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Functions
primarycensored.stan File Reference

Go to the source code of this file.

Functions

real expgrowth_cdf (real x, real xmin, real xmax, real r)
 
real expgrowth_lcdf (real x, real xmin, real xmax, real r)
 
real expgrowth_lpdf (real x, real xmin, real xmax, real r)
 
vector primary_lcdf_vec (vector p, int primary_id, array[] real primary_params, data real pwindow)
 
real discretestep_lcdf (data real d, vector boundaries, vector pmf, int primary_id, array[] real primary_params, data real pwindow)
 
vector hazards_to_pmf (vector hazards)
 
real discretehazard_lcdf (data real d, vector boundaries, vector hazards, int primary_id, array[] real primary_params, data real pwindow)
 
real pstep_lcdf (real t, vector boundaries, vector pmf)
 
real phazard_lcdf (real t, vector boundaries, vector hazards)
 
int check_for_uniform_terms (int dist_id, int primary_id)
 
int check_for_analytical (int dist_id, int primary_id)
 
real primarycensored_uniform_lcdf_from_terms (vector terms_d, vector terms_q, data real pwindow)
 
vector primarycensored_gamma_uniform_terms (real t, array[] real params)
 
real primarycensored_gamma_uniform_lcdf (data real d, real q, array[] real params, data real pwindow)
 
vector primarycensored_lognormal_uniform_terms (real t, array[] real params)
 
real primarycensored_lognormal_uniform_lcdf (data real d, real q, array[] real params, data real pwindow)
 
real log_weibull_g (real t, real shape, real scale)
 
vector primarycensored_weibull_uniform_terms (real t, array[] real params)
 
real primarycensored_weibull_uniform_lcdf (data real d, real q, array[] real params, data real pwindow)
 
vector primarycensored_gengamma_uniform_terms (real t, array[] real params)
 
real primarycensored_gengamma_uniform_lcdf (data real d, real q, array[] real params, data real pwindow)
 
real primarycensored_analytical_lcdf_raw (data real d, int dist_id, array[] real params, data real pwindow, int primary_id, array[] real primary_params)
 
real primarycensored_analytical_lcdf (data real d, int dist_id, array[] real params, data real pwindow, data real L, data real D, int primary_id, array[] real primary_params)
 
real primarycensored_analytical_cdf (data real d, int dist_id, array[] real params, data real pwindow, data real L, data real D, int primary_id, array[] real primary_params)
 
int check_for_analytical_vectorized (int dist_id, int primary_id, data real pwindow)
 
vector primarycensored_uniform_terms (real t, data int dist_id, array[] real params)
 
vector primarycensored_analytical_lcdf_vectorized (data int start, data int n, data int dist_id, array[] real params, data real pwindow)
 
int dist_has_positive_support (data int dist_id)
 
real primary_lcdf (real p, int primary_id, array[] real primary_params, data real pwindow)
 
int lognormal_lcdf_underflows (real y, real mu, real sigma)
 
real gengamma_lcdf (real y, real shape, real scale, real k)
 
real dist_lcdf (real delay, array[] real params, int dist_id)
 
real primary_lpdf (real x, int primary_id, array[] real params, real xmin, real xmax)
 
vector primarycensored_ode (real t, vector y, array[] real theta, array[] real x_r, array[] int x_i)
 
real primarycensored_log_normalizer (real log_cdf_D, real log_cdf_L, real L)
 
real primarycensored_apply_truncation (real log_cdf, real log_cdf_L, real log_normalizer, real L)
 
vector primarycensored_truncation_bounds (data real L, data real D, data int dist_id, array[] real params, data real pwindow, data int primary_id, array[] real primary_params)
 
real primarycensored_cdf (data real d, data int dist_id, array[] real params, data real pwindow, data real L, data real D, data int primary_id, array[] real primary_params)
 
real primarycensored_lcdf (data real d, data int dist_id, array[] real params, data real pwindow, data real L, data real D, data int primary_id, array[] real primary_params)
 
vector primarycensored_lcdf_vectorized (data int start, data int n, data int dist_id, array[] real params, data real pwindow, data int primary_id, array[] real primary_params)
 
vector primarycensored_sone_lpmf_vectorized (data int max_delay, data real L, data real D, data int dist_id, array[] real params, data real pwindow, data int primary_id, array[] real primary_params)
 

Function Documentation

◆ check_for_analytical()

int check_for_analytical ( int dist_id,
int primary_id )

Definition at line 164 of file primarycensored.stan.

◆ check_for_analytical_vectorized()

int check_for_analytical_vectorized ( int dist_id,
int primary_id,
data real pwindow )

Definition at line 350 of file primarycensored.stan.

◆ check_for_uniform_terms()

int check_for_uniform_terms ( int dist_id,
int primary_id )

Definition at line 160 of file primarycensored.stan.

◆ discretehazard_lcdf()

real discretehazard_lcdf ( data real d,
vector boundaries,
vector hazards,
int primary_id,
array[]real primary_params,
data real pwindow )

Definition at line 134 of file primarycensored.stan.

◆ discretestep_lcdf()

real discretestep_lcdf ( data real d,
vector boundaries,
vector pmf,
int primary_id,
array[]real primary_params,
data real pwindow )

Definition at line 67 of file primarycensored.stan.

◆ dist_has_positive_support()

int dist_has_positive_support ( data int dist_id)

Definition at line 387 of file primarycensored.stan.

◆ dist_lcdf()

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

Definition at line 423 of file primarycensored.stan.

◆ expgrowth_cdf()

real expgrowth_cdf ( real x,
real xmin,
real xmax,
real r )

Vendored primary event censored distribution functions

AUTO-GENERATED by inst/dev/vendor-primarycensored.R from the installed primarycensored package (version 1.6.0), part of the epinowcast organisation: https://github.com/epinowcast/primarycensored (https://primarycensored.epinowcast.org). Do not edit by hand; rerun the vendoring script instead.

These functions implement the double interval censoring discretisation used by epinowcast's parametric reference delay model (a continuous delay convolved with a uniform primary event window, interval censored on the secondary side, with optional right truncation).

primarycensored is distributed under the MIT licence (Copyright (c) 2024 primarycensored authors), reproduced in inst/stan/functions/LICENSE.primarycensored. Both primarycensored and epinowcast are MIT licensed and maintained by the epinowcast organisation.

Note: a few non-ASCII characters in upstream doc comments (the Greek letters lambda and gamma) are transliterated to ASCII by the vendoring script so the concatenated functions block lexes on all stanc versions.

Definition at line 27 of file primarycensored.stan.

◆ expgrowth_lcdf()

real expgrowth_lcdf ( real x,
real xmin,
real xmax,
real r )

Definition at line 39 of file primarycensored.stan.

◆ expgrowth_lpdf()

real expgrowth_lpdf ( real x,
real xmin,
real xmax,
real r )

Definition at line 48 of file primarycensored.stan.

◆ gengamma_lcdf()

real gengamma_lcdf ( real y,
real shape,
real scale,
real k )

Definition at line 420 of file primarycensored.stan.

◆ hazards_to_pmf()

vector hazards_to_pmf ( vector hazards)

Definition at line 125 of file primarycensored.stan.

◆ log_weibull_g()

real log_weibull_g ( real t,
real shape,
real scale )

Definition at line 233 of file primarycensored.stan.

◆ lognormal_lcdf_underflows()

int lognormal_lcdf_underflows ( real y,
real mu,
real sigma )

Definition at line 414 of file primarycensored.stan.

◆ phazard_lcdf()

real phazard_lcdf ( real t,
vector boundaries,
vector hazards )

Definition at line 157 of file primarycensored.stan.

◆ primary_lcdf()

real primary_lcdf ( real p,
int primary_id,
array[]real primary_params,
data real pwindow )

Definition at line 401 of file primarycensored.stan.

◆ primary_lcdf_vec()

vector primary_lcdf_vec ( vector p,
int primary_id,
array[]real primary_params,
data real pwindow )

Definition at line 58 of file primarycensored.stan.

◆ primary_lpdf()

real primary_lpdf ( real x,
int primary_id,
array[]real params,
real xmin,
real xmax )

Definition at line 474 of file primarycensored.stan.

◆ primarycensored_analytical_cdf()

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

Definition at line 343 of file primarycensored.stan.

◆ primarycensored_analytical_lcdf()

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

Definition at line 317 of file primarycensored.stan.

◆ primarycensored_analytical_lcdf_raw()

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

Definition at line 281 of file primarycensored.stan.

◆ primarycensored_analytical_lcdf_vectorized()

vector primarycensored_analytical_lcdf_vectorized ( data int start,
data int n,
data int dist_id,
array[]real params,
data real pwindow )

Definition at line 368 of file primarycensored.stan.

◆ primarycensored_apply_truncation()

real primarycensored_apply_truncation ( real log_cdf,
real log_cdf_L,
real log_normalizer,
real L )

Definition at line 513 of file primarycensored.stan.

◆ primarycensored_cdf()

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

Definition at line 558 of file primarycensored.stan.

◆ primarycensored_gamma_uniform_lcdf()

real primarycensored_gamma_uniform_lcdf ( data real d,
real q,
array[]real params,
data real pwindow )

Definition at line 202 of file primarycensored.stan.

◆ primarycensored_gamma_uniform_terms()

vector primarycensored_gamma_uniform_terms ( real t,
array[]real params )

Definition at line 185 of file primarycensored.stan.

◆ primarycensored_gengamma_uniform_lcdf()

real primarycensored_gengamma_uniform_lcdf ( data real d,
real q,
array[]real params,
data real pwindow )

Definition at line 273 of file primarycensored.stan.

◆ primarycensored_gengamma_uniform_terms()

vector primarycensored_gengamma_uniform_terms ( real t,
array[]real params )

Definition at line 258 of file primarycensored.stan.

◆ primarycensored_lcdf()

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

Definition at line 614 of file primarycensored.stan.

◆ primarycensored_lcdf_vectorized()

vector primarycensored_lcdf_vectorized ( data int start,
data int n,
data int dist_id,
array[]real params,
data real pwindow,
data int primary_id,
array[]real primary_params )

Definition at line 662 of file primarycensored.stan.

◆ primarycensored_log_normalizer()

real primarycensored_log_normalizer ( real log_cdf_D,
real log_cdf_L,
real L )

Definition at line 506 of file primarycensored.stan.

◆ primarycensored_lognormal_uniform_lcdf()

real primarycensored_lognormal_uniform_lcdf ( data real d,
real q,
array[]real params,
data real pwindow )

Definition at line 225 of file primarycensored.stan.

◆ primarycensored_lognormal_uniform_terms()

vector primarycensored_lognormal_uniform_terms ( real t,
array[]real params )

Definition at line 210 of file primarycensored.stan.

◆ primarycensored_ode()

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

Definition at line 481 of file primarycensored.stan.

◆ primarycensored_sone_lpmf_vectorized()

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

Definition at line 684 of file primarycensored.stan.

◆ primarycensored_truncation_bounds()

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

Definition at line 521 of file primarycensored.stan.

◆ primarycensored_uniform_lcdf_from_terms()

real primarycensored_uniform_lcdf_from_terms ( vector terms_d,
vector terms_q,
data real pwindow )

Definition at line 173 of file primarycensored.stan.

◆ primarycensored_uniform_terms()

vector primarycensored_uniform_terms ( real t,
data int dist_id,
array[]real params )

Definition at line 355 of file primarycensored.stan.

◆ primarycensored_weibull_uniform_lcdf()

real primarycensored_weibull_uniform_lcdf ( data real d,
real q,
array[]real params,
data real pwindow )

Definition at line 250 of file primarycensored.stan.

◆ primarycensored_weibull_uniform_terms()

vector primarycensored_weibull_uniform_terms ( real t,
array[]real params )

Definition at line 238 of file primarycensored.stan.

◆ pstep_lcdf()

real pstep_lcdf ( real t,
vector boundaries,
vector pmf )

Definition at line 143 of file primarycensored.stan.