DPModel_impl

Builds the source attribution model. Is not intended to be used by a regular user.
Developers only here!

datasets

Implements a non-parametric source attribution model to attribute
cases of disease to sources in Bayesian framework with source and type effects.
Type effects are clustered using a Dirichlet Process. Multiple times and
locations are supported.

Poppy Miller

sourceR

Fits a Non-Parametric Bayesian Source Attribution Model

Chris Jewell

Jonathan Marshall

Nigel French

DPModel_impl function

<code><a rd-options="" href="/link/R6Class?package=sourceR&version=1.0.1" data-mini-rdoc="sourceR::R6Class">R6Class</a></code> object.

Format

<dl class="dl-horizontal">
<dt><code>y</code></dt><dd>3D array of [type, time, location] of the number of human cases</dd></dl><dt><code>X</code></dt><dd>3D array of the number of positive samples for each type, source and time
[type, source, time]</dd><dt><code>R</code></dt><dd>3D array of normalised relative prevalences for each timepoint
[type, source, time]</dd><dt><code>Time</code></dt><dd>a character vector of timepoint ids matching time dimension in y and R</dd><dt><code>Location</code></dt><dd>a character vector of location ids matching location dimension in y</dd><dt><code>Sources</code></dt><dd>a character vector of source ids matching the source dimension in X</dd><dt><code>Type</code></dt><dd>a character vector of type ids matching the type dimension in X</dd><dt><code>prev</code></dt><dd>a 2D array (matrix) of [source, time].</dd><dt><code>a_q</code></dt><dd>concentration parameter for the DP</dd><dt><code>a_theta</code></dt><dd>shape parameter for the Gamma base distribution for the DP</dd><dt><code>b_theta</code></dt><dd>rate parameter for the Gamma base distribution for the DP</dd><dt><code>a_r</code></dt><dd>3D array of [type, src, time] for the hyperprior on the relative prevalences R</dd><dt><code>a_alpha</code></dt><dd>3D array of [source, time, location] for the prior on the alpha parameters</dd><dt><code>s</code></dt><dd>vector giving initial group allocation for each type for the DP</dd><dt><code>theta</code></dt><dd>vector giving initial values for each group in the DP</dd><dt><code>alpha</code></dt><dd>3D array of [source, time, location] giving initial values for the alpha
parameters</dd>

Fields

Builds the source attribution model. Is not intended to be used by a regular user.
 — DPModel_impl

<code><a rd-options='' href='R6Class'>R6Class</a></code> object.

DPModel_impl: Builds the source attribution model. Is not intended to be used by a regular user.

Description

Usage

Arguments

Value

Format

Fields