Functions for delay distribution handling. More...

Collaboration diagram for Delay Handlers:

Functions
array[] int	get_delay_type_max (int delay_types, array[] int delay_types_p, array[] int delay_types_id, array[] int delay_types_groups, array[] int delay_max, array[] int delay_np_pmf_groups)

vector	get_delay_rev_pmf (int delay_id, int len, array[] int delay_types_p, array[] int delay_types_id, array[] int delay_types_groups, array[] int delay_max, vector delay_np_pmf, array[] int delay_np_pmf_groups, vector delay_params, array[] int delay_params_groups, array[] int delay_dist, int left_truncate, int reverse_pmf, int cumulative)

void	delays_lp (vector delay_params, vector delay_params_mean, vector delay_params_sd, array[] int delay_params_groups, array[] int delay_dist, array[] int weight)

void	delays_np_lp (vector delay_np_est_raw, vector delay_np_est_alpha)

vector	combine_np_pmf (vector delay_np_pmf, int delay_n_np_est, array[] int delay_np_est_groups, array[] int delay_np_est_pos, vector delay_np_est_raw)

vector	normal_lb_rng (vector mu, vector sigma, vector lb)

Description

Functions for delay distribution handling.

Functions from delays.stan for creating, parameterizing and applying delay distributions.

Function Documentation

◆ combine_np_pmf()

vector combine_np_pmf	(	vector	delay_np_pmf,
		int	delay_n_np_est,
		array[]int	delay_np_est_groups,
		array[]int	delay_np_est_pos,
		vector	delay_np_est_raw )

Combine fixed and estimated nonparametric delay PMFs

Returns a copy of the fixed PMF vector with the estimated entries overwritten by per-segment normalisation of the raw gamma values. Fixed entries and structural zeros are left unchanged.

Parameters

delay_np_pmf	Fixed PMF vector (concatenated ragged array).
delay_n_np_est	Number of estimated nonparametric delays.
delay_np_est_groups	Ragged-array boundaries into delay_np_est_raw (length delay_n_np_est + 1).
delay_np_est_pos	For each estimated element, its position within delay_np_pmf.
delay_np_est_raw	Raw gamma values backing each segment.

Returns: A vector of length num_elements(delay_np_pmf) containing the combined PMF.

Definition at line 206 of file delays.stan.

◆ delays_lp()

void delays_lp	(	vector	delay_params,
		vector	delay_params_mean,
		vector	delay_params_sd,
		array[]int	delay_params_groups,
		array[]int	delay_dist,
		array[]int	weight )

Update log density for delay distribution priors

Parameters

delay_params	Vector of parameters for parametric delay distributions
delay_params_mean	Vector of prior means for delay parameters
delay_params_sd	Vector of prior standard deviations for delay parameters
delay_params_groups	Array of indices for accessing delay parameters
delay_dist	Array of distribution types using primarycensored convention (1: lognormal, 2: gamma, 3: weibull, 4: exponential)
weight	Array of weights for each delay distribution in the log density

Definition at line 138 of file delays.stan.

◆ delays_np_lp()

void delays_np_lp	(	vector	delay_np_est_raw,
		vector	delay_np_est_alpha )

Update log prior density for estimated nonparametric delays

Applies Gamma(alpha, 1) priors to the raw vector that backs the estimated nonparametric PMFs. Once normalised within each ragged segment, this induces a Dirichlet(alpha) prior on the segment. See https://mc-stan.org/docs/stan-users-guide/simplexes.html for the gamma-normalisation construction.

Parameters

delay_np_est_raw	Raw gamma-distributed values backing each estimated nonparametric PMF segment.
delay_np_est_alpha	Dirichlet concentration parameters, matched element-wise to delay_np_est_raw.

Definition at line 180 of file delays.stan.

◆ get_delay_rev_pmf()

vector get_delay_rev_pmf	(	int	delay_id,
		int	len,
		array[]int	delay_types_p,
		array[]int	delay_types_id,
		array[]int	delay_types_groups,
		array[]int	delay_max,
		vector	delay_np_pmf,
		array[]int	delay_np_pmf_groups,
		vector	delay_params,
		array[]int	delay_params_groups,
		array[]int	delay_dist,
		int	left_truncate,
		int	reverse_pmf,
		int	cumulative )

Get the reversed probability mass function for a delay

Parameters

delay_id	Identifier for the specific delay distribution
len	Length of the output PMF
delay_types_p	Array indicating whether each delay is parametric (1) or non-parametric (0)
delay_types_id	Array mapping delay types to their respective IDs
delay_types_groups	Array of indices defining groups of delay types
delay_max	Array of maximum delays for parametric distributions
delay_np_pmf	Vector of probability mass functions for non-parametric delays
delay_np_pmf_groups	Array of indices for accessing non-parametric PMFs
delay_params	Vector of parameters for parametric delay distributions
delay_params_groups	Array of indices for accessing delay parameters
delay_dist	Array of distribution types using primarycensored convention (1: lognormal, 2: gamma, 3: weibull, 4: exponential)
left_truncate	Left truncation point (0 for no truncation)
reverse_pmf	Whether to reverse the PMF (1) or not (0)
cumulative	Whether to return cumulative (1) or daily (0) values

Returns: A vector containing the (reversed) PMF of length len

Definition at line 65 of file delays.stan.

References convolve_with_rev_pmf(), and discretised_pmf().

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◆ get_delay_type_max()

array[] int get_delay_type_max	(	int	delay_types,
		array[]int	delay_types_p,
		array[]int	delay_types_id,
		array[]int	delay_types_groups,
		array[]int	delay_max,
		array[]int	delay_np_pmf_groups )

Delay Distribution Functions

This group of functions handles the creation, manipulation, and application of delay distributions in the model. Delay distributions represent the time between events (e.g., infection to symptom onset, symptom onset to reporting). Get the maximum delay for each delay type

Parameters

delay_types	Number of delay types
delay_types_p	Array indicating whether each delay is parametric (1) or non-parametric (0)
delay_types_id	Array mapping delay types to their respective IDs
delay_types_groups	Array of indices defining groups of delay types
delay_max	Array of maximum delays for parametric distributions
delay_np_pmf_groups	Array of indices for accessing non-parametric PMFs

Returns: An array of maximum delays for each delay type

Definition at line 23 of file delays.stan.

◆ normal_lb_rng()

vector normal_lb_rng	(	vector	mu,
		vector	sigma,
		vector	lb )

Generate random samples from a normal distribution with lower bounds

Parameters

mu	Vector of means
sigma	Vector of standard deviations
lb	Vector of lower bounds

Returns: A vector of random samples from the truncated normal distribution

Definition at line 233 of file delays.stan.