Adjust from Case Counts by Infection Date to Date of Report — adjust_infection_to

Maps from cases by date of infection to date of report via date of onset.

Usage

adjust_infection_to_report(
  infections,
  delay_defs,
  reporting_model,
  reporting_effect,
  type = "sample",
  truncate_future = TRUE
)

Arguments

infections: <data.table> containing a date variable and a numeric cases variable.
delay_defs: A list of single row data.tables that each defines a delay distribution (model, parameters and maximum delay for each model). See lognorm_dist_def() for an example of the structure.
reporting_model: A function that takes a single numeric vector as an argument and returns a single numeric vector. Can be used to apply stochastic reporting effects. See the examples for details.
reporting_effect: A numeric vector of length 7 that allows the scaling of reported cases by the day on which they report (1 = Monday, 7 = Sunday). By default no scaling occurs.
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.
truncate_future: Logical, should cases be truncated if they occur after the first date reported in the data. Defaults to TRUE.

Value

A data.table containing a date variable (date of report) and a cases variable. If return_onset = TRUE there will be a third variable reference which indicates what the date variable refers to.