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Functions
primarycensored.stan File Reference

Go to the source code of this file.

Functions

real expgrowth_lpdf (real x, real xmin, real xmax, real r)
 
int check_for_analytical (int dist_id, int primary_id)
 
real primarycensored_gamma_uniform_lcdf (data real d, real q, array[] real params, data real pwindow)
 
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)
 
real primarycensored_weibull_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)
 
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 dist_has_positive_support (data int dist_id)
 
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_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 37 of file primarycensored.stan.

◆ dist_has_positive_support()

int dist_has_positive_support ( data int dist_id)

Definition at line 200 of file primarycensored.stan.

◆ dist_lcdf()

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

Definition at line 213 of file primarycensored.stan.

◆ expgrowth_lpdf()

real expgrowth_lpdf ( 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 1.5.0), 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.

◆ log_weibull_g()

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

Definition at line 116 of file primarycensored.stan.

◆ primary_lpdf()

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

Definition at line 239 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 193 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 167 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 )

Definition at line 152 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 278 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 323 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 43 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 377 of file primarycensored.stan.

◆ primarycensored_log_normalizer()

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

Definition at line 271 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 83 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 246 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 423 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 286 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 121 of file primarycensored.stan.