log_expected_latent_from_r.stan File Reference

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Functions
vector	extract_group_rates (vector r, array[] int r_g, int k, int r_t)
array[] vector	log_expected_latent_from_r (matrix lexp_latent_int, vector r, array[] int r_g, int r_t, int r_seed, int gt_n, vector lrgt, int t, int g, vector pop, int use_pop, real pop_floor)

Function Documentation

extract_group_rates()

vector extract_group_rates	(	vector	r,
		array[]int	r_g,
		int	k,
		int	r_t )

Extract log growth rates for a specific group

Parameters

r	Vector of all group growth rates concatenated.
r_g	Array of indices marking the start of each group in r.
k	Group index (1-indexed).
r_t	Number of time periods.

Returns

Vector of log growth rates for group k.

Definition at line 11 of file log_expected_latent_from_r.stan.

log_expected_latent_from_r()

array[] vector log_expected_latent_from_r	(	matrix	lexp_latent_int,
		vector	r,
		array[]int	r_g,
		int	r_t,
		int	r_seed,
		int	gt_n,
		vector	lrgt,
		int	t,
		int	g,
		vector	pop,
		int	use_pop,
		real	pop_floor )

Iteratively compute expected latent values using the renewal equation

This function calculates expected latent values over time for different groups using the renewal equation. It's designed to handle scenarios where the generation time is represented either as a constant (leading to exponential growth) or as a vector (requiring a dot product calculation). The function operates on the natural scale for stability and then transforms the results back to the log scale when the generation time is a vector.

Parameters

lexp_latent_int	Matrix of initial log expected latent values.
r	Vector representing growth rate or the log of the effective reproduction number.
r_g	Array of indices marking the start of each group in the rate vector.
r_t	Number of time periods for rate adjustments.
r_seed	Seed time period for rate-based adjustments.
gt_n	Length of the generation time vector (1 for constant generation time).
lrgt	Log of the generation time vector or scalar.
t	Total number of time periods.
g	Number of groups.
pop	Initial susceptible population per group. Ignored when use_pop == 0.
use_pop	Susceptible-depletion switch (0 = off, 1 = on). When on, transmission is scaled by the remaining susceptible fraction over the whole post-seed series.
pop_floor	Minimum susceptible population, floored on the transmission-rate denominator only. Matches EpiNow2's rt_opts(pop_floor). Only used when use_pop > 0.

Returns

An array of vectors of log-transformed expected latent values by group and time.

Note

For each group: when gt_n == 1 exponential growth is computed as a cumulative sum on the log scale; when gt_n > 1 the renewal equation is applied on the natural scale (more stable) and logged afterwards.

When use_pop > 0, new cases are capped by the remaining susceptibles (fmax(0, pop - cum_cases)) so depletion cannot exceed the pool, and a small 1e-8 floor keeps the subsequent log() finite near exhaustion. Groups are independent well-mixed populations with no waning or vital dynamics. Adapted from EpiNow2's generate_infections() (epiforecasts/EpiNow2, MIT licence).

Definition at line 70 of file log_expected_latent_from_r.stan.