pcd_load_stan_functions

Provides functions for working with primary
event censored distributions and 'Stan' implementations for use in Bayesian
modeling. Primary event censored distributions are useful for modeling
delayed reporting scenarios in epidemiology and other fields (Charniga et
al. (2024) <doi:10.48550/arXiv.2405.08841>). It also provides support for
arbitrary delay distributions, a range of common primary distributions, and
allows for truncation and secondary event censoring to be accounted for
(Park et al. (2024) <doi:10.1101/2024.01.12.24301247>). A subset of
common distributions also have analytical solutions implemented, allowing
for faster computation. In addition, it provides multiple methods for
fitting primary event censored distributions to data via optional
dependencies.

Sam Abbott 

primarycensored

Primary Event Censored Distributions

Sam Abbott

Sam Brand

Adam Howes

James Mba Azam

Carl Pearson

Sebastian Funk

Kelly Charniga

pcd_load_stan_functions function

<dl><dt>functions</dt>
<dd>Character vector of function names to load. Defaults to all
functions.</dd>
<dt>stan_path</dt>
<dd>Character string, the path to the Stan code. Defaults to the
path to the Stan code in the primarycensored package.</dd>
<dt>wrap_in_block</dt>
<dd>Logical, whether to wrap the functions in a
<code>functions{}</code> block. Default is FALSE.</dd>
<dt>write_to_file</dt>
<dd>Logical, whether to write the output to a file. Default
is FALSE.</dd>
<dt>output_file</dt>
<dd>Character string, the path to write the output file if
write_to_file is TRUE. Defaults to "pcd_functions.stan".</dd>
<dt>dependencies</dt>
<dd>Logical, whether to include all functions that the
requested functions depend on. When TRUE, recursively finds and includes
all dependencies in the correct order (dependencies before the functions
that use them). Default is FALSE.</dd></dl>

Arguments

Load Stan functions as a string — pcd_load_stan_functions

<dl>

<dt>functions</dt>
<dd>Character vector of function names to load. Defaults to all
functions.</dd>


<dt>stan_path</dt>
<dd>Character string, the path to the Stan code. Defaults to the
path to the Stan code in the primarycensored package.</dd>


<dt>wrap_in_block</dt>
<dd>Logical, whether to wrap the functions in a
<code>functions{}</code> block. Default is FALSE.</dd>


<dt>write_to_file</dt>
<dd>Logical, whether to write the output to a file. Default
is FALSE.</dd>


<dt>output_file</dt>
<dd>Character string, the path to write the output file if
write_to_file is TRUE. Defaults to "pcd_functions.stan".</dd>


<dt>dependencies</dt>
<dd>Logical, whether to include all functions that the
requested functions depend on. When TRUE, recursively finds and includes
all dependencies in the correct order (dependencies before the functions
that use them). Default is FALSE.</dd>

</dl>

Load Stan functions as a string

pcd_load_stan_functions: Load Stan functions as a string

Description

Usage

Value

Arguments

See Also