plot_seroprev_estimates

Plot seroprevalence estimates on top of the serosurvey

Estimating the force of infection from time varying, age varying, or constant
serocatalytic models from population based seroprevalence studies using a Bayesian framework,
including data simulation functions enabling the generation of serological surveys based on this
models. This tool also provides a flexible prior specification syntax for the force of infection
and the seroreversion rate, as well as methods to assess model convergence and comparison
criteria along with useful visualisation functions.

Zulma M. Cucunubá

serofoi

Bayesian Estimation of the Force of Infection from Serological
Data

Nicolás T. Domínguez

Ben Lambert

Pierre Nouvellet

Geraldine Gómez

Jaime A. Pavlich-Mariscal

Hugo Gruson

David Santiago Quevedo

Miguel Gámez

Sumali Bajaj

Everlyn Kamau

Richard Creswell

International Development Research Center (IDRC) 

Pontificia Universidad Javeriana 

plot_seroprev_estimates function

<dl><dt>seromodel</dt>
<dd>stan_fit object obtained from sampling a model
with fit_seromodel</dd>
<dt>serosurvey</dt>
<dd><dl>
<dt><code>survey_year</code></dt>
<dd>Year in which the survey took place
(only needed to plot time models)</dd></dl></dd><dt><code>age_min</code></dt>
<dd>Floor value of the average between age_min and age_max</dd><dt><code>age_max</code></dt>
<dd>The size of the sample</dd><dt><code>n_sample</code></dt>
<dd>Number of samples for each age group</dd><dt><code>n_seropositive</code></dt>
<dd>Number of positive samples for each age group</dd>
</dl>
<dt>alpha</dt>
<dd>1 - alpha indicates the credibility level to be used</dd>
<dt>size_text</dt>
<dd>Size of text for plotting (<code>base_size</code> in
ggplot2)</dd>
<dt>bin_serosurvey</dt>
<dd>If <code>TRUE</code>, <code>serodata</code> is binned by means of
<code>prepare_bin_serosurvey</code>.
Otherwise, age groups are kept as originally input.</dd>
<dt>bin_step</dt>
<dd>Integer specifying the age groups bin size to be used when
<code>bin_serosurvey</code> is set to <code>TRUE</code>.</dd>

Arguments

Plot seroprevalence estimates on top of the serosurvey — plot_seroprev_estimates

<dl>

<dt>seromodel</dt>
<dd>stan_fit object obtained from sampling a model
with fit_seromodel</dd>


<dt>serosurvey</dt>
<dd><dl>
<dt><code>survey_year</code></dt>
<dd>Year in which the survey took place
(only needed to plot time models)</dd>

<dt><code>age_min</code></dt>
<dd>Floor value of the average between age_min and age_max</dd>

<dt><code>age_max</code></dt>
<dd>The size of the sample</dd>

<dt><code>n_sample</code></dt>
<dd>Number of samples for each age group</dd>

<dt><code>n_seropositive</code></dt>
<dd>Number of positive samples for each age group</dd>


</dl></dd>


<dt>alpha</dt>
<dd>1 - alpha indicates the credibility level to be used</dd>


<dt>size_text</dt>
<dd>Size of text for plotting (<code>base_size</code> in
ggplot2)</dd>


<dt>bin_serosurvey</dt>
<dd>If <code>TRUE</code>, <code>serodata</code> is binned by means of
<code>prepare_bin_serosurvey</code>.
Otherwise, age groups are kept as originally input.</dd>


<dt>bin_step</dt>
<dd>Integer specifying the age groups bin size to be used when
<code>bin_serosurvey</code> is set to <code>TRUE</code>.</dd>

</dl>

Plot seroprevalence estimates on top of the serosurvey

plot_seroprev_estimates: Plot seroprevalence estimates on top of the serosurvey

Description

Usage

Value

Arguments

Examples