primary_censored_dist.stan File Reference

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Functions
real	dist_lcdf (real delay, array[] real params, int dist_id)
real	primary_dist_lpdf (real x, int primary_dist_id, array[] real params, real min, real max)
vector	primary_censored_ode (real t, vector y, array[] real theta, array[] real x_r, array[] int x_i)
real	primary_censored_dist_cdf (data real d, int dist_id, array[] real params, data real pwindow, data real D, int primary_dist_id, array[] real primary_params)
real	primary_censored_dist_lcdf (data real d, int dist_id, array[] real params, data real pwindow, data real D, int primary_dist_id, array[] real primary_params)
real	primary_censored_dist_lpmf (data int d, int dist_id, array[] real params, data real pwindow, data real d_upper, data real D, int primary_dist_id, array[] real primary_params)
real	primary_censored_dist_pmf (data int d, int dist_id, array[] real params, data real pwindow, data real d_upper, data real D, int primary_dist_id, array[] real primary_params)
vector	primary_censored_sone_lpmf_vectorized (int max_delay, data real D, int dist_id, array[] real params, data real pwindow, int primary_dist_id, array[] real primary_params)
vector	primary_censored_sone_pmf_vectorized (int max_delay, data real D, int dist_id, array[] real params, data real pwindow, int primary_dist_id, array[] real primary_params)

Function Documentation

dist_lcdf()

real dist_lcdf	(	real	delay,
		array[]real	params,
		int	dist_id
	)

Primary event censored distribution functions Compute the log CDF of the delay distribution

Parameters

delay	Time delay
params	Distribution parameters
dist_id	Distribution identifier 1: Lognormal, 2: Gamma, 3: Normal, 4: Exponential, 5: Weibull, 6: Beta, 7: Cauchy, 8: Chi-square, 9: Inverse Chi-square, 10: Double Exponential, 11: Inverse Gamma, 12: Logistic, 13: Pareto, 14: Scaled Inverse Chi-square, 15: Student's t, 16: Uniform, 17: von Mises

Returns

Log CDF of the delay distribution

// Example: Lognormal distribution
real delay = 5.0;
array[2] real params = {0.0, 1.0}; // mean and standard deviation on log scale
int dist_id = 1; // Lognormal
real log_cdf = dist_lcdf(delay, params, dist_id);

Definition at line 27 of file primary_censored_dist.stan.

primary_censored_dist_cdf()

real primary_censored_dist_cdf	(	data real	d,
		int	dist_id,
		array[]real	params,
		data real	pwindow,
		data real	D,
		int	primary_dist_id,
		array[]real	primary_params
	)

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_dist_id	Primary distribution identifier
primary_params	Primary distribution parameters

Returns

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

Definition at line 130 of file primary_censored_dist.stan.

primary_censored_dist_lcdf()

real primary_censored_dist_lcdf	(	data real	d,
		int	dist_id,
		array[]real	params,
		data real	pwindow,
		data real	D,
		int	primary_dist_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_dist_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_dist_id = 1; // Uniform
array[0] real primary_params = {};
real log_cdf = primary_censored_dist_lcdf(
  d, dist_id, params, pwindow, D, primary_dist_id, primary_params
);

Definition at line 196 of file primary_censored_dist.stan.

primary_censored_dist_lpmf()

real primary_censored_dist_lpmf	(	data int	d,
		int	dist_id,
		array[]real	params,
		data real	pwindow,
		data real	d_upper,
		data real	D,
		int	primary_dist_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_dist_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_dist_id = 1; // Uniform
array[0] real primary_params = {};
real log_pmf = primary_censored_dist_lpmf(
  d, dist_id, params, pwindow, d_upper, D, primary_dist_id, primary_params
);

Definition at line 262 of file primary_censored_dist.stan.

primary_censored_dist_pmf()

real primary_censored_dist_pmf	(	data int	d,
		int	dist_id,
		array[]real	params,
		data real	pwindow,
		data real	d_upper,
		data real	D,
		int	primary_dist_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_dist_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_dist_id = 1; // Uniform
array[0] real primary_params = {};
real pmf = primary_censored_dist_pmf(d, dist_id, params, pwindow, swindow, D, primary_dist_id, primary_params);

Definition at line 324 of file primary_censored_dist.stan.

primary_censored_ode()

vector primary_censored_ode	(	real	t,
		vector	y,
		array[]real	theta,
		array[]real	x_r,
		array[]int	x_i
	)

ODE system for the primary censored distribution

Parameters

t	Time
y	State variables
theta	Parameters
x_r	Real data
x_i	Integer data

Returns

Derivatives of the state variables

Definition at line 91 of file primary_censored_dist.stan.

primary_censored_sone_lpmf_vectorized()

vector primary_censored_sone_lpmf_vectorized	(	int	max_delay,
		data real	D,
		int	dist_id,
		array[]real	params,
		data real	pwindow,
		int	primary_dist_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_dist_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 primary_censored_dist_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_dist_id = 1; // Uniform
array[0] real primary_params = {};
 
vector[max_delay] log_pmf =
  primary_censored_sone_lpmf_vectorized(
     max_delay, D, dist_id, params, pwindow, primary_dist_id,
     primary_params
  );

Definition at line 373 of file primary_censored_dist.stan.

primary_censored_sone_pmf_vectorized()

vector primary_censored_sone_pmf_vectorized	(	int	max_delay,
		data real	D,
		int	dist_id,
		array[]real	params,
		data real	pwindow,
		int	primary_dist_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_dist_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 primary_censored_dist_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_dist_id = 1; // Uniform
array[0] real primary_params = {};
vector[max_delay] pmf =
  primary_censored_sone_pmf_vectorized(
     max_delay, D, dist_id, params, pwindow, primary_dist_id, primary_params
  );

Definition at line 455 of file primary_censored_dist.stan.

primary_dist_lpdf()

real primary_dist_lpdf	(	real	x,
		int	primary_dist_id,
		array[]real	params,
		real	min,
		real	max
	)

Compute the log PDF of the primary distribution

Parameters

x	Value
primary_dist_id	Primary distribution identifier
params	Distribution parameters
min	Minimum value
max	Maximum value

Returns

Log PDF of the primary distribution

// Example: Uniform distribution
real x = 0.5;
int primary_dist_id = 1; // Uniform
array[0] real params = {}; // No additional parameters for uniform
real min = 0;
real max = 1;
real log_pdf = primary_dist_lpdf(x, primary_dist_id, params, min, max);

Definition at line 72 of file primary_censored_dist.stan.