<!DOCTYPE html> <!-- Generated by pkgdown: do not edit by hand --><html lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <title>Using stochastic individual compartment models (ICMs) to simulate COVID-19 spread • sirplus</title> <!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css"> <script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> <script src="pkgdown.js"></script><meta property="og:title" content="Using stochastic individual compartment models (ICMs) to simulate COVID-19 spread"> <meta property="og:description" content="sirplus is a package for the modeling of COVID-19 spread with extensions to the classical Susceptible-Infectious-Recovered (SIR) model, using stochastic individual compartment models (ICMs). It provides a simple interface for creating experiments to demonstrate how factors like social-distancing and epidemiological parameters will change the curve of an epidemic's trajectory. "> <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> </head> <body data-spy="scroll" data-target="#toc"> <div class="container template-home"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">sirplus</a> <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.0</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> <a href="index.html"> <span class="fas fa fas fa-home fa-lg"></span> </a> </li> <li> <a href="reference/index.html">Reference</a> </li> <li class="dropdown"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> Articles <span class="caret"></span> </a> <ul class="dropdown-menu" role="menu"> <li> <a href="articles/sirplus_intro_v2.html">Introduction to sirplus (V2)</a> </li> </ul> </li> </ul> <ul class="nav navbar-nav navbar-right"></ul> </div> <!--/.nav-collapse --> </div> <!--/.container --> </div> <!--/.navbar --> </header><div class="row"> <div class="contents col-md-9"> <div id="sirplus" class="section level1"> <div class="page-header"><h1 class="hasAnchor"> <a href="#sirplus" class="anchor"></a>sirplus</h1></div> <p><img src="articles/sirplus-logo-small.png"></p> <p>sirplus is a package for the modeling of COVID-19 spread using stochastic individual compartment models (ICMs). The model implemented extends the classical Susceptible-Infectious-Recovered (SIR) model by adding compartments for Exposed, Quarantined, Hospitalised and Case Fatality individuals. The package provides a simple interface for creating experiments to demonstrate how factors like social-distancing and epidemiological parameters will change the curve.</p> <div id="installation-and-vignette" class="section level2"> <h2 class="hasAnchor"> <a href="#installation-and-vignette" class="anchor"></a>Installation and vignette</h2> <p>To view the vignette install the package then:</p> <pre><code><a href="https://devtools.r-lib.org//reference/install.html">devtools::install(build_vignettes=TRUE) library(sirplus) browseVignettes("sirplus") </a></code></pre> </div> </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> <div class="license"> <h2>License</h2> <ul class="list-unstyled"> <li> <a href="https://www.r-project.org/Licenses/GPL-3">GPL-3</a> + file <a href="LICENSE-text.html">LICENSE</a> </li> </ul> </div> <div class="developers"> <h2>Developers</h2> <ul class="list-unstyled"> <li>Puxue Qiao <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0002-1521-9086" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li> <li>Christina Azodi <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0002-6097-606X" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li> <li>Ruqian Lyu <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-7736-6612" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li> <li>Sam Tanner <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0001-9197-6970" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li> <li>Tim Churches <br><small class="roles"> Author </small> </li> <li>Davis McCarthy <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-2218-6833" target="orcid.widget" aria-label="ORCID"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li> </ul> </div> </div> </div> <footer><div class="copyright"> <p>Developed by Puxue Qiao, Christina Azodi, Ruqian Lyu, Sam Tanner, Tim Churches, Davis McCarthy.</p> </div> <div class="pkgdown"> <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> </div> </body> </html>