disaggregate_positive

Pycnophylactic disaggregation with spatial smoothness on rates

Supports modelling real-time case data to facilitate the real-time
surveillance of infectious diseases and other point phenomena. The package provides automated computational grid generation over
an area of interest with methods to map covariates between geographies, model fitting including spatially aggregated case counts,
and predictions and visualisation. Both Bayesian and maximum likelihood methods are provided. Log-Gaussian Cox Processes are described by
Diggle et al. (2013) <doi:10.1214/13-STS441> and we provide both the low-rank approximation for Gaussian processes
described by Solin and Särkkä (2020) <doi:10.1007/s11222-019-09886-w> and Riutort-Mayol et al (2023) <doi:10.1007/s11222-022-10167-2> and the
nearest neighbour Gaussian process described by Datta et al (2016) <doi:10.1080/01621459.2015.1044091>.

Sam Watson

rts2

Real-Time Disease Surveillance

disaggregate_positive function

<dl><dt>W</dt>
<dd>m x n aggregation matrix</dd>
<dt>y_r</dt>
<dd>length m vector (observed regional counts)</dd>
<dt>pop</dt>
<dd>length n vector (population per cell)</dd>
<dt>adj</dt>
<dd>n x n adjacency matrix (1 if neighbours, 0 otherwise)
or a sparse Matrix from the Matrix package</dd>
<dt>lambda_smooth</dt>
<dd>weight on spatial smoothness</dd>
<dt>lambda_entropy</dt>
<dd>weight on entropy (0 = pure QP, &gt;0 = nonlinear)</dd>
<dt>weights</dt>
<dd>optional n x n matrix of edge weights (e.g., inverse distance)</dd></dl>

Arguments

Disaggregation function for strictly positive covariates — disaggregate_positive

<dl>

<dt>W</dt>
<dd>m x n aggregation matrix</dd>


<dt>y_r</dt>
<dd>length m vector (observed regional counts)</dd>


<dt>pop</dt>
<dd>length n vector (population per cell)</dd>


<dt>adj</dt>
<dd>n x n adjacency matrix (1 if neighbours, 0 otherwise)
or a sparse Matrix from the Matrix package</dd>


<dt>lambda_smooth</dt>
<dd>weight on spatial smoothness</dd>


<dt>lambda_entropy</dt>
<dd>weight on entropy (0 = pure QP, &gt;0 = nonlinear)</dd>


<dt>weights</dt>
<dd>optional n x n matrix of edge weights (e.g., inverse distance)</dd>

</dl>

disaggregate_positive: Disaggregation function for strictly positive covariates

Description

Usage

Value

Arguments

Details