estimate_from_mixture

An easy-to-use and efficient tool to estimate infectious diseases parameters using serological data. Implemented models include SIR models (basic_sir_model(), static_sir_model(), mseir_model(), sir_subpops_model()), parametric models (polynomial_model(), fp_model()), nonparametric models (lp_model()), semiparametric models (penalized_splines_model()), hierarchical models (hierarchical_bayesian_model()).
The package is based on the book "Modeling Infectious Disease Parameters Based on Serological and Social Contact Data: A Modern Statistical Perspective" (Hens, Niel & Shkedy, Ziv & Aerts, Marc & Faes, Christel & Damme, Pierre & Beutels, Philippe., 2013) <doi:10.1007/978-1-4614-4072-7>.

Anh Phan Truong Quynh

serosv

Model Infectious Disease Parameters from Serosurveys

Nguyen Pham Nguyen The

Long Bui Thanh

Tuyen Huynh

Thinh Ong

Marc Choisy

estimate_from_mixture function

<dl><dt>age</dt>
<dd>- vector of age</dd>
<dt>antibody_level</dt>
<dd>- vector of the corresponding raw antibody level</dd>
<dt>threshold_status</dt>
<dd>- sero status using threshold approach in line listing (optional, for visualization and comparison only)</dd>
<dt>mixture_model</dt>
<dd>- mixture_model object generated by serosv::mixture_model()</dd>
<dt>s</dt>
<dd>- smoothing basis used to fit antibody level</dd>
<dt>sp</dt>
<dd>- smoothing parameter</dd>
<dt>monotonize</dt>
<dd>- whether to monotonize seroprevalence (default to TRUE)</dd></dl>

Arguments

Estimate seroprevalence and foi by combining mixture model and regression — estimate_from_mixture

<dl>

<dt>age</dt>
<dd>- vector of age</dd>


<dt>antibody_level</dt>
<dd>- vector of the corresponding raw antibody level</dd>


<dt>threshold_status</dt>
<dd>- sero status using threshold approach in line listing (optional, for visualization and comparison only)</dd>


<dt>mixture_model</dt>
<dd>- mixture_model object generated by serosv::mixture_model()</dd>


<dt>s</dt>
<dd>- smoothing basis used to fit antibody level</dd>


<dt>sp</dt>
<dd>- smoothing parameter</dd>


<dt>monotonize</dt>
<dd>- whether to monotonize seroprevalence (default to TRUE)</dd>

</dl>

Estimate seroprevalence and foi by combining mixture model and regression

estimate_from_mixture: Estimate seroprevalence and foi by combining mixture model and regression

Description

Usage

Value

Arguments

See Also