Empirical delays parameters

Arguments

empirical_delays, delays	dataframe containing the empirical data. See Details.
n_report_time_steps	integer. Length of the incidence time series in the accompanying analysis. This argument is needed to determine the dimensions of the output matrix.
min_number_cases	integer. Minimal number of cases to build the empirical distribution from. If `num_steps_in_a_unit` is `NULL`, for any time step T, the `min_number_cases` records prior to T are used. If less than `min_number_cases` delays were recorded before T, then T is ignored and the `min_number_cases` earliest-recorded delays are used. If `num_steps_in_a_unit` is given a value, a similar same procedure is applied, except that, now at least `min_number_cases` must be taken over a round number of time units. For example, if `num_steps_in_a_unit = 7`, and time steps represent consecutive days, to build the distribution for time step T, we find the smallest number of weeks starting from T and going in the past, for which at least `min_number_cases` delays were recorded. We then use all the delays recorded during these weeks. Weeks are not meant as necessarily being Monday to Sunday, but simply 7 days in a row, e.g. it can be Thursday-Wednesday. Again, if less than `min_number_cases` delays were recorded before T, then T is ignored. We then find the minimum number of weeks, starting from the first recorded delay that contains at least `min_number_cases`.
min_number_cases_fraction	numeric. Between 0 and 1. If `min_number_cases` is not provided (kept to `NULL`), the number of most-recent cases used to build the instant delay distribution is `min_number_cases_fraction` times the total number of reported delays.
min_min_number_cases	numeric. Lower bound for number of cases used to build an instant delay distribution.
upper_quantile_threshold	numeric. Between 0 and 1. Argument for internal use.
fit	string. One of "gamma" or "none". Specifies the type of fit that is applied to the columns of the delay matrix
date_of_interest	Date. Date for which the most recent recorded delays are sought.
num_steps_in_a_unit	Optional argument. Number of time steps in a full time unit (e.g. 7 if looking at weeks). If set, the delays used to build a particular delay distribution will span over a round number of such time units. This option is included for comparison with legacy code.