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+ <main id="main" class="col-md-9"><div class="page-header">
+ <img src="../logo.svg" class="logo" alt=""><h1>Introduction to Rnaught</h1>
+
+
+ <small class="dont-index">Source: <a href="https://github.com/MI2YorkU/Rnaught/blob/master/vignettes/Rnaught.Rmd" class="external-link"><code>vignettes/Rnaught.Rmd</code></a></small>
+ <div class="d-none name"><code>Rnaught.Rmd</code></div>
+ </div>
+
+
+
+<p>The goal of Rnaught is to provide a a collection of methods for
+estimating the <a href="https://en.wikipedia.org/wiki/Basic_reproduction_number" class="external-link">basic
+reproduction number</a>
+(<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><msub><mi>R</mi><mn>0</mn></msub><annotation encoding="application/x-tex">R_0</annotation></semantics></math>)
+of infectious diseases.</p>
+<div class="section level2">
+<h2 id="estimators">Estimators<a class="anchor" aria-label="anchor" href="#estimators"></a>
+</h2>
+<p>The following estimators are currently available:</p>
+<ul>
+<li>
+<code><a href="../reference/id.html">id()</a></code>: Incidence Decay (ID)</li>
+<li>
+<code><a href="../reference/idea.html">idea()</a></code>: Incidence Decay and Exponential Adjustment
+(IDEA)</li>
+<li>
+<code><a href="../reference/seq_bayes.html">seq_bayes()</a></code>: Sequential Bayes (seqB)</li>
+<li>
+<code><a href="../reference/wp.html">wp()</a></code>: White and Pagano (WP)</li>
+</ul>
+<p>Every estimator employs its own model, has its own set of parameters,
+and is better suited to particular scenarios. You should consult each
+methodβs documentation for technical details. Below is a short example
+computing estimates for a given set of case counts.</p>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://MI2YorkU.github.io/Rnaught">Rnaught</a></span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># Weekly case counts.</span></span>
+<span><span class="va">cases</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">4</span>, <span class="fl">10</span>, <span class="fl">5</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">19</span>, <span class="fl">3</span>, <span class="fl">3</span>, <span class="fl">14</span>, <span class="fl">4</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># Compute estimates of R0, assuming a serial interval of five days.</span></span>
+<span><span class="va">mu</span> <span class="op"><-</span> <span class="fl">5</span> <span class="op">/</span> <span class="fl">7</span></span>
+<span></span>
+<span><span class="fu"><a href="../reference/id.html">id</a></span><span class="op">(</span><span class="va">cases</span>, <span class="va">mu</span><span class="op">)</span></span>
+<span><span class="co">#> [1] 1.245734</span></span>
+<span><span class="fu"><a href="../reference/idea.html">idea</a></span><span class="op">(</span><span class="va">cases</span>, <span class="va">mu</span><span class="op">)</span></span>
+<span><span class="co">#> [1] 1.419546</span></span>
+<span><span class="fu"><a href="../reference/seq_bayes.html">seq_bayes</a></span><span class="op">(</span><span class="va">cases</span>, <span class="va">mu</span><span class="op">)</span></span>
+<span><span class="co">#> [1] 1.026563</span></span>
+<span><span class="fu"><a href="../reference/wp.html">wp</a></span><span class="op">(</span><span class="va">cases</span>, <span class="va">mu</span><span class="op">)</span></span>
+<span><span class="co">#> [1] 1.107862</span></span></code></pre></div>
+</div>
+<div class="section level2">
+<h2 id="web-application">Web Application<a class="anchor" aria-label="anchor" href="#web-application"></a>
+</h2>
+<p>This serves as a graphical interface for the package. An instance is
+available at <a href="https://immune.math.yorku.ca/Rnaught" class="external-link uri">https://immune.math.yorku.ca/Rnaught</a>. It can also be run
+locally by invoking the <code><a href="../reference/web.html">web()</a></code> function.</p>
+<p>Datasets can be uploaded as a CSV file, or entered manually. The data
+is visualized in the application through plots that show the case counts
+(either daily or weekly). If multiple datasets are added, the trends
+corresponding to these datasets are populated in the same plot. This
+plot can be exported as a PNG image. Furthermore, the datasets entered
+can be exported as a CSV.</p>
+<p>Two sample datasets are included: weekly Canadian COVID-19 case count
+data from March 3rd, 2020 to March 31st, 2020, and weekly Ontario
+COVID-19 case count data from March 3rd, 2020 to March 31st, 2020.</p>
+<p>To estimate the basic reproductive number, the user can choose their
+preferred estimator, and if applicable, must enter the known <a href="https://en.wikipedia.org/wiki/Serial_interval" class="external-link">serial interval</a>
+prior to estimation. If multiple estimates of the basic reproductive
+number are calculated, they are all included in a table where each row
+represents an estimate. If multiple datasets are being considered, the
+basic reproduction number is estimated for all datasets and the columns
+of the table correspond to the different datasets. The table also
+consists of a column corresponding to the value of the serial interval.
+This table can also be exported as a CSV.</p>
+</div>
+<div class="section level2">
+<h2 id="datasets">Datasets<a class="anchor" aria-label="anchor" href="#datasets"></a>
+</h2>
+<p>The package includes two datasets provided by the <a href="https://github.com/ccodwg/CovidTimelineCanada" class="external-link">COVID-19 Canada
+Open Data Working Group</a>. These report the national and provincial
+case counts of COVID-19 in Canada. For details, see
+<code><a href="../reference/COVIDCanada.html">?COVIDCanada</a></code> and <code><a href="../reference/COVIDCanadaPT.html">?COVIDCanadaPT</a></code>. They are also
+available as <a href="https://github.com/MI2YorkU/Rnaught/tree/master/inst/extdata" class="external-link">CSV
+files</a>.</p>
+</div>
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+ <dl><dt><a href="Rnaught.html">Introduction to Rnaught</a></dt>
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<p>In the Sequential Bayes method, the probability distribution of R0 is
updated sequentially from one case count to the next, starting from a
(discretized) uniform prior. By default, the function
-<code>seq_bayes</code> returns the mean of the last updated posterior
+<code><a href="../reference/seq_bayes.html">seq_bayes()</a></code> returns the mean of the last updated posterior
distribution as its estimate of R0. However, by setting the parameter
<code>post</code> to <code>TRUE</code>, it is possible to return the
final distribution itself:</p>
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<title>White and Pagano: Utilizing the Serial Distribution β’ Rnaught</title>
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becomes symptomatic. The serial interval refers to a range of likely
values from this distribution, although it is typically reported as the
mean.</p>
-<p>In the White and Pagano method, the serial distribution is assumed to
-be a discretized, finite version of a gamma distribution. Setting the
-parameter <code>serial</code> to <code>TRUE</code> causes this
-discretized distribution to be returned in addition to the estimate of
-R0. Furthermore, the method can be used whether or not the serial
-interval (specified as the parameter <code>mu</code>) is known. When
-<code>mu</code> is specified, it is taken to be the mean of a continuous
-gamma distribution (i.e., before the discretization). As such, the mean
-computed from the returned serial distribution may differ slightly from
-<code>mu</code>:</p>
+<p>In the White and Pagano method, <code><a href="../reference/wp.html">wp()</a></code>, the serial
+distribution is assumed to be a discretized, finite version of a gamma
+distribution. Setting the parameter <code>serial</code> to
+<code>TRUE</code> causes this discretized distribution to be returned in
+addition to the estimate of R0. Furthermore, the method can be used
+whether or not the serial interval (specified as the parameter
+<code>mu</code>) is known. When <code>mu</code> is specified, it is
+taken to be the mean of a continuous gamma distribution (i.e., before
+the discretization). As such, the mean computed from the returned serial
+distribution may differ slightly from <code>mu</code>:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Case counts.</span></span>
<span><span class="va">cases</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">4</span>, <span class="fl">10</span>, <span class="fl">5</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">19</span>, <span class="fl">3</span>, <span class="fl">3</span>, <span class="fl">14</span>, <span class="fl">4</span><span class="op">)</span></span>
<!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, shrink-to-fit=no"><title>Authors and Citation β’ Rnaught</title><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"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><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"><link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><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="Authors and Citation"><meta property="og:image" content="https://MI2YorkU.github.io/Rnaught/logo.svg"></head><body>
+<!-- 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, shrink-to-fit=no"><title>Authors and Citation β’ Rnaught</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><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"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><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"><link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><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="Authors and Citation"><meta property="og:image" content="https://MI2YorkU.github.io/Rnaught/logo.svg"></head><body>
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+ <ul class="navbar-nav me-auto"><li class="nav-item"><a class="nav-link" href="articles/Rnaught.html">Get started</a></li>
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--- /dev/null
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<title>Estimate the Basic Reproduction Number (R0) of Infectious Diseases β’ Rnaught</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
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+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
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+<li class="nav-item"><a class="nav-link" href="articles/Rnaught.html">Get started</a></li>
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</h1>
</div>
+<!-- badges: start -->
+
<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>
-<p>Currently, this estimation can be done in the web application via four different methods: White and Panago (WP), sequential Bayes (seqB), incidence decay (ID), and incidence decay and exponential adjustment (IDEA).</p>
-<p>Datasets can be uploaded as a .csv file, or can be entered manually into the application. The data is visualized in the application through plots that show the case counts (either weekly or daily). If multiple datasets are uploaded/manually entered, the trends corresponding to these datasets are populated in the same plot and can be compared. This plot can be exported as a .png file. Further, the dataset entered can be exported into a .csv file. Two sample datasets are included: weekly Canadian COVID-19 case count data from March 3rd, 2020 to March 31st, 2020, and weekly Ontario COVID-19 case count data from March 3rd, 2020 to March 31st, 2020.</p>
-<p>To estimate the basic reproductive number, the user can choose their preferred estimator, and if applicable, must enter the known serial interval prior to estimation. If multiple estimates of the basic reproductive number are calculated, they are all included in a table where each row represents an estimate. If multiple datasets are being considered, the basic reproductive number is estimated for all datasets and the columns of the table correspond to the different datasets uploaded into the application. The table also consists of a column corresponding to the value of the <a href="https://en.wikipedia.org/wiki/Serial_interval" class="external-link">serial interval (SI)</a>. This table can be exported as a .csv file.</p>
-<p>In progressβ¦</p>
+<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>
+<div class="section level2">
+<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
+</h2>
+<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>
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<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>
+<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>
+</div>
+<div class="section level2">
+<h2 id="documentation">Documentation<a class="anchor" aria-label="anchor" href="#documentation"></a>
+</h2>
+<p>The package documentation is available online at <a href="https://MI2YorkU.github.io/Rnaught" class="uri">https://MI2YorkU.github.io/Rnaught</a>.</p>
+<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>
+<p>To view the documentation locally, run <code>?Rnaught::<function></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>
+</div>
+<div class="section level2">
+<h2 id="contributing">Contributing<a class="anchor" aria-label="anchor" href="#contributing"></a>
+</h2>
+<p>The source code for this package is available on <a href="https://github.com/MI2YorkU/Rnaught" class="external-link">GitHub</a>.</p>
+<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>
+<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>
+</div>
+<div class="section level2">
+<h2 id="license">License<a class="anchor" aria-label="anchor" href="#license"></a>
+</h2>
+<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>
+<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>
+<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>
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Bettencourt and Riberio (PloS One, 2008). See details for important
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in Medicine, 2008). The method is based on maximum likelihood estimation in a
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in Medicine, 2008). The method is based on maximum likelihood estimation in a
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-[{"path":"https://MI2YorkU.github.io/Rnaught/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Naeem Model. Author, maintainer. Sawitree Boonpatcharanon. Author. Jane Heffernan. Author. Hanna Jankowski. Author. Tatiana Krikella. Contributor.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Model N, Boonpatcharanon S, Heffernan J, Jankowski H (????). Rnaught: Estimate Basic Reproduction Number (R0) Infectious Diseases. R package version 0.1.0, https://github.com/MI2YorkU/Rnaught, https://MI2YorkU.github.io/Rnaught. Boonpatcharanon S, Heffernan JM, Jankowski H (2022). βEstimating basic reproduction number beginning outbreak.β PLOS ONE, 17(6), 1-24. doi:10.1371/journal.pone.0269306.","code":"@Manual{, title = {Rnaught: Estimate the Basic Reproduction Number (R0) of Infectious Diseases}, author = {Naeem Model and Sawitree Boonpatcharanon and Jane Heffernan and Hanna Jankowski}, note = {R package version 0.1.0, https://github.com/MI2YorkU/Rnaught}, url = {https://MI2YorkU.github.io/Rnaught}, } @Article{, doi = {10.1371/journal.pone.0269306}, author = {Sawitree Boonpatcharanon and Jane M. Heffernan and Hanna Jankowski}, journal = {PLOS ONE}, publisher = {Public Library of Science}, title = {Estimating the basic reproduction number at the beginning of an outbreak}, year = {2022}, month = {6}, volume = {17}, pages = {1-24}, number = {6}, }"},{"path":"https://MI2YorkU.github.io/Rnaught/index.html","id":"rnaught-","dir":"","previous_headings":"","what":"Estimate the Basic Reproduction Number (R0) of Infectious Diseases","title":"Estimate the Basic Reproduction Number (R0) of Infectious Diseases","text":"Rnaught R package web application estimating basic reproduction number (R0) infectious diseases. Currently, estimation can done web application via four different methods: White Panago (WP), sequential Bayes (seqB), incidence decay (ID), incidence decay exponential adjustment (IDEA). Datasets can uploaded .csv file, can entered manually application. data visualized application plots show case counts (either weekly daily). multiple datasets uploaded/manually entered, trends corresponding datasets populated plot can compared. plot can exported .png file. , dataset entered can exported .csv file. Two sample datasets included: weekly Canadian COVID-19 case count data March 3rd, 2020 March 31st, 2020, weekly Ontario COVID-19 case count data March 3rd, 2020 March 31st, 2020. estimate basic reproductive number, user can choose preferred estimator, applicable, must enter known serial interval prior estimation. multiple estimates basic reproductive number calculated, included table row represents estimate. multiple datasets considered, basic reproductive number estimated datasets columns table correspond different datasets uploaded application. table also consists column corresponding value serial interval (SI). table can exported .csv file. progressβ¦","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanada.html","id":null,"dir":"Reference","previous_headings":"","what":"COVID-19 Canada National Case Counts, 2020-2023 β COVIDCanada","title":"COVID-19 Canada National Case Counts, 2020-2023 β COVIDCanada","text":"Daily national COVID-19 case counts Canada, start pandemic end 2023. Retrieved COVID-19 Canada Open Data Working Group 2024-05-11.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanada.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COVID-19 Canada National Case Counts, 2020-2023 β COVIDCanada","text":"","code":"COVIDCanada"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanada.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COVID-19 Canada National Case Counts, 2020-2023 β COVIDCanada","text":"data frame 1439 observations 3 variables: date date reporting YYYY-MM-DD format. cases daily number cases. cumulative_cases cumulative number cases.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanada.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"COVID-19 Canada National Case Counts, 2020-2023 β COVIDCanada","text":"https://github.com/ccodwg/CovidTimelineCanada","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanadaPT.html","id":null,"dir":"Reference","previous_headings":"","what":"COVID-19 Canada Provincial and Territorial Case Counts, 2020-2023 β COVIDCanadaPT","title":"COVID-19 Canada Provincial and Territorial Case Counts, 2020-2023 β COVIDCanadaPT","text":"Daily COVID-19 case counts Canadian province territory, start pandemic end 2023. Retrieved COVID-19 Canada Open Data Working Group 2024-05-11.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanadaPT.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COVID-19 Canada Provincial and Territorial Case Counts, 2020-2023 β COVIDCanadaPT","text":"","code":"COVIDCanadaPT"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanadaPT.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COVID-19 Canada Provincial and Territorial Case Counts, 2020-2023 β COVIDCanadaPT","text":"data frame 16799 observations 4 variables: region two-letter code Canadian province territory. date date reporting YYYY-MM-DD format. cases daily number cases. cumulative_cases cumulative number cases.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanadaPT.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"COVID-19 Canada Provincial and Territorial Case Counts, 2020-2023 β COVIDCanadaPT","text":"https://github.com/ccodwg/CovidTimelineCanada","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/Rnaught-package.html","id":null,"dir":"Reference","previous_headings":"","what":"Rnaught: Estimate the Basic Reproduction Number (R0) of Infectious Diseases β Rnaught-package","title":"Rnaught: Estimate the Basic Reproduction Number (R0) of Infectious Diseases β Rnaught-package","text":"R package web application estimating basic reproduction number (R0) infectious diseases.","code":""},{"path":[]},{"path":"https://MI2YorkU.github.io/Rnaught/reference/Rnaught-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Rnaught: Estimate the Basic Reproduction Number (R0) of Infectious Diseases β Rnaught-package","text":"Maintainer: Naeem Model @nmode.ca Authors: Sawitree Boonpatcharanon Jane Heffernan Hanna Jankowski contributors: Tatiana Krikella [contributor]","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":null,"dir":"Reference","previous_headings":"","what":"Incidence Decay (ID) β id","title":"Incidence Decay (ID) β id","text":"function implements least squares estimation method R0 due Fisman et al. (PloS One, 2013). See details implementation notes.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Incidence Decay (ID) β id","text":"","code":"id(cases, mu)"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Incidence Decay (ID) β id","text":"cases Vector case counts. vector must non-empty contain positive integers. mu Mean serial distribution. must positive number. value match case counts time units. example, case counts weekly serial distribution mean seven days, mu set 1. case counts daily serial distribution mean seven days, mu set 7.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Incidence Decay (ID) β id","text":"estimate basic reproduction number (R0).","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Incidence Decay (ID) β id","text":"method based straightforward incidence decay model. estimate R0 value minimizes sum squares observed case counts cases counts expected model. method based approximation SIR model, valid beginning epidemic. method assumes mean serial distribution (sometimes called serial interval) known. final estimate can quite sensitive value, sensitivity testing strongly recommended. Users careful units time (e.g., counts observed daily weekly?) implementing.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Incidence Decay (ID) β id","text":"Fisman et al. (PloS One, 2013)","code":""},{"path":[]},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Incidence Decay (ID) β id","text":"","code":"# Weekly data. cases <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4) # Obtain R0 when the serial distribution has a mean of five days. id(cases, mu = 5 / 7) #> [1] 1.245734 # Obtain R0 when the serial distribution has a mean of three days. id(cases, mu = 3 / 7) #> [1] 1.14092"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":null,"dir":"Reference","previous_headings":"","what":"Incidence Decay and Exponential Adjustment (IDEA) β idea","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"function implements least squares estimation method R0 due Fisman et al. (PloS One, 2013). See details implementation notes.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"","code":"idea(cases, mu)"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"cases Vector case counts. vector must length least two contain positive integers. mu Mean serial distribution. must positive number. value match case counts time units. example, case counts weekly serial distribution mean seven days, mu set 1. case counts daily serial distribution mean seven days, mu set 7.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"estimate basic reproduction number (R0).","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"method closely related implemented id(). method based incidence decay model. estimate R0 value minimizes sum squares observed case counts case counts expected model. method based approximation SIR model, valid beginning epidemic. method assumes mean serial distribution (sometimes called serial interval) known. final estimate can quite sensitive value, sensitivity testing strongly recommended. Users careful units time (e.g., counts observed daily weekly?) implementing.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"Fisman et al. (PloS One, 2013)","code":""},{"path":[]},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"","code":"# Weekly data. cases <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4) # Obtain R0 when the serial distribution has a mean of five days. idea(cases, mu = 5 / 7) #> [1] 1.419546 # Obtain R0 when the serial distribution has a mean of three days. idea(cases, mu = 3 / 7) #> [1] 1.233927"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":null,"dir":"Reference","previous_headings":"","what":"Sequential Bayes (seqB) β seq_bayes","title":"Sequential Bayes (seqB) β seq_bayes","text":"function implements sequential Bayesian estimation method R0 due Bettencourt Riberio (PloS One, 2008). See details important implementation notes.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sequential Bayes (seqB) β seq_bayes","text":"","code":"seq_bayes(cases, mu, kappa = 20, post = FALSE)"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sequential Bayes (seqB) β seq_bayes","text":"cases Vector case counts. vector must contain non-negative integers, least two positive integers. mu Mean serial distribution. must positive number. value match case counts time units. example, case counts weekly serial distribution mean seven days, mu set 1. case counts daily serial distribution mean seven days, mu set 7. kappa Largest possible value uniform prior (defaults 20). must number greater equal 1. describes prior belief ranges R0, set higher value R0 believed larger. post Whether return posterior distribution R0 instead estimate R0 (defaults FALSE). must value identical TRUE FALSE.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sequential Bayes (seqB) β seq_bayes","text":"post identical TRUE, list containing following components returned: supp - support posterior distribution R0 pmf - probability mass function posterior distribution R0 Otherwise, post identical FALSE, estimate R0 returned. Note estimate equal sum(supp * pmf) (.e., posterior mean).","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sequential Bayes (seqB) β seq_bayes","text":"method sets uniform prior distribution R0 possible values 0 kappa, discretized fine grid. distribution R0 updated sequentially, one update new case count observation. final estimate R0 mean (last) posterior distribution. prior distribution initial belief distribution R0, uninformative uniform distribution values 0 kappa. Users can change value kappa (.e., prior distribution changed uniform). case counts observed, influence prior distribution lessen final estimate. method based approximation SIR model, valid beginning epidemic. method assumes mean serial distribution (sometimes called serial interval) known. final estimate can quite sensitive value, sensitivity testing strongly recommended. Users careful units time (e.g., counts observed daily weekly?) implementing. code modified provide estimate even case counts equal zero present time intervals. done grouping counts periods time. Without grouping, presence zero counts, estimate can provided.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Sequential Bayes (seqB) β seq_bayes","text":"Bettencourt Riberio (PloS One, 2008)","code":""},{"path":[]},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sequential Bayes (seqB) β seq_bayes","text":"","code":"# Weekly data. cases <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4) # Obtain R0 when the serial distribution has a mean of five days. seq_bayes(cases, mu = 5 / 7) #> [1] 1.026563 # Obtain R0 when the serial distribution has a mean of three days. seq_bayes(cases, mu = 3 / 7) #> [1] 1.015938 # Obtain R0 when the serial distribution has a mean of seven days, and R0 is # believed to be at most 4. estimate <- seq_bayes(cases, mu = 1, kappa = 4) # Same as above, but return the posterior distribution of R0 instead of the # estimate. posterior <- seq_bayes(cases, mu = 1, kappa = 4, post = TRUE) # Display the support and probability mass function of the posterior. posterior$supp #> [1] 0.00 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10 0.11 0.12 0.13 0.14 #> [16] 0.15 0.16 0.17 0.18 0.19 0.20 0.21 0.22 0.23 0.24 0.25 0.26 0.27 0.28 0.29 #> [31] 0.30 0.31 0.32 0.33 0.34 0.35 0.36 0.37 0.38 0.39 0.40 0.41 0.42 0.43 0.44 #> [46] 0.45 0.46 0.47 0.48 0.49 0.50 0.51 0.52 0.53 0.54 0.55 0.56 0.57 0.58 0.59 #> [61] 0.60 0.61 0.62 0.63 0.64 0.65 0.66 0.67 0.68 0.69 0.70 0.71 0.72 0.73 0.74 #> [76] 0.75 0.76 0.77 0.78 0.79 0.80 0.81 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89 #> [91] 0.90 0.91 0.92 0.93 0.94 0.95 0.96 0.97 0.98 0.99 1.00 1.01 1.02 1.03 1.04 #> [106] 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 #> [121] 1.20 1.21 1.22 1.23 1.24 1.25 1.26 1.27 1.28 1.29 1.30 1.31 1.32 1.33 1.34 #> [136] 1.35 1.36 1.37 1.38 1.39 1.40 1.41 1.42 1.43 1.44 1.45 1.46 1.47 1.48 1.49 #> [151] 1.50 1.51 1.52 1.53 1.54 1.55 1.56 1.57 1.58 1.59 1.60 1.61 1.62 1.63 1.64 #> [166] 1.65 1.66 1.67 1.68 1.69 1.70 1.71 1.72 1.73 1.74 1.75 1.76 1.77 1.78 1.79 #> [181] 1.80 1.81 1.82 1.83 1.84 1.85 1.86 1.87 1.88 1.89 1.90 1.91 1.92 1.93 1.94 #> [196] 1.95 1.96 1.97 1.98 1.99 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 #> [211] 2.10 2.11 2.12 2.13 2.14 2.15 2.16 2.17 2.18 2.19 2.20 2.21 2.22 2.23 2.24 #> [226] 2.25 2.26 2.27 2.28 2.29 2.30 2.31 2.32 2.33 2.34 2.35 2.36 2.37 2.38 2.39 #> [241] 2.40 2.41 2.42 2.43 2.44 2.45 2.46 2.47 2.48 2.49 2.50 2.51 2.52 2.53 2.54 #> [256] 2.55 2.56 2.57 2.58 2.59 2.60 2.61 2.62 2.63 2.64 2.65 2.66 2.67 2.68 2.69 #> [271] 2.70 2.71 2.72 2.73 2.74 2.75 2.76 2.77 2.78 2.79 2.80 2.81 2.82 2.83 2.84 #> [286] 2.85 2.86 2.87 2.88 2.89 2.90 2.91 2.92 2.93 2.94 2.95 2.96 2.97 2.98 2.99 #> [301] 3.00 3.01 3.02 3.03 3.04 3.05 3.06 3.07 3.08 3.09 3.10 3.11 3.12 3.13 3.14 #> [316] 3.15 3.16 3.17 3.18 3.19 3.20 3.21 3.22 3.23 3.24 3.25 3.26 3.27 3.28 3.29 #> [331] 3.30 3.31 3.32 3.33 3.34 3.35 3.36 3.37 3.38 3.39 3.40 3.41 3.42 3.43 3.44 #> [346] 3.45 3.46 3.47 3.48 3.49 3.50 3.51 3.52 3.53 3.54 3.55 3.56 3.57 3.58 3.59 #> [361] 3.60 3.61 3.62 3.63 3.64 3.65 3.66 3.67 3.68 3.69 3.70 3.71 3.72 3.73 3.74 #> [376] 3.75 3.76 3.77 3.78 3.79 3.80 3.81 3.82 3.83 3.84 3.85 3.86 3.87 3.88 3.89 #> [391] 3.90 3.91 3.92 3.93 3.94 3.95 3.96 3.97 3.98 3.99 4.00 posterior$pmf #> [1] 4.396081e-14 6.866777e-14 1.069979e-13 1.663113e-13 2.578585e-13 #> [6] 3.987896e-13 6.151736e-13 9.465244e-13 1.452563e-12 2.223289e-12 #> [11] 3.393931e-12 5.167074e-12 7.845296e-12 1.187914e-11 1.793742e-11 #> [16] 2.700983e-11 4.055633e-11 6.072366e-11 9.065827e-11 1.349567e-10 #> [21] 2.003117e-10 2.964355e-10 4.373744e-10 6.433725e-10 9.435054e-10 #> [26] 1.379386e-09 2.010358e-09 2.920742e-09 4.229916e-09 6.106257e-09 #> [31] 8.786364e-09 1.260143e-08 1.801328e-08 2.566338e-08 3.643912e-08 #> [36] 5.156328e-08 7.271379e-08 1.021837e-07 1.430935e-07 1.996715e-07 #> [41] 2.776227e-07 3.846102e-07 5.308815e-07 7.300785e-07 1.000278e-06 #> [46] 1.365319e-06 1.856496e-06 2.514686e-06 3.393017e-06 4.560205e-06 #> [51] 6.104659e-06 8.139541e-06 1.080892e-05 1.429523e-05 1.882819e-05 #> [56] 2.469542e-05 3.225496e-05 4.194988e-05 5.432506e-05 7.004650e-05 #> [61] 8.992291e-05 1.149299e-04 1.462361e-04 1.852322e-04 2.335598e-04 #> [66] 2.931434e-04 3.662201e-04 4.553696e-04 5.635406e-04 6.940727e-04 #> [71] 8.507116e-04 1.037615e-03 1.259347e-03 1.520857e-03 1.827440e-03 #> [76] 2.184679e-03 2.598363e-03 3.074378e-03 3.618573e-03 4.236597e-03 #> [81] 4.933708e-03 5.714562e-03 6.582973e-03 7.541662e-03 8.591990e-03 #> [86] 9.733699e-03 1.096466e-02 1.228062e-02 1.367503e-02 1.513890e-02 #> [91] 1.666067e-02 1.822624e-02 1.981901e-02 2.142007e-02 2.300844e-02 #> [96] 2.456146e-02 2.605520e-02 2.746508e-02 2.876640e-02 2.993509e-02 #> [101] 3.094837e-02 3.178548e-02 3.242832e-02 3.286214e-02 3.307605e-02 #> [106] 3.306344e-02 3.282231e-02 3.235539e-02 3.167013e-02 3.077854e-02 #> [111] 2.969682e-02 2.844487e-02 2.704571e-02 2.552471e-02 2.390888e-02 #> [116] 2.222595e-02 2.050365e-02 1.876888e-02 1.704700e-02 1.536123e-02 #> [121] 1.373213e-02 1.217724e-02 1.071084e-02 9.343864e-03 8.083917e-03 #> [126] 6.935429e-03 5.899896e-03 4.976201e-03 4.160989e-03 3.449076e-03 #> [131] 2.833858e-03 2.307727e-03 1.862441e-03 1.489475e-03 1.180313e-03 #> [136] 9.266886e-04 7.207803e-04 5.553459e-04 4.238132e-04 3.203273e-04 #> [141] 2.397617e-04 1.777009e-04 1.304008e-04 9.473459e-05 6.812875e-05 #> [146] 4.849552e-05 3.416469e-05 2.381841e-05 1.643092e-05 1.121447e-05 #> [151] 7.572111e-06 5.057422e-06 3.340936e-06 2.182658e-06 1.410047e-06 #> [156] 9.006636e-07 5.687529e-07 3.550312e-07 2.190488e-07 1.335660e-07 #> [161] 8.047851e-08 4.791165e-08 2.817909e-08 1.637135e-08 9.394205e-09 #> [166] 5.323528e-09 2.978849e-09 1.645703e-09 8.975385e-10 4.831664e-10 #> [171] 2.566999e-10 1.345806e-10 6.961600e-11 3.552605e-11 1.788285e-11 #> [176] 8.878079e-12 4.346434e-12 2.098061e-12 9.984180e-13 4.683320e-13 #> [181] 2.165108e-13 9.863385e-14 4.427200e-14 1.957601e-14 8.526007e-15 #> [186] 3.657023e-15 1.544555e-15 6.422519e-16 2.628849e-16 1.059047e-16 #> [191] 4.198412e-17 1.637588e-17 6.283525e-18 2.371425e-18 8.801378e-19 #> [196] 3.211841e-19 1.152248e-19 4.063045e-20 1.407979e-20 4.794057e-21 #> [201] 1.603601e-21 5.268629e-22 1.699923e-22 5.385323e-23 1.674809e-23 #> [206] 5.112219e-24 1.531308e-24 4.500307e-25 1.297374e-25 3.668155e-26 #> [211] 1.016962e-26 2.764082e-27 7.363758e-28 1.922485e-28 4.917601e-29 #> [216] 1.232200e-29 3.023823e-30 7.265876e-31 1.709166e-31 3.935069e-32 #> [221] 8.865403e-33 1.954015e-33 4.212549e-34 8.880821e-35 1.830437e-35 #> [226] 3.687665e-36 7.260114e-37 1.396466e-37 2.623677e-38 4.813725e-39 #> [231] 8.622619e-40 1.507577e-40 2.572153e-41 4.281381e-42 6.950773e-43 #> [236] 1.100362e-43 1.698170e-44 2.554224e-45 3.743317e-46 5.343929e-47 #> [241] 7.429450e-48 1.005609e-48 1.324832e-49 1.698377e-50 2.118019e-51 #> [246] 2.568782e-52 3.029042e-53 3.471688e-54 3.866425e-55 4.182989e-56 #> [251] 4.394865e-57 4.482891e-58 4.438084e-59 4.263117e-60 3.972112e-61 #> [256] 3.588768e-62 3.143145e-63 2.667736e-64 2.193531e-65 1.746742e-66 #> [261] 1.346659e-67 1.004822e-68 7.254056e-70 5.065108e-71 3.419533e-72 #> [266] 2.231354e-73 1.406840e-74 8.567343e-76 5.037567e-77 2.859011e-78 #> [271] 1.565585e-79 8.268889e-81 4.210849e-82 2.066735e-83 9.773085e-85 #> [276] 4.450901e-86 1.951504e-87 8.234368e-89 3.342436e-90 1.304664e-91 #> [281] 4.895156e-93 1.764793e-94 6.110914e-96 2.031551e-97 6.481579e-99 #> [286] 1.983744e-100 5.821848e-102 1.637658e-103 4.413549e-105 1.139116e-106 #> [291] 2.814324e-108 6.652979e-110 1.504185e-111 3.251137e-113 6.714617e-115 #> [296] 1.324527e-116 2.494329e-118 4.482263e-120 7.682227e-122 1.255211e-123 #> [301] 1.954236e-125 2.897728e-127 4.090211e-129 5.493210e-131 7.015875e-133 #> [306] 8.517133e-135 9.822891e-137 1.075711e-138 1.117987e-140 1.102133e-142 #> [311] 1.030047e-144 9.121635e-147 7.649726e-149 6.072101e-151 4.559445e-153 #> [316] 3.236849e-155 2.171329e-157 1.375543e-159 8.224662e-162 4.638796e-164 #> [321] 2.466499e-166 1.235627e-168 5.828612e-171 2.587326e-173 1.080141e-175 #> [326] 4.238233e-178 1.562047e-180 5.404238e-183 1.754003e-185 5.337064e-188 #> [331] 1.521491e-190 4.061129e-193 1.014255e-195 2.368537e-198 5.168362e-201 #> [336] 1.053099e-203 2.002304e-206 3.550040e-209 5.865079e-212 9.022847e-215 #> [341] 1.291610e-217 1.719185e-220 2.126178e-223 2.441418e-226 2.600913e-229 #> [346] 2.568760e-232 2.350200e-235 1.990379e-238 1.559119e-241 1.128742e-244 #> [351] 7.546371e-248 4.655454e-251 2.647985e-254 1.387535e-257 6.692519e-261 #> [356] 2.968866e-264 1.210268e-267 4.529956e-271 1.555446e-274 4.895396e-278 #> [361] 1.410954e-281 3.720881e-285 8.970133e-289 1.975060e-292 3.968208e-296 #> [366] 7.268446e-300 1.212601e-303 1.840840e-307 2.540527e-311 3.184384e-315 #> [371] 3.621946e-319 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [376] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [381] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [386] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [391] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [396] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [401] 0.000000e+00 # Note that the following always holds: estimate == sum(posterior$supp * posterior$pmf) #> [1] TRUE"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/web.html","id":null,"dir":"Reference","previous_headings":"","what":"Launch the Rnaught Web Application β web","title":"Launch the Rnaught Web Application β web","text":"entry point Rnaught web application, creates returns Shiny app object. invoked directly, web application launched.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/web.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Launch the Rnaught Web Application β web","text":"","code":"web()"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/web.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Launch the Rnaught Web Application β web","text":"Shiny app object Rnaught web application.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/web.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Launch the Rnaught Web Application β web","text":"following dependencies required run application: shiny bslib DT plotly packages missing launch, prompt appear install . configure settings port, host default browser, set Shiny's global options (see shiny::runApp()).","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":null,"dir":"Reference","previous_headings":"","what":"White and Pagano (WP) β wp","title":"White and Pagano (WP) β wp","text":"function implements R0 estimation due White Pagano (Statistics Medicine, 2008). method based maximum likelihood estimation Poisson transmission model. See details important implementation notes.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"White and Pagano (WP) β wp","text":"","code":"wp( cases, mu = NA, serial = FALSE, grid_length = 100, max_shape = 10, max_scale = 10 )"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"White and Pagano (WP) β wp","text":"cases Vector case counts. vector must length least two contain positive integers. mu Mean serial distribution (defaults NA). must positive number NA. number specified, value match case counts time units. example, case counts weekly serial distribution mean seven days, mu set 1. case counts daily serial distribution mean seven days, mu set 7. serial Whether return estimated serial distribution addition estimate R0 (defaults FALSE). must value identical TRUE FALSE. grid_length length grid grid search (defaults 100). must positive integer. used mu set NA. grid search go combinations shape scale parameters gamma distribution, grid_length evenly spaced values 0 (exclusive) max_shape max_scale (inclusive), respectively. Note larger values result longer search time. max_shape largest possible value shape parameter grid search (defaults 10). must positive number. used mu set NA. Note larger values result longer search time, may cause numerical instabilities. max_scale largest possible value scale parameter grid search (defaults 10). must positive number. used mu set NA. Note larger values result longer search time, may cause numerical instabilities.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"White and Pagano (WP) β wp","text":"serial identical TRUE, list containing following components returned: r0 - estimate R0 supp - support estimated serial distribution pmf - probability mass function estimated serial distribution Otherwise, serial identical FALSE, estimate R0 returned.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"White and Pagano (WP) β wp","text":"method based Poisson transmission model, hence may valid beginning epidemic. model, serial distribution assumed discrete finite number possible values. implementation, mu NA, serial distribution taken discretized version gamma distribution shape parameter 1 scale parameter mu (hence mean mu). mu NA, function implements grid search algorithm find maximum likelihood estimator possible gamma distributions unknown shape scale, restricting prespecified grid (see parameters grid_length, max_shape max_scale). cases, largest value support chosen cumulative distribution function original (pre-discretized) gamma distribution cumulative probability 0.999 value. serial distribution known (.e., mu NA), sensitivity testing mu strongly recommended. serial distribution unknown (.e., mu NA), likelihood function can flat near maximum, resulting numerical instability optimizer. mu NA, implementation takes considerably longer run. Users careful units time (e.g., counts observed daily weekly?) implementing. model developed White Pagano (2008) discrete, hence serial distribution finite discrete. implementation, input value mu continuous distribution. algorithm discretizes input, mean estimated serial distribution returned (serial set TRUE) differ mu somewhat. say, user notices input mu mean estimated serial distribution different, expected, caused discretization.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"White and Pagano (WP) β wp","text":"White Pagano (Statistics Medicine, 2008)","code":""},{"path":[]},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"White and Pagano (WP) β wp","text":"","code":"# Weekly data. cases <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4) # Obtain R0 when the serial distribution has a mean of five days. wp(cases, mu = 5 / 7) #> [1] 1.107862 # Obtain R0 when the serial distribution has a mean of three days. wp(cases, mu = 3 / 7) #> [1] 1.067642 # Obtain R0 when the serial distribution is unknown. # Note that this will take longer to run than when `mu` is known. wp(cases) #> [1] 1.495574 # Same as above, but specify custom grid search parameters. The larger any of # the parameters, the longer the search will take, but with potentially more # accurate estimates. wp(cases, grid_length = 40, max_shape = 4, max_scale = 4) #> [1] 1.495574 # Return the estimated serial distribution in addition to the estimate of R0. estimate <- wp(cases, serial = TRUE) # Display the estimate of R0, as well as the support and probability mass # function of the estimated serial distribution returned by the grid search. estimate$r0 #> [1] 1.495574 estimate$supp #> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 estimate$pmf #> [1] 0.3295449612 0.1855210503 0.1282030815 0.0920057871 0.0672100630 #> [6] 0.0496097863 0.0368701329 0.0275354532 0.0206388543 0.0155131855 #> [11] 0.0116867019 0.0088202295 0.0066670102 0.0050459517 0.0038232730 #> [16] 0.0028996361 0.0022009767 0.0016718921 0.0012708261 0.0009665381 #> [21] 0.0007354976 0.0005599523 0.0004264906 0.0003249676 0.0002477014"}]
+[{"path":"https://MI2YorkU.github.io/Rnaught/articles/Rnaught.html","id":"estimators","dir":"Articles","previous_headings":"","what":"Estimators","title":"Introduction to Rnaught","text":"following estimators currently available: id(): Incidence Decay (ID) idea(): Incidence Decay Exponential Adjustment (IDEA) seq_bayes(): Sequential Bayes (seqB) wp(): White Pagano (WP) Every estimator employs model, set parameters, better suited particular scenarios. consult methodβs documentation technical details. short example computing estimates given set case counts.","code":"library(Rnaught) # Weekly case counts. cases <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4) # Compute estimates of R0, assuming a serial interval of five days. mu <- 5 / 7 id(cases, mu) #> [1] 1.245734 idea(cases, mu) #> [1] 1.419546 seq_bayes(cases, mu) #> [1] 1.026563 wp(cases, mu) #> [1] 1.107862"},{"path":"https://MI2YorkU.github.io/Rnaught/articles/Rnaught.html","id":"web-application","dir":"Articles","previous_headings":"","what":"Web Application","title":"Introduction to Rnaught","text":"serves graphical interface package. instance available https://immune.math.yorku.ca/Rnaught. can also run locally invoking web() function. Datasets can uploaded CSV file, entered manually. data visualized application plots show case counts (either daily weekly). multiple datasets added, trends corresponding datasets populated plot. plot can exported PNG image. Furthermore, datasets entered can exported CSV. Two sample datasets included: weekly Canadian COVID-19 case count data March 3rd, 2020 March 31st, 2020, weekly Ontario COVID-19 case count data March 3rd, 2020 March 31st, 2020. estimate basic reproductive number, user can choose preferred estimator, applicable, must enter known serial interval prior estimation. multiple estimates basic reproductive number calculated, included table row represents estimate. multiple datasets considered, basic reproduction number estimated datasets columns table correspond different datasets. table also consists column corresponding value serial interval. table can also exported CSV.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/articles/Rnaught.html","id":"datasets","dir":"Articles","previous_headings":"","what":"Datasets","title":"Introduction to Rnaught","text":"package includes two datasets provided COVID-19 Canada Open Data Working Group. report national provincial case counts COVID-19 Canada. details, see ?COVIDCanada ?COVIDCanadaPT. also available CSV files.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Naeem Model. Author, maintainer. Sawitree Boonpatcharanon. Author. Jane Heffernan. Author. Hanna Jankowski. Author. Tatiana Krikella. Contributor.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Model N, Boonpatcharanon S, Heffernan J, Jankowski H (????). Rnaught: Estimate Basic Reproduction Number (R0) Infectious Diseases. R package version 0.1.0, https://github.com/MI2YorkU/Rnaught, https://MI2YorkU.github.io/Rnaught. Boonpatcharanon S, Heffernan JM, Jankowski H (2022). βEstimating basic reproduction number beginning outbreak.β PLOS ONE, 17(6), 1-24. doi:10.1371/journal.pone.0269306.","code":"@Manual{, title = {Rnaught: Estimate the Basic Reproduction Number (R0) of Infectious Diseases}, author = {Naeem Model and Sawitree Boonpatcharanon and Jane Heffernan and Hanna Jankowski}, note = {R package version 0.1.0, https://github.com/MI2YorkU/Rnaught}, url = {https://MI2YorkU.github.io/Rnaught}, } @Article{, doi = {10.1371/journal.pone.0269306}, author = {Sawitree Boonpatcharanon and Jane M. Heffernan and Hanna Jankowski}, journal = {PLOS ONE}, publisher = {Public Library of Science}, title = {Estimating the basic reproduction number at the beginning of an outbreak}, year = {2022}, month = {6}, volume = {17}, pages = {1-24}, number = {6}, }"},{"path":"https://MI2YorkU.github.io/Rnaught/index.html","id":"rnaught-","dir":"","previous_headings":"","what":"Estimate the Basic Reproduction Number (R0) of Infectious Diseases","title":"Estimate the Basic Reproduction Number (R0) of Infectious Diseases","text":"Rnaught R package web application estimating basic reproduction number (R0) infectious diseases. instance web application available https://immune.math.yorku.ca/Rnaught.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Estimate the Basic Reproduction Number (R0) of Infectious Diseases","text":"can install development version Rnaught using devtools package. Run following commands R session:","code":"install.packages(\"devtools\") # If not already installed. devtools::install_github(\"MI2YorkU/Rnaught\", build_vignettes = TRUE)"},{"path":"https://MI2YorkU.github.io/Rnaught/index.html","id":"documentation","dir":"","previous_headings":"","what":"Documentation","title":"Estimate the Basic Reproduction Number (R0) of Infectious Diseases","text":"package documentation available online https://MI2YorkU.github.io/Rnaught. quick introduction, see Get started page. can also accessed R session vignette(\"Rnaught\", package = \"Rnaught\"). view documentation locally, run ?Rnaught::<function>. list functions shown package index executing help(package = \"Rnaught\").","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/index.html","id":"contributing","dir":"","previous_headings":"","what":"Contributing","title":"Estimate the Basic Reproduction Number (R0) of Infectious Diseases","text":"source code package available GitHub. report bug, request new feature, give feedback, ask questions, open new issue. Submit new estimators, features, bug fixes, patches creating pull request.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Estimate the Basic Reproduction Number (R0) of Infectious Diseases","text":"program free software: can redistribute /modify terms GNU Affero General Public License published Free Software Foundation, either version 3 License, (option) later version. program distributed hope useful, WITHOUT WARRANTY; without even implied warranty MERCHANTABILITY FITNESS PARTICULAR PURPOSE. See GNU Affero General Public License details. received copy GNU Affero General Public License along program. , see https://www.gnu.org/licenses.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanada.html","id":null,"dir":"Reference","previous_headings":"","what":"COVID-19 Canada National Case Counts, 2020-2023 β COVIDCanada","title":"COVID-19 Canada National Case Counts, 2020-2023 β COVIDCanada","text":"Daily national COVID-19 case counts Canada, start pandemic end 2023. Retrieved COVID-19 Canada Open Data Working Group 2024-05-11.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanada.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COVID-19 Canada National Case Counts, 2020-2023 β COVIDCanada","text":"","code":"COVIDCanada"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanada.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COVID-19 Canada National Case Counts, 2020-2023 β COVIDCanada","text":"data frame 1439 observations 3 variables: date date reporting YYYY-MM-DD format. cases daily number cases. cumulative_cases cumulative number cases.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanada.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"COVID-19 Canada National Case Counts, 2020-2023 β COVIDCanada","text":"https://github.com/ccodwg/CovidTimelineCanada","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanadaPT.html","id":null,"dir":"Reference","previous_headings":"","what":"COVID-19 Canada Provincial and Territorial Case Counts, 2020-2023 β COVIDCanadaPT","title":"COVID-19 Canada Provincial and Territorial Case Counts, 2020-2023 β COVIDCanadaPT","text":"Daily COVID-19 case counts Canadian province territory, start pandemic end 2023. Retrieved COVID-19 Canada Open Data Working Group 2024-05-11.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanadaPT.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"COVID-19 Canada Provincial and Territorial Case Counts, 2020-2023 β COVIDCanadaPT","text":"","code":"COVIDCanadaPT"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanadaPT.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"COVID-19 Canada Provincial and Territorial Case Counts, 2020-2023 β COVIDCanadaPT","text":"data frame 16799 observations 4 variables: region two-letter code Canadian province territory. date date reporting YYYY-MM-DD format. cases daily number cases. cumulative_cases cumulative number cases.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/COVIDCanadaPT.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"COVID-19 Canada Provincial and Territorial Case Counts, 2020-2023 β COVIDCanadaPT","text":"https://github.com/ccodwg/CovidTimelineCanada","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/Rnaught-package.html","id":null,"dir":"Reference","previous_headings":"","what":"Rnaught: Estimate the Basic Reproduction Number (R0) of Infectious Diseases β Rnaught-package","title":"Rnaught: Estimate the Basic Reproduction Number (R0) of Infectious Diseases β Rnaught-package","text":"R package web application estimating basic reproduction number (R0) infectious diseases.","code":""},{"path":[]},{"path":"https://MI2YorkU.github.io/Rnaught/reference/Rnaught-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Rnaught: Estimate the Basic Reproduction Number (R0) of Infectious Diseases β Rnaught-package","text":"Maintainer: Naeem Model @nmode.ca Authors: Sawitree Boonpatcharanon Jane Heffernan Hanna Jankowski contributors: Tatiana Krikella [contributor]","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":null,"dir":"Reference","previous_headings":"","what":"Incidence Decay (ID) β id","title":"Incidence Decay (ID) β id","text":"function implements least squares estimation method R0 due Fisman et al. (PloS One, 2013). See details implementation notes.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Incidence Decay (ID) β id","text":"","code":"id(cases, mu)"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Incidence Decay (ID) β id","text":"cases Vector case counts. vector must non-empty contain positive integers. mu Mean serial distribution. must positive number. value match case counts time units. example, case counts weekly serial distribution mean seven days, mu set 1. case counts daily serial distribution mean seven days, mu set 7.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Incidence Decay (ID) β id","text":"estimate basic reproduction number (R0).","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Incidence Decay (ID) β id","text":"method based straightforward incidence decay model. estimate R0 value minimizes sum squares observed case counts cases counts expected model. method based approximation SIR model, valid beginning epidemic. method assumes mean serial distribution (sometimes called serial interval) known. final estimate can quite sensitive value, sensitivity testing strongly recommended. Users careful units time (e.g., counts observed daily weekly?) implementing.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Incidence Decay (ID) β id","text":"Fisman et al. (PloS One, 2013)","code":""},{"path":[]},{"path":"https://MI2YorkU.github.io/Rnaught/reference/id.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Incidence Decay (ID) β id","text":"","code":"# Weekly data. cases <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4) # Obtain R0 when the serial distribution has a mean of five days. id(cases, mu = 5 / 7) #> [1] 1.245734 # Obtain R0 when the serial distribution has a mean of three days. id(cases, mu = 3 / 7) #> [1] 1.14092"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":null,"dir":"Reference","previous_headings":"","what":"Incidence Decay and Exponential Adjustment (IDEA) β idea","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"function implements least squares estimation method R0 due Fisman et al. (PloS One, 2013). See details implementation notes.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"","code":"idea(cases, mu)"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"cases Vector case counts. vector must length least two contain positive integers. mu Mean serial distribution. must positive number. value match case counts time units. example, case counts weekly serial distribution mean seven days, mu set 1. case counts daily serial distribution mean seven days, mu set 7.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"estimate basic reproduction number (R0).","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"method closely related implemented id(). method based incidence decay model. estimate R0 value minimizes sum squares observed case counts case counts expected model. method based approximation SIR model, valid beginning epidemic. method assumes mean serial distribution (sometimes called serial interval) known. final estimate can quite sensitive value, sensitivity testing strongly recommended. Users careful units time (e.g., counts observed daily weekly?) implementing.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"Fisman et al. (PloS One, 2013)","code":""},{"path":[]},{"path":"https://MI2YorkU.github.io/Rnaught/reference/idea.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Incidence Decay and Exponential Adjustment (IDEA) β idea","text":"","code":"# Weekly data. cases <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4) # Obtain R0 when the serial distribution has a mean of five days. idea(cases, mu = 5 / 7) #> [1] 1.419546 # Obtain R0 when the serial distribution has a mean of three days. idea(cases, mu = 3 / 7) #> [1] 1.233927"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":null,"dir":"Reference","previous_headings":"","what":"Sequential Bayes (seqB) β seq_bayes","title":"Sequential Bayes (seqB) β seq_bayes","text":"function implements sequential Bayesian estimation method R0 due Bettencourt Riberio (PloS One, 2008). See details important implementation notes.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sequential Bayes (seqB) β seq_bayes","text":"","code":"seq_bayes(cases, mu, kappa = 20, post = FALSE)"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sequential Bayes (seqB) β seq_bayes","text":"cases Vector case counts. vector must contain non-negative integers, least two positive integers. mu Mean serial distribution. must positive number. value match case counts time units. example, case counts weekly serial distribution mean seven days, mu set 1. case counts daily serial distribution mean seven days, mu set 7. kappa Largest possible value uniform prior (defaults 20). must number greater equal 1. describes prior belief ranges R0, set higher value R0 believed larger. post Whether return posterior distribution R0 instead estimate R0 (defaults FALSE). must value identical TRUE FALSE.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sequential Bayes (seqB) β seq_bayes","text":"post identical TRUE, list containing following components returned: supp - support posterior distribution R0 pmf - probability mass function posterior distribution R0 Otherwise, post identical FALSE, estimate R0 returned. Note estimate equal sum(supp * pmf) (.e., posterior mean).","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Sequential Bayes (seqB) β seq_bayes","text":"method sets uniform prior distribution R0 possible values 0 kappa, discretized fine grid. distribution R0 updated sequentially, one update new case count observation. final estimate R0 mean (last) posterior distribution. prior distribution initial belief distribution R0, uninformative uniform distribution values 0 kappa. Users can change value kappa (.e., prior distribution changed uniform). case counts observed, influence prior distribution lessen final estimate. method based approximation SIR model, valid beginning epidemic. method assumes mean serial distribution (sometimes called serial interval) known. final estimate can quite sensitive value, sensitivity testing strongly recommended. Users careful units time (e.g., counts observed daily weekly?) implementing. code modified provide estimate even case counts equal zero present time intervals. done grouping counts periods time. Without grouping, presence zero counts, estimate can provided.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Sequential Bayes (seqB) β seq_bayes","text":"Bettencourt Riberio (PloS One, 2008)","code":""},{"path":[]},{"path":"https://MI2YorkU.github.io/Rnaught/reference/seq_bayes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sequential Bayes (seqB) β seq_bayes","text":"","code":"# Weekly data. cases <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4) # Obtain R0 when the serial distribution has a mean of five days. seq_bayes(cases, mu = 5 / 7) #> [1] 1.026563 # Obtain R0 when the serial distribution has a mean of three days. seq_bayes(cases, mu = 3 / 7) #> [1] 1.015938 # Obtain R0 when the serial distribution has a mean of seven days, and R0 is # believed to be at most 4. estimate <- seq_bayes(cases, mu = 1, kappa = 4) # Same as above, but return the posterior distribution of R0 instead of the # estimate. posterior <- seq_bayes(cases, mu = 1, kappa = 4, post = TRUE) # Display the support and probability mass function of the posterior. posterior$supp #> [1] 0.00 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10 0.11 0.12 0.13 0.14 #> [16] 0.15 0.16 0.17 0.18 0.19 0.20 0.21 0.22 0.23 0.24 0.25 0.26 0.27 0.28 0.29 #> [31] 0.30 0.31 0.32 0.33 0.34 0.35 0.36 0.37 0.38 0.39 0.40 0.41 0.42 0.43 0.44 #> [46] 0.45 0.46 0.47 0.48 0.49 0.50 0.51 0.52 0.53 0.54 0.55 0.56 0.57 0.58 0.59 #> [61] 0.60 0.61 0.62 0.63 0.64 0.65 0.66 0.67 0.68 0.69 0.70 0.71 0.72 0.73 0.74 #> [76] 0.75 0.76 0.77 0.78 0.79 0.80 0.81 0.82 0.83 0.84 0.85 0.86 0.87 0.88 0.89 #> [91] 0.90 0.91 0.92 0.93 0.94 0.95 0.96 0.97 0.98 0.99 1.00 1.01 1.02 1.03 1.04 #> [106] 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 #> [121] 1.20 1.21 1.22 1.23 1.24 1.25 1.26 1.27 1.28 1.29 1.30 1.31 1.32 1.33 1.34 #> [136] 1.35 1.36 1.37 1.38 1.39 1.40 1.41 1.42 1.43 1.44 1.45 1.46 1.47 1.48 1.49 #> [151] 1.50 1.51 1.52 1.53 1.54 1.55 1.56 1.57 1.58 1.59 1.60 1.61 1.62 1.63 1.64 #> [166] 1.65 1.66 1.67 1.68 1.69 1.70 1.71 1.72 1.73 1.74 1.75 1.76 1.77 1.78 1.79 #> [181] 1.80 1.81 1.82 1.83 1.84 1.85 1.86 1.87 1.88 1.89 1.90 1.91 1.92 1.93 1.94 #> [196] 1.95 1.96 1.97 1.98 1.99 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 #> [211] 2.10 2.11 2.12 2.13 2.14 2.15 2.16 2.17 2.18 2.19 2.20 2.21 2.22 2.23 2.24 #> [226] 2.25 2.26 2.27 2.28 2.29 2.30 2.31 2.32 2.33 2.34 2.35 2.36 2.37 2.38 2.39 #> [241] 2.40 2.41 2.42 2.43 2.44 2.45 2.46 2.47 2.48 2.49 2.50 2.51 2.52 2.53 2.54 #> [256] 2.55 2.56 2.57 2.58 2.59 2.60 2.61 2.62 2.63 2.64 2.65 2.66 2.67 2.68 2.69 #> [271] 2.70 2.71 2.72 2.73 2.74 2.75 2.76 2.77 2.78 2.79 2.80 2.81 2.82 2.83 2.84 #> [286] 2.85 2.86 2.87 2.88 2.89 2.90 2.91 2.92 2.93 2.94 2.95 2.96 2.97 2.98 2.99 #> [301] 3.00 3.01 3.02 3.03 3.04 3.05 3.06 3.07 3.08 3.09 3.10 3.11 3.12 3.13 3.14 #> [316] 3.15 3.16 3.17 3.18 3.19 3.20 3.21 3.22 3.23 3.24 3.25 3.26 3.27 3.28 3.29 #> [331] 3.30 3.31 3.32 3.33 3.34 3.35 3.36 3.37 3.38 3.39 3.40 3.41 3.42 3.43 3.44 #> [346] 3.45 3.46 3.47 3.48 3.49 3.50 3.51 3.52 3.53 3.54 3.55 3.56 3.57 3.58 3.59 #> [361] 3.60 3.61 3.62 3.63 3.64 3.65 3.66 3.67 3.68 3.69 3.70 3.71 3.72 3.73 3.74 #> [376] 3.75 3.76 3.77 3.78 3.79 3.80 3.81 3.82 3.83 3.84 3.85 3.86 3.87 3.88 3.89 #> [391] 3.90 3.91 3.92 3.93 3.94 3.95 3.96 3.97 3.98 3.99 4.00 posterior$pmf #> [1] 4.396081e-14 6.866777e-14 1.069979e-13 1.663113e-13 2.578585e-13 #> [6] 3.987896e-13 6.151736e-13 9.465244e-13 1.452563e-12 2.223289e-12 #> [11] 3.393931e-12 5.167074e-12 7.845296e-12 1.187914e-11 1.793742e-11 #> [16] 2.700983e-11 4.055633e-11 6.072366e-11 9.065827e-11 1.349567e-10 #> [21] 2.003117e-10 2.964355e-10 4.373744e-10 6.433725e-10 9.435054e-10 #> [26] 1.379386e-09 2.010358e-09 2.920742e-09 4.229916e-09 6.106257e-09 #> [31] 8.786364e-09 1.260143e-08 1.801328e-08 2.566338e-08 3.643912e-08 #> [36] 5.156328e-08 7.271379e-08 1.021837e-07 1.430935e-07 1.996715e-07 #> [41] 2.776227e-07 3.846102e-07 5.308815e-07 7.300785e-07 1.000278e-06 #> [46] 1.365319e-06 1.856496e-06 2.514686e-06 3.393017e-06 4.560205e-06 #> [51] 6.104659e-06 8.139541e-06 1.080892e-05 1.429523e-05 1.882819e-05 #> [56] 2.469542e-05 3.225496e-05 4.194988e-05 5.432506e-05 7.004650e-05 #> [61] 8.992291e-05 1.149299e-04 1.462361e-04 1.852322e-04 2.335598e-04 #> [66] 2.931434e-04 3.662201e-04 4.553696e-04 5.635406e-04 6.940727e-04 #> [71] 8.507116e-04 1.037615e-03 1.259347e-03 1.520857e-03 1.827440e-03 #> [76] 2.184679e-03 2.598363e-03 3.074378e-03 3.618573e-03 4.236597e-03 #> [81] 4.933708e-03 5.714562e-03 6.582973e-03 7.541662e-03 8.591990e-03 #> [86] 9.733699e-03 1.096466e-02 1.228062e-02 1.367503e-02 1.513890e-02 #> [91] 1.666067e-02 1.822624e-02 1.981901e-02 2.142007e-02 2.300844e-02 #> [96] 2.456146e-02 2.605520e-02 2.746508e-02 2.876640e-02 2.993509e-02 #> [101] 3.094837e-02 3.178548e-02 3.242832e-02 3.286214e-02 3.307605e-02 #> [106] 3.306344e-02 3.282231e-02 3.235539e-02 3.167013e-02 3.077854e-02 #> [111] 2.969682e-02 2.844487e-02 2.704571e-02 2.552471e-02 2.390888e-02 #> [116] 2.222595e-02 2.050365e-02 1.876888e-02 1.704700e-02 1.536123e-02 #> [121] 1.373213e-02 1.217724e-02 1.071084e-02 9.343864e-03 8.083917e-03 #> [126] 6.935429e-03 5.899896e-03 4.976201e-03 4.160989e-03 3.449076e-03 #> [131] 2.833858e-03 2.307727e-03 1.862441e-03 1.489475e-03 1.180313e-03 #> [136] 9.266886e-04 7.207803e-04 5.553459e-04 4.238132e-04 3.203273e-04 #> [141] 2.397617e-04 1.777009e-04 1.304008e-04 9.473459e-05 6.812875e-05 #> [146] 4.849552e-05 3.416469e-05 2.381841e-05 1.643092e-05 1.121447e-05 #> [151] 7.572111e-06 5.057422e-06 3.340936e-06 2.182658e-06 1.410047e-06 #> [156] 9.006636e-07 5.687529e-07 3.550312e-07 2.190488e-07 1.335660e-07 #> [161] 8.047851e-08 4.791165e-08 2.817909e-08 1.637135e-08 9.394205e-09 #> [166] 5.323528e-09 2.978849e-09 1.645703e-09 8.975385e-10 4.831664e-10 #> [171] 2.566999e-10 1.345806e-10 6.961600e-11 3.552605e-11 1.788285e-11 #> [176] 8.878079e-12 4.346434e-12 2.098061e-12 9.984180e-13 4.683320e-13 #> [181] 2.165108e-13 9.863385e-14 4.427200e-14 1.957601e-14 8.526007e-15 #> [186] 3.657023e-15 1.544555e-15 6.422519e-16 2.628849e-16 1.059047e-16 #> [191] 4.198412e-17 1.637588e-17 6.283525e-18 2.371425e-18 8.801378e-19 #> [196] 3.211841e-19 1.152248e-19 4.063045e-20 1.407979e-20 4.794057e-21 #> [201] 1.603601e-21 5.268629e-22 1.699923e-22 5.385323e-23 1.674809e-23 #> [206] 5.112219e-24 1.531308e-24 4.500307e-25 1.297374e-25 3.668155e-26 #> [211] 1.016962e-26 2.764082e-27 7.363758e-28 1.922485e-28 4.917601e-29 #> [216] 1.232200e-29 3.023823e-30 7.265876e-31 1.709166e-31 3.935069e-32 #> [221] 8.865403e-33 1.954015e-33 4.212549e-34 8.880821e-35 1.830437e-35 #> [226] 3.687665e-36 7.260114e-37 1.396466e-37 2.623677e-38 4.813725e-39 #> [231] 8.622619e-40 1.507577e-40 2.572153e-41 4.281381e-42 6.950773e-43 #> [236] 1.100362e-43 1.698170e-44 2.554224e-45 3.743317e-46 5.343929e-47 #> [241] 7.429450e-48 1.005609e-48 1.324832e-49 1.698377e-50 2.118019e-51 #> [246] 2.568782e-52 3.029042e-53 3.471688e-54 3.866425e-55 4.182989e-56 #> [251] 4.394865e-57 4.482891e-58 4.438084e-59 4.263117e-60 3.972112e-61 #> [256] 3.588768e-62 3.143145e-63 2.667736e-64 2.193531e-65 1.746742e-66 #> [261] 1.346659e-67 1.004822e-68 7.254056e-70 5.065108e-71 3.419533e-72 #> [266] 2.231354e-73 1.406840e-74 8.567343e-76 5.037567e-77 2.859011e-78 #> [271] 1.565585e-79 8.268889e-81 4.210849e-82 2.066735e-83 9.773085e-85 #> [276] 4.450901e-86 1.951504e-87 8.234368e-89 3.342436e-90 1.304664e-91 #> [281] 4.895156e-93 1.764793e-94 6.110914e-96 2.031551e-97 6.481579e-99 #> [286] 1.983744e-100 5.821848e-102 1.637658e-103 4.413549e-105 1.139116e-106 #> [291] 2.814324e-108 6.652979e-110 1.504185e-111 3.251137e-113 6.714617e-115 #> [296] 1.324527e-116 2.494329e-118 4.482263e-120 7.682227e-122 1.255211e-123 #> [301] 1.954236e-125 2.897728e-127 4.090211e-129 5.493210e-131 7.015875e-133 #> [306] 8.517133e-135 9.822891e-137 1.075711e-138 1.117987e-140 1.102133e-142 #> [311] 1.030047e-144 9.121635e-147 7.649726e-149 6.072101e-151 4.559445e-153 #> [316] 3.236849e-155 2.171329e-157 1.375543e-159 8.224662e-162 4.638796e-164 #> [321] 2.466499e-166 1.235627e-168 5.828612e-171 2.587326e-173 1.080141e-175 #> [326] 4.238233e-178 1.562047e-180 5.404238e-183 1.754003e-185 5.337064e-188 #> [331] 1.521491e-190 4.061129e-193 1.014255e-195 2.368537e-198 5.168362e-201 #> [336] 1.053099e-203 2.002304e-206 3.550040e-209 5.865079e-212 9.022847e-215 #> [341] 1.291610e-217 1.719185e-220 2.126178e-223 2.441418e-226 2.600913e-229 #> [346] 2.568760e-232 2.350200e-235 1.990379e-238 1.559119e-241 1.128742e-244 #> [351] 7.546371e-248 4.655454e-251 2.647985e-254 1.387535e-257 6.692519e-261 #> [356] 2.968866e-264 1.210268e-267 4.529956e-271 1.555446e-274 4.895396e-278 #> [361] 1.410954e-281 3.720881e-285 8.970133e-289 1.975060e-292 3.968208e-296 #> [366] 7.268446e-300 1.212601e-303 1.840840e-307 2.540527e-311 3.184384e-315 #> [371] 3.621946e-319 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [376] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [381] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [386] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [391] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [396] 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 0.000000e+00 #> [401] 0.000000e+00 # Note that the following always holds: estimate == sum(posterior$supp * posterior$pmf) #> [1] TRUE"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/web.html","id":null,"dir":"Reference","previous_headings":"","what":"Launch the Rnaught Web Application β web","title":"Launch the Rnaught Web Application β web","text":"entry point Rnaught web application, creates returns Shiny app object. invoked directly, web application launched.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/web.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Launch the Rnaught Web Application β web","text":"","code":"web()"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/web.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Launch the Rnaught Web Application β web","text":"Shiny app object Rnaught web application.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/web.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Launch the Rnaught Web Application β web","text":"following dependencies required run application: shiny bslib DT plotly packages missing launch, prompt appear install . configure settings port, host default browser, set Shiny's global options (see shiny::runApp()).","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":null,"dir":"Reference","previous_headings":"","what":"White and Pagano (WP) β wp","title":"White and Pagano (WP) β wp","text":"function implements R0 estimation due White Pagano (Statistics Medicine, 2008). method based maximum likelihood estimation Poisson transmission model. See details important implementation notes.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"White and Pagano (WP) β wp","text":"","code":"wp( cases, mu = NA, serial = FALSE, grid_length = 100, max_shape = 10, max_scale = 10 )"},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"White and Pagano (WP) β wp","text":"cases Vector case counts. vector must length least two contain positive integers. mu Mean serial distribution (defaults NA). must positive number NA. number specified, value match case counts time units. example, case counts weekly serial distribution mean seven days, mu set 1. case counts daily serial distribution mean seven days, mu set 7. serial Whether return estimated serial distribution addition estimate R0 (defaults FALSE). must value identical TRUE FALSE. grid_length length grid grid search (defaults 100). must positive integer. used mu set NA. grid search go combinations shape scale parameters gamma distribution, grid_length evenly spaced values 0 (exclusive) max_shape max_scale (inclusive), respectively. Note larger values result longer search time. max_shape largest possible value shape parameter grid search (defaults 10). must positive number. used mu set NA. Note larger values result longer search time, may cause numerical instabilities. max_scale largest possible value scale parameter grid search (defaults 10). must positive number. used mu set NA. Note larger values result longer search time, may cause numerical instabilities.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"White and Pagano (WP) β wp","text":"serial identical TRUE, list containing following components returned: r0 - estimate R0 supp - support estimated serial distribution pmf - probability mass function estimated serial distribution Otherwise, serial identical FALSE, estimate R0 returned.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"White and Pagano (WP) β wp","text":"method based Poisson transmission model, hence may valid beginning epidemic. model, serial distribution assumed discrete finite number possible values. implementation, mu NA, serial distribution taken discretized version gamma distribution shape parameter 1 scale parameter mu (hence mean mu). mu NA, function implements grid search algorithm find maximum likelihood estimator possible gamma distributions unknown shape scale, restricting prespecified grid (see parameters grid_length, max_shape max_scale). cases, largest value support chosen cumulative distribution function original (pre-discretized) gamma distribution cumulative probability 0.999 value. serial distribution known (.e., mu NA), sensitivity testing mu strongly recommended. serial distribution unknown (.e., mu NA), likelihood function can flat near maximum, resulting numerical instability optimizer. mu NA, implementation takes considerably longer run. Users careful units time (e.g., counts observed daily weekly?) implementing. model developed White Pagano (2008) discrete, hence serial distribution finite discrete. implementation, input value mu continuous distribution. algorithm discretizes input, mean estimated serial distribution returned (serial set TRUE) differ mu somewhat. say, user notices input mu mean estimated serial distribution different, expected, caused discretization.","code":""},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"White and Pagano (WP) β wp","text":"White Pagano (Statistics Medicine, 2008)","code":""},{"path":[]},{"path":"https://MI2YorkU.github.io/Rnaught/reference/wp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"White and Pagano (WP) β wp","text":"","code":"# Weekly data. cases <- c(1, 4, 10, 5, 3, 4, 19, 3, 3, 14, 4) # Obtain R0 when the serial distribution has a mean of five days. wp(cases, mu = 5 / 7) #> [1] 1.107862 # Obtain R0 when the serial distribution has a mean of three days. wp(cases, mu = 3 / 7) #> [1] 1.067642 # Obtain R0 when the serial distribution is unknown. # Note that this will take longer to run than when `mu` is known. wp(cases) #> [1] 1.495574 # Same as above, but specify custom grid search parameters. The larger any of # the parameters, the longer the search will take, but with potentially more # accurate estimates. wp(cases, grid_length = 40, max_shape = 4, max_scale = 4) #> [1] 1.495574 # Return the estimated serial distribution in addition to the estimate of R0. estimate <- wp(cases, serial = TRUE) # Display the estimate of R0, as well as the support and probability mass # function of the estimated serial distribution returned by the grid search. estimate$r0 #> [1] 1.495574 estimate$supp #> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 estimate$pmf #> [1] 0.3295449612 0.1855210503 0.1282030815 0.0920057871 0.0672100630 #> [6] 0.0496097863 0.0368701329 0.0275354532 0.0206388543 0.0155131855 #> [11] 0.0116867019 0.0088202295 0.0066670102 0.0050459517 0.0038232730 #> [16] 0.0028996361 0.0022009767 0.0016718921 0.0012708261 0.0009665381 #> [21] 0.0007354976 0.0005599523 0.0004264906 0.0003249676 0.0002477014"}]
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git.nmode.ca / Rnaught / commitdiff
