primarycensored.stan File Reference

Go to the source code of this file.

Functions
real	primarycensored_cdf (data real d, int dist_id, array[] real params, data real pwindow, data real D, int primary_id, array[] real primary_params)
real	primarycensored_lcdf (data real d, int dist_id, array[] real params, data real pwindow, data real D, int primary_id, array[] real primary_params)
real	primarycensored_lpmf (data int d, int dist_id, array[] real params, data real pwindow, data real d_upper, data real D, int primary_id, array[] real primary_params)
real	primarycensored_pmf (data int d, int dist_id, array[] real params, data real pwindow, data real d_upper, data real D, int primary_id, array[] real primary_params)
vector	primarycensored_sone_lpmf_vectorized (int max_delay, data real D, int dist_id, array[] real params, data real pwindow, int primary_id, array[] real primary_params)
vector	primarycensored_sone_pmf_vectorized (int max_delay, data real D, int dist_id, array[] real params, data real pwindow, int primary_id, array[] real primary_params)

Function Documentation

primarycensored_cdf()

real primarycensored_cdf	(	data real	d,
		int	dist_id,
		array[]real	params,
		data real	pwindow,
		data real	D,
		int	primary_id,
		array[]real	primary_params )

Primary event censored distribution functions Compute the primary event censored CDF for a single delay

Parameters

d	Delay
dist_id	Distribution identifier
params	Array of distribution parameters
pwindow	Primary event window
D	Maximum delay (truncation point)
primary_id	Primary distribution identifier
primary_params	Primary distribution parameters

Returns

Primary event censored CDF, normalized by D if finite (truncation adjustment)

Definition at line 18 of file primarycensored.stan.

primarycensored_lcdf()

real primarycensored_lcdf	(	data real	d,
		int	dist_id,
		array[]real	params,
		data real	pwindow,
		data real	D,
		int	primary_id,
		array[]real	primary_params )

Compute the primary event censored log CDF for a single delay

Parameters

d	Delay
dist_id	Distribution identifier
params	Array of distribution parameters
pwindow	Primary event window
D	Maximum delay (truncation point)
primary_id	Primary distribution identifier
primary_params	Primary distribution parameters

Returns

Primary event censored log CDF, normalized by D if finite (truncation adjustment)

// Example: Weibull delay distribution with uniform primary distribution
real d = 3.0;
int dist_id = 5; // Weibull
array[2] real params = {2.0, 1.5}; // shape and scale
real pwindow = 1.0;
real D = positive_infinity();
int primary_id = 1; // Uniform
array[0] real primary_params = rep_array(0.0, 0);
real log_cdf = primarycensored_lcdf(
  d, dist_id, params, pwindow, D, primary_id, primary_params
);

Definition at line 86 of file primarycensored.stan.

primarycensored_lpmf()

real primarycensored_lpmf	(	data int	d,
		int	dist_id,
		array[]real	params,
		data real	pwindow,
		data real	d_upper,
		data real	D,
		int	primary_id,
		array[]real	primary_params )

Compute the primary event censored log PMF for a single delay

Parameters

d	Delay (integer)
dist_id	Distribution identifier
params	Array of distribution parameters
pwindow	Primary event window
d_upper	Upper bound for the delay interval
D	Maximum delay (truncation point)
primary_id	Primary distribution identifier
primary_params	Primary distribution parameters

Returns

Primary event censored log PMF, normalized by D if finite (truncation adjustment)

// Example: Weibull delay distribution with uniform primary distribution
int d = 3;
int dist_id = 5; // Weibull
array[2] real params = {2.0, 1.5}; // shape and scale
real pwindow = 1.0;
real d_upper = 4.0;
real D = positive_infinity();
int primary_id = 1; // Uniform
array[0] real primary_params = {};
real log_pmf = primarycensored_lpmf(
  d, dist_id, params, pwindow, d_upper, D, primary_id, primary_params
);

Definition at line 152 of file primarycensored.stan.

primarycensored_pmf()

real primarycensored_pmf	(	data int	d,
		int	dist_id,
		array[]real	params,
		data real	pwindow,
		data real	d_upper,
		data real	D,
		int	primary_id,
		array[]real	primary_params )

Compute the primary event censored PMF for a single delay

Parameters

d	Delay (integer)
dist_id	Distribution identifier
params	Array of distribution parameters
pwindow	Primary event window
d_upper	Upper bound for the delay interval
D	Maximum delay (truncation point)
primary_id	Primary distribution identifier
primary_params	Primary distribution parameters

Returns

Primary event censored PMF, normalized by D if finite (truncation adjustment)

// Example: Weibull delay distribution with uniform primary distribution
int d = 3;
real d = 3.0;
int dist_id = 5; // Weibull
array[2] real params = {2.0, 1.5}; // shape and scale
real pwindow = 1.0;
real swindow = 0.1;
real D = positive_infinity();
int primary_id = 1; // Uniform
array[0] real primary_params = {};
real pmf = primarycensored_pmf(d, dist_id, params, pwindow, swindow, D, primary_id, primary_params);

Definition at line 214 of file primarycensored.stan.

primarycensored_sone_lpmf_vectorized()

vector primarycensored_sone_lpmf_vectorized	(	int	max_delay,
		data real	D,
		int	dist_id,
		array[]real	params,
		data real	pwindow,
		int	primary_id,
		array[]real	primary_params )

Compute the primary event censored log PMF for integer delays up to max_delay

Parameters

max_delay	Maximum delay to compute PMF for
D	Maximum delay (truncation point), must be at least max_delay + 1
dist_id	Distribution identifier
params	Array of distribution parameters
pwindow	Primary event window
primary_id	Primary distribution identifier
primary_params	Primary distribution parameters

Returns

Vector of primary event censored log PMFs for delays [0, 1] to [max_delay, max_delay + 1].

This function differs from primarycensored_lpmf in that it:

1. Computes PMFs for all integer delays from [0, 1] to [max_delay, max_delay + 1] in one call.
2. Assumes integer delays (swindow = 1)
3. Is more computationally efficient for multiple delay calculation as it reduces the number of integration calls.

// Example: Weibull delay distribution with uniform primary distribution
int max_delay = 10;
real D = 15.0;
int dist_id = 5; // Weibull
array[2] real params = {2.0, 1.5}; // shape and scale
real pwindow = 7.0;
int primary_id = 1; // Uniform
array[0] real primary_params = {};
 
vector[max_delay] log_pmf =
  primarycensored_sone_lpmf_vectorized(
     max_delay, D, dist_id, params, pwindow, primary_id,
     primary_params
  );

Definition at line 263 of file primarycensored.stan.

primarycensored_sone_pmf_vectorized()

vector primarycensored_sone_pmf_vectorized	(	int	max_delay,
		data real	D,
		int	dist_id,
		array[]real	params,
		data real	pwindow,
		int	primary_id,
		array[]real	primary_params )

Compute the primary event censored PMF for integer delays up to max_delay

Parameters

max_delay	Maximum delay to compute PMF for
D	Maximum delay (truncation point), must be at least max_delay + 1
dist_id	Distribution identifier
params	Array of distribution parameters
pwindow	Primary event window
primary_id	Primary distribution identifier
primary_params	Primary distribution parameters

Returns

Vector of primary event censored PMFs for integer delays 1 to max_delay

This function differs from primarycensored_pmf in that it:

1. Computes PMFs for all integer delays from [0, 1] to [max_delay, max_delay + 1] in one call.
2. Assumes integer delays (swindow = 1)
3. Is more computationally efficient for multiple delay calculations

// Example: Weibull delay distribution with uniform primary distribution
int max_delay = 10;
real D = 15.0;
int dist_id = 5; // Weibull
array[2] real params = {2.0, 1.5}; // shape and scale
real pwindow = 7.0;
int primary_id = 1; // Uniform
array[0] real primary_params = {};
vector[max_delay] pmf =
  primarycensored_sone_lpmf_vectorized(
     max_delay, D, dist_id, params, pwindow, primary_id, primary_params
  );

Definition at line 345 of file primarycensored.stan.