build_np_est_data: Build Stan data for estimated nonparametric delays

In EpiNow2: Estimate and Forecast Real-Time Infection Dynamics

Build Stan data for estimated nonparametric delays

Description

Takes the nonparametric delays and the PMF group boundaries and returns the ragged-array fields that Stan needs to map a normalised Dirichlet draw back into delay_np_pmf.

Usage

build_np_est_data(np_delays, np_pmf_groups)

Arguments

np_delays	A list of nonparametric dist_spec objects in their original order. Each estimated entry must carry an ⁠$alpha⁠ numeric vector aligned with its PMF.
np_pmf_groups	Integer vector of 1-indexed PMF group boundaries (output of create_stan_delays()).

Details

Structural zeros (entries where the prior alpha is zero, e.g. the t = 0 generation-time bin) are dropped from the estimated parameter vector so Stan never sees a Gamma(0, 1) rate. Their positions are still held by the fixed delay_np_pmf entries and are left untouched at sampling time.

Value

A named list with n_np_est, np_est_which, np_est_alpha, np_est_pos, np_est_groups, and np_est_length. Empty arrays are returned when no delays are estimated.

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