dot-prepare_linelist_data: Prepare linelist data for delay estimation

In EpiNow2: Estimate and Forecast Real-Time Infection Dynamics

Prepare linelist data for delay estimation

Description

Converts date-based or numeric delay data into an aggregated format suitable for the primarycensored Stan model. Handles date-to-numeric conversion, computation of derived columns, an obs-time-to-Inf heuristic, and aggregation by unique delay/censoring combinations.

Usage

.prepare_linelist_data(data, obs_time_threshold = 2, verbose = FALSE)

Arguments

data	A data frame with date columns (pdate_lwr, sdate_lwr, and optionally pdate_upr, sdate_upr, obs_date, n).
obs_time_threshold	Numeric multiplier for the obs-time-to-Inf heuristic. Observations where relative_obs_time > max(delay_upr) * obs_time_threshold are treated as untruncated. Set to Inf to disable.
verbose	Logical, print progress messages?

Value

A data frame with columns: delay_lwr, delay_upr, pwindow, relative_obs_time, n.

EpiNow2 documentation built on June 17, 2026, 1:07 a.m.