nmode's Git Repositories - Rnaught/blob - index.html

   1 <!DOCTYPE html>
   2 <!-- Generated by pkgdown: do not edit by hand --><html lang="en">
   3 <head>
   4 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
   5 <meta charset="utf-8">
   6 <meta http-equiv="X-UA-Compatible" content="IE=edge">
   7 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
   8 <title>Estimate the Basic Reproduction Number (R0) of Infectious Diseases • Rnaught</title>
   9 <!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="favicon-96x96.png">
  10 <link rel="icon" type="”image/svg+xml”" href="favicon.svg">
  11 <link rel="apple-touch-icon" sizes="180x180" href="apple-touch-icon.png">
  12 <link rel="icon" sizes="any" href="favicon.ico">
  13 <link rel="manifest" href="site.webmanifest">
  14 <script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
  15 <link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
  16 <script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
  17 <link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
  18 <script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Estimate the Basic Reproduction Number (R0) of Infectious Diseases">
  19 <meta name="description" content="An R package and web application for estimating the basic reproduction number (R0) of infectious diseases.">
  20 <meta property="og:description" content="An R package and web application for estimating the basic reproduction number (R0) of infectious diseases.">
  21 <meta property="og:image" content="https://MI2YorkU.github.io/Rnaught/logo.svg">
  22 </head>
  23 <body>
  24     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
  25
  26
  27     <nav class="navbar navbar-expand-lg fixed-top bg-light" data-bs-theme="light" aria-label="Site navigation"><div class="container">
  28
  29     <a class="navbar-brand me-2" href="index.html">Rnaught</a>
  30
  31     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.0</small>
  32
  33
  34     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
  35       <span class="navbar-toggler-icon"></span>
  36     </button>
  37
  38     <div id="navbar" class="collapse navbar-collapse ms-3">
  39       <ul class="navbar-nav me-auto">
  40 <li class="nav-item"><a class="nav-link" href="articles/Rnaught.html">Get started</a></li>
  41 <li class="nav-item"><a class="nav-link" href="reference/index.html">Reference</a></li>
  42 <li class="nav-item dropdown">
  43   <button class="nav-link dropdown-toggle" type="button" id="dropdown-articles" data-bs-toggle="dropdown" aria-expanded="false" aria-haspopup="true">Articles</button>
  44   <ul class="dropdown-menu" aria-labelledby="dropdown-articles">
  45 <li><a class="dropdown-item" href="articles/seq_bayes_post.html">Sequential Bayes: Utilizing the Posterior Distribution</a></li>
  46     <li><a class="dropdown-item" href="articles/wp_serial.html">White and Pagano: Utilizing the Serial Distribution</a></li>
  47   </ul>
  48 </li>
  49       </ul>
  50 <ul class="navbar-nav">
  51 <li class="nav-item"><form class="form-inline" role="search">
  52  <input class="form-control" type="search" name="search-input" id="search-input" autocomplete="off" aria-label="Search site" placeholder="Search for" data-search-index="search.json">
  53 </form></li>
  54 <li class="nav-item"><a class="external-link nav-link" href="https://github.com/MI2YorkU/Rnaught/" aria-label="GitHub"><span class="fa fab fa-github fa-lg"></span></a></li>
  55       </ul>
  56 </div>
  57
  58
  59   </div>
  60 </nav><div class="container template-home">
  61 <div class="row">
  62   <main id="main" class="col-md-9"><div class="section level1">
  63 <div class="page-header">
  64 <img src="logo.svg" class="logo" alt=""><h1 id="rnaught-">Rnaught
  65 <a class="anchor" aria-label="anchor" href="#rnaught-"></a>
  66 </h1>
  67 </div>
  68 <!-- badges: start -->
  69
  70 <p>Rnaught is an R package and web application for estimating the <a href="https://en.wikipedia.org/wiki/Basic_reproduction_number" class="external-link">basic reproduction number (<em>R</em><sub>0</sub>)</a> of infectious diseases.</p>
  71 <p>An instance of the web application is available at <a href="https://immune.math.yorku.ca/Rnaught" class="external-link uri">https://immune.math.yorku.ca/Rnaught</a>.</p>
  72 <div class="section level2">
  73 <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
  74 </h2>
  75 <p>You can install the development version of Rnaught using the <a href="https://devtools.r-lib.org" class="external-link">devtools</a> package. Run the following commands in an R session:</p>
  76 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
  77 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"devtools"</span><span class="op">)</span> <span class="co"># If not already installed.</span></span>
  78 <span><span class="fu">devtools</span><span class="fu">::</span><span class="fu">install_github</span><span class="op">(</span><span class="st">"MI2YorkU/Rnaught"</span>, build_vignettes <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
  79 </div>
  80 <div class="section level2">
  81 <h2 id="documentation">Documentation<a class="anchor" aria-label="anchor" href="#documentation"></a>
  82 </h2>
  83 <p>The package documentation is available online at <a href="https://MI2YorkU.github.io/Rnaught" class="uri">https://MI2YorkU.github.io/Rnaught</a>.</p>
  84 <p>For a quick introduction, see the <a href="https://MI2YorkU.github.io/Rnaught/articles/Rnaught.html">Get started</a> page. This can also be accessed from an R session with <code><a href="articles/Rnaught.html">vignette("Rnaught", package = "Rnaught")</a></code>.</p>
  85 <p>To view the documentation locally, run <code>?Rnaught::&lt;function&gt;</code>. A list of all functions is shown in the package index by executing <code><a href="https://MI2YorkU.github.io/Rnaught/reference">help(package = "Rnaught")</a></code>.</p>
  86 </div>
  87 <div class="section level2">
  88 <h2 id="contributing">Contributing<a class="anchor" aria-label="anchor" href="#contributing"></a>
  89 </h2>
  90 <p>The source code for this package is available on <a href="https://github.com/MI2YorkU/Rnaught" class="external-link">GitHub</a>.</p>
  91 <p>To report a bug, request a new feature, give feedback, or ask questions, open a new <a href="https://github.com/MI2YorkU/Rnaught/issues" class="external-link">issue</a>.</p>
  92 <p>Submit new estimators, features, bug fixes, or patches by creating a <a href="https://github.com/MI2YorkU/Rnaught/pulls" class="external-link">pull request</a>.</p>
  93 </div>
  94 <div class="section level2">
  95 <h2 id="license">License<a class="anchor" aria-label="anchor" href="#license"></a>
  96 </h2>
  97 <p>This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.</p>
  98 <p>This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.</p>
  99 <p>You should have received a copy of the GNU Affero General Public License along with this program. If not, see <a href="https://www.gnu.org/licenses" class="external-link uri">https://www.gnu.org/licenses</a>.</p>
 100 </div>
 101 </div>
 102   </main><aside class="col-md-3"><div class="links">
 103 <h2 data-toc-skip>Links</h2>
 104 <ul class="list-unstyled">
 105 <li><a href="https://github.com/MI2YorkU/Rnaught/" class="external-link">Browse source code</a></li>
 106 <li><a href="https://github.com/MI2YorkU/Rnaught/issues" class="external-link">Report a bug</a></li>
 107 </ul>
 108 </div>
 109
 110 <div class="license">
 111 <h2 data-toc-skip>License</h2>
 112 <ul class="list-unstyled">
 113 <li>AGPL (&gt;= 3)</li>
 114 </ul>
 115 </div>
 116
 117
 118 <div class="citation">
 119 <h2 data-toc-skip>Citation</h2>
 120 <ul class="list-unstyled">
 121 <li><a href="authors.html#citation">Citing Rnaught</a></li>
 122 </ul>
 123 </div>
 124
 125 <div class="developers">
 126 <h2 data-toc-skip>Developers</h2>
 127 <ul class="list-unstyled">
 128 <li>Naeem Model <br><small class="roles"> Author, maintainer </small>   </li>
 129 <li>Sawitree Boonpatcharanon <br><small class="roles"> Author </small>   </li>
 130 <li>Jane Heffernan <br><small class="roles"> Author </small>   </li>
 131 <li>Hanna Jankowski <br><small class="roles"> Author </small>   </li>
 132 <li>Tatiana Krikella <br><small class="roles"> Author </small>   </li>
 133 </ul>
 134 </div>
 135
 136 <div class="dev-status">
 137 <h2 data-toc-skip>Dev status</h2>
 138 <ul class="list-unstyled">
 139 <li><a href="https://github.com/MI2YorkU/Rnaught/actions/workflows/R-CMD-check.yaml" class="external-link"><img src="https://github.com/MI2YorkU/Rnaught/actions/workflows/R-CMD-check.yaml/badge.svg" alt="R-CMD-check"></a></li>
 140 </ul>
 141 </div>
 142
 143   </aside>
 144 </div>
 145
 146
 147     <footer><div class="pkgdown-footer-left">
 148   <p>Developed by Naeem Model, Sawitree Boonpatcharanon, Jane Heffernan, Hanna Jankowski, Tatiana Krikella.</p>
 149 </div>
 150
 151 <div class="pkgdown-footer-right">
 152   <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.3.</p>
 153 </div>
 154
 155     </footer>
 156 </div>
 157
 158
 159
 160
 161
 162   </body>
 163 </html>