diff --git a/public/404.html b/public/404.html
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-<pre> GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
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- Copyright (C) {year} {name of author}
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- This program is free software: you can redistribute it and/or modify
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- but WITHOUT ANY WARRANTY; without even the implied warranty of
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-Also add information on how to contact you by electronic and paper mail.
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- {project} Copyright (C) {year} {fullname}
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
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-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
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- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
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-<http://www.gnu.org/philosophy/why-not-lgpl.html>.
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- <h1 data-toc-skip>Introduction to sirplus (V2)</h1>
-
- <h4 class="date">Last updated: 12 April 2020</h4>
-
-
- <div class="hidden name"><code>sirplus_intro_v2.Rmd</code></div>
-
- </div>
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-
-
-<p><img src="sirplus-logo-small.png"></p>
-<p>The sirplus package makes it easy to generate stochastic individual compartment models (ICMs) to simulate contagious disease spread using compartments not available in standard SIR packages. This method and most of the code was originally written by Tim Churches (see his <a href="https://timchurches.github.io/blog/posts/2020-03-18-modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-2/">blog post</a>). The sirplus package was developed by the Bioinformatics & Cellular Genomics team at St. Vincent’s Institute of Medical Research in order to help St. Vincents’ Hospital model the COVID-19 pandemic.</p>
-<p>The compartments available in this package include:</p>
-<table class="table">
-<colgroup>
-<col width="13%">
-<col width="86%">
-</colgroup>
-<thead><tr class="header">
-<th>Compartment</th>
-<th>Functional definition</th>
-</tr></thead>
-<tbody>
-<tr class="odd">
-<td><strong>S</strong></td>
-<td>Susceptible individuals</td>
-</tr>
-<tr class="even">
-<td><strong>E</strong></td>
-<td>Exposed <strong>and</strong> infected, not yet symptomatic but potentially infectious</td>
-</tr>
-<tr class="odd">
-<td><strong>I</strong></td>
-<td>Infected, symptomatic <strong>and</strong> infectious</td>
-</tr>
-<tr class="even">
-<td><strong>Q</strong></td>
-<td>Infectious, but (self-)isolated</td>
-</tr>
-<tr class="odd">
-<td><strong>H</strong></td>
-<td>Requiring hospitalisation (would normally be hospitalised if capacity available)</td>
-</tr>
-<tr class="even">
-<td><strong>R</strong></td>
-<td>Recovered, immune from further infection</td>
-</tr>
-<tr class="odd">
-<td><strong>F</strong></td>
-<td>Case fatality (death due to infection, not other causes)</td>
-</tr>
-</tbody>
-</table>
-<p>The diagram below shows the model structure and how the parameters and compartments associate with each other. See Tim Churches’s <a href="https://timchurches.github.io/blog/posts/2020-03-18-modelling-the-effects-of-public-health-interventions-on-covid-19-transmission-part-2/">blog post</a> for more details.</p>
-<p><img src="model_diagram.png"></p>
-<table class="table">
-<colgroup>
-<col width="13%">
-<col width="16%">
-<col width="69%">
-</colgroup>
-<thead><tr class="header">
-<th>trasnitions</th>
-<th>Description</th>
-<th>Parameters (with default values)</th>
-</tr></thead>
-<tbody>
-<tr class="odd">
-<td><strong>inf</strong></td>
-<td>Infection due to contact</td>
-<td>
-<code>act.rate.*</code> and <code>inf.prob.*</code>, where <code><a href="https://rdrr.io/r/base/Arithmetic.html">*</a></code> = <code>i</code>, <code>e</code>, <code>q</code>
-</td>
-</tr>
-<tr class="even">
-<td><strong>prog</strong></td>
-<td>Progress from asymptomatic to symptomatic</td>
-<td>
-<code>prog.rand = FALSE</code>, <code>prog.rate</code>, <code>prog.dist.scale = 5</code>, <code>prog.dist.shape = 1.5</code>
-</td>
-</tr>
-<tr class="odd">
-<td><strong>quar</strong></td>
-<td>From infectious to quarantine</td>
-<td>
-<code>quar.rand = TRUE</code>, <code>quar.rate = 1/30</code>
-</td>
-</tr>
-<tr class="even">
-<td><strong>hosp</strong></td>
-<td>From infected (both before and during quarantine) to require hospitalisation</td>
-<td>
-<code>quar.rand = TRUE</code>, <code>quar.rate = 1/30</code>
-</td>
-</tr>
-<tr class="odd">
-<td><strong>rec</strong></td>
-<td>From infected to recovered without hospitalization</td>
-<td>
-<code>rec.rand = FALSE</code>, <code>prog.dist.scale = 35</code>, <code>prog.dist.shape = 1.5</code>
-</td>
-</tr>
-<tr class="even">
-<td><strong>arec</strong></td>
-<td>Exposed individuals recovered before symptomatic</td>
-<td>
-<code>arec.rand = TRUE</code>, <code>arec.rate = 0.05</code>
-</td>
-</tr>
-<tr class="odd">
-<td><strong>disch</strong></td>
-<td>recovery after hospitalization</td>
-<td>
-<code>disch.rand = TRUE</code>, <code>disch.rate = 1/15</code>
-</td>
-</tr>
-<tr class="even">
-<td><strong>fat</strong></td>
-<td>Fatality</td>
-<td>
-<code>fat.rate.base = 1/50</code>, <code>hosp.cap = 40</code>, <code>fat.rate.overcap = 1/25</code>, <code>fat.tcoeff = 0.5</code>
-</td>
-</tr>
-</tbody>
-</table>
-<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="co">#library(sirplus)</span>
-<span class="kw pkg">devtools</span><span class="kw ns">::</span><span class="fu"><a href="https://devtools.r-lib.org//reference/load_all.html">load_all</a></span>(<span class="st">"."</span>)
-<span class="co">## Loading sirplus</span></pre></body></html></div>
-<div id="simulate-and-inspect-a-baseline-sirplus-model" class="section level2">
-<h2 class="hasAnchor">
-<a href="#simulate-and-inspect-a-baseline-sirplus-model" class="anchor"></a>Simulate and inspect a baseline sirplus model</h2>
-<div id="set-parameters" class="section level3">
-<h3 class="hasAnchor">
-<a href="#set-parameters" class="anchor"></a>Set parameters</h3>
-<p>Here we will simulate the epidemiological data for a made-up population with 1000 susceptible individuals (S), 50 that are infected but not in the hospital or in self-quarantine (I; maybe people that are infected/symptomatic but not tested/ aware), 10 confirmed cases that have self-isolated (Q), and 1 confirmed case that has been hospitalized (H). We call this the baseline model because it uses default parameters for disease spread (i.e. no additional interventions).</p>
-<div class="sourceCode" id="cb2"><html><body><pre class="r"><span class="no">s.num</span> <span class="kw"><-</span> <span class="fl">2000</span> <span class="co"># number susceptible</span>
-<span class="no">i.num</span> <span class="kw"><-</span> <span class="fl">15</span> <span class="co"># number infected </span>
-<span class="no">q.num</span> <span class="kw"><-</span> <span class="fl">5</span> <span class="co"># number in self-isolation</span>
-<span class="no">h.num</span> <span class="kw"><-</span> <span class="fl">1</span> <span class="co"># number in the hospital</span>
-<span class="no">nsteps</span> <span class="kw"><-</span> <span class="fl">90</span> <span class="co"># number of steps (e.g. days) to simulate</span>
-
-<span class="no">control</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/control_seiqhrf.html">control_seiqhrf</a></span>(<span class="kw">nsteps</span> <span class="kw">=</span> <span class="no">nsteps</span>)
-<span class="no">param</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/param_seiqhrf.html">param_seiqhrf</a></span>()
-<span class="no">init</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/init_seiqhrf.html">init_seiqhrf</a></span>(<span class="kw">s.num</span> <span class="kw">=</span> <span class="no">s.num</span>, <span class="kw">i.num</span> <span class="kw">=</span> <span class="no">i.num</span>, <span class="kw">q.num</span> <span class="kw">=</span> <span class="no">q.num</span>, <span class="kw">h.num</span> <span class="kw">=</span> <span class="no">h.num</span>)
-
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">init</span>)
-<span class="co">## SEIQHRF Initial Conditions</span>
-<span class="co">## ===========================</span>
-<span class="co">## </span>
-<span class="co">## User specified control parameters:</span>
-<span class="co">## ---------------------------</span>
-<span class="co">## s.num = 2000</span>
-<span class="co">## i.num = 15</span>
-<span class="co">## q.num = 5</span>
-<span class="co">## h.num = 1</span>
-<span class="co">## </span>
-<span class="co">## Default control parameters:</span>
-<span class="co">## ---------------------------</span>
-<span class="co">## e.num = 0</span>
-<span class="co">## r.num = 0</span>
-<span class="co">## f.num = 0</span>
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">control</span>)
-<span class="co">## SEIQHRF Control Settings</span>
-<span class="co">## ===========================</span>
-<span class="co">## </span>
-<span class="co">## User specified control parameters:</span>
-<span class="co">## ---------------------------</span>
-<span class="co">## nsteps = 90</span>
-<span class="co">## </span>
-<span class="co">## Default control parameters:</span>
-<span class="co">## ---------------------------</span>
-<span class="co">## type = SEIQHRF</span>
-<span class="co">## nsims = 8</span>
-<span class="co">## prog.rand = FALSE</span>
-<span class="co">## quar.rand = TRUE</span>
-<span class="co">## hosp.rand = TRUE</span>
-<span class="co">## disch.rand = TRUE</span>
-<span class="co">## rec.rand = FALSE</span>
-<span class="co">## arec.rand = TRUE</span>
-<span class="co">## fat.rand = TRUE</span>
-<span class="co">## a.rand = TRUE</span>
-<span class="co">## d.rand = TRUE</span>
-<span class="co">## verbose = FALSE</span>
-<span class="co">## verbose.int = 0</span>
-<span class="co">## skip.check = FALSE</span>
-<span class="co">## ncores = 4</span>
-<span class="co">## bi.mods = initialize.FUN infection.FUN recovery.FUN departures.FUN arrivals.FUN </span>
-<span class="co">## get_prev.FUN</span>
-<span class="co">## Base Modules: initialize.FUN infection.FUN recovery.FUN departures.FUN </span>
-<span class="co">## arrivals.FUN get_prev.FUN</span>
-<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">param</span>)
-<span class="co">## SEIQHRF Parameters</span>
-<span class="co">## ===========================</span>
-<span class="co">## </span>
-<span class="co">## User specified control parameters:</span>
-<span class="co">## ---------------------------</span>
-<span class="co">## </span>
-<span class="co">## Default control parameters:</span>
-<span class="co">## ---------------------------</span>
-<span class="co">## inf.prob.e = 0.02</span>
-<span class="co">## act.rate.e = 10</span>
-<span class="co">## inf.prob.i = 0.05</span>
-<span class="co">## act.rate.i = 10</span>
-<span class="co">## inf.prob.q = 0.02</span>
-<span class="co">## act.rate.q = 2.5</span>
-<span class="co">## prog.rate = 0.1</span>
-<span class="co">## quar.rate = 0.03333333</span>
-<span class="co">## hosp.rate = 0.01</span>
-<span class="co">## disch.rate = 0.06666667</span>
-<span class="co">## rec.rate = 0.071</span>
-<span class="co">## arec.rate = 0.05</span>
-<span class="co">## prog.dist.scale = 5</span>
-<span class="co">## prog.dist.shape = 1.5</span>
-<span class="co">## quar.dist.scale = 1</span>
-<span class="co">## quar.dist.shape = 1</span>
-<span class="co">## hosp.dist.scale = 1</span>
-<span class="co">## hosp.dist.shape = 1</span>
-<span class="co">## disch.dist.scale = 1</span>
-<span class="co">## disch.dist.shape = 1</span>
-<span class="co">## rec.dist.scale = 35</span>
-<span class="co">## rec.dist.shape = 1.5</span>
-<span class="co">## arec.dist.scale = 35</span>
-<span class="co">## arec.dist.shape = 1.5</span>
-<span class="co">## fat.rate.base = 0.02</span>
-<span class="co">## hosp.cap = 40</span>
-<span class="co">## fat.rate.overcap = 0.04</span>
-<span class="co">## fat.tcoeff = 0.5</span>
-<span class="co">## a.rate = 2.876712e-05</span>
-<span class="co">## a.prop.e = 0.01</span>
-<span class="co">## a.prop.i = 0.001</span>
-<span class="co">## a.prop.q = 0.01</span>
-<span class="co">## ds.rate = 1.917808e-05</span>
-<span class="co">## de.rate = 1.917808e-05</span>
-<span class="co">## di.rate = 1.917808e-05</span>
-<span class="co">## dq.rate = 1.917808e-05</span>
-<span class="co">## dh.rate = 5.479452e-05</span>
-<span class="co">## dr.rate = 1.917808e-05</span>
-<span class="co">## act.rate = 1</span>
-<span class="co">## groups = 1</span></pre></body></html></div>
-</div>
-<div id="simulate-baseline" class="section level3">
-<h3 class="hasAnchor">
-<a href="#simulate-baseline" class="anchor"></a>Simulate baseline</h3>
-<p>This will produce an seiqhrf object.</p>
-<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">baseline_sim</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/seiqhrf.html">seiqhrf</a></span>(<span class="no">init</span>, <span class="no">control</span>, <span class="no">param</span>)
-<span class="no">baseline_sim</span>
-<span class="co">## SEIQHRF Model Simulation</span>
-<span class="co">## =======================</span>
-<span class="co">## Model class: seiqhrf</span>
-<span class="co">## </span>
-<span class="co">## Simulation Summary</span>
-<span class="co">## -----------------------</span>
-<span class="co">## Model type: SEIQHRF</span>
-<span class="co">## Number of simulations: 8</span>
-<span class="co">## Number of time steps: 90</span>
-<span class="co">## </span>
-<span class="co">## Model Output (variable names)</span>
-<span class="co">## -----------------------</span>
-<span class="co">## s.num i.num num se.flow is.flow iq.flow iq2h.flow hf.flow </span>
-<span class="co">## ds.flow de.flow di.flow dq.flow dh.flow dr.flow a.flow </span>
-<span class="co">## a.e.flow a.i.flow a.q.flow e.num r.num q.num h.num f.num</span></pre></body></html></div>
-</div>
-<div id="extract-summary-of-the-simulation" class="section level3">
-<h3 class="hasAnchor">
-<a href="#extract-summary-of-the-simulation" class="anchor"></a>Extract summary of the simulation</h3>
-<div class="sourceCode" id="cb4"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">baseline_sim</span>)
-<span class="co">## Peaks of SEIQHRF Model Simulation: </span>
-<span class="co">## ===============================</span>
-<span class="co">## Max Time</span>
-<span class="co">## s.num 2000.00 1</span>
-<span class="co">## e.num 340.50 21</span>
-<span class="co">## i.num 532.25 26</span>
-<span class="co">## q.num 110.25 29</span>
-<span class="co">## h.num 58.88 35</span>
-<span class="co">## r.num 1928.88 90</span>
-<span class="co">## f.num 3.62 78</span>
-<span class="fu"><a href="https://rdrr.io/r/utils/ls_str.html">ls.str</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">baseline_sim</span>))
-<span class="co">## e.num : List of 4</span>
-<span class="co">## $ mean : Named num [1:90] NaN 9 19.2 27.2 36.5 ...</span>
-<span class="co">## $ sd : Named num [1:90] NA 3.34 6.5 7.25 6.72 ...</span>
-<span class="co">## $ CI : num [1:90, 1:2] NaN 2.46 6.52 13.05 23.33 ...</span>
-<span class="co">## $ qntCI: num [1:90, 1:2] NA 4.53 11.7 17.52 28 ...</span>
-<span class="co">## f.num : List of 4</span>
-<span class="co">## $ mean : Named num [1:90] NaN 0 0 0 0 0 0 0 0 0 ...</span>
-<span class="co">## $ sd : Named num [1:90] NA 0 0 0 0 0 0 0 0 0 ...</span>
-<span class="co">## $ CI : num [1:90, 1:2] NaN 0 0 0 0 0 0 0 0 0 ...</span>
-<span class="co">## $ qntCI: num [1:90, 1:2] NA 0 0 0 0 0 0 0 0 0 ...</span>
-<span class="co">## h.num : List of 4</span>
-<span class="co">## $ mean : Named num [1:90] NaN 1.25 1.12 1 1.38 ...</span>
-<span class="co">## $ sd : Named num [1:90] NA 0.707 1.126 1.069 1.061 ...</span>
-<span class="co">## $ CI : num [1:90, 1:2] NaN -0.136 -1.082 -1.095 -0.704 ...</span>
-<span class="co">## $ qntCI: num [1:90, 1:2] NA 1 0 0 0.175 0 1 1 1 1 ...</span>
-<span class="co">## i.num : List of 4</span>
-<span class="co">## $ mean : Named num [1:90] 15 14.8 14.9 16.4 19.9 ...</span>
-<span class="co">## $ sd : Named num [1:90] 0 0.707 1.246 1.061 2.997 ...</span>
-<span class="co">## $ CI : num [1:90, 1:2] 15 13.4 12.4 14.3 14 ...</span>
-<span class="co">## $ qntCI: num [1:90, 1:2] 15 13.4 13.2 15 17.2 ...</span>
-<span class="co">## q.num : List of 4</span>
-<span class="co">## $ mean : Named num [1:90] NaN 5 5.38 6.5 7.75 ...</span>
-<span class="co">## $ sd : Named num [1:90] NA 0 0.916 0.535 1.035 ...</span>
-<span class="co">## $ CI : num [1:90, 1:2] NaN 5 3.58 5.45 5.72 ...</span>
-<span class="co">## $ qntCI: num [1:90, 1:2] NA 5 4.17 6 6.17 ...</span>
-<span class="co">## r.num : List of 4</span>
-<span class="co">## $ mean : Named num [1:90] NaN 0.5 1.75 3 5.12 ...</span>
-<span class="co">## $ sd : Named num [1:90] NA 0.535 1.581 2.138 1.458 ...</span>
-<span class="co">## $ CI : num [1:90, 1:2] NaN -0.548 -1.349 -1.191 2.268 ...</span>
-<span class="co">## $ qntCI: num [1:90, 1:2] NA 0 0 0 4 ...</span>
-<span class="co">## s.num : List of 4</span>
-<span class="co">## $ mean : Named num [1:90] 2000 1990 1979 1967 1950 ...</span>
-<span class="co">## $ sd : Named num [1:90] 0 3.16 6.25 7.38 8.26 ...</span>
-<span class="co">## $ CI : num [1:90, 1:2] 2000 1984 1966 1952 1934 ...</span>
-<span class="co">## $ qntCI: num [1:90, 1:2] 2000 1986 1968 1955 1936 ...</span></pre></body></html></div>
-</div>
-<div id="inspect-baseline-transition-distributions" class="section level3">
-<h3 class="hasAnchor">
-<a href="#inspect-baseline-transition-distributions" class="anchor"></a>Inspect baseline transition distributions</h3>
-<p>The sirplus model controls transitions between compartments, i.e. a change in state for an individual (e.g. going from self-isolation to hospital), using a variety of transition parameters. You can use the <code><a href="https://rdrr.io/r/graphics/plot.html">plot()</a></code> functions, and set parameter <code>method</code> as <code>times</code> to examine the distributions of timings for various transitions based on these parameters. In the case of a disease with observed data available, these plots can be used to sanity check parameter settings.</p>
-<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(<span class="no">baseline_sim</span>, <span class="st">"times"</span>)</pre></body></html></div>
-<p><img src="sirplus_intro_v2_files/figure-html/baseline%20sims-1.png" width="700"></p>
-</div>
-<div id="plot-baseline-sirplus-results" class="section level3">
-<h3 class="hasAnchor">
-<a href="#plot-baseline-sirplus-results" class="anchor"></a>Plot baseline sirplus results</h3>
-<p>To visualise your sirplus model, you can plot the change in prevalence (i.e. people) over time in each compartment. By default, this plotting function shows the mean count across all simulations and the 95th quantile in the ribbon. You can hide the CI by setting parameter <code>ci</code> to <code>FALSE</code>.</p>
-<div class="sourceCode" id="cb6"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(<span class="no">baseline_sim</span>,
- <span class="kw">start_date</span> <span class="kw">=</span> <span class="kw pkg">lubridate</span><span class="kw ns">::</span><span class="fu"><a href="http://lubridate.tidyverse.org/reference/ymd.html">ymd</a></span>(<span class="st">"2020-01-01"</span>),
- <span class="kw">comp_remove</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">'s.num'</span>, <span class="st">'r.num'</span>),
- <span class="kw">plot_title</span> <span class="kw">=</span> <span class="st">'Baseline Model'</span>)
-<span class="co">## Scale for 'colour' is already present. Adding another scale for 'colour',</span>
-<span class="co">## which will replace the existing scale.</span>
-<span class="co">## Warning: Removed 4 row(s) containing missing values (geom_path).</span></pre></body></html></div>
-<p><img src="sirplus_intro_v2_files/figure-html/viz%20prevalence-1.png" width="700"></p>
-</div>
-</div>
-<div id="run-an-experiment" class="section level2">
-<h2 class="hasAnchor">
-<a href="#run-an-experiment" class="anchor"></a>Run an experiment</h2>
-<p>With the sirplus package you can also set up experiments. We will set up two experiments here:</p>
-<ul>
-<li>Experiment #1: One week after the beginning of the epidemic, schools and non-essential businesses are closed to encourage social distancing. This causes the act.rate to gradually drop from 10 to 6 over the course of the next week. In this experiment, we imagine these policies are never lifted, so act.rate remains at 6 for the duration of the simulation.</li>
-<li>Experiment #2: Again, one week after the beginning of the epidemic, social distancing policies are put into place resulting in act.rate dropping from 10 to 6 over the next week. But after two weeks these policies are lifted and the act.rate returns to normal within the next week.</li>
-</ul>
-<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="co"># Experiment #1</span>
-<span class="no">vals</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">10</span>, <span class="fl">7</span>)
-<span class="no">timing</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">7</span>, <span class="fl">14</span>)
-<span class="no">act_rate</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/vary_param.html">vary_param</a></span>(<span class="kw">nstep</span> <span class="kw">=</span> <span class="no">nsteps</span>, <span class="kw">vals</span> <span class="kw">=</span> <span class="no">vals</span>, <span class="kw">timing</span> <span class="kw">=</span> <span class="no">timing</span>)
-
-<span class="no">control</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/control_seiqhrf.html">control_seiqhrf</a></span>(<span class="kw">nsteps</span> <span class="kw">=</span> <span class="no">nsteps</span>)
-<span class="no">param</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/param_seiqhrf.html">param_seiqhrf</a></span>(<span class="kw">act.rate.e</span> <span class="kw">=</span> <span class="no">act_rate</span>, <span class="kw">act.rate.i</span> <span class="kw">=</span> <span class="no">act_rate</span> * <span class="fl">0.5</span>)
-<span class="no">init</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/init_seiqhrf.html">init_seiqhrf</a></span>(<span class="kw">s.num</span> <span class="kw">=</span> <span class="no">s.num</span>, <span class="kw">i.num</span> <span class="kw">=</span> <span class="no">i.num</span>, <span class="kw">q.num</span> <span class="kw">=</span> <span class="no">q.num</span>, <span class="kw">h.num</span> <span class="kw">=</span> <span class="no">h.num</span>)
-<span class="no">sim_exp</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/seiqhrf.html">seiqhrf</a></span>(<span class="no">init</span>, <span class="no">control</span>, <span class="no">param</span>)
-
-<span class="co"># Experiment #2</span>
-<span class="no">vals</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">10</span>, <span class="fl">7</span>, <span class="fl">7</span>, <span class="fl">10</span>)
-<span class="no">timing</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">21</span>, <span class="fl">28</span>)
-<span class="no">act_rate_relax</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/vary_param.html">vary_param</a></span>(<span class="kw">nstep</span> <span class="kw">=</span> <span class="no">nsteps</span>, <span class="kw">vals</span> <span class="kw">=</span> <span class="no">vals</span>, <span class="kw">timing</span> <span class="kw">=</span> <span class="no">timing</span>)
-
-<span class="no">param</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/param_seiqhrf.html">param_seiqhrf</a></span>(<span class="kw">act.rate.e</span> <span class="kw">=</span> <span class="no">act_rate_relax</span>, <span class="kw">act.rate.i</span> <span class="kw">=</span> <span class="no">act_rate_relax</span> * <span class="fl">0.5</span>)
-<span class="no">sim_exp_relax</span> <span class="kw"><-</span> <span class="fu"><a href="../reference/seiqhrf.html">seiqhrf</a></span>(<span class="no">init</span>, <span class="no">control</span>, <span class="no">param</span>)
-
-<span class="co"># Compare experiments 1 and 2 to the baseline simulation</span>
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="st">"Baseline"</span> <span class="kw">=</span> <span class="no">baseline_sim</span>, <span class="st">"Closures"</span> <span class="kw">=</span> <span class="no">sim_exp</span>,
- <span class="st">"Closures (2 mo)"</span> <span class="kw">=</span> <span class="no">sim_exp_relax</span>),
- <span class="kw">start_date</span> <span class="kw">=</span> <span class="kw pkg">lubridate</span><span class="kw ns">::</span><span class="fu"><a href="http://lubridate.tidyverse.org/reference/ymd.html">ymd</a></span>(<span class="st">"2020-01-01"</span>),
- <span class="kw">comp_remove</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">'s.num'</span>, <span class="st">'r.num'</span>), <span class="kw">plot_title</span> <span class="kw">=</span> <span class="st">'Closures Experiment'</span>)
-<span class="co">## Scale for 'colour' is already present. Adding another scale for 'colour',</span>
-<span class="co">## which will replace the existing scale.</span>
-<span class="co">## Warning: Removed 64 row(s) containing missing values (geom_path).</span></pre></body></html></div>
-<p><img src="sirplus_intro_v2_files/figure-html/Experiment%20example%20with%20act.rate-1.png" width="700"></p>
-<p>From these results we see that this policy would likely reduce the peak number of infections from 500 to 300 and would “flatten the curve†for infections and thus hospitalizations (the peak in number of infected people is lower, but the number of people infected declines more slowly after the peak of the epidemic than in the baseline model).</p>
-</div>
-<div id="visualize-sirplus-advanced-plotting-options" class="section level2">
-<h2 class="hasAnchor">
-<a href="#visualize-sirplus-advanced-plotting-options" class="anchor"></a>Visualize sirplus: Advanced Plotting Options</h2>
-<div id="a--adding-known-data" class="section level3">
-<h3 class="hasAnchor">
-<a href="#a--adding-known-data" class="anchor"></a>A. Adding known data</h3>
-<p>You can use the <code><a href="https://rdrr.io/r/graphics/plot.html">plot()</a></code> function to include known compartment values alongside your simulations by supplying the known values as a dataframe to parameter <code>known</code>. This can be helpful when wanting to know how well experiments are simulating the epidemic progression to the point where you have data.</p>
-<p>For example, if we know the hospitalization numbers have been growing exponentially (by 0.2) at each step, we can see how that compares to our experiments.</p>
-<div class="sourceCode" id="cb8"><html><body><pre class="r"><span class="no">known</span> <span class="kw"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span>(<span class="st">'time'</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html">seq</a></span>(<span class="fl">1</span>:<span class="fl">30</span>), <span class="st">'h.num'</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html">seq</a></span>(<span class="fl">0</span>, <span class="fl">10</span>, <span class="kw">by</span><span class="kw">=</span><span class="fl">0.2</span>)[<span class="fl">1</span>:<span class="fl">30</span>])
-
-<span class="fu"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(<span class="fu"><a href="https://rdrr.io/r/base/list.html">list</a></span>(<span class="st">"Baseline"</span> <span class="kw">=</span> <span class="no">baseline_sim</span>, <span class="st">"Closures"</span> <span class="kw">=</span> <span class="no">sim_exp</span>,
- <span class="st">"Closures (2 mo)"</span> <span class="kw">=</span> <span class="no">sim_exp_relax</span>), <span class="kw">time_lim</span> <span class="kw">=</span> <span class="fl">45</span>,
- <span class="kw">known</span> <span class="kw">=</span> <span class="no">known</span>,
- <span class="kw">start_date</span> <span class="kw">=</span> <span class="kw pkg">lubridate</span><span class="kw ns">::</span><span class="fu"><a href="http://lubridate.tidyverse.org/reference/ymd.html">ymd</a></span>(<span class="st">"2020-01-01"</span>),
- <span class="kw">comp_remove</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">'s.num'</span>, <span class="st">'r.num'</span>, <span class="st">'e.num'</span>, <span class="st">'i.num'</span>, <span class="st">'q.num'</span>),
- <span class="kw">plot_title</span> <span class="kw">=</span> <span class="st">'Closures Experiment'</span>)
-<span class="co">## Scale for 'colour' is already present. Adding another scale for 'colour',</span>
-<span class="co">## which will replace the existing scale.</span>
-<span class="co">## Warning: Removed 32 row(s) containing missing values (geom_path).</span></pre></body></html></div>
-<p><img src="sirplus_intro_v2_files/figure-html/sirplus%20plot%20with%20known-1.png" width="700"> From this, we can see that the closure for 2 months is slightly pessimistic, while the closures simulation is close to the known hospitalization rate.</p>
-</div>
-<div id="b--plotting-compartment-separately" class="section level3">
-<h3 class="hasAnchor">
-<a href="#b--plotting-compartment-separately" class="anchor"></a>B. Plotting compartment separately</h3>
-<p>You can use the <code><a href="https://rdrr.io/r/graphics/plot.html">plot()</a></code> function to plot counts for each compartment separately by specifying <code>sep_compartments</code> as ‘y’. This can be useful when visualizing compartments on different scales (e.g. i.num v f.num) without using log transformations.</p>
-<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(<span class="no">sim_exp</span>,
- <span class="kw">sep_compartments</span> <span class="kw">=</span> <span class="fl">TRUE</span>,
- <span class="kw">start_date</span> <span class="kw">=</span> <span class="kw pkg">lubridate</span><span class="kw ns">::</span><span class="fu"><a href="http://lubridate.tidyverse.org/reference/ymd.html">ymd</a></span>(<span class="st">"2020-01-01"</span>),
- <span class="kw">plot_title</span> <span class="kw">=</span> <span class="st">'Closures Experiment'</span>)
-<span class="co">## Scale for 'colour' is already present. Adding another scale for 'colour',</span>
-<span class="co">## which will replace the existing scale.</span>
-<span class="co">## Warning: Removed 5 row(s) containing missing values (geom_path).</span></pre></body></html></div>
-<p><img src="sirplus_intro_v2_files/figure-html/sirplus%20plot%20by%20compartment-1.png" width="700"></p>
-</div>
-<div id="c--weekly-hospitalization-numbers" class="section level3">
-<h3 class="hasAnchor">
-<a href="#c--weekly-hospitalization-numbers" class="anchor"></a>C. Weekly hospitalization numbers</h3>
-<p>Use the <code><a href="https://rdrr.io/r/graphics/plot.html">plot()</a></code> function with parameter <code>method = "weekly_local"</code> to extract and plot the number of weekly expected patients in a hospital. If <code>return_df</code> is <code>TRUE</code>, the function returns a dataframe that generates the plot, otherwise, it returns a ggplot object.</p>
-<p>This function takes the following input:</p>
-<ul>
-<li>
-<code>sims</code>: Single or list of outputs from simulate.seiqhrf().</li>
-<li>
-<code>market.share</code>: Percent of cases in your model population (s.num) that are anticipated at the hospital of interest. Default = 4% (0.04).</li>
-<li>
-<code>icu_percent</code>: Percent of hospitalised cases are are likely to need treatment in an intensive care unit (ICU). Default = 10% (0.1).</li>
-<li>
-<code>start_date</code>: Epidemic start date. Default is <code>NA</code>.</li>
-<li>
-<code>show_start_date</code>: First date to show in plots. Default is to show from beginning</li>
-<li>
-<code>time_lim</code>: Number of days (nsteps) to include. Default = 90.</li>
-<li>
-<code>total_population</code>: True population size. This parameter is only needed if the simulation size (s.num) was smaller than the true population size (i.e. scaled down) to reduce computational cost.</li>
-</ul>
-<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(<span class="no">baseline_sim</span>, <span class="kw">method</span> <span class="kw">=</span> <span class="st">"weekly_local"</span>,
- <span class="kw">time_lim</span> <span class="kw">=</span> <span class="fl">40</span>,
- <span class="kw">start_date</span> <span class="kw">=</span> <span class="fu">ymd</span>(<span class="st">"2020-01-01"</span>),
- <span class="kw">show_start_date</span> <span class="kw">=</span> <span class="fu">ymd</span>(<span class="st">"2020-01-06"</span>),
- <span class="kw">return_df</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
-<span class="co">## $plot</span></pre></body></html></div>
-<p><img src="sirplus_intro_v2_files/figure-html/hospital%20visualization-1.png" width="700"></p>
-<pre><code>##
-## $result
-## # A tibble: 6 x 7
-## yr_wk h.num h.ci5 h.ci95 icu.num icu.ci5 icu.ci95
-## <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
-## 1 2020-01-06 14.5 4.66 27.9 1.61 0.518 3.10
-## 2 2020-01-13 54.4 36.1 72.4 6.05 4.01 8.04
-## 3 2020-01-20 192. 129. 241. 21.4 14.3 26.8
-## 4 2020-01-27 349. 299. 393. 38.8 33.2 43.6
-## 5 2020-02-03 361. 301. 413. 40.1 33.4 45.9
-## 6 2020-02-10 45.9 37.7 55.4 5.1 4.19 6.16</code></pre>
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- <div class="container template-citation-authors">
- <header>
- <div class="navbar navbar-default navbar-fixed-top" role="navigation">
- <div class="container">
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-</li>
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- Articles
-
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- </a>
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- <li>
- <a href="articles/sirplus_intro_v2.html">Introduction to sirplus (V2)</a>
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- <h1>Citation</h1>
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-
- <p>Zappia L, Phipson B, Oshlack A. Splatter: Simulation of single-cell RNA sequencing data. Genome Biology. 2017; doi:10.1186/s13059-017-1305-0</p>
- <pre>@Article{,
- author = {Luke Zappia and Belinda Phipson and Alicia Oshlack},
- title = {Splatter: simulation of single-cell RNA sequencing data},
- journal = {Genome Biology},
- year = {2017},
- url = {http://dx.doi.org/10.1186/s13059-017-1305-0},
- doi = {10.1186/s13059-017-1305-0},
-}</pre>
-
- <div class="page-header">
- <h1>Authors</h1>
- </div>
-
- <ul class="list-unstyled">
- <li>
- <p><strong>Christina Azodi</strong>. Author. <a href='https://orcid.org/0000-0002-6097-606X' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
- </p>
- </li>
- <li>
- <p><strong>Puxue Qiao</strong>. Author.
- </p>
- </li>
- <li>
- <p><strong>Ruqian Lyu</strong>. Author.
- </p>
- </li>
- <li>
- <p><strong>Sam Tanner</strong>. Author.
- </p>
- </li>
- <li>
- <p><strong>Tim Churches</strong>. Author.
- </p>
- </li>
- <li>
- <p><strong>Davis McCarthy</strong>. Author, maintainer. <a href='https://orcid.org/0000-0002-2218-6833' target='orcid.widget' aria-label='ORCID'><span class='fab fa-orcid orcid' aria-hidden='true'></span></a>
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diff --git a/public/bootstrap-toc.css b/public/bootstrap-toc.css
deleted file mode 100644
index 5a859415c1f7eacfd94920968bc910e2f1f1427e..0000000000000000000000000000000000000000
--- a/public/bootstrap-toc.css
+++ /dev/null
@@ -1,60 +0,0 @@
-/*!
- * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
- * Copyright 2015 Aidan Feldman
- * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
-
-/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */
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-/* All levels of nav */
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- padding-left: 19px;
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- background-color: transparent;
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-nav[data-toggle='toc'] .nav > .active:hover > a,
-nav[data-toggle='toc'] .nav > .active:focus > a {
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- font-weight: bold;
- color: #563d7c;
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- border-left: 2px solid #563d7c;
-}
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-/* Nav: second level (shown on .active) */
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- padding-left: 28px;
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-nav[data-toggle='toc'] .nav > .active > ul {
- display: block;
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diff --git a/public/bootstrap-toc.js b/public/bootstrap-toc.js
deleted file mode 100644
index 1cdd573b20f53b3ebe31c021e154c4338ca456af..0000000000000000000000000000000000000000
--- a/public/bootstrap-toc.js
+++ /dev/null
@@ -1,159 +0,0 @@
-/*!
- * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/)
- * Copyright 2015 Aidan Feldman
- * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */
-(function() {
- 'use strict';
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- // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/
- // http://stackoverflow.com/a/12731439/358804
- var $descendants = $el.find(selector);
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- },
-
- generateUniqueIdBase: function(el) {
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- },
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- generateUniqueId: function(el) {
- var anchorBase = this.generateUniqueIdBase(el);
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- if (i > 0) {
- // add suffix
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- }
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- if (!document.getElementById(anchor)) {
- return anchor;
- }
- }
- },
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- generateAnchor: function(el) {
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- } else {
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- createNavList: function() {
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- },
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- // Find the first heading level (`<h1>`, then `<h2>`, etc.) that has more than one element. Defaults to 1 (for `<h1>`).
- getTopLevel: function($scope) {
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- // returns the elements for the top level, and the next below it
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- return parseInt(el.tagName.charAt(1), 10);
- },
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- populateNav: function($topContext, topLevel, $headings) {
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- $headings.each(function(i, el) {
- var $newNav = helpers.generateNavItem(el);
- var navLevel = helpers.getNavLevel(el);
-
- // determine the proper $context
- if (navLevel === topLevel) {
- // use top level
- $context = $topContext;
- } else if ($prevNav && $context === $topContext) {
- // create a new level of the tree and switch to it
- $context = helpers.createChildNavList($prevNav);
- } // else use the current $context
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- $context.append($newNav);
-
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- });
- },
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- parseOps: function(arg) {
- var opts;
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- // accepts a jQuery object, or an options object
- init: function(opts) {
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-
- // ensure that the data attribute is in place for styling
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-
- var $topContext = this.helpers.createChildNavList(opts.$nav);
- var topLevel = this.helpers.getTopLevel(opts.$scope);
- var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
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- }
- };
-
- $(function() {
- $('nav[data-toggle="toc"]').each(function(i, el) {
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diff --git a/public/docsearch.css b/public/docsearch.css
deleted file mode 100644
index e5f1fe1dfa2c34c51fe941829b511acd8c763301..0000000000000000000000000000000000000000
--- a/public/docsearch.css
+++ /dev/null
@@ -1,148 +0,0 @@
-/* Docsearch -------------------------------------------------------------- */
-/*
- Source: https://github.com/algolia/docsearch/
- License: MIT
-*/
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-.algolia-autocomplete {
- display: block;
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-.algolia-autocomplete .ds-dropdown-menu {
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- max-width: none;
- padding: .75rem 0;
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- background-clip: padding-box;
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- box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
-}
-
-@media (min-width:768px) {
- .algolia-autocomplete .ds-dropdown-menu {
- width: 175%
- }
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-.algolia-autocomplete .ds-dropdown-menu::before {
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-.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
- padding: 0;
- background-color: rgb(255,255,255);
- border: 0;
- max-height: 80vh;
-}
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-.algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
- margin-top: 0
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-.algolia-autocomplete .algolia-docsearch-suggestion {
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-.algolia-autocomplete .algolia-docsearch-suggestion--category-header {
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-.algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
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- padding-top: 0
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-.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
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-.algolia-autocomplete .algolia-docsearch-suggestion--content::before {
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-.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
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- /* display: none */
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-.algolia-autocomplete .algolia-docsearch-suggestion--title {
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- padding: .25rem 1rem;
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-.algolia-autocomplete .algolia-docsearch-suggestion--text {
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-.algolia-autocomplete .algolia-docsearch-footer {
- width: 110px;
- height: 20px;
- z-index: 3;
- margin-top: 10.66667px;
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- line-height: 0;
-}
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-.algolia-autocomplete .algolia-docsearch-footer--logo {
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- <h1 data-toc-skip>Changelog <small></small></h1>
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-
- <div id="version-1-10-0-2019-10-30" class="section level1">
-<h1 class="page-header" data-toc-text="1.10.0">
-<a href="#version-1-10-0-2019-10-30" class="anchor"></a>Version 1.10.0 (2019-10-30)</h1>
-<ul>
-<li>Bioconductor 3.10 release</li>
-</ul>
-<div id="version-1-9-11-2019-10-20" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-11-2019-10-20" class="anchor"></a>Version 1.9.11 (2019-10-20)</h2>
-<ul>
-<li>Update NEWS.Rd</li>
-</ul>
-</div>
-<div id="version-1-9-10-2019-10-20" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-10-2019-10-20" class="anchor"></a>Version 1.9.10 (2019-10-20)</h2>
-<ul>
-<li>Update scater QC function names</li>
-</ul>
-</div>
-<div id="version-1-9-9-2019-10-16" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-9-2019-10-16" class="anchor"></a>Version 1.9.9 (2019-10-16)</h2>
-<ul>
-<li>Add missing documentation for sce argument in getCounts</li>
-<li>Update maintainer email address</li>
-</ul>
-</div>
-<div id="version-1-9-8-2019-10-11" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-8-2019-10-11" class="anchor"></a>Version 1.9.8 (2019-10-11)</h2>
-<ul>
-<li>Add Kersplat simulation! Still experimental but is useable.</li>
-<li>Check for counts assay when estimating from SingleCellExperiment objects (Fixes #82)</li>
-<li>Fix where simpleSimulate stores parameters (Fixes #72)</li>
-</ul>
-<div id="version-1-9-7-9019-2019-10-11" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-7-9019-2019-10-11" class="anchor"></a>Version 1.9.7.9019 (2019-10-11)</h3>
-<ul>
-<li>Run checks</li>
-</ul>
-</div>
-<div id="version-1-9-7-9018-2019-10-10" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-7-9018-2019-10-10" class="anchor"></a>Version 1.9.7.9018 (2019-10-10)</h3>
-<ul>
-<li>Document Splotch estimation functions</li>
-<li>Add Splotch to listSims</li>
-<li>Rename Splotch to Kersplat</li>
-</ul>
-</div>
-<div id="version-1-9-7-9017-2019-10-09" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-7-9017-2019-10-09" class="anchor"></a>Version 1.9.7.9017 (2019-10-09)</h3>
-<ul>
-<li>Document Splotch simulation functions</li>
-</ul>
-</div>
-<div id="version-1-9-7-9016-2019-10-01" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-7-9016-2019-10-01" class="anchor"></a>Version 1.9.7.9016 (2019-10-01)</h3>
-<ul>
-<li>Change the default SplotchParams cell design to place cells at end of path</li>
-<li>Add one time warning for Splotch simulation</li>
-<li>Avoid unnecessarily resetting cells.design in SplotchParams</li>
-</ul>
-</div>
-<div id="version-1-9-7-9015-2019-09-26" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-7-9015-2019-09-26" class="anchor"></a>Version 1.9.7.9015 (2019-09-26)</h3>
-<ul>
-<li>Add doublets to splotchSimulate</li>
-</ul>
-</div>
-<div id="version-1-9-7-9014-2019-09-24" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-7-9014-2019-09-24" class="anchor"></a>Version 1.9.7.9014 (2019-09-24)</h3>
-<ul>
-<li>Add ambient expression and empty cells to splotchSimulate</li>
-</ul>
-</div>
-<div id="version-1-9-7-9013-2019-09-19" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-7-9013-2019-09-19" class="anchor"></a>Version 1.9.7.9013 (2019-09-19)</h3>
-<ul>
-<li>Merge master into splotch branch</li>
-</ul>
-</div>
-</div>
-<div id="version-1-9-7-2019-09-19" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-7-2019-09-19" class="anchor"></a>Version 1.9.7 (2019-09-19)</h2>
-<ul>
-<li>Rescale when sampling Phi in BASiCSSimulate</li>
-</ul>
-</div>
-<div id="version-1-9-6-2019-09-17" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-6-2019-09-17" class="anchor"></a>Version 1.9.6 (2019-09-17)</h2>
-<ul>
-<li>Adjust BASiCSSimulate to match development version of BASiCS</li>
-</ul>
-<div id="version-1-9-5-9012-2019-09-09" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-5-9012-2019-09-09" class="anchor"></a>Version 1.9.5.9012 (2019-09-09)</h3>
-<ul>
-<li>Merge master into splotch branch</li>
-</ul>
-</div>
-</div>
-<div id="version-1-9-5-2019-09-09" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-5-2019-09-09" class="anchor"></a>Version 1.9.5 (2019-09-09)</h2>
-<ul>
-<li>Fix bug in NAMESPACE</li>
-</ul>
-<div id="version-1-9-4-9011-2019-08-29" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-4-9011-2019-08-29" class="anchor"></a>Version 1.9.4.9011 (2019-08-29)</h3>
-<ul>
-<li>Add BCV adjustment to Splotch simulation</li>
-<li>Use new exponential correction for bcv.common</li>
-</ul>
-</div>
-<div id="version-1-9-4-9010-2019-08-22" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-4-9010-2019-08-22" class="anchor"></a>Version 1.9.4.9010 (2019-08-22)</h3>
-<ul>
-<li>Add density sampling options for means and library sizes</li>
-</ul>
-</div>
-<div id="version-1-9-4-9009-2019-08-21" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-4-9009-2019-08-21" class="anchor"></a>Version 1.9.4.9009 (2019-08-21)</h3>
-<ul>
-<li>Replace library size log-normal with density and rejection sampling</li>
-<li>Add violins to comparison plots</li>
-</ul>
-</div>
-<div id="version-1-9-4-9008-2019-08-20" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-4-9008-2019-08-20" class="anchor"></a>Version 1.9.4.9008 (2019-08-20)</h3>
-<ul>
-<li>Merge master into splotch branch</li>
-<li>Fix dataset in splotchEstimate example</li>
-</ul>
-</div>
-</div>
-<div id="version-1-9-4-2019-08-20" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-4-2019-08-20" class="anchor"></a>Version 1.9.4 (2019-08-20)</h2>
-<ul>
-<li>Fix deprecated column name in diffSCEs QQ plots</li>
-<li>Fix bugs where parameters were not being passed correctly in BASiCSEstimate and sparseDCEstimate</li>
-<li>Replace the sc_example_counts dataset from scater with the mockSCE function</li>
-<li>Tidy and improve estimation function examples</li>
-</ul>
-<div id="version-1-9-3-9008-2019-08-20" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-3-9008-2019-08-20" class="anchor"></a>Version 1.9.3.9008 (2019-08-20)</h3>
-<ul>
-<li>Add expression outliers to Splotch</li>
-</ul>
-</div>
-<div id="version-1-9-3-9007-2019-08-14" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-3-9007-2019-08-14" class="anchor"></a>Version 1.9.3.9007 (2019-08-14)</h3>
-<ul>
-<li>Fix bug in selectFit</li>
-</ul>
-</div>
-<div id="version-1-9-3-9006-2019-08-13" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-3-9006-2019-08-13" class="anchor"></a>Version 1.9.3.9006 (2019-08-13)</h3>
-<ul>
-<li>Add splotchEstimate function</li>
-</ul>
-</div>
-<div id="version-1-9-3-9005-2019-08-08" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-3-9005-2019-08-08" class="anchor"></a>Version 1.9.3.9005 (2019-08-08)</h3>
-<ul>
-<li>Simulate counts in splotchSimulate</li>
-<li>Split splotchSimulate into separate functions for each stage</li>
-</ul>
-</div>
-<div id="version-1-9-3-9004-2019-08-08" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-3-9004-2019-08-08" class="anchor"></a>Version 1.9.3.9004 (2019-08-08)</h3>
-<ul>
-<li>Merge master into splotch branch</li>
-</ul>
-</div>
-</div>
-<div id="version-1-9-3-2019-08-08" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-3-2019-08-08" class="anchor"></a>Version 1.9.3 (2019-08-08)</h2>
-<ul>
-<li>Remove deprecated scater functions</li>
-</ul>
-<div id="version-1-9-2-9003-2019-07-17" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-2-9003-2019-07-17" class="anchor"></a>Version 1.9.2.9003 (2019-07-17)</h3>
-<ul>
-<li>Topologically sort Splotch paths</li>
-<li>Add library size parameters to SplotchParams</li>
-<li>Simulate cell means in splotchSimulate</li>
-</ul>
-</div>
-<div id="version-1-9-2-9002-2019-07-16" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-2-9002-2019-07-16" class="anchor"></a>Version 1.9.2.9002 (2019-07-16)</h3>
-<ul>
-<li>Add paths parameters to SplotchParams</li>
-</ul>
-</div>
-<div id="version-1-9-2-9001-2019-07-16" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-2-9001-2019-07-16" class="anchor"></a>Version 1.9.2.9001 (2019-07-16)</h3>
-<ul>
-<li>Add mean parameters to SplotchParams</li>
-</ul>
-</div>
-<div id="version-1-9-2-9000-2019-07-11" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-9-2-9000-2019-07-11" class="anchor"></a>Version 1.9.2.9000 (2019-07-11)</h3>
-<ul>
-<li>Add SplotchParams object</li>
-</ul>
-</div>
-</div>
-<div id="version-1-9-2-2019-06-13" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-2-2019-06-13" class="anchor"></a>Version 1.9.2 (2019-06-13)</h2>
-<ul>
-<li>Add variable gene correlation plot to compareSCEs</li>
-</ul>
-</div>
-<div id="version-1-9-1-2019-06-05" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-1-2019-06-05" class="anchor"></a>Version 1.9.1 (2019-06-05)</h2>
-<ul>
-<li>Refactor the summariseDiff function</li>
-<li>Add the KS statistic to summariseDiff</li>
-<li>Set gam method for fitted lines in comparison plots</li>
-<li>Add checks for suggested packages in examples</li>
-</ul>
-</div>
-<div id="version-1-9-0-2019-05-03" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-9-0-2019-05-03" class="anchor"></a>Version 1.9.0 (2019-05-03)</h2>
-<ul>
-<li>Bioconductor 3.10 devel</li>
-</ul>
-</div>
-</div>
- <div id="version-1-8-0-2019-05-03" class="section level1">
-<h1 class="page-header" data-toc-text="1.8.0">
-<a href="#version-1-8-0-2019-05-03" class="anchor"></a>Version 1.8.0 (2019-05-03)</h1>
-<ul>
-<li>Bioconductor 3.9 release</li>
-</ul>
-<div id="version-1-7-5-2018-04-18" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-7-5-2018-04-18" class="anchor"></a>Version 1.7.5 (2018-04-18)</h2>
-<ul>
-<li>Add Splat parameters vignette</li>
-<li>Fix spelling</li>
-</ul>
-</div>
-<div id="version-1-7-4-2018-04-17" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-7-4-2018-04-17" class="anchor"></a>Version 1.7.4 (2018-04-17)</h2>
-<ul>
-<li>Allow SplatParams parameters to be set in any order</li>
-</ul>
-</div>
-<div id="version-1-7-3-2018-04-15" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-7-3-2018-04-15" class="anchor"></a>Version 1.7.3 (2018-04-15)</h2>
-<ul>
-<li>Minor changes to documentation</li>
-<li>Protect against integer overflow in simulation functions</li>
-<li>Fix order of groups in splatSimulate</li>
-</ul>
-</div>
-<div id="version-1-7-2-2018-12-06" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-7-2-2018-12-06" class="anchor"></a>Version 1.7.2 (2018-12-06)</h2>
-<ul>
-<li>Add ImmunoOncology biocViews tag at request of Bioconductor team</li>
-</ul>
-</div>
-<div id="version-1-7-1-2018-11-17" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-7-1-2018-11-17" class="anchor"></a>Version 1.7.1 (2018-11-17)</h2>
-<ul>
-<li>Fix bugs in vignette</li>
-</ul>
-</div>
-<div id="version-1-7-0-2018-11-01" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-7-0-2018-11-01" class="anchor"></a>Version 1.7.0 (2018-11-01)</h2>
-<ul>
-<li>Bioconductor 3.9 devel</li>
-</ul>
-</div>
-<div id="version-1-6-1-2018-12-06" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-6-1-2018-12-06" class="anchor"></a>Version 1.6.1 (2018-12-06)</h2>
-<ul>
-<li>Add ImmunoOncology biocViews tag at request of Bioconductor team</li>
-</ul>
-</div>
-</div>
- <div id="version-1-6-0-2018-11-01" class="section level1">
-<h1 class="page-header" data-toc-text="1.6.0">
-<a href="#version-1-6-0-2018-11-01" class="anchor"></a>Version 1.6.0 (2018-11-01)</h1>
-<ul>
-<li>Bioconductor 3.8 release</li>
-</ul>
-<div id="version-1-5-8-2018-10-22" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-5-8-2018-10-22" class="anchor"></a>Version 1.5.8 (2018-10-22)</h2>
-<ul>
-<li>Add WithSpikes argument when calling BASiCS::BASiCS_MCMC()</li>
-</ul>
-</div>
-<div id="version-1-5-7-2018-10-03" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-5-7-2018-10-03" class="anchor"></a>Version 1.5.7 (2018-10-03)</h2>
-<ul>
-<li>Fix BASiCSEstimate tests</li>
-</ul>
-</div>
-<div id="version-1-5-4-2018-08-30" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-5-4-2018-08-30" class="anchor"></a>Version 1.5.4 (2018-08-30)</h2>
-<ul>
-<li>Fix installation instructions</li>
-</ul>
-</div>
-<div id="version-1-5-3-2018-08-20" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-5-3-2018-08-20" class="anchor"></a>Version 1.5.3 (2018-08-20)</h2>
-<ul>
-<li>Fix bug in BASiCSEstimate when no spike-ins provided</li>
-</ul>
-<div id="version-1-5-2-9000-2018-08-16" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-5-2-9000-2018-08-16" class="anchor"></a>Version 1.5.2.9000 (2018-08-16)</h3>
-<ul>
-<li>Add missing regression argument to BASiCSEstimate</li>
-<li>Add new BASiCS tests</li>
-</ul>
-</div>
-</div>
-<div id="version-1-5-2-2018-08-16" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-5-2-2018-08-16" class="anchor"></a>Version 1.5.2 (2018-08-16)</h2>
-<ul>
-<li>Fix bug in getLNormFactors when reversing factors less than one</li>
-<li>Update documentation to new Roxygen version (6.1.0)</li>
-<li>Change variable name in vignette for compatibility with scater</li>
-<li>Add suggested package checks to tests</li>
-</ul>
-</div>
-<div id="version-1-5-1-2018-06-12" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-5-1-2018-06-12" class="anchor"></a>Version 1.5.1 (2018-06-12)</h2>
-<ul>
-<li>Fix normality testing error in splatEstLib</li>
-<li>Correct p-value cutoff in normality test</li>
-<li>Sample library sizes for normality testing if > 5000 cells</li>
-</ul>
-</div>
-<div id="version-1-5-0-2018-05-02" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-5-0-2018-05-02" class="anchor"></a>Version 1.5.0 (2018-05-02)</h2>
-<ul>
-<li>Bioconductor 3.7 devel</li>
-</ul>
-</div>
-<div id="version-1-4-3-2018-08-20" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-4-3-2018-08-20" class="anchor"></a>Version 1.4.3 (2018-08-20)</h2>
-<ul>
-<li>Fix bug in BASiCSEstimate when no spike-ins provided</li>
-</ul>
-</div>
-<div id="version-1-4-2-2018-08-16" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-4-2-2018-08-16" class="anchor"></a>Version 1.4.2 (2018-08-16)</h2>
-<ul>
-<li>Add missing regression argument to BASiCSEstimate</li>
-<li>Add new BASiCS tests</li>
-</ul>
-</div>
-<div id="version-1-4-1-2018-06-12" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-4-1-2018-06-12" class="anchor"></a>Version 1.4.1 (2018-06-12)</h2>
-<ul>
-<li>Fix normality testing error in splatEstLib</li>
-<li>Correct p-value cutoff in normality test</li>
-<li>Sample library sizes for normality testing if > 5000 cells</li>
-</ul>
-</div>
-</div>
- <div id="version-1-4-0-2018-05-02" class="section level1">
-<h1 class="page-header" data-toc-text="1.4.0">
-<a href="#version-1-4-0-2018-05-02" class="anchor"></a>Version 1.4.0 (2018-05-02)</h1>
-<ul>
-<li>Bioconductor 3.7 release</li>
-</ul>
-<div id="version-1-3-6-2018-04-30" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-3-6-2018-04-30" class="anchor"></a>Version 1.3.6 (2018-04-30)</h2>
-<ul>
-<li>Set seed in sparseDCEstimate tests</li>
-</ul>
-</div>
-<div id="version-1-3-5-2018-04-25" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-3-5-2018-04-25" class="anchor"></a>Version 1.3.5 (2018-04-25)</h2>
-<ul>
-<li>Replace dropout.present with dropout.type in SplatParams
-<ul>
-<li>Allows users to set dropout by experiment, batch, group or cell</li>
-</ul>
-</li>
-</ul>
-</div>
-<div id="version-1-3-4-2018-04-19" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-3-4-2018-04-19" class="anchor"></a>Version 1.3.4 (2018-04-19)</h2>
-<ul>
-<li>Add option to use a normal distribution for library sizes in Splat simulations</li>
-<li>Add SparseDC simulation</li>
-<li>Rename params in metadata slot of simulation to Params for consistency</li>
-<li>Add checks to SplatParams to reset path.from if nGroups changes</li>
-<li>Improve printing of parameters stored as data.frames</li>
-<li>Colourise Params print output and listSims output</li>
-<li>Improve warning message when fitting means in splatEstimate fails</li>
-<li>Simplify problematic documentation links</li>
-</ul>
-<div id="version-1-3-3-9010-2018-04-12" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-3-3-9010-2018-04-12" class="anchor"></a>Version 1.3.3.9010 (2018-04-12)</h3>
-<ul>
-<li>Add option to use a normal distribution for library sizes in Splat simulations</li>
-</ul>
-</div>
-<div id="version-1-3-3-9000-2018-04-12" class="section level3">
-<h3 class="hasAnchor">
-<a href="#version-1-3-3-9000-2018-04-12" class="anchor"></a>Version 1.3.3.9000 (2018-04-12)</h3>
-<ul>
-<li>Replace dropout.present with dropout.type in SplatParams
-<ul>
-<li>Allows more control over dropout.mid and dropout.shape</li>
-</ul>
-</li>
-</ul>
-</div>
-</div>
-<div id="version-1-3-3-2018-03-27" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-3-3-2018-03-27" class="anchor"></a>Version 1.3.3 (2018-03-27)</h2>
-<ul>
-<li>Fix parameter passing bug in scDDEstimate</li>
-</ul>
-</div>
-<div id="version-1-3-2-2018-01-31" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-3-2-2018-01-31" class="anchor"></a>Version 1.3.2 (2018-01-31)</h2>
-<ul>
-<li>Fix QC names that have been changed in scater</li>
-<li>Move scater to Imports and add scater version</li>
-<li>Remove lingering references to SCESets</li>
-<li>Add more tests</li>
-</ul>
-</div>
-<div id="version-1-3-1-2018-01-03" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-3-1-2018-01-03" class="anchor"></a>Version 1.3.1 (2018-01-03)</h2>
-<ul>
-<li>Fix error in vignette caused by changes in scater</li>
-</ul>
-</div>
-<div id="version-1-3-0-2017-10-13" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-3-0-2017-10-13" class="anchor"></a>Version 1.3.0 (2017-10-13)</h2>
-<ul>
-<li>Bioconductor 3.7 devel</li>
-</ul>
-</div>
-<div id="version-1-2-2-2018-03-27" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-2-2-2018-03-27" class="anchor"></a>Version 1.2.2 (2018-03-27)</h2>
-<ul>
-<li>Fix parameter passing bug in scDDEstimate</li>
-</ul>
-</div>
-<div id="version-1-2-1-2017-11-23" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-2-1-2017-11-23" class="anchor"></a>Version 1.2.1 (2017-11-23)</h2>
-<ul>
-<li>Fix zinbwave installation error</li>
-</ul>
-</div>
-</div>
- <div id="version-1-2-0-2017-10-30" class="section level1">
-<h1 class="page-header" data-toc-text="1.2.0">
-<a href="#version-1-2-0-2017-10-30" class="anchor"></a>Version 1.2.0 (2017-10-30)</h1>
-<ul>
-<li>Bioconductor 3.6 release</li>
-</ul>
-<div id="version-1-1-8-2017-10-13" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-8-2017-10-13" class="anchor"></a>Version 1.1.8 (2017-10-13)</h2>
-<ul>
-<li>Add BASiCS simulation</li>
-<li>Update Splatter citation</li>
-<li>Update Lun2 reference</li>
-</ul>
-</div>
-<div id="version-1-1-7-2017-10-05" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-7-2017-10-05" class="anchor"></a>Version 1.1.7 (2017-10-05)</h2>
-<ul>
-<li>Add PhenoPath simulation</li>
-<li>Add ZINB-WaVE simulation</li>
-<li>Adjust mfaSimulate output</li>
-</ul>
-</div>
-<div id="version-1-1-6-2017-10-02" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-6-2017-10-02" class="anchor"></a>Version 1.1.6 (2017-10-02)</h2>
-<ul>
-<li>Update scDD version</li>
-<li>Add mfa simulation</li>
-</ul>
-</div>
-<div id="version-1-1-5-2017-09-13" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-5-2017-09-13" class="anchor"></a>Version 1.1.5 (2017-09-13)</h2>
-<ul>
-<li>Convert to SingleCellExperiment</li>
-</ul>
-</div>
-<div id="version-1-1-4-2017-08-04" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-4-2017-08-04" class="anchor"></a>Version 1.1.4 (2017-08-04)</h2>
-<ul>
-<li>Fix group factors bug</li>
-</ul>
-</div>
-<div id="version-1-1-3-2017-07-20" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-3-2017-07-20" class="anchor"></a>Version 1.1.3 (2017-07-20)</h2>
-<ul>
-<li>Add verbose option to scDDEstimate</li>
-<li>Change “mean-dropout†to “mean-zeros†in compareSCESets</li>
-</ul>
-</div>
-<div id="version-1-1-2-2017-07-16" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-2-2017-07-16" class="anchor"></a>Version 1.1.2 (2017-07-16)</h2>
-<ul>
-<li>Update summariseDiff</li>
-<li>Update scDDEstimate, now estimates gene types</li>
-<li>Fix error in lun2Estimate</li>
-<li>Import SummarizedExperiment to avoid warnings</li>
-</ul>
-</div>
-<div id="version-1-1-1-2017-07-07" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-1-2017-07-07" class="anchor"></a>Version 1.1.1 (2017-07-07)</h2>
-<ul>
-<li>Add batch effects to Splat simulation</li>
-<li>Make Splat group assignment probabilistic</li>
-<li>Update SplatParams with new parameters</li>
-</ul>
-</div>
-<div id="version-1-1-0-2017-07-07" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-1-0-2017-07-07" class="anchor"></a>Version 1.1.0 (2017-07-07)</h2>
-<ul>
-<li>Bioconductor 3.6 devel</li>
-</ul>
-</div>
-<div id="version-1-0-3-2017-05-26" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-0-3-2017-05-26" class="anchor"></a>Version 1.0.3 (2017-05-26)</h2>
-<ul>
-<li>Update citation</li>
-</ul>
-</div>
-<div id="version-1-0-2-2017-05-15" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-0-2-2017-05-15" class="anchor"></a>Version 1.0.2 (2017-05-15)</h2>
-<ul>
-<li>Fix error handling when fitting means</li>
-</ul>
-</div>
-<div id="version-1-0-1-2017-04-28" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-1-0-1-2017-04-28" class="anchor"></a>Version 1.0.1 (2017-04-28)</h2>
-<ul>
-<li>Fix scales in some difference plots</li>
-<li>Fix colours in difference plots</li>
-<li>Fix panel legends</li>
-</ul>
-</div>
-</div>
- <div id="version-1-0-0-2017-04-28" class="section level1">
-<h1 class="page-header" data-toc-text="1.0.0">
-<a href="#version-1-0-0-2017-04-28" class="anchor"></a>Version 1.0.0 (2017-04-28)</h1>
-<ul>
-<li>Bioconductor 3.5 release</li>
-</ul>
-<div id="version-0-99-15-2017-04-14" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-15-2017-04-14" class="anchor"></a>Version 0.99.15 (2017-04-14)</h2>
-<ul>
-<li>Add summariseDiff function</li>
-<li>Add BPPARAM argument to scDDSimulate</li>
-<li>Adjust default Splat DE factor parameters</li>
-<li>Add limits to zeros diff plots</li>
-<li>Remove estimation of dropout.present</li>
-</ul>
-</div>
-<div id="version-0-99-14-2017-03-28" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-14-2017-03-28" class="anchor"></a>Version 0.99.14 (2017-03-28)</h2>
-<ul>
-<li>Add functions for making comparison panels</li>
-<li>Add panel section to vignette</li>
-<li>Change variance plot scale (for consistency)</li>
-</ul>
-</div>
-<div id="version-0-99-13-2017-03-25" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-13-2017-03-25" class="anchor"></a>Version 0.99.13 (2017-03-25)</h2>
-<ul>
-<li>Modify how Lun2Params stores gene parameters to use data.frame</li>
-<li>Move sampling of genes/cells to lun2Simulate</li>
-<li>Return to old Lun2 nGenes estimate</li>
-</ul>
-</div>
-<div id="version-0-99-12-2017-03-22" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-12-2017-03-22" class="anchor"></a>Version 0.99.12 (2017-03-22)</h2>
-<ul>
-<li>Add diffSCESets function</li>
-<li>Update compareSCESets plots</li>
-<li>Modify Lun2 nGenes estimate</li>
-<li>Modify how addFeatureStats names columns</li>
-<li>Add infinite bcv.df warning to splatSimulate</li>
-</ul>
-</div>
-<div id="version-0-99-11-2017-03-20" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-11-2017-03-20" class="anchor"></a>Version 0.99.11 (2017-03-20)</h2>
-<ul>
-<li>Add parallel option to lun2Estimate</li>
-<li>Allow non-integer library sizes in Lun2Params</li>
-<li>Adjust dropout eta value</li>
-<li>Adjust comparison plots</li>
-</ul>
-</div>
-<div id="version-0-99-10-2017-03-07" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-10-2017-03-07" class="anchor"></a>Version 0.99.10 (2017-03-07)</h2>
-<ul>
-<li>Improve Splat estimation procedure</li>
-<li>Update default Splat parameters</li>
-<li>Remove out.loProb Splat parameter</li>
-<li>Add MeanZeros plot to compareSCESets</li>
-</ul>
-</div>
-<div id="version-0-99-9-2017-02-02" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-9-2017-02-02" class="anchor"></a>Version 0.99.9 (2017-02-02)</h2>
-<ul>
-<li>Add addGeneLengths function</li>
-<li>Update scDD reference</li>
-</ul>
-</div>
-<div id="version-0-99-8-2017-01-23" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-8-2017-01-23" class="anchor"></a>Version 0.99.8 (2017-01-23)</h2>
-<ul>
-<li>Fix bug that meant non-linear path factors weren’t stored in output</li>
-</ul>
-</div>
-<div id="version-0-99-7-2017-01-10" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-7-2017-01-10" class="anchor"></a>Version 0.99.7 (2017-01-10)</h2>
-<ul>
-<li>Small changes to avoid NOTEs and reduce check time</li>
-</ul>
-</div>
-<div id="version-0-99-6-2016-12-29" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-6-2016-12-29" class="anchor"></a>Version 0.99.6 (2016-12-29)</h2>
-<ul>
-<li>Add installation to vignette</li>
-<li>Add detail about counts matrix to vignette</li>
-<li>Replace 1:x with seq_len/seq_along</li>
-</ul>
-</div>
-<div id="version-0-99-5-2016-12-28" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-5-2016-12-28" class="anchor"></a>Version 0.99.5 (2016-12-28)</h2>
-<ul>
-<li>Set R_TESTS environment</li>
-</ul>
-</div>
-<div id="version-0-99-4-2016-12-23" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-4-2016-12-23" class="anchor"></a>Version 0.99.4 (2016-12-23)</h2>
-<ul>
-<li>Version bump to start build</li>
-</ul>
-</div>
-<div id="version-0-99-3-2016-12-21" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-3-2016-12-21" class="anchor"></a>Version 0.99.3 (2016-12-21)</h2>
-<ul>
-<li>Fix to match Bioconductor version of scDD</li>
-<li>Add logo to repository</li>
-</ul>
-</div>
-<div id="version-0-99-2-2016-12-13" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-2-2016-12-13" class="anchor"></a>Version 0.99.2 (2016-12-13)</h2>
-<ul>
-<li>Add rownames, colnames to matrices in splatSimulate, lunSimulate</li>
-<li>Bump R version to 3.4</li>
-</ul>
-</div>
-<div id="version-0-99-1-2016-12-12" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-99-1-2016-12-12" class="anchor"></a>Version 0.99.1 (2016-12-12)</h2>
-<ul>
-<li>Address Biocondutor build warnings, notes</li>
-</ul>
-</div>
-</div>
- <div id="version-0-99-0-2016-12-05" class="section level1">
-<h1 class="page-header" data-toc-text="0.99.0">
-<a href="#version-0-99-0-2016-12-05" class="anchor"></a>Version 0.99.0 (2016-12-05)</h1>
-<ul>
-<li>Submit to Bioconductor</li>
-</ul>
-<div id="version-0-12-1-2016-11-25" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-12-1-2016-11-25" class="anchor"></a>Version 0.12.1 (2016-11-25)</h2>
-<ul>
-<li>Fix bug in compareSCESets</li>
-<li>Dataset order is now kept in plots</li>
-</ul>
-</div>
-<div id="version-0-12-0-2016-10-25" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-12-0-2016-10-25" class="anchor"></a>Version 0.12.0 (2016-10-25)</h2>
-<ul>
-<li>Add compareSCESets function</li>
-<li>Update vignette</li>
-<li>Fix LunParams validity bug</li>
-<li>Add logo</li>
-</ul>
-</div>
-<div id="version-0-11-1-2016-11-23" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-11-1-2016-11-23" class="anchor"></a>Version 0.11.1 (2016-11-23)</h2>
-<ul>
-<li>Fix bug in splatSimulatePaths that caused NAs</li>
-</ul>
-</div>
-<div id="version-0-11-0-2016-11-22" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-11-0-2016-11-22" class="anchor"></a>Version 0.11.0 (2016-11-22)</h2>
-<ul>
-<li>Make compatible with Bioconductor 3.4</li>
-</ul>
-</div>
-<div id="version-0-10-1-2016-10-17" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-10-1-2016-10-17" class="anchor"></a>Version 0.10.1 (2016-10-17)</h2>
-<ul>
-<li>Fix error for SCESets in lun2Estimate, scDDEstimate</li>
-</ul>
-</div>
-<div id="version-0-10-0-2016-10-16" class="section level2">
-<h2 class="hasAnchor">
-<a href="#version-0-10-0-2016-10-16" class="anchor"></a>Version 0.10.0 (2016-10-16)</h2>
-<ul>
-<li>Add listSims function</li>
-<li>Add vignette</li>
-</ul>
-</div>
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- <h1>Add known counts to sims dataframe for ggplot</h1>
-
- <div class="hidden name"><code>add_known.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Add known counts to sims dataframe for ggplot</p>
- </div>
-
- <pre class="usage"><span class='fu'>add_known</span>(<span class='no'>plot_df</span>, <span class='no'>known</span>, <span class='no'>start_date</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>plot_df</th>
- <td><p>An seiqhrf object returned from function <code><a href='seiqhrf.html'>seiqhrf</a></code>.</p></td>
- </tr>
- <tr>
- <th>known</th>
- <td><p>Dataframe with known compartment numbers to plot alongside
-projections</p></td>
- </tr>
- <tr>
- <th>start_date</th>
- <td><p>Date for day 0.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>dataframe with known data added</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
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-<meta property="og:description" content="Function to handle background demographics for the SEIQHRF model.
-Specifically arrivals (births and immigration). Uses the original EpiModel
-code currently. A replacement that implements modelling the arrival of
-infected individuals is under development -- but for now, all arrivals
-go into the S compartment.." />
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- <h1>Arrivals function</h1>
-
- <div class="hidden name"><code>arrivals.FUN.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Function to handle background demographics for the SEIQHRF model.
-Specifically arrivals (births and immigration). Uses the original EpiModel
-code currently. A replacement that implements modelling the arrival of
-infected individuals is under development -- but for now, all arrivals
-go into the S compartment..</p>
- </div>
-
- <pre class="usage"><span class='fu'>arrivals.FUN</span>(<span class='no'>dat</span>, <span class='no'>at</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>dat</th>
- <td><p>Input data needed.</p></td>
- </tr>
- <tr>
- <th>at</th>
- <td><p>time point</p></td>
- </tr>
- <tr>
- <th>seed</th>
- <td><p>random seed for checking consistency</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>Updated dat</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
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- <p>Developed by Christina Azodi, Puxue Qiao, Ruqian Lyu, Sam Tanner, Tim Churches, Davis McCarthy.</p>
-</div>
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diff --git a/public/reference/as.data.frame.seiqhrf.html b/public/reference/as.data.frame.seiqhrf.html
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-<meta property="og:description" content="This function extracts model simulations for objects of classes
- seiqhrf into a data frame using
- the generic as.data.frame function." />
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- <h1>Extract Model Data for Stochastic Models</h1>
-
- <div class="hidden name"><code>as.data.frame.seiqhrf.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>This function extracts model simulations for objects of classes
- <code>seiqhrf</code> into a data frame using
- the generic <code>as.data.frame</code> function.</p>
- </div>
-
- <pre class="usage"><span class='co'># S3 method for seiqhrf</span>
-<span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span>(
- <span class='no'>x</span>,
- <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>optional</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>out</span> <span class='kw'>=</span> <span class='st'>"vals"</span>,
- <span class='no'>sim</span>,
- <span class='no'>qval</span>,
- <span class='no'>...</span>
-)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>x</th>
- <td><p>An <code>EpiModel</code> object of class <code>icm</code> or <code>netsim</code>.</p></td>
- </tr>
- <tr>
- <th>row.names</th>
- <td><p>See <code><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame.default</a></code>.</p></td>
- </tr>
- <tr>
- <th>optional</th>
- <td><p>See <code><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame.default</a></code>.</p></td>
- </tr>
- <tr>
- <th>out</th>
- <td><p>Data output to data frame: <code>"mean"</code> for row means across
-simulations, <code>"sd"</code> for row standard deviations across simulations,
-<code>"qnt"</code> for row quantiles at the level specified in <code>qval</code>,
-or <code>"vals"</code> for values from individual simulations.</p></td>
- </tr>
- <tr>
- <th>sim</th>
- <td><p>If <code>out="vals"</code>, the simulation number to output. If not
-specified, then data from all simulations will be output.</p></td>
- </tr>
- <tr>
- <th>qval</th>
- <td><p>Quantile value required when <code>out="qnt"</code>.</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>See <code><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame.default</a></code>.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
- <p>These methods work for both <code>seiqhrf</code> class models. The
-available output includes time-specific means, standard deviations, quantiles,
-and simulation values (compartment and flow sizes) from these stochastic model
-classes. Means, standard deviations, and quantiles are calculated by taking the
-row summary (i.e., each row of data is corresponds to a time step) across all
-simulations in the model output.</p>
-
- <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='co'>## Stochastic SEIQHRF model</span>
-<span class='no'>param</span> <span class='kw'><-</span> <span class='fu'><a href='param_seiqhrf.html'>param_seiqhrf</a></span>()
-<span class='no'>init</span> <span class='kw'><-</span> <span class='fu'><a href='init_seiqhrf.html'>init_seiqhrf</a></span>(<span class='kw'>s.num</span> <span class='kw'>=</span> <span class='fl'>500</span>, <span class='kw'>i.num</span> <span class='kw'>=</span> <span class='fl'>1</span>)
-<span class='no'>control</span> <span class='kw'><-</span> <span class='fu'><a href='control_seiqhrf.html'>control_seiqhrf</a></span>(<span class='kw'>nsteps</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>nsims</span> <span class='kw'>=</span> <span class='fl'>3</span>)
-<span class='no'>mod</span> <span class='kw'><-</span> <span class='fu'><a href='seiqhrf.html'>seiqhrf</a></span>(<span class='no'>init</span>, <span class='no'>control</span>, <span class='no'>param</span>)
-
-<span class='co'># Default output all simulation runs, default to all in stacked data.frame</span>
-<span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span>(<span class='no'>mod</span>)</div><div class='output co'>#> sim time s.num i.num num se.flow is.flow iq.flow iq2h.flow hf.flow ds.flow
-#> 1 1 1 500 1 501 0 0 0 0 0 0
-#> 2 1 2 500 1 501 0 0 0 0 0 0
-#> 3 1 3 500 1 501 0 0 0 0 0 0
-#> 4 1 4 499 1 501 1 0 0 0 0 0
-#> 5 1 5 499 1 501 0 0 0 0 0 0
-#> 6 1 6 498 1 501 0 0 0 0 0 0
-#> 7 1 7 497 1 501 1 0 0 0 0 0
-#> 8 1 8 496 2 501 1 0 0 0 0 0
-#> 9 1 9 494 3 501 0 0 0 0 0 0
-#> 10 1 10 492 4 501 0 0 0 0 0 0
-#> 11 2 1 500 1 501 0 0 0 0 0 0
-#> 12 2 2 500 1 501 0 0 0 0 0 0
-#> 13 2 3 500 0 501 0 0 1 0 0 0
-#> 14 2 4 500 0 501 0 0 0 0 0 0
-#> 15 2 5 499 0 501 1 0 0 0 0 0
-#> 16 2 6 499 0 501 0 0 0 0 0 0
-#> 17 2 7 498 0 501 0 1 0 0 0 0
-#> 18 2 8 498 0 501 0 1 0 0 0 0
-#> 19 2 9 498 0 501 0 0 0 0 0 0
-#> 20 2 10 498 0 501 0 0 0 0 0 0
-#> 21 3 1 500 1 501 0 0 0 0 0 0
-#> 22 3 2 499 1 501 1 0 0 0 0 0
-#> 23 3 3 499 1 501 0 0 0 0 0 0
-#> 24 3 4 498 1 501 1 0 0 0 0 0
-#> 25 3 5 496 1 501 1 0 0 0 0 0
-#> 26 3 6 496 2 501 0 2 0 0 0 0
-#> 27 3 7 493 2 501 3 2 0 0 0 0
-#> 28 3 8 492 1 501 1 0 0 1 0 0
-#> 29 3 9 489 2 501 1 0 0 0 0 0
-#> 30 3 10 485 3 501 1 1 0 0 0 0
-#> de.flow di.flow dq.flow dh.flow dr.flow a.flow a.e.flow a.i.flow a.q.flow
-#> 1 0 0 0 0 0 0 0 0 0
-#> 2 0 0 0 0 0 0 0 0 0
-#> 3 0 0 0 0 0 0 0 0 0
-#> 4 0 0 0 0 0 0 0 0 0
-#> 5 0 0 0 0 0 0 0 0 0
-#> 6 0 0 0 0 0 0 0 0 0
-#> 7 0 0 0 0 0 0 0 0 0
-#> 8 0 0 0 0 0 0 0 0 0
-#> 9 0 0 0 0 0 0 0 0 0
-#> 10 0 0 0 0 0 0 0 0 0
-#> 11 0 0 0 0 0 0 0 0 0
-#> 12 0 0 0 0 0 0 0 0 0
-#> 13 0 0 0 0 0 0 0 0 0
-#> 14 0 0 0 0 0 0 0 0 0
-#> 15 0 0 0 0 0 0 0 0 0
-#> 16 0 0 0 0 0 0 0 0 0
-#> 17 0 0 0 0 0 0 0 0 0
-#> 18 0 0 0 0 0 0 0 0 0
-#> 19 0 0 0 0 0 0 0 0 0
-#> 20 0 0 0 0 0 0 0 0 0
-#> 21 0 0 0 0 0 0 0 0 0
-#> 22 0 0 0 0 0 0 0 0 0
-#> 23 0 0 0 0 0 0 0 0 0
-#> 24 0 0 0 0 0 0 0 0 0
-#> 25 0 0 0 0 0 0 0 0 0
-#> 26 0 0 0 0 0 0 0 0 0
-#> 27 0 0 0 0 0 0 0 0 0
-#> 28 0 0 0 0 0 0 0 0 0
-#> 29 0 0 0 0 0 0 0 0 0
-#> 30 0 0 0 0 0 0 0 0 0
-#> e.num r.num q.num h.num f.num
-#> 1 NA NA NA NA NA
-#> 2 0 0 0 0 0
-#> 3 0 0 0 0 0
-#> 4 1 0 0 0 0
-#> 5 1 0 0 0 0
-#> 6 2 0 0 0 0
-#> 7 3 0 0 0 0
-#> 8 3 0 0 0 0
-#> 9 4 0 0 0 0
-#> 10 5 0 0 0 0
-#> 11 NA NA NA NA NA
-#> 12 0 0 0 0 0
-#> 13 0 0 1 0 0
-#> 14 0 0 1 0 0
-#> 15 1 0 1 0 0
-#> 16 1 0 1 0 0
-#> 17 1 1 1 0 0
-#> 18 0 2 1 0 0
-#> 19 0 2 1 0 0
-#> 20 0 2 1 0 0
-#> 21 NA NA NA NA NA
-#> 22 1 0 0 0 0
-#> 23 1 0 0 0 0
-#> 24 2 0 0 0 0
-#> 25 4 0 0 0 0
-#> 26 1 2 0 0 0
-#> 27 2 4 0 0 0
-#> 28 3 5 0 0 0
-#> 29 5 5 0 0 0
-#> 30 7 6 0 0 0</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span>(<span class='no'>mod</span>, <span class='kw'>sim</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#> sim time s.num i.num num se.flow is.flow iq.flow iq2h.flow hf.flow ds.flow
-#> 1 2 1 500 1 501 0 0 0 0 0 0
-#> 2 2 2 500 1 501 0 0 0 0 0 0
-#> 3 2 3 500 0 501 0 0 1 0 0 0
-#> 4 2 4 500 0 501 0 0 0 0 0 0
-#> 5 2 5 499 0 501 1 0 0 0 0 0
-#> 6 2 6 499 0 501 0 0 0 0 0 0
-#> 7 2 7 498 0 501 0 1 0 0 0 0
-#> 8 2 8 498 0 501 0 1 0 0 0 0
-#> 9 2 9 498 0 501 0 0 0 0 0 0
-#> 10 2 10 498 0 501 0 0 0 0 0 0
-#> de.flow di.flow dq.flow dh.flow dr.flow a.flow a.e.flow a.i.flow a.q.flow
-#> 1 0 0 0 0 0 0 0 0 0
-#> 2 0 0 0 0 0 0 0 0 0
-#> 3 0 0 0 0 0 0 0 0 0
-#> 4 0 0 0 0 0 0 0 0 0
-#> 5 0 0 0 0 0 0 0 0 0
-#> 6 0 0 0 0 0 0 0 0 0
-#> 7 0 0 0 0 0 0 0 0 0
-#> 8 0 0 0 0 0 0 0 0 0
-#> 9 0 0 0 0 0 0 0 0 0
-#> 10 0 0 0 0 0 0 0 0 0
-#> e.num r.num q.num h.num f.num
-#> 1 NA NA NA NA NA
-#> 2 0 0 0 0 0
-#> 3 0 0 1 0 0
-#> 4 0 0 1 0 0
-#> 5 1 0 1 0 0
-#> 6 1 0 1 0 0
-#> 7 1 1 1 0 0
-#> 8 0 2 1 0 0
-#> 9 0 2 1 0 0
-#> 10 0 2 1 0 0</div><div class='input'>
-<span class='co'># Time-specific means across simulations</span>
-<span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span>(<span class='no'>mod</span>, <span class='kw'>out</span> <span class='kw'>=</span> <span class='st'>"mean"</span>)</div><div class='output co'>#> time s.num i.num num se.flow is.flow iq.flow iq2h.flow hf.flow
-#> 1 1 500.0000 1.0000000 501 0.0000000 0.0000000 0.0000000 0.0000000 0
-#> 2 2 499.6667 1.0000000 501 0.3333333 0.0000000 0.0000000 0.0000000 0
-#> 3 3 499.6667 0.6666667 501 0.0000000 0.0000000 0.3333333 0.0000000 0
-#> 4 4 499.0000 0.6666667 501 0.6666667 0.0000000 0.0000000 0.0000000 0
-#> 5 5 498.0000 0.6666667 501 0.6666667 0.0000000 0.0000000 0.0000000 0
-#> 6 6 497.6667 1.0000000 501 0.0000000 0.6666667 0.0000000 0.0000000 0
-#> 7 7 496.0000 1.0000000 501 1.3333333 1.0000000 0.0000000 0.0000000 0
-#> 8 8 495.3333 1.0000000 501 0.6666667 0.3333333 0.0000000 0.3333333 0
-#> 9 9 493.6667 1.6666667 501 0.3333333 0.0000000 0.0000000 0.0000000 0
-#> 10 10 491.6667 2.3333333 501 0.3333333 0.3333333 0.0000000 0.0000000 0
-#> ds.flow de.flow di.flow dq.flow dh.flow dr.flow a.flow a.e.flow a.i.flow
-#> 1 0 0 0 0 0 0 0 0 0
-#> 2 0 0 0 0 0 0 0 0 0
-#> 3 0 0 0 0 0 0 0 0 0
-#> 4 0 0 0 0 0 0 0 0 0
-#> 5 0 0 0 0 0 0 0 0 0
-#> 6 0 0 0 0 0 0 0 0 0
-#> 7 0 0 0 0 0 0 0 0 0
-#> 8 0 0 0 0 0 0 0 0 0
-#> 9 0 0 0 0 0 0 0 0 0
-#> 10 0 0 0 0 0 0 0 0 0
-#> a.q.flow e.num r.num q.num h.num f.num
-#> 1 0 NaN NaN NaN NaN NaN
-#> 2 0 0.3333333 0.0000000 0.0000000 0 0
-#> 3 0 0.3333333 0.0000000 0.3333333 0 0
-#> 4 0 1.0000000 0.0000000 0.3333333 0 0
-#> 5 0 2.0000000 0.0000000 0.3333333 0 0
-#> 6 0 1.3333333 0.6666667 0.3333333 0 0
-#> 7 0 2.0000000 1.6666667 0.3333333 0 0
-#> 8 0 2.0000000 2.3333333 0.3333333 0 0
-#> 9 0 3.0000000 2.3333333 0.3333333 0 0
-#> 10 0 4.0000000 2.6666667 0.3333333 0 0</div><div class='input'>
-<span class='co'># Time-specific standard deviations across simulations</span>
-<span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span>(<span class='no'>mod</span>, <span class='kw'>out</span> <span class='kw'>=</span> <span class='st'>"sd"</span>)</div><div class='output co'>#> time s.num i.num num se.flow is.flow iq.flow iq2h.flow hf.flow
-#> 1 1 0.0000000 0.0000000 0 0.0000000 0.0000000 0.0000000 0.0000000 0
-#> 2 2 0.5773503 0.0000000 0 0.5773503 0.0000000 0.0000000 0.0000000 0
-#> 3 3 0.5773503 0.5773503 0 0.0000000 0.0000000 0.5773503 0.0000000 0
-#> 4 4 1.0000000 0.5773503 0 0.5773503 0.0000000 0.0000000 0.0000000 0
-#> 5 5 1.7320508 0.5773503 0 0.5773503 0.0000000 0.0000000 0.0000000 0
-#> 6 6 1.5275252 1.0000000 0 0.0000000 1.1547005 0.0000000 0.0000000 0
-#> 7 7 2.6457513 1.0000000 0 1.5275252 1.0000000 0.0000000 0.0000000 0
-#> 8 8 3.0550505 1.0000000 0 0.5773503 0.5773503 0.0000000 0.5773503 0
-#> 9 9 4.5092498 1.5275252 0 0.5773503 0.0000000 0.0000000 0.0000000 0
-#> 10 10 6.5064071 2.0816660 0 0.5773503 0.5773503 0.0000000 0.0000000 0
-#> ds.flow de.flow di.flow dq.flow dh.flow dr.flow a.flow a.e.flow a.i.flow
-#> 1 0 0 0 0 0 0 0 0 0
-#> 2 0 0 0 0 0 0 0 0 0
-#> 3 0 0 0 0 0 0 0 0 0
-#> 4 0 0 0 0 0 0 0 0 0
-#> 5 0 0 0 0 0 0 0 0 0
-#> 6 0 0 0 0 0 0 0 0 0
-#> 7 0 0 0 0 0 0 0 0 0
-#> 8 0 0 0 0 0 0 0 0 0
-#> 9 0 0 0 0 0 0 0 0 0
-#> 10 0 0 0 0 0 0 0 0 0
-#> a.q.flow e.num r.num q.num h.num f.num
-#> 1 0 NA NA NA NA NA
-#> 2 0 0.5773503 0.000000 0.0000000 0 0
-#> 3 0 0.5773503 0.000000 0.5773503 0 0
-#> 4 0 1.0000000 0.000000 0.5773503 0 0
-#> 5 0 1.7320508 0.000000 0.5773503 0 0
-#> 6 0 0.5773503 1.154701 0.5773503 0 0
-#> 7 0 1.0000000 2.081666 0.5773503 0 0
-#> 8 0 1.7320508 2.516611 0.5773503 0 0
-#> 9 0 2.6457513 2.516611 0.5773503 0 0
-#> 10 0 3.6055513 3.055050 0.5773503 0 0</div><div class='input'>
-<span class='co'># Time-specific quantile values across simulations</span>
-<span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span>(<span class='no'>mod</span>, <span class='kw'>out</span> <span class='kw'>=</span> <span class='st'>"qnt"</span>, <span class='kw'>qval</span> <span class='kw'>=</span> <span class='fl'>0.25</span>)</div><div class='output co'>#> time s.num i.num num se.flow is.flow iq.flow iq2h.flow hf.flow ds.flow
-#> 1 1 500.0 1.0 501 0.0 0.0 0 0 0 0
-#> 2 2 499.5 1.0 501 0.0 0.0 0 0 0 0
-#> 3 3 499.5 0.5 501 0.0 0.0 0 0 0 0
-#> 4 4 498.5 0.5 501 0.5 0.0 0 0 0 0
-#> 5 5 497.5 0.5 501 0.5 0.0 0 0 0 0
-#> 6 6 497.0 0.5 501 0.0 0.0 0 0 0 0
-#> 7 7 495.0 0.5 501 0.5 0.5 0 0 0 0
-#> 8 8 494.0 0.5 501 0.5 0.0 0 0 0 0
-#> 9 9 491.5 1.0 501 0.0 0.0 0 0 0 0
-#> 10 10 488.5 1.5 501 0.0 0.0 0 0 0 0
-#> de.flow di.flow dq.flow dh.flow dr.flow a.flow a.e.flow a.i.flow a.q.flow
-#> 1 0 0 0 0 0 0 0 0 0
-#> 2 0 0 0 0 0 0 0 0 0
-#> 3 0 0 0 0 0 0 0 0 0
-#> 4 0 0 0 0 0 0 0 0 0
-#> 5 0 0 0 0 0 0 0 0 0
-#> 6 0 0 0 0 0 0 0 0 0
-#> 7 0 0 0 0 0 0 0 0 0
-#> 8 0 0 0 0 0 0 0 0 0
-#> 9 0 0 0 0 0 0 0 0 0
-#> 10 0 0 0 0 0 0 0 0 0
-#> e.num r.num q.num h.num f.num
-#> 1 NA NA NA NA NA
-#> 2 0.0 0.0 0 0 0
-#> 3 0.0 0.0 0 0 0
-#> 4 0.5 0.0 0 0 0
-#> 5 1.0 0.0 0 0 0
-#> 6 1.0 0.0 0 0 0
-#> 7 1.5 0.5 0 0 0
-#> 8 1.5 1.0 0 0 0
-#> 9 2.0 1.0 0 0 0
-#> 10 2.5 1.0 0 0 0</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span>(<span class='no'>mod</span>, <span class='kw'>out</span> <span class='kw'>=</span> <span class='st'>"qnt"</span>, <span class='kw'>qval</span> <span class='kw'>=</span> <span class='fl'>0.75</span>)</div><div class='output co'>#> time s.num i.num num se.flow is.flow iq.flow iq2h.flow hf.flow ds.flow
-#> 1 1 500.0 1.0 501 0.0 0.0 0.0 0.0 0 0
-#> 2 2 500.0 1.0 501 0.5 0.0 0.0 0.0 0 0
-#> 3 3 500.0 1.0 501 0.0 0.0 0.5 0.0 0 0
-#> 4 4 499.5 1.0 501 1.0 0.0 0.0 0.0 0 0
-#> 5 5 499.0 1.0 501 1.0 0.0 0.0 0.0 0 0
-#> 6 6 498.5 1.5 501 0.0 1.0 0.0 0.0 0 0
-#> 7 7 497.5 1.5 501 2.0 1.5 0.0 0.0 0 0
-#> 8 8 497.0 1.5 501 1.0 0.5 0.0 0.5 0 0
-#> 9 9 496.0 2.5 501 0.5 0.0 0.0 0.0 0 0
-#> 10 10 495.0 3.5 501 0.5 0.5 0.0 0.0 0 0
-#> de.flow di.flow dq.flow dh.flow dr.flow a.flow a.e.flow a.i.flow a.q.flow
-#> 1 0 0 0 0 0 0 0 0 0
-#> 2 0 0 0 0 0 0 0 0 0
-#> 3 0 0 0 0 0 0 0 0 0
-#> 4 0 0 0 0 0 0 0 0 0
-#> 5 0 0 0 0 0 0 0 0 0
-#> 6 0 0 0 0 0 0 0 0 0
-#> 7 0 0 0 0 0 0 0 0 0
-#> 8 0 0 0 0 0 0 0 0 0
-#> 9 0 0 0 0 0 0 0 0 0
-#> 10 0 0 0 0 0 0 0 0 0
-#> e.num r.num q.num h.num f.num
-#> 1 NA NA NA NA NA
-#> 2 0.5 0.0 0.0 0 0
-#> 3 0.5 0.0 0.5 0 0
-#> 4 1.5 0.0 0.5 0 0
-#> 5 2.5 0.0 0.5 0 0
-#> 6 1.5 1.0 0.5 0 0
-#> 7 2.5 2.5 0.5 0 0
-#> 8 3.0 3.5 0.5 0 0
-#> 9 4.5 3.5 0.5 0 0
-#> 10 6.0 4.0 0.5 0 0</div><div class='input'>
-</div></pre>
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-with simulate_seiqhrf. Similar to EpiModel::control.icm, but allows for
-model types with additional compartments (e.g. 'SEIQHRF')." />
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- <h1>Control Settings for Stochastic Individual Contact Models</h1>
-
- <div class="hidden name"><code>control_seiqhrf.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Sets the controls for stochastic individual contact models simulated
-with <code><a href='simulate_seiqhrf.html'>simulate_seiqhrf</a></code>. Similar to EpiModel::control.icm, but allows for
-model types with additional compartments (e.g. 'SEIQHRF').</p>
- </div>
-
- <pre class="usage"><span class='fu'>control_seiqhrf</span>(
- <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SEIQHRF"</span>,
- <span class='kw'>nsteps</span> <span class='kw'>=</span> <span class='fl'>366</span>,
- <span class='kw'>nsims</span> <span class='kw'>=</span> <span class='fl'>8</span>,
- <span class='kw'>prog.rand</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>quar.rand</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>hosp.rand</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>disch.rand</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>rec.rand</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>arec.rand</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>fat.rand</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>a.rand</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>d.rand</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>initialize.FUN</span> <span class='kw'>=</span> <span class='st'>"initialize.FUN"</span>,
- <span class='kw'>infection.FUN</span> <span class='kw'>=</span> <span class='st'>"infection.FUN"</span>,
- <span class='kw'>recovery.FUN</span> <span class='kw'>=</span> <span class='st'>"recovery.FUN"</span>,
- <span class='kw'>departures.FUN</span> <span class='kw'>=</span> <span class='st'>"departures.FUN"</span>,
- <span class='kw'>arrivals.FUN</span> <span class='kw'>=</span> <span class='st'>"arrivals.FUN"</span>,
- <span class='kw'>get_prev.FUN</span> <span class='kw'>=</span> <span class='st'>"get_prev.FUN"</span>,
- <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>verbose.int</span> <span class='kw'>=</span> <span class='fl'>0</span>,
- <span class='kw'>skip.check</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>ncores</span> <span class='kw'>=</span> <span class='fl'>4</span>,
- <span class='no'>...</span>
-)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>type</th>
- <td><p>Disease type to be modeled, with the choice of <code>"SI"</code> for
-Susceptible-Infected diseases, <code>"SIR"</code> for
-Susceptible-Infected-Recovered diseases, and <code>"SIS"</code> for
-Susceptible-Infected-Susceptible diseases.</p></td>
- </tr>
- <tr>
- <th>nsteps</th>
- <td><p>Number of time steps to solve the model over. This must be a
-positive integer.</p></td>
- </tr>
- <tr>
- <th>nsims</th>
- <td><p>Number of simulations to run.</p></td>
- </tr>
- <tr>
- <th>prog.rand</th>
- <td><p>Method for progression from E compartment to I. If TRUE,
-random binomial draws at prog.rate, if FALSE, random draws from a
-Weibull distribution (yes, I know it should be a discrete Weibull
-distribution but it makes little difference and speed of computation
-matters), with parameters prog.dist.scale and prog.dist.shape</p></td>
- </tr>
- <tr>
- <th>quar.rand</th>
- <td><p>Method for self-isolation transition from I to Q. If TRUE,
-random binomial draws at quar.rate, if FALSE, random sample with a
-sample fraction also given by `quar.rate.</p></td>
- </tr>
- <tr>
- <th>hosp.rand</th>
- <td><p>Method for transition from I or Q to H -- that is, from
-infectious or from self-isolated to requiring hospitalisation. If
-TRUE, random binomial draws at hosp.rate, if FALSE, random sample
-with a sample fraction also given by `hosp.rate.</p></td>
- </tr>
- <tr>
- <th>disch.rand</th>
- <td><p>Method for transition from H to R -- that is, from
-requiring hospitalisation to recovered. If TRUE, random binomial
-draws at disch.rate, if FALSE, random sample with a sample fraction
-also given by disch.rate. Note that the only way out of the H
-compartment is recovery or death.</p></td>
- </tr>
- <tr>
- <th>rec.rand</th>
- <td><p>If <code>TRUE</code>, use a stochastic recovery model, with the
-number of recovered at each time step a function of random draws from
-a binomial distribution with the probability equal to <code>rec.rate</code>.
-If <code>FALSE</code>, then a deterministic rounded count of the expectation
-implied by that rate.</p></td>
- </tr>
- <tr>
- <th>arec.rand</th>
- <td><p>Method for recovery transition from E to R. If TRUE,
-random binomial draws at arec.rate, if FALSE, random draws from a
-random draws from a Weibull distribution, with parameters
-arec.dist.scale and arec.dist.shape.</p></td>
- </tr>
- <tr>
- <th>fat.rand</th>
- <td><p>Method for case fatality transition from H to F. If TRUE,
-random binomial draws at fat.rate.base, if FALSE, random sample with
-a sample fraction also given by fat.rate.base. However, if the
-current number of patients in the H (needs hospitalisation)
-compartment is above a hospital capacity level specified by
-hosp.cap, then the fatality rate is the mean of the base fatality
-rate weighted by the hospital capacity, plus a higher rate,
-specified by fat.rate.overcap, weighted by the balance of those
-requiring hospitalisation (but who can't be accommodated). By
-setting fat.rate.overcap higher, the effect of exceeding the
-capacity of the health care system can be simulated. There is also
-a coefficient fat.tcoeff for the fatality rates that increases them
-as a linear function of the number of days the individual has been
-in the H compartment. Use of the co-efficient better approximates
-the trapezoid survival time distribution typical of ICU patients.</p></td>
- </tr>
- <tr>
- <th>a.rand</th>
- <td><p>If <code>TRUE</code>, use a stochastic arrival model, with the
-number of arrivals at each time step a function of random draws from a
-binomial distribution with the probability equal to the governing arrival
-rates. If <code>FALSE</code>, then a deterministic rounded count of the
-expectation implied by those rates.</p></td>
- </tr>
- <tr>
- <th>d.rand</th>
- <td><p>If <code>TRUE</code>, use a stochastic departure model, with the number of
-departures at each time step a function of random draws from a binomial
-distribution with the probability equal to the governing departure rates.
-If <code>FALSE</code>, then a deterministic rounded count of the expectation
-implied by those rates.</p></td>
- </tr>
- <tr>
- <th>initialize.FUN</th>
- <td><p>Module to initialize the model at the outset, with the
-default function of <code>initialize.icm</code>.</p></td>
- </tr>
- <tr>
- <th>infection.FUN</th>
- <td><p>Module to simulate disease infection, with the default
-function of <code>infection.icm</code>.</p></td>
- </tr>
- <tr>
- <th>recovery.FUN</th>
- <td><p>Module to simulate disease recovery, with the default
-function of <code>recovery.icm</code>.</p></td>
- </tr>
- <tr>
- <th>departures.FUN</th>
- <td><p>Module to simulate departures or exits, with the default
-function of <code>departures.icm</code>.</p></td>
- </tr>
- <tr>
- <th>arrivals.FUN</th>
- <td><p>Module to simulate arrivals or entries, with the default
-function of <code>arrivals.icm</code>.</p></td>
- </tr>
- <tr>
- <th>get_prev.FUN</th>
- <td><p>Module to calculate disease prevalence at each time step,
-with the default function of <code>get_prev.icm</code>.</p></td>
- </tr>
- <tr>
- <th>verbose</th>
- <td><p>If <code>TRUE</code>, print model progress to the console.</p></td>
- </tr>
- <tr>
- <th>verbose.int</th>
- <td><p>Time step interval for printing progress to console, where
-0 (the default) prints completion status of entire simulation and
-positive integer <code>x</code> prints progress after each <code>x</code> time
-steps.</p></td>
- </tr>
- <tr>
- <th>skip.check</th>
- <td><p>If <code>TRUE</code>, skips the default error checking for the
-structure and consistency of the parameter values, initial conditions,
-and control settings before running base epidemic models. Setting
-this to <code>FALSE</code> is recommended when running models with new modules
-specified.</p></td>
- </tr>
- <tr>
- <th>ncores</th>
- <td><p>Number of physical CPU cores used for parallel computation.</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Additional control settings passed to model.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>A list of control parameters and core functions</p>
- <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
- <p><code>control</code> sets the required control settings for any stochastic
-individual contact model solved with the <code>simulate_seiqhrf</code> function. Controls
-are required for both base model types and when passing original process
-modules. For an overview of control settings for base ICM class models,
-consult the <a href='http://statnet.github.io/tut/BasicICMs.html'>Basic ICMs</a>
-tutorial. For all base models, the <code>type</code> argument is a necessary
-parameter and it has no default.</p>
- <h2 class="hasAnchor" id="new-modules"><a class="anchor" href="#new-modules"></a>New Modules</h2>
-
-
-
-<p>Base ICM models use a set of module functions that specify
-how the individual agents in the population are subjected to infection, recovery,
-demographics, and other processes. Core modules are those listed in the
-<code>.FUN</code> arguments. For each module, there is a default function used in
-the simulation. The default infection module, for example, is contained in
-the <code><a href='infection.FUN.html'>infection.FUN</a></code> function.</p>
-<p>For original models, one may substitute replacement module functions for any of
-the default functions. New modules may be added to the workflow at each time
-step by passing a module function via the <code>...</code> argument.</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
- </nav>
- </div>
-</div>
-
-
- <footer>
- <div class="copyright">
- <p>Developed by Christina Azodi, Puxue Qiao, Ruqian Lyu, Sam Tanner, Tim Churches, Davis McCarthy.</p>
-</div>
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- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
- </footer>
- </div>
-
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-</html>
-
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diff --git a/public/reference/crosscheck_seiqhrf.html b/public/reference/crosscheck_seiqhrf.html
deleted file mode 100644
index c1284d0be2d8f44d89457faca1cfb70df8b4902e..0000000000000000000000000000000000000000
--- a/public/reference/crosscheck_seiqhrf.html
+++ /dev/null
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-<meta property="og:description" content="This function checks that the three parameter lists from
- param_seiqhrf, init.icm, and
- control_seiqhrf are consistent." />
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- <div class="page-header">
- <h1>Cross Checking of Inputs for Stochastic Individual Contact Models</h1>
-
- <div class="hidden name"><code>crosscheck_seiqhrf.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>This function checks that the three parameter lists from
- <code><a href='param_seiqhrf.html'>param_seiqhrf</a></code>, <code>init.icm</code>, and
- <code><a href='control_seiqhrf.html'>control_seiqhrf</a></code> are consistent.</p>
- </div>
-
- <pre class="usage"><span class='fu'>crosscheck_seiqhrf</span>(<span class='no'>param</span>, <span class='no'>init</span>, <span class='no'>control</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>param</th>
- <td><p>An <code>EpiModel</code> object of class <code>param.seiqhrf</code>.</p></td>
- </tr>
- <tr>
- <th>init</th>
- <td><p>An <code>EpiModel</code> object of class <code>init.icm</code>.</p></td>
- </tr>
- <tr>
- <th>control</th>
- <td><p>A list returned by <code><a href='control_seiqhrf.html'>control_seiqhrf</a></code>.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>This function returns no objects.</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
- </nav>
- </div>
-</div>
-
-
- <footer>
- <div class="copyright">
- <p>Developed by Christina Azodi, Puxue Qiao, Ruqian Lyu, Sam Tanner, Tim Churches, Davis McCarthy.</p>
-</div>
-
-<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
- </footer>
- </div>
-
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-</html>
-
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diff --git a/public/reference/cum_discr_si.html b/public/reference/cum_discr_si.html
deleted file mode 100644
index 53e85a5e8541b4b4f52f59b16df49f38e76b413d..0000000000000000000000000000000000000000
--- a/public/reference/cum_discr_si.html
+++ /dev/null
@@ -1,182 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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-<meta property="og:description" content="Function to sample values from a Weibull distribution with parameters shape
-and rate" />
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- <h1>Sample value from Weibull distribution</h1>
-
- <div class="hidden name"><code>cum_discr_si.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Function to sample values from a Weibull distribution with parameters shape
-and rate</p>
- </div>
-
- <pre class="usage"><span class='fu'>cum_discr_si</span>(<span class='no'>vecTimeSinceExp</span>, <span class='no'>scale</span>, <span class='no'>shape</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>vecTimeSinceExp</th>
- <td><p>?</p></td>
- </tr>
- <tr>
- <th>scale</th>
- <td><p>scale parameter value</p></td>
- </tr>
- <tr>
- <th>shape</th>
- <td><p>shape parameter value</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>Value of coefficient of variation for vector</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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diff --git a/public/reference/departures.FUN.html b/public/reference/departures.FUN.html
deleted file mode 100644
index aa58b8b7276c31409f0bfcb4155669e784017ba4..0000000000000000000000000000000000000000
--- a/public/reference/departures.FUN.html
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-<meta property="og:description" content="Function to handle background demographics for the SEIQHRF model.
-Specifically departures (deaths not due to the virus, and emigration)." />
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-
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- </div>
-
- <div class="ref-description">
- <p>Function to handle background demographics for the SEIQHRF model.
-Specifically departures (deaths not due to the virus, and emigration).</p>
- </div>
-
- <pre class="usage"><span class='fu'>departures.FUN</span>(<span class='no'>dat</span>, <span class='no'>at</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>dat</th>
- <td><p>Merged input parameters.</p></td>
- </tr>
- <tr>
- <th>at</th>
- <td><p>Step number</p></td>
- </tr>
- <tr>
- <th>seed</th>
- <td><p>random seed for checking consistency</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>Updated dat</p>
-
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diff --git a/public/reference/format_sims.html b/public/reference/format_sims.html
deleted file mode 100644
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--- a/public/reference/format_sims.html
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- <h1>Format seiqhrf objects into dataframe for ggplot</h1>
-
- <div class="hidden name"><code>format_sims.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Format seiqhrf objects into dataframe for ggplot</p>
- </div>
-
- <pre class="usage"><span class='fu'>format_sims</span>(<span class='no'>x</span>, <span class='no'>time_limit</span>, <span class='no'>start_date</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>x</th>
- <td><p>An seiqhrf object returned from function <code><a href='seiqhrf.html'>seiqhrf</a></code>.</p></td>
- </tr>
- <tr>
- <th>time_limit</th>
- <td><p>Number of steps (days) to plot.</p></td>
- </tr>
- <tr>
- <th>start_date</th>
- <td><p>Date for day 0. Default: ymd("2020-03-21"),</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>dataframe</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
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diff --git a/public/reference/get_ci.html b/public/reference/get_ci.html
deleted file mode 100644
index 6f7c96b3ff59c4d9af40f1e242455a18d86e2875..0000000000000000000000000000000000000000
--- a/public/reference/get_ci.html
+++ /dev/null
@@ -1,177 +0,0 @@
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- <h1>Get 95% confidence intervals</h1>
-
- <div class="hidden name"><code>get_ci.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Get 95% confidence intervals</p>
- </div>
-
- <pre class="usage"><span class='fu'>get_ci</span>(<span class='no'>x</span>, <span class='no'>plot_df</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>x</th>
- <td><p>An seiqhrf object returned from function <code><a href='seiqhrf.html'>seiqhrf</a></code>.</p></td>
- </tr>
- <tr>
- <th>plot_df</th>
- <td><p>Dataframe with known compartment numbers to plot alongside
-projections</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>dataframe with CIs and sd added</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
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-</div>
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diff --git a/public/reference/get_prev.FUN.html b/public/reference/get_prev.FUN.html
deleted file mode 100644
index a27fc4a3c61ec747c5be46473abd10b239248525..0000000000000000000000000000000000000000
--- a/public/reference/get_prev.FUN.html
+++ /dev/null
@@ -1,178 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
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- <p>Utility function that collects prevalence and transition time data from each
-run and stores it away in the simulation result object.</p>
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- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>dat</th>
- <td><p>Merged input parameters.</p></td>
- </tr>
- <tr>
- <th>at</th>
- <td><p>Step number</p></td>
- </tr>
- </table>
-
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-
- <p>Updated dat</p>
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diff --git a/public/reference/get_weekly_local.html b/public/reference/get_weekly_local.html
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- <h1>Extract and plot information of local and weekly estimates from simulation</h1>
-
- <div class="hidden name"><code>get_weekly_local.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Extract and plot information of local and weekly estimates from simulation</p>
- </div>
-
- <pre class="usage"><span class='fu'>get_weekly_local</span>(
- <span class='no'>sim</span>,
- <span class='kw'>market.share</span> <span class='kw'>=</span> <span class='no'>market.share</span>,
- <span class='kw'>icu_percent</span> <span class='kw'>=</span> <span class='no'>icu_percent</span>,
- <span class='kw'>start_date</span> <span class='kw'>=</span> <span class='no'>start_date</span>,
- <span class='kw'>show_start_date</span> <span class='kw'>=</span> <span class='no'>show_start_date</span>,
- <span class='kw'>time_limit</span> <span class='kw'>=</span> <span class='no'>time_limit</span>,
- <span class='kw'>total_population</span> <span class='kw'>=</span> <span class='no'>total_population</span>
-)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>sim</th>
- <td><p>An <code>seiqhrf</code> object returned by <a href='simulate_seiqhrf.html'>simulate_seiqhrf</a>.</p></td>
- </tr>
- <tr>
- <th>market.share</th>
- <td><p>between 0 and 1, percentage of local hospital beds in
-the simulated unit (e.g. state)</p></td>
- </tr>
- <tr>
- <th>icu_percent</th>
- <td><p>between 0 and 1, percentage of patients that should go to
-ICU among the ones that need hospitalization</p></td>
- </tr>
- <tr>
- <th>start_date</th>
- <td><p>Epidemic start date. Default is 'na', if not provided will
-plot week numbers, if provided will plot the first day (Sunday) of the
-week.</p></td>
- </tr>
- <tr>
- <th>show_start_date</th>
- <td><p>First date to show in plots. Use ymd format. If FALSE,
-shows from step 1. Default: FALSE</p></td>
- </tr>
- <tr>
- <th>time_limit</th>
- <td><p>Number of days to include. Default = 90.</p></td>
- </tr>
- <tr>
- <th>total_population</th>
- <td><p>True population size, needed only if simulation size
-is smaller than the true population size due to computational cost
-etc.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
-
-<ul>
-<li><p><code>plot:</code> A <code>ggplot</code> object, bar charts of count of patients
- requiring hospitalization and ICU respectively</p></li>
-<li><p><code>result:</code> A dataframe</p><ul>
-<li><p><code>hosp:</code> the number of patients that require hospitalization locally,</p></li>
-<li><p><code>icu:</code> the number of patients that require ICU locally.</p></li>
-</ul></li>
-</ul>
-
-
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- </div>
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- <colgroup>
-
- <col class="alias" />
- <col class="title" />
- </colgroup>
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- <tbody>
- <tr>
- <th colspan="2">
- <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
- <p class="section-desc"></p>
- </th>
- </tr>
-
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- </tbody><tbody>
-
-
- <tr>
-
- <td>
- <p><code><a href="add_known.html">add_known()</a></code> </p>
- </td>
- <td><p>Add known counts to sims dataframe for ggplot</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="arrivals.FUN.html">arrivals.FUN()</a></code> </p>
- </td>
- <td><p>Arrivals function</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="as.data.frame.seiqhrf.html">as.data.frame(<i><seiqhrf></i>)</a></code> </p>
- </td>
- <td><p>Extract Model Data for Stochastic Models</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="control_seiqhrf.html">control_seiqhrf()</a></code> </p>
- </td>
- <td><p>Control Settings for Stochastic Individual Contact Models</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="cum_discr_si.html">cum_discr_si()</a></code> </p>
- </td>
- <td><p>Sample value from Weibull distribution</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="departures.FUN.html">departures.FUN()</a></code> </p>
- </td>
- <td><p>Departures function</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="format_sims.html">format_sims()</a></code> </p>
- </td>
- <td><p>Format seiqhrf objects into dataframe for ggplot</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="get_ci.html">get_ci()</a></code> </p>
- </td>
- <td><p>Get 95% confidence intervals</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="get_prev.FUN.html">get_prev.FUN()</a></code> </p>
- </td>
- <td><p>Get previous function</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="get_weekly_local.html">get_weekly_local()</a></code> </p>
- </td>
- <td><p>Extract and plot information of local and weekly estimates from simulation</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="infection.FUN.html">infection.FUN()</a></code> </p>
- </td>
- <td><p>Infection function</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="init_seiqhrf.html">init_seiqhrf()</a></code> </p>
- </td>
- <td><p>Initial Conditions for Stochastic Individual Contact Models</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="init_status.icm.html">init_status.icm()</a></code> </p>
- </td>
- <td><p>Initialize status of ICM</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="initialize.FUN.html">initialize.FUN()</a></code> </p>
- </td>
- <td><p>Initialize ICM</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="merge.seiqhrf.icm.html">merge(<i><seiqhrf.icm></i>)</a></code> </p>
- </td>
- <td><p>Merge icm</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="param_seiqhrf.html">param_seiqhrf()</a></code> </p>
- </td>
- <td><p>Epidemic Parameters for Stochastic Individual Contact Models</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="plot.list.html">plot(<i><list></i>)</a></code> </p>
- </td>
- <td><p>Plot simulation result given list</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="plot.seiqhrf.html">plot(<i><seiqhrf></i>)</a></code> </p>
- </td>
- <td><p>Plot simulation result</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="plot_models.html">plot_models()</a></code> </p>
- </td>
- <td><p>Plot models</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="plot_sirplus.html">plot_sirplus()</a></code> </p>
- </td>
- <td><p>Wrapper for primary sirplus plotting function</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="plot_times.html">plot_times()</a></code> </p>
- </td>
- <td><p>Plot compartment duration distributions</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="recovery.FUN.html">recovery.FUN()</a></code> </p>
- </td>
- <td><p>Progress icm</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="saveout_seiqhrf.html">saveout_seiqhrf()</a></code> </p>
- </td>
- <td><p>Save icm</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="seiqhrf.html">seiqhrf()</a></code> </p>
- </td>
- <td><p>SEIQHRF function</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="simulate_seiqhrf.html">simulate_seiqhrf()</a></code> </p>
- </td>
- <td><p>SEIQHRF Simulation Wrapper</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="summary.seiqhrf.html">summary(<i><seiqhrf></i>)</a></code> </p>
- </td>
- <td><p>summary function</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="vary_param.html">vary_param()</a></code> </p>
- </td>
- <td><p>Generating time-dependent parameters</p></td>
- </tr>
- </tbody>
- </table>
- </div>
-
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
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diff --git a/public/reference/infection.FUN.html b/public/reference/infection.FUN.html
deleted file mode 100644
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--- a/public/reference/infection.FUN.html
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- <h1>Infection function</h1>
-
- <div class="hidden name"><code>infection.FUN.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Function to implement infection processes for SEIQHRF model</p>
- </div>
-
- <pre class="usage"><span class='fu'>infection.FUN</span>(<span class='no'>dat</span>, <span class='no'>at</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>dat</th>
- <td><p>Merged input parameters.</p></td>
- </tr>
- <tr>
- <th>at</th>
- <td><p>Step number</p></td>
- </tr>
- <tr>
- <th>seed</th>
- <td><p>random seed</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>Updated dat</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
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diff --git a/public/reference/init_seiqhrf.html b/public/reference/init_seiqhrf.html
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- <h1>Initial Conditions for Stochastic Individual Contact Models</h1>
-
- <div class="hidden name"><code>init_seiqhrf.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Sets the initial conditions for stochastic individual contact
- models simulated with <code>icm</code>.</p>
- </div>
-
- <pre class="usage"><span class='fu'>init_seiqhrf</span>(
- <span class='kw'>s.num</span> <span class='kw'>=</span> <span class='fl'>9997</span>,
- <span class='kw'>e.num</span> <span class='kw'>=</span> <span class='fl'>0</span>,
- <span class='kw'>i.num</span> <span class='kw'>=</span> <span class='fl'>3</span>,
- <span class='kw'>q.num</span> <span class='kw'>=</span> <span class='fl'>0</span>,
- <span class='kw'>h.num</span> <span class='kw'>=</span> <span class='fl'>0</span>,
- <span class='kw'>r.num</span> <span class='kw'>=</span> <span class='fl'>0</span>,
- <span class='kw'>f.num</span> <span class='kw'>=</span> <span class='fl'>0</span>,
- <span class='no'>...</span>
-)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>s.num</th>
- <td><p>Initial number of *S compartment individuals in
-the simulated population. An overall population of 10,000 is a good
-compromise. A set of models will still take several minutes or more
-to run, in parallel.</p></td>
- </tr>
- <tr>
- <th>e.num</th>
- <td><p>Initial number of E compartment individuals in
-the simulated population.</p></td>
- </tr>
- <tr>
- <th>i.num</th>
- <td><p>Initial number of I compartment individuals in
-the simulated population.</p></td>
- </tr>
- <tr>
- <th>q.num</th>
- <td><p>Initial number of Q compartment individuals in
-the simulated population.</p></td>
- </tr>
- <tr>
- <th>h.num</th>
- <td><p>Initial number of H compartment individuals in
-the simulated population.</p></td>
- </tr>
- <tr>
- <th>r.num</th>
- <td><p>Initial number of R compartment individuals in
-the simulated population.</p></td>
- </tr>
- <tr>
- <th>f.num</th>
- <td><p>Initial number of F compartment individuals in
-the simulated population.</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Additional initial conditions passed to model.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
- <p>The initial conditions for a model solved with <code>icm</code> should be
-input into the <code>init.icm</code> function. This function handles initial
-conditions for both base models and original models using new modules. For
-an overview of initial conditions for base ICM class models, consult the
-<a href='http://statnet.github.io/tut/BasicICMs.html'>Basic ICMs</a> tutorial.</p>
- <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
- <div class='dont-index'><p>Use <code>param.icm</code> to specify model parameters and
- <code>control.icm</code> to specify the control settings. Run the
- parameterized model with <code>icm</code>.</p></div>
-
- </div>
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diff --git a/public/reference/init_status.icm.html b/public/reference/init_status.icm.html
deleted file mode 100644
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--- a/public/reference/init_status.icm.html
+++ /dev/null
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- <h1>Initialize status of ICM</h1>
-
- <div class="hidden name"><code>init_status.icm.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Function to get the status of the initialized icm</p>
- </div>
-
- <pre class="usage"><span class='fu'>init_status.icm</span>(<span class='no'>dat</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>dat</th>
- <td><p>Object containing all data</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>Updated dat</p>
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diff --git a/public/reference/initialize.FUN.html b/public/reference/initialize.FUN.html
deleted file mode 100644
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--- a/public/reference/initialize.FUN.html
+++ /dev/null
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- <h1>Initialize ICM</h1>
-
- <div class="hidden name"><code>initialize.FUN.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Function to initialize the icm</p>
- </div>
-
- <pre class="usage"><span class='fu'>initialize.FUN</span>(<span class='no'>param</span>, <span class='no'>init</span>, <span class='no'>control</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>param</th>
- <td><p>ICM parameters.</p></td>
- </tr>
- <tr>
- <th>init</th>
- <td><p>Initial value parameters.</p></td>
- </tr>
- <tr>
- <th>control</th>
- <td><p>Control parameters</p></td>
- </tr>
- <tr>
- <th>seed</th>
- <td><p>random seed for checking consistency with other versions.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>Updated dat</p>
-
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diff --git a/public/reference/merge.seiqhrf.icm.html b/public/reference/merge.seiqhrf.icm.html
deleted file mode 100644
index 8db8bf9b1ed835eb4128b7c32ec020162cace9ee..0000000000000000000000000000000000000000
--- a/public/reference/merge.seiqhrf.icm.html
+++ /dev/null
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- <h1>Merge icm</h1>
-
- <div class="hidden name"><code>merge.seiqhrf.icm.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Function to merge icms</p>
- </div>
-
- <pre class="usage"><span class='co'># S3 method for seiqhrf.icm</span>
-<span class='fu'><a href='https://rdrr.io/r/base/merge.html'>merge</a></span>(<span class='no'>x</span>, <span class='no'>y</span>, <span class='no'>...</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>x</th>
- <td><p>First to merge</p></td>
- </tr>
- <tr>
- <th>y</th>
- <td><p>Second to merge</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>other parameters</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>Combined</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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- <h1>Epidemic Parameters for Stochastic Individual Contact Models</h1>
-
- <div class="hidden name"><code>param_seiqhrf.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Sets the epidemic parameters for stochastic individual contact
- models simulated with <code>seiqhrf</code>.</p>
- </div>
-
- <pre class="usage"><span class='fu'>param_seiqhrf</span>(
- <span class='kw'>inf.prob.e</span> <span class='kw'>=</span> <span class='fl'>0.02</span>,
- <span class='kw'>act.rate.e</span> <span class='kw'>=</span> <span class='fl'>10</span>,
- <span class='kw'>inf.prob.i</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
- <span class='kw'>act.rate.i</span> <span class='kw'>=</span> <span class='fl'>10</span>,
- <span class='kw'>inf.prob.q</span> <span class='kw'>=</span> <span class='fl'>0.02</span>,
- <span class='kw'>act.rate.q</span> <span class='kw'>=</span> <span class='fl'>2.5</span>,
- <span class='kw'>prog.rate</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>10</span>,
- <span class='kw'>quar.rate</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>30</span>,
- <span class='kw'>hosp.rate</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>100</span>,
- <span class='kw'>disch.rate</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>15</span>,
- <span class='kw'>rec.rate</span> <span class='kw'>=</span> <span class='fl'>0.071</span>,
- <span class='kw'>arec.rate</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
- <span class='kw'>prog.dist.scale</span> <span class='kw'>=</span> <span class='fl'>5</span>,
- <span class='kw'>prog.dist.shape</span> <span class='kw'>=</span> <span class='fl'>1.5</span>,
- <span class='kw'>quar.dist.scale</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>quar.dist.shape</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>hosp.dist.scale</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>hosp.dist.shape</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>disch.dist.scale</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>disch.dist.shape</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>rec.dist.scale</span> <span class='kw'>=</span> <span class='fl'>35</span>,
- <span class='kw'>rec.dist.shape</span> <span class='kw'>=</span> <span class='fl'>1.5</span>,
- <span class='kw'>arec.dist.scale</span> <span class='kw'>=</span> <span class='fl'>35</span>,
- <span class='kw'>arec.dist.shape</span> <span class='kw'>=</span> <span class='fl'>1.5</span>,
- <span class='kw'>fat.rate.base</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>50</span>,
- <span class='kw'>hosp.cap</span> <span class='kw'>=</span> <span class='fl'>40</span>,
- <span class='kw'>fat.rate.overcap</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>25</span>,
- <span class='kw'>fat.tcoeff</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
- <span class='kw'>vital</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>a.rate</span> <span class='kw'>=</span> (<span class='fl'>10.5</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='kw'>a.prop.e</span> <span class='kw'>=</span> <span class='fl'>0.01</span>,
- <span class='kw'>a.prop.i</span> <span class='kw'>=</span> <span class='fl'>0.001</span>,
- <span class='kw'>a.prop.q</span> <span class='kw'>=</span> <span class='fl'>0.01</span>,
- <span class='kw'>ds.rate</span> <span class='kw'>=</span> (<span class='fl'>7</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='kw'>de.rate</span> <span class='kw'>=</span> (<span class='fl'>7</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='kw'>di.rate</span> <span class='kw'>=</span> (<span class='fl'>7</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='kw'>dq.rate</span> <span class='kw'>=</span> (<span class='fl'>7</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='kw'>dh.rate</span> <span class='kw'>=</span> (<span class='fl'>20</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='kw'>dr.rate</span> <span class='kw'>=</span> (<span class='fl'>7</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='no'>...</span>
-)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>inf.prob.e</th>
- <td><p>Probability of passing on infection at each
-exposure event for interactions between infectious people in the E
-compartment and susceptible in S. Note the default is lower than for
-inf.prob.i reflecting the reduced infectivity of infected but
-asymptomatic people (the E compartment). Otherwise as for inf.exp.i.</p></td>
- </tr>
- <tr>
- <th>act.rate.e</th>
- <td><p>The number of exposure events (acts) between
-infectious individuals in the E compartment and susceptible individuals
-in the S compartment, per day. Otherwise as for act.rate.i.</p></td>
- </tr>
- <tr>
- <th>inf.prob.i</th>
- <td><p>Probability of passing on infection at each
-exposure event for interactions between infectious people in the I
-compartment and susceptible in S. Reducing inf.prob.i is equivalent to
-increasing hygiene measures, such as not putting hands in eyes, nose or
-moth, use of hand sanitisers, wearing masks by the infected, and so on.</p></td>
- </tr>
- <tr>
- <th>act.rate.i</th>
- <td><p>The number of exposure events (acts) between
-infectious individuals in the I compartment and susceptible individuals
-in the S compartment, per day. It's stochastic, so the rate is an
-average, some individuals may have more or less. Note that not every
-exposure event results in infection - that is governed by the inf.prob.i
-parameters (see below). Reducing act.rate.i is equivalent to increasing
-social distancing by people in the I compartment.</p></td>
- </tr>
- <tr>
- <th>inf.prob.q</th>
- <td><p>Probability of passing on infection at each
-exposure event for interactions between infectious people in the Q
-compartment and susceptible in S. Note the default is lower than for
-inf.prob.i reflecting the greater care that self-isolated individuals
-will, on average, take regarding hygiene measures, such as wearing masks,
-to limit spread to others. Otherwise as for inf.exp.i.</p></td>
- </tr>
- <tr>
- <th>act.rate.q</th>
- <td><p>The number of exposure events (acts) between
-infectious individuals in the Q compartment (isolated, self or otherwise)
-and susceptible individuals in the S compartment, per day. Note the much
-lower rate than for the I and E compartments, reflecting the much
-greater degree of social isolation for someone in (self-)isolation. The
-exposure event rate is not zero for this group, just much less.
-Otherwise as for act.rate.i.</p></td>
- </tr>
- <tr>
- <th>prog.rate</th>
- <td><p>Rate per day at which people who are infected
-but asymptomatic (E compartment) progress to becoming symptomatic (or
-test-positive), the I compartment. See prog.rand above for more details.</p></td>
- </tr>
- <tr>
- <th>quar.rate</th>
- <td><p>Rate per day at which symptomatic (or tested
-positive), infected I compartment people enter self-isolation (Q
-compartment). Asymptomatic E compartment people can't enter
-self-isolation because they don't yet know they are infected. Default is
-a low rate reflecting low community awareness or compliance with
-self-isolation requirements or practices, but this can be tweaked when
-exploring scenarios.</p></td>
- </tr>
- <tr>
- <th>hosp.rate</th>
- <td><p>Rate per day at which symptomatic (or tested
-positive), infected I compartment people or self-isolated Q compartment
-people enter the state of requiring hospital care -- that is, become
-serious cases. A default rate of 1<!-- % per day with an average illness -->
-duration of about 10 days means a bit less than 10<!-- % of cases will -->
-require hospitalisation, which seems about right (but can be tweaked,
-of course).</p></td>
- </tr>
- <tr>
- <th>disch.rate</th>
- <td><p>Rate per day at which people needing
-hospitalisation recover.</p></td>
- </tr>
- <tr>
- <th>rec.rate</th>
- <td><p>Rate per day at which people who are infected and
-symptomatic (I compartment) recover, thus entering the R compartment.
-See rec.rand above for more details.</p></td>
- </tr>
- <tr>
- <th>arec.rate</th>
- <td><p>Rate per day at which people who are exposed but asymptotic
-(E compartment) recover, thus entering the R compartment.
-See arec.rand above for more details.</p></td>
- </tr>
- <tr>
- <th>prog.dist.scale</th>
- <td><p>Scale parameter for Weibull distribution
-for progression, see prog.rand for details.</p></td>
- </tr>
- <tr>
- <th>prog.dist.shape</th>
- <td><p>Shape parameter for Weibull distribution
-for progression, see prog.rand for details. Read up on the Weibull
-distribution before changing the default.</p></td>
- </tr>
- <tr>
- <th>quar.dist.scale</th>
- <td><p>Scale parameter for Weibull distribution for
-recovery, see quar.rand for details.</p></td>
- </tr>
- <tr>
- <th>quar.dist.shape</th>
- <td><p>Shape parameter for Weibull distribution for
-recovery, see quar.rand for details. Read up on the Weibull distribution
-before changing the default.</p></td>
- </tr>
- <tr>
- <th>hosp.dist.scale</th>
- <td><p>Scale parameter for Weibull distribution for
-recovery, see hosp.rand for details.</p></td>
- </tr>
- <tr>
- <th>hosp.dist.shape</th>
- <td><p>Shape parameter for Weibull distribution for
-recovery, see hosp.rand for details. Read up on the Weibull distribution
-before changing the default.</p></td>
- </tr>
- <tr>
- <th>disch.dist.scale</th>
- <td><p>Scale parameter for Weibull distribution for
-recovery, see disch.rand for details.</p></td>
- </tr>
- <tr>
- <th>disch.dist.shape</th>
- <td><p>Shape parameter for Weibull distribution for
-recovery, see disch.rand for details. Read up on the Weibull distribution
-before changing the default.</p></td>
- </tr>
- <tr>
- <th>rec.dist.scale</th>
- <td><p>Scale parameter for Weibull distribution for
-recovery, see rec.rand for details.</p></td>
- </tr>
- <tr>
- <th>rec.dist.shape</th>
- <td><p>Shape parameter for Weibull distribution for
-recovery, see rec.rand for details. Read up on the Weibull distribution
-before changing the default.</p></td>
- </tr>
- <tr>
- <th>arec.dist.scale</th>
- <td><p>Scale parameter for Weibull distribution for
-recovery, see arec.rand for details.</p></td>
- </tr>
- <tr>
- <th>arec.dist.shape</th>
- <td><p>Shape parameter for Weibull distribution for
-recovery, see arec.rand for details.</p></td>
- </tr>
- <tr>
- <th>fat.rate.base</th>
- <td><p>Baseline mortality rate per day for people
-needing hospitalisation (deaths due to the virus). See fat.rand for more
-details.</p></td>
- </tr>
- <tr>
- <th>hosp.cap</th>
- <td><p>Number of available hospital beds for the modelled
-population. See fat.rand for more details.</p></td>
- </tr>
- <tr>
- <th>fat.rate.overcap</th>
- <td><p>Mortality rate per day for people needing
-hospitalisation but who can't get into hospital due to the hospitals
-being full (see hosp.cap and fat.rand). The default rate is twice that
-for those who do get into hospital.</p></td>
- </tr>
- <tr>
- <th>fat.tcoeff</th>
- <td><p>Time co-efficient for increasing mortality rate
-as time in the H compartment increases for each individual in it. See
-fat.rand for details.</p></td>
- </tr>
- <tr>
- <th>vital</th>
- <td><p>Enables demographics, that is, arrivals and
-departures, to and from the simulated population.</p></td>
- </tr>
- <tr>
- <th>a.rate</th>
- <td><p>Background demographic arrival rate. Currently all
-arrivals go into the S compartment, the default is approximately the
-daily birth rate for Australia. Will be extended to cover immigration in
-future versions.</p></td>
- </tr>
- <tr>
- <th>a.prop.e</th>
- <td><p>Arrivals proportion that goes to E (immigration).</p></td>
- </tr>
- <tr>
- <th>a.prop.i</th>
- <td><p>Arrivals proportion that goes to I (immigration).</p></td>
- </tr>
- <tr>
- <th>a.prop.q</th>
- <td><p>Arrivals proportion that goes to Q (immigration).</p></td>
- </tr>
- <tr>
- <th>ds.rate</th>
- <td><p>Background demographic departure (death not due to
-virus) rates. Defaults based on Australian crude death rates. Can be
-used to model emigration as well as deaths.</p></td>
- </tr>
- <tr>
- <th>de.rate</th>
- <td><p>Background demographic departure (death not due to
-virus) rates. Defaults based on Australian crude death rates. Can be
-used to model emigration as well as deaths.</p></td>
- </tr>
- <tr>
- <th>di.rate</th>
- <td><p>Background demographic departure (death not due to
-virus) rates. Defaults based on Australian crude death rates. Can be used
-to model emigration as well as deaths.</p></td>
- </tr>
- <tr>
- <th>dq.rate</th>
- <td><p>Background demographic departure (death not due to
-virus) rates. Defaults based on Australian crude death rates. Can be used
-to model emigration as well as deaths.</p></td>
- </tr>
- <tr>
- <th>dh.rate</th>
- <td><p>Background demographic departure (death not due to
-virus) rates. Defaults based on Australian crude death rates. Can be used
-to model emigration as well as deaths.</p></td>
- </tr>
- <tr>
- <th>dr.rate</th>
- <td><p>Background demographic departure (death not due to
-virus) rates. Defaults based on Australian crude death rates. Can be used
-to model emigration as well as deaths.</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Other parameters.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
-
- <p><code>param_seiqhrf</code> sets the epidemic parameters for the stochastic individual
-contact models simulated with the <code><a href='seiqhrf.html'>seiqhrf</a></code> function. Models
-may use the base types, for which these parameters are used, or new process
-modules which may use these parameters (but not necessarily). A detailed
-description of ICM parameterization for base models is found in the
-<a href='http://statnet.github.io/tut/BasicICMs.html'>Basic ICMs</a> tutorial.</p>
-<p>For base models, the model specification will be chosen as a result of
-the model parameters entered here and the control settings in
-<code><a href='control_seiqhrf.html'>control_seiqhrf</a></code>.</p>
- <h2 class="hasAnchor" id="new-modules"><a class="anchor" href="#new-modules"></a>New Modules</h2>
-
-
-
-<p>To build original models outside of the base models, new process modules
-may be constructed to replace the existing modules or to supplement the existing
-set. These are passed into the control settings in <code><a href='control_seiqhrf.html'>control_seiqhrf</a></code>.
-New modules may use either the existing model parameters named here, an
-original set of parameters, or a combination of both. The <code>...</code> allows
-the user to pass an arbitrary set of original model parameters into
-<code>param_seiqhrf</code>. Whereas there are strict checks with default modules for
-parameter validity, these checks are the user's responsibility with new modules.</p>
- <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
-
- <div class='dont-index'><p>Use <code>init.icm</code> to specify the initial conditions and
- <code><a href='control_seiqhrf.html'>control_seiqhrf</a></code> to specify the control settings. Run the
- parameterized model with <code><a href='seiqhrf.html'>seiqhrf</a></code>.</p></div>
-
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- <h1>Plot simulation result given list</h1>
-
- <div class="hidden name"><code>plot.list.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Plot simulation result given list</p>
- </div>
-
- <pre class="usage"><span class='co'># S3 method for list</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(
- <span class='no'>x</span>,
- <span class='kw'>comp_remove</span> <span class='kw'>=</span> <span class='st'>"none"</span>,
- <span class='kw'>time_limit</span> <span class='kw'>=</span> <span class='fl'>90</span>,
- <span class='kw'>ci</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>sep_compartments</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>trans</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>known</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>start_date</span> <span class='kw'>=</span> <span class='fu'>ymd</span>(<span class='st'>"2020-03-21"</span>),
- <span class='kw'>x_axis</span> <span class='kw'>=</span> <span class='st'>"Days since beginning of epidemic"</span>,
- <span class='kw'>plot_title</span> <span class='kw'>=</span> <span class='st'>"SEIQHRF"</span>,
- <span class='no'>...</span>
-)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>x</th>
- <td><p>A list of seiqhrf objects returned from <code><a href='seiqhrf.html'>seiqhrf</a></code>.</p></td>
- </tr>
- <tr>
- <th>comp_remove</th>
- <td><p>Compartments to remove. Suggest c(s.num, r.num)</p></td>
- </tr>
- <tr>
- <th>time_limit</th>
- <td><p>Number of steps (days) to plot.</p></td>
- </tr>
- <tr>
- <th>ci</th>
- <td><p>T/F to include 95% confidence intervals in sirplus plot.</p></td>
- </tr>
- <tr>
- <th>sep_compartments</th>
- <td><p>T/F use faceting to show each compartment in a
-separate plot, only works if plotting a single simulation.</p></td>
- </tr>
- <tr>
- <th>trans</th>
- <td><p>Y-axis transformation (e.g. log2, log10). Default = none.</p></td>
- </tr>
- <tr>
- <th>known</th>
- <td><p>Dataframe with known compartment numbers to plot alongside
-projections</p></td>
- </tr>
- <tr>
- <th>start_date</th>
- <td><p>Date for day 0. Default: ymd("2020-03-21"),</p></td>
- </tr>
- <tr>
- <th>x_axis</th>
- <td><p>Title for x-axis. Default: 'Days since beginning of epidemic'</p></td>
- </tr>
- <tr>
- <th>plot_title</th>
- <td><p>Title for whole plot. Default: 'SEIQHRF plot'</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Additional parameters</p></td>
- </tr>
- </table>
-
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
- </nav>
- </div>
-</div>
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- <footer>
- <div class="copyright">
- <p>Developed by Christina Azodi, Puxue Qiao, Ruqian Lyu, Sam Tanner, Tim Churches, Davis McCarthy.</p>
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diff --git a/public/reference/plot.seiqhrf.html b/public/reference/plot.seiqhrf.html
deleted file mode 100644
index 0746a72e6dfce65c806180b0097c1be6ebee8970..0000000000000000000000000000000000000000
--- a/public/reference/plot.seiqhrf.html
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- <div class="page-header">
- <h1>Plot simulation result</h1>
-
- <div class="hidden name"><code>plot.seiqhrf.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Plot simulation result</p>
- </div>
-
- <pre class="usage"><span class='co'># S3 method for seiqhrf</span>
-<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(
- <span class='no'>x</span>,
- <span class='kw'>method</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>comp_remove</span> <span class='kw'>=</span> <span class='st'>"none"</span>,
- <span class='kw'>time_limit</span> <span class='kw'>=</span> <span class='fl'>90</span>,
- <span class='kw'>ci</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>sep_compartments</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>trans</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>known</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>start_date</span> <span class='kw'>=</span> <span class='fu'>ymd</span>(<span class='st'>"2020-03-21"</span>),
- <span class='kw'>show_start_date</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>x_axis</span> <span class='kw'>=</span> <span class='st'>"Days since beginning of epidemic"</span>,
- <span class='kw'>plot_title</span> <span class='kw'>=</span> <span class='st'>"SEIQHRF"</span>,
- <span class='kw'>return_df</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>market.share</span> <span class='kw'>=</span> <span class='fl'>0.04</span>,
- <span class='kw'>icu_percent</span> <span class='kw'>=</span> <span class='fl'>0.1</span>,
- <span class='kw'>total_population</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='no'>...</span>
-)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>x</th>
- <td><p>An seiqhrf object returned from function <code><a href='seiqhrf.html'>seiqhrf</a></code>.</p></td>
- </tr>
- <tr>
- <th>method</th>
- <td><p>If "times", plot Duration frequency distributions.
-If "weekly_local", plot local weekly estimates from simulation.
-If NULL, plot sirplus plots.</p></td>
- </tr>
- <tr>
- <th>comp_remove</th>
- <td><p>Compartments to remove. Suggest c(s.num, r.num)</p></td>
- </tr>
- <tr>
- <th>time_limit</th>
- <td><p>Number of steps (days) to plot.</p></td>
- </tr>
- <tr>
- <th>ci</th>
- <td><p>T/F to include 95% confidence intervals in sirplus plot.</p></td>
- </tr>
- <tr>
- <th>sep_compartments</th>
- <td><p>T/F use faceting to show each compartment in a
-separate plot, only works if plotting a single simulation.</p></td>
- </tr>
- <tr>
- <th>trans</th>
- <td><p>Y-axis transformation (e.g. log2, log10). Default = none.</p></td>
- </tr>
- <tr>
- <th>known</th>
- <td><p>Dataframe with known compartment numbers to plot alongside
-projections</p></td>
- </tr>
- <tr>
- <th>start_date</th>
- <td><p>Date for day 0. Default: ymd("2020-03-21"),</p></td>
- </tr>
- <tr>
- <th>show_start_date</th>
- <td><p>First date to show in plots. Use ymd format. If FALSE,
-shows from step 1. Default: FALSE</p></td>
- </tr>
- <tr>
- <th>x_axis</th>
- <td><p>Title for x-axis. Default: 'Days since beginning of epidemic'</p></td>
- </tr>
- <tr>
- <th>plot_title</th>
- <td><p>Title for whole plot. Default: 'SEIQHRF plot'</p></td>
- </tr>
- <tr>
- <th>return_df</th>
- <td><p>In effect only when method == "weekly", if TRUE returns
-also the dataframe used for plotting as well as the ggplot object.</p></td>
- </tr>
- <tr>
- <th>market.share</th>
- <td><p>between 0 and 1, percentage of local hospital beds in
-the simulated unit (e.g. state)</p></td>
- </tr>
- <tr>
- <th>icu_percent</th>
- <td><p>between 0 and 1, percentage of patients that should go to
-ICU among the ones that need hospitalization</p></td>
- </tr>
- <tr>
- <th>total_population</th>
- <td><p>True population size, needed only if simulation size
-is smaller than the true population size due to computational cost
-etc.</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Additional parameters</p></td>
- </tr>
- </table>
-
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
- </nav>
- </div>
-</div>
-
-
- <footer>
- <div class="copyright">
- <p>Developed by Christina Azodi, Puxue Qiao, Ruqian Lyu, Sam Tanner, Tim Churches, Davis McCarthy.</p>
-</div>
-
-<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
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diff --git a/public/reference/plot_models.html b/public/reference/plot_models.html
deleted file mode 100644
index fa84c8c82ed9025919bbc0b4a43d527b85a20487..0000000000000000000000000000000000000000
--- a/public/reference/plot_models.html
+++ /dev/null
@@ -1,215 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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- Articles
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- <div class="col-md-9 contents">
- <div class="page-header">
- <h1>Plot models</h1>
-
- <div class="hidden name"><code>plot_models.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Function to plot individuals models or multiple models for comparison.</p>
- </div>
-
- <pre class="usage"><span class='fu'>plot_models</span>(
- <span class='kw'>sims</span> <span class='kw'>=</span> <span class='no'>baseline_sim</span>,
- <span class='kw'>sim_id</span> <span class='kw'>=</span> <span class='st'>"baseline"</span>,
- <span class='kw'>comp_remove</span> <span class='kw'>=</span> <span class='st'>"none"</span>,
- <span class='kw'>time_lim</span> <span class='kw'>=</span> <span class='fl'>100</span>,
- <span class='kw'>trans</span> <span class='kw'>=</span> <span class='st'>"na"</span>,
- <span class='kw'>known</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
- <span class='kw'>start_date</span> <span class='kw'>=</span> <span class='fu'>ymd</span>(<span class='st'>"2020-03-21"</span>),
- <span class='kw'>x_axis</span> <span class='kw'>=</span> <span class='st'>"Days since beginning of epidemic"</span>,
- <span class='kw'>plot_title</span> <span class='kw'>=</span> <span class='st'>"SEIQHRF"</span>
-)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>sims</th>
- <td><p>Single or list of sims to plot</p></td>
- </tr>
- <tr>
- <th>sim_id</th>
- <td><p>String or list of strings to name each facet</p></td>
- </tr>
- <tr>
- <th>comp_remove</th>
- <td><p>Compartments to remove. Suggest c(s.num, r.num)</p></td>
- </tr>
- <tr>
- <th>time_lim</th>
- <td><p>Number of steps (days) to plot.</p></td>
- </tr>
- <tr>
- <th>trans</th>
- <td><p>Y-axis transformation (e.g. log2, log10). Default = none.</p></td>
- </tr>
- <tr>
- <th>known</th>
- <td><p>Dataframe with known compartment numbers to plot alongside
-projections</p></td>
- </tr>
- <tr>
- <th>start_date</th>
- <td><p>Date for day 0. Default: ymd("2020-03-21"),</p></td>
- </tr>
- <tr>
- <th>x_axis</th>
- <td><p>Title for x-axis. Default: 'Days since beginning of epidemic'</p></td>
- </tr>
- <tr>
- <th>plot_title</th>
- <td><p>Title for whole plot. Default: 'SEIQHRF plot'</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>ggplot2 object</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
- </nav>
- </div>
-</div>
-
-
- <footer>
- <div class="copyright">
- <p>Developed by Christina Azodi, Puxue Qiao, Ruqian Lyu, Sam Tanner, Tim Churches, Davis McCarthy.</p>
-</div>
-
-<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
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diff --git a/public/reference/plot_sirplus.html b/public/reference/plot_sirplus.html
deleted file mode 100644
index e72995cc1da4fb02fe47d4759cb3983dcb410026..0000000000000000000000000000000000000000
--- a/public/reference/plot_sirplus.html
+++ /dev/null
@@ -1,233 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
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- <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
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-<title>Wrapper for primary sirplus plotting function — plot_sirplus • sirplus</title>
-
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-<!-- jquery -->
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-<meta property="og:description" content="Flexible function to generate sirplus plots (i.e. compartment counts over
-time). This function allows for plotting multiple experiments, viewing the
-plots of different scales (e.g. log2), plotting compartments separately,
-adding 95% CIs, and plotting known data along side the simulations." />
-
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-<!-- mathjax -->
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- Articles
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- <a href="../articles/sirplus_intro_v2.html">Introduction to sirplus (V2)</a>
- </li>
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- <a href="../news/index.html">Changelog</a>
-</li>
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- <ul class="nav navbar-nav navbar-right">
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-
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-<div class="row">
- <div class="col-md-9 contents">
- <div class="page-header">
- <h1>Wrapper for primary sirplus plotting function</h1>
-
- <div class="hidden name"><code>plot_sirplus.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Flexible function to generate sirplus plots (i.e. compartment counts over
-time). This function allows for plotting multiple experiments, viewing the
-plots of different scales (e.g. log2), plotting compartments separately,
-adding 95% CIs, and plotting known data along side the simulations.</p>
- </div>
-
- <pre class="usage"><span class='fu'>plot_sirplus</span>(
- <span class='no'>x</span>,
- <span class='no'>comp_remove</span>,
- <span class='no'>time_limit</span>,
- <span class='no'>ci</span>,
- <span class='no'>sep_compartments</span>,
- <span class='no'>trans</span>,
- <span class='no'>known</span>,
- <span class='no'>start_date</span>,
- <span class='no'>x_axis</span>,
- <span class='no'>plot_title</span>,
- <span class='no'>...</span>
-)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>x</th>
- <td><p>A seiqhrf object (or list of multiple seiqhrf objects) returned
-from <code><a href='seiqhrf.html'>seiqhrf</a></code>.</p></td>
- </tr>
- <tr>
- <th>comp_remove</th>
- <td><p>Compartments to remove. Suggest c(s.num, r.num)</p></td>
- </tr>
- <tr>
- <th>time_limit</th>
- <td><p>Number of steps (days) to plot.</p></td>
- </tr>
- <tr>
- <th>ci</th>
- <td><p>T/F to include 95% confidence intervals in sirplus plot.</p></td>
- </tr>
- <tr>
- <th>sep_compartments</th>
- <td><p>T/F use faceting to show each compartment in a
-separate plot, only works if plotting a single simulation.</p></td>
- </tr>
- <tr>
- <th>trans</th>
- <td><p>Y-axis transformation (e.g. log2, log10). Default = none.</p></td>
- </tr>
- <tr>
- <th>known</th>
- <td><p>Dataframe with known compartment numbers to plot alongside
-projections</p></td>
- </tr>
- <tr>
- <th>start_date</th>
- <td><p>Date for day 0. Default: ymd("2020-03-21"),</p></td>
- </tr>
- <tr>
- <th>x_axis</th>
- <td><p>Title for x-axis. Default: 'Days since beginning of epidemic'</p></td>
- </tr>
- <tr>
- <th>plot_title</th>
- <td><p>Title for whole plot. Default: 'SEIQHRF plot'</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Additional parameters</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>ggplot2 object</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
- </nav>
- </div>
-</div>
-
-
- <footer>
- <div class="copyright">
- <p>Developed by Christina Azodi, Puxue Qiao, Ruqian Lyu, Sam Tanner, Tim Churches, Davis McCarthy.</p>
-</div>
-
-<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
-</div>
-
- </footer>
- </div>
-
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-</html>
-
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diff --git a/public/reference/plot_times.html b/public/reference/plot_times.html
deleted file mode 100644
index f1dbdfe2892404758c87b94a3b8a86170f1247c8..0000000000000000000000000000000000000000
--- a/public/reference/plot_times.html
+++ /dev/null
@@ -1,174 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Plot compartment duration distributions — plot_times • sirplus</title>
-
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-<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
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-
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-<script src="../bootstrap-toc.js"></script>
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-<!-- headroom.js -->
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-<meta property="og:title" content="Plot compartment duration distributions — plot_times" />
-<meta property="og:description" content="Function to plot Duration frequency distributions. If multiple simulations
-were performed (nsim &gt;1), durations from sims are appended to each other." />
-
-
-
-
-<!-- mathjax -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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- <span class="icon-bar"></span>
- </button>
- <span class="navbar-brand">
- <a class="navbar-link" href="../index.html">sirplus</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.1.0</span>
- </span>
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-
- <div id="navbar" class="navbar-collapse collapse">
- <ul class="nav navbar-nav">
- <li>
- <a href="../index.html">
- <span class="fas fa fas fa-home fa-lg"></span>
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- <a href="../reference/index.html">Reference</a>
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- <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
- Articles
-
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- </a>
- <ul class="dropdown-menu" role="menu">
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- <a href="../articles/sirplus_intro_v2.html">Introduction to sirplus (V2)</a>
- </li>
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- <a href="../news/index.html">Changelog</a>
-</li>
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- <ul class="nav navbar-nav navbar-right">
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- <h1>Plot compartment duration distributions</h1>
-
- <div class="hidden name"><code>plot_times.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Function to plot Duration frequency distributions. If multiple simulations
-were performed (nsim >1), durations from sims are appended to each other.</p>
- </div>
-
- <pre class="usage"><span class='fu'>plot_times</span>(<span class='no'>sim</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>sim</th>
- <td><p>An seiqhrf object returned from function <code><a href='seiqhrf.html'>seiqhrf</a></code>.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>ggplot2 object</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
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-</div>
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diff --git a/public/reference/recovery.FUN.html b/public/reference/recovery.FUN.html
deleted file mode 100644
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--- a/public/reference/recovery.FUN.html
+++ /dev/null
@@ -1,180 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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- <a href="../articles/sirplus_intro_v2.html">Introduction to sirplus (V2)</a>
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- <a href="../news/index.html">Changelog</a>
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- <h1>Progress icm</h1>
-
- <div class="hidden name"><code>recovery.FUN.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Function to get progress of icms</p>
- </div>
-
- <pre class="usage"><span class='fu'>recovery.FUN</span>(<span class='no'>dat</span>, <span class='no'>at</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>dat</th>
- <td><p>Object containing all data</p></td>
- </tr>
- <tr>
- <th>at</th>
- <td><p>time point</p></td>
- </tr>
- <tr>
- <th>seed</th>
- <td><p>random seed for checking consistency</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>progress</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
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diff --git a/public/reference/saveout_seiqhrf.html b/public/reference/saveout_seiqhrf.html
deleted file mode 100644
index fd9d798381c4467a9ac4e692632db6422c4cdb44..0000000000000000000000000000000000000000
--- a/public/reference/saveout_seiqhrf.html
+++ /dev/null
@@ -1,180 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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- <h1>Save icm</h1>
-
- <div class="hidden name"><code>saveout_seiqhrf.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Function to organize simulation outputs</p>
- </div>
-
- <pre class="usage"><span class='fu'>saveout_seiqhrf</span>(<span class='no'>dat</span>, <span class='no'>s</span>, <span class='kw'>out</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>dat</th>
- <td><p>Merged input parameters.</p></td>
- </tr>
- <tr>
- <th>s</th>
- <td><p>Step number or time point.</p></td>
- </tr>
- <tr>
- <th>out</th>
- <td><p>initial out. Default = NULL</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>list of output in the same format as <code>icm</code> object in <code>EpiModel</code>.</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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diff --git a/public/reference/seiqhrf.html b/public/reference/seiqhrf.html
deleted file mode 100644
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--- a/public/reference/seiqhrf.html
+++ /dev/null
@@ -1,184 +0,0 @@
-<!-- Generated by pkgdown: do not edit by hand -->
-<!DOCTYPE html>
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-<meta http-equiv="X-UA-Compatible" content="IE=edge">
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- <h1>SEIQHRF function</h1>
-
- <div class="hidden name"><code>seiqhrf.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Function to implement infection processes for SEIQHRF model</p>
- </div>
-
- <pre class="usage"><span class='fu'>seiqhrf</span>(<span class='no'>init</span>, <span class='no'>control</span>, <span class='no'>param</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>init</th>
- <td><p>Initial state values, returned by <code><a href='init_seiqhrf.html'>init_seiqhrf</a></code>.</p></td>
- </tr>
- <tr>
- <th>control</th>
- <td><p>Control parameters of the model, returned by <code><a href='control_seiqhrf.html'>control_seiqhrf</a></code>.</p></td>
- </tr>
- <tr>
- <th>param</th>
- <td><p>Model parameters, returned by <code><a href='param_seiqhrf.html'>param_seiqhrf</a></code>.</p></td>
- </tr>
- <tr>
- <th>seed</th>
- <td><p>random seed for checking consistency</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>Updated dat</p>
-
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- <h1>SEIQHRF Simulation Wrapper</h1>
-
- <div class="hidden name"><code>simulate_seiqhrf.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Wrapper to implement SEIQHRF model</p>
- </div>
-
- <pre class="usage"><span class='fu'>simulate_seiqhrf</span>(
- <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SEIQHRF"</span>,
- <span class='kw'>nsteps</span> <span class='kw'>=</span> <span class='fl'>366</span>,
- <span class='kw'>nsims</span> <span class='kw'>=</span> <span class='fl'>8</span>,
- <span class='kw'>ncores</span> <span class='kw'>=</span> <span class='fl'>4</span>,
- <span class='kw'>prog.rand</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>quar.rand</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>hosp.rand</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>disch.rand</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>rec.rand</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
- <span class='kw'>arec.rand</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>fat.rand</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>infection.FUN</span> <span class='kw'>=</span> <span class='st'>"infection.FUN"</span>,
- <span class='kw'>recovery.FUN</span> <span class='kw'>=</span> <span class='st'>"recovery.FUN"</span>,
- <span class='kw'>departures.FUN</span> <span class='kw'>=</span> <span class='st'>"departures.FUN"</span>,
- <span class='kw'>arrivals.FUN</span> <span class='kw'>=</span> <span class='st'>"arrivals.FUN"</span>,
- <span class='kw'>get_prev.FUN</span> <span class='kw'>=</span> <span class='st'>"get_prev.FUN"</span>,
- <span class='kw'>s.num</span> <span class='kw'>=</span> <span class='fl'>9997</span>,
- <span class='kw'>e.num</span> <span class='kw'>=</span> <span class='fl'>0</span>,
- <span class='kw'>i.num</span> <span class='kw'>=</span> <span class='fl'>3</span>,
- <span class='kw'>q.num</span> <span class='kw'>=</span> <span class='fl'>0</span>,
- <span class='kw'>h.num</span> <span class='kw'>=</span> <span class='fl'>0</span>,
- <span class='kw'>r.num</span> <span class='kw'>=</span> <span class='fl'>0</span>,
- <span class='kw'>f.num</span> <span class='kw'>=</span> <span class='fl'>0</span>,
- <span class='kw'>inf.prob.e</span> <span class='kw'>=</span> <span class='fl'>0.02</span>,
- <span class='kw'>act.rate.e</span> <span class='kw'>=</span> <span class='fl'>10</span>,
- <span class='kw'>inf.prob.i</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
- <span class='kw'>act.rate.i</span> <span class='kw'>=</span> <span class='fl'>10</span>,
- <span class='kw'>inf.prob.q</span> <span class='kw'>=</span> <span class='fl'>0.02</span>,
- <span class='kw'>act.rate.q</span> <span class='kw'>=</span> <span class='fl'>2.5</span>,
- <span class='kw'>prog.rate</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>10</span>,
- <span class='kw'>quar.rate</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>30</span>,
- <span class='kw'>hosp.rate</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>100</span>,
- <span class='kw'>disch.rate</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>15</span>,
- <span class='kw'>rec.rate</span> <span class='kw'>=</span> <span class='fl'>0.071</span>,
- <span class='kw'>arec.rate</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
- <span class='kw'>prog.dist.scale</span> <span class='kw'>=</span> <span class='fl'>5</span>,
- <span class='kw'>prog.dist.shape</span> <span class='kw'>=</span> <span class='fl'>1.5</span>,
- <span class='kw'>quar.dist.scale</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>quar.dist.shape</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>hosp.dist.scale</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>hosp.dist.shape</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>disch.dist.scale</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>disch.dist.shape</span> <span class='kw'>=</span> <span class='fl'>1</span>,
- <span class='kw'>rec.dist.scale</span> <span class='kw'>=</span> <span class='fl'>35</span>,
- <span class='kw'>rec.dist.shape</span> <span class='kw'>=</span> <span class='fl'>1.5</span>,
- <span class='kw'>arec.dist.scale</span> <span class='kw'>=</span> <span class='fl'>35</span>,
- <span class='kw'>arec.dist.shape</span> <span class='kw'>=</span> <span class='fl'>1.5</span>,
- <span class='kw'>fat.rate.base</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>50</span>,
- <span class='kw'>hosp.cap</span> <span class='kw'>=</span> <span class='fl'>40</span>,
- <span class='kw'>fat.rate.overcap</span> <span class='kw'>=</span> <span class='fl'>1</span>/<span class='fl'>25</span>,
- <span class='kw'>fat.tcoeff</span> <span class='kw'>=</span> <span class='fl'>0.5</span>,
- <span class='kw'>vital</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>a.rate</span> <span class='kw'>=</span> (<span class='fl'>10.5</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='kw'>a.prop.e</span> <span class='kw'>=</span> <span class='fl'>0.01</span>,
- <span class='kw'>a.prop.i</span> <span class='kw'>=</span> <span class='fl'>0.001</span>,
- <span class='kw'>a.prop.q</span> <span class='kw'>=</span> <span class='fl'>0.01</span>,
- <span class='kw'>ds.rate</span> <span class='kw'>=</span> (<span class='fl'>7</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='kw'>de.rate</span> <span class='kw'>=</span> (<span class='fl'>7</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='kw'>di.rate</span> <span class='kw'>=</span> (<span class='fl'>7</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='kw'>dq.rate</span> <span class='kw'>=</span> (<span class='fl'>7</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='kw'>dh.rate</span> <span class='kw'>=</span> (<span class='fl'>20</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='kw'>dr.rate</span> <span class='kw'>=</span> (<span class='fl'>7</span>/<span class='fl'>365</span>)/<span class='fl'>1000</span>,
- <span class='kw'>out</span> <span class='kw'>=</span> <span class='st'>"mean"</span>,
- <span class='kw'>seed</span> <span class='kw'>=</span> <span class='kw'>NULL</span>
-)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>type</th>
- <td><p>Type of model: SI, SIR, SIS, SEIR, SEIQHR and
-SEIQHRF available, but only SEIQHRF is likely to work in the
-current version of the code.</p></td>
- </tr>
- <tr>
- <th>nsteps</th>
- <td><p>Number of time steps to solve the model over. This must be a
-positive integer.</p></td>
- </tr>
- <tr>
- <th>nsims</th>
- <td><p>Number of simulations to run.</p></td>
- </tr>
- <tr>
- <th>ncores</th>
- <td><p>Number of physical CPU cores used for parallel computation.</p></td>
- </tr>
- <tr>
- <th>prog.rand</th>
- <td><p>Method for progression from E compartment to I. If TRUE,
-random binomial draws at prog.rate, if FALSE, random draws from a
-Weibull distribution (yes, I know it should be a discrete Weibull
-distribution but it makes little difference and speed of computation
-matters), with parameters prog.dist.scale and prog.dist.shape</p></td>
- </tr>
- <tr>
- <th>quar.rand</th>
- <td><p>Method for self-isolation transition from I to Q. If TRUE,
-random binomial draws at quar.rate, if FALSE, random sample with a
-sample fraction also given by `quar.rate.</p></td>
- </tr>
- <tr>
- <th>hosp.rand</th>
- <td><p>Method for transition from I or Q to H -- that is, from
-infectious or from self-isolated to requiring hospitalisation. If
-TRUE, random binomial draws at hosp.rate, if FALSE, random sample
-with a sample fraction also given by `hosp.rate.</p></td>
- </tr>
- <tr>
- <th>disch.rand</th>
- <td><p>Method for transition from H to R -- that is, from
-requiring hospitalisation to recovered. If TRUE, random binomial
-draws at disch.rate, if FALSE, random sample with a sample fraction
-also given by disch.rate. Note that the only way out of the H
-compartment is recovery or death.</p></td>
- </tr>
- <tr>
- <th>rec.rand</th>
- <td><p>Method for recovery transition from I, Q or H to R. If TRUE,
-random binomial draws at rec.rate, if FALSE, random draws from a
-random draws from a Weibull distribution, with parameters
-rec.dist.scale and rec.dist.shape.</p></td>
- </tr>
- <tr>
- <th>arec.rand</th>
- <td><p>Method for recovery transition from E to R. If TRUE,
-random binomial draws at arec.rate, if FALSE, random draws from a
-random draws from a Weibull distribution, with parameters
-arec.dist.scale and arec.dist.shape.</p></td>
- </tr>
- <tr>
- <th>fat.rand</th>
- <td><p>Method for case fatality transition from H to F. If TRUE,
-random binomial draws at fat.rate.base, if FALSE, random sample with
-a sample fraction also given by fat.rate.base. However, if the
-current number of patients in the H (needs hospitalisation)
-compartment is above a hospital capacity level specified by
-hosp.cap, then the fatality rate is the mean of the base fatality
-rate weighted by the hospital capacity, plus a higher rate,
-specified by fat.rate.overcap, weighted by the balance of those
-requiring hospitalisation (but who can't be accommodated). By
-setting fat.rate.overcap higher, the effect of exceeding the
-capacity of the health care system can be simulated. There is also
-a coefficient fat.tcoeff for the fatality rates that increases them
-as a linear function of the number of days the individual has been
-in the H compartment. Use of the co-efficient better approximates
-the trapezoid survival time distribution typical of ICU patients.</p></td>
- </tr>
- <tr>
- <th>infection.FUN</th>
- <td><p>No, being infected with SARS-CoV2 is not fun. Rather
-this is the the name of the function to implement infection
-processes. Use the default.</p></td>
- </tr>
- <tr>
- <th>recovery.FUN</th>
- <td><p>Function to implement recovery processes. Use the
-default.</p></td>
- </tr>
- <tr>
- <th>departures.FUN</th>
- <td><p>Handles background demographics, specifically
-departures (deaths not due to the virus, and emigration). Use the
-default.</p></td>
- </tr>
- <tr>
- <th>arrivals.FUN</th>
- <td><p>Handles background demographics, specifically arrivals
-(births and immigration). Uses the original EpiModel code
-currently. A replacement that implements modelling the arrival of
-infected individuals is under development -- but for now, all
-arrivals go into the S compartment.</p></td>
- </tr>
- <tr>
- <th>get_prev.FUN</th>
- <td><p>Utility function that collects prevalence and transition
-time data from each run and stores it away in the simulation result
-object. Use the default.</p></td>
- </tr>
- <tr>
- <th>s.num</th>
- <td><p>Initial number of *S compartment individuals in
-the simulated population. An overall population of 10,000 is a good
-compromise. A set of models will still take several minutes or more
-to run, in parallel.</p></td>
- </tr>
- <tr>
- <th>e.num</th>
- <td><p>Initial number of E compartment individuals in
-the simulated population.</p></td>
- </tr>
- <tr>
- <th>i.num</th>
- <td><p>Initial number of I compartment individuals in
-the simulated population.</p></td>
- </tr>
- <tr>
- <th>q.num</th>
- <td><p>Initial number of Q compartment individuals in
-the simulated population.</p></td>
- </tr>
- <tr>
- <th>h.num</th>
- <td><p>Initial number of H compartment individuals in
-the simulated population.</p></td>
- </tr>
- <tr>
- <th>r.num</th>
- <td><p>Initial number of R compartment individuals in
-the simulated population.</p></td>
- </tr>
- <tr>
- <th>f.num</th>
- <td><p>Initial number of F compartment individuals in
-the simulated population.</p></td>
- </tr>
- <tr>
- <th>inf.prob.e</th>
- <td><p>Probability of passing on infection at each
-exposure event for interactions between infectious people in the E
-compartment and susceptible in S. Note the default is lower than for
-inf.prob.i reflecting the reduced infectivity of infected but
-asymptomatic people (the E compartment). Otherwise as for inf.exp.i.</p></td>
- </tr>
- <tr>
- <th>act.rate.e</th>
- <td><p>The number of exposure events (acts) between
-infectious individuals in the E compartment and susceptible individuals
-in the S compartment, per day. Otherwise as for act.rate.i.</p></td>
- </tr>
- <tr>
- <th>inf.prob.i</th>
- <td><p>Probability of passing on infection at each
-exposure event for interactions between infectious people in the I
-compartment and susceptible in S. Reducing inf.prob.i is equivalent to
-increasing hygiene measures, such as not putting hands in eyes, nose or
-moth, use of hand sanitisers, wearing masks by the infected, and so on.</p></td>
- </tr>
- <tr>
- <th>act.rate.i</th>
- <td><p>The number of exposure events (acts) between
-infectious individuals in the I compartment and susceptible individuals
-in the S compartment, per day. It's stochastic, so the rate is an
-average, some individuals may have more or less. Note that not every
-exposure event results in infection - that is governed by the inf.prob.i
-parameters (see below). Reducing act.rate.i is equivalent to increasing
-social distancing by people in the I compartment.</p></td>
- </tr>
- <tr>
- <th>inf.prob.q</th>
- <td><p>Probability of passing on infection at each
-exposure event for interactions between infectious people in the Q
-compartment and susceptible in S. Note the default is lower than for
-inf.prob.i reflecting the greater care that self-isolated individuals
-will, on average, take regarding hygiene measures, such as wearing masks,
-to limit spread to others. Otherwise as for inf.exp.i.</p></td>
- </tr>
- <tr>
- <th>act.rate.q</th>
- <td><p>The number of exposure events (acts) between
-infectious individuals in the Q compartment (isolated, self or otherwise)
-and susceptible individuals in the S compartment, per day. Note the much
-lower rate than for the I and E compartments, reflecting the much
-greater degree of social isolation for someone in (self-)isolation. The
-exposure event rate is not zero for this group, just much less.
-Otherwise as for act.rate.i.</p></td>
- </tr>
- <tr>
- <th>prog.rate</th>
- <td><p>Rate per day at which people who are infected
-but asymptomatic (E compartment) progress to becoming symptomatic (or
-test-positive), the I compartment. See prog.rand above for more details.</p></td>
- </tr>
- <tr>
- <th>quar.rate</th>
- <td><p>Rate per day at which symptomatic (or tested
-positive), infected I compartment people enter self-isolation (Q
-compartment). Asymptomatic E compartment people can't enter
-self-isolation because they don't yet know they are infected. Default is
-a low rate reflecting low community awareness or compliance with
-self-isolation requirements or practices, but this can be tweaked when
-exploring scenarios.</p></td>
- </tr>
- <tr>
- <th>hosp.rate</th>
- <td><p>Rate per day at which symptomatic (or tested
-positive), infected I compartment people or self-isolated Q compartment
-people enter the state of requiring hospital care -- that is, become
-serious cases. A default rate of 1<!-- % per day with an average illness -->
-duration of about 10 days means a bit less than 10<!-- % of cases will -->
-require hospitalisation, which seems about right (but can be tweaked,
-of course).</p></td>
- </tr>
- <tr>
- <th>disch.rate</th>
- <td><p>Rate per day at which people needing
-hospitalisation recover.</p></td>
- </tr>
- <tr>
- <th>rec.rate</th>
- <td><p>Rate per day at which people who are infected and
-symptomatic (I compartment) recover, thus entering the R compartment.
-See rec.rand above for more details.</p></td>
- </tr>
- <tr>
- <th>arec.rate</th>
- <td><p>Rate per day at which people who are exposed but asymptotic
-(E compartment) recover, thus entering the R compartment.
-See arec.rand above for more details.</p></td>
- </tr>
- <tr>
- <th>prog.dist.scale</th>
- <td><p>Scale parameter for Weibull distribution
-for progression, see prog.rand for details.</p></td>
- </tr>
- <tr>
- <th>prog.dist.shape</th>
- <td><p>Shape parameter for Weibull distribution
-for progression, see prog.rand for details. Read up on the Weibull
-distribution before changing the default.</p></td>
- </tr>
- <tr>
- <th>quar.dist.scale</th>
- <td><p>Scale parameter for Weibull distribution for
-recovery, see quar.rand for details.</p></td>
- </tr>
- <tr>
- <th>quar.dist.shape</th>
- <td><p>Shape parameter for Weibull distribution for
-recovery, see quar.rand for details. Read up on the Weibull distribution
-before changing the default.</p></td>
- </tr>
- <tr>
- <th>hosp.dist.scale</th>
- <td><p>Scale parameter for Weibull distribution for
-recovery, see hosp.rand for details.</p></td>
- </tr>
- <tr>
- <th>hosp.dist.shape</th>
- <td><p>Shape parameter for Weibull distribution for
-recovery, see hosp.rand for details. Read up on the Weibull distribution
-before changing the default.</p></td>
- </tr>
- <tr>
- <th>disch.dist.scale</th>
- <td><p>Scale parameter for Weibull distribution for
-recovery, see disch.rand for details.</p></td>
- </tr>
- <tr>
- <th>disch.dist.shape</th>
- <td><p>Shape parameter for Weibull distribution for
-recovery, see disch.rand for details. Read up on the Weibull distribution
-before changing the default.</p></td>
- </tr>
- <tr>
- <th>rec.dist.scale</th>
- <td><p>Scale parameter for Weibull distribution for
-recovery, see rec.rand for details.</p></td>
- </tr>
- <tr>
- <th>rec.dist.shape</th>
- <td><p>Shape parameter for Weibull distribution for
-recovery, see rec.rand for details. Read up on the Weibull distribution
-before changing the default.</p></td>
- </tr>
- <tr>
- <th>arec.dist.scale</th>
- <td><p>Scale parameter for Weibull distribution for
-recovery, see arec.rand for details.</p></td>
- </tr>
- <tr>
- <th>arec.dist.shape</th>
- <td><p>Shape parameter for Weibull distribution for
-recovery, see arec.rand for details.</p></td>
- </tr>
- <tr>
- <th>fat.rate.base</th>
- <td><p>Baseline mortality rate per day for people
-needing hospitalisation (deaths due to the virus). See fat.rand for more
-details.</p></td>
- </tr>
- <tr>
- <th>hosp.cap</th>
- <td><p>Number of available hospital beds for the modelled
-population. See fat.rand for more details.</p></td>
- </tr>
- <tr>
- <th>fat.rate.overcap</th>
- <td><p>Mortality rate per day for people needing
-hospitalisation but who can't get into hospital due to the hospitals
-being full (see hosp.cap and fat.rand). The default rate is twice that
-for those who do get into hospital.</p></td>
- </tr>
- <tr>
- <th>fat.tcoeff</th>
- <td><p>Time co-efficient for increasing mortality rate
-as time in the H compartment increases for each individual in it. See
-fat.rand for details.</p></td>
- </tr>
- <tr>
- <th>vital</th>
- <td><p>Enables demographics, that is, arrivals and
-departures, to and from the simulated population.</p></td>
- </tr>
- <tr>
- <th>a.rate</th>
- <td><p>Background demographic arrival rate. Currently all
-arrivals go into the S compartment, the default is approximately the
-daily birth rate for Australia. Will be extended to cover immigration in
-future versions.</p></td>
- </tr>
- <tr>
- <th>a.prop.e</th>
- <td><p>Arrivals proportion that goes to E (immigration).</p></td>
- </tr>
- <tr>
- <th>a.prop.i</th>
- <td><p>Arrivals proportion that goes to I (immigration).</p></td>
- </tr>
- <tr>
- <th>a.prop.q</th>
- <td><p>Arrivals proportion that goes to Q (immigration).</p></td>
- </tr>
- <tr>
- <th>ds.rate</th>
- <td><p>Background demographic departure (death not due to
-virus) rates. Defaults based on Australian crude death rates. Can be
-used to model emigration as well as deaths.</p></td>
- </tr>
- <tr>
- <th>de.rate</th>
- <td><p>Background demographic departure (death not due to
-virus) rates. Defaults based on Australian crude death rates. Can be
-used to model emigration as well as deaths.</p></td>
- </tr>
- <tr>
- <th>di.rate</th>
- <td><p>Background demographic departure (death not due to
-virus) rates. Defaults based on Australian crude death rates. Can be used
-to model emigration as well as deaths.</p></td>
- </tr>
- <tr>
- <th>dq.rate</th>
- <td><p>Background demographic departure (death not due to
-virus) rates. Defaults based on Australian crude death rates. Can be used
-to model emigration as well as deaths.</p></td>
- </tr>
- <tr>
- <th>dh.rate</th>
- <td><p>Background demographic departure (death not due to
-virus) rates. Defaults based on Australian crude death rates. Can be used
-to model emigration as well as deaths.</p></td>
- </tr>
- <tr>
- <th>dr.rate</th>
- <td><p>Background demographic departure (death not due to
-virus) rates. Defaults based on Australian crude death rates. Can be used
-to model emigration as well as deaths.</p></td>
- </tr>
- <tr>
- <th>out</th>
- <td><p>Summary function for the simulation runs. median is
-also available, or percentiles, see the EpiModel documentation.</p></td>
- </tr>
- <tr>
- <th>seed</th>
- <td><p>Random see for checking consistency.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>list with simulation and simulation dataframe</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
- </nav>
- </div>
-</div>
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- <div class="copyright">
- <p>Developed by Christina Azodi, Puxue Qiao, Ruqian Lyu, Sam Tanner, Tim Churches, Davis McCarthy.</p>
-</div>
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- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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diff --git a/public/reference/summary.seiqhrf.html b/public/reference/summary.seiqhrf.html
deleted file mode 100644
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--- a/public/reference/summary.seiqhrf.html
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- <h1>summary function</h1>
-
- <div class="hidden name"><code>summary.seiqhrf.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Function to extract mean and standard deviation of all compartments
-for SEIQHRF model</p>
- </div>
-
- <pre class="usage"><span class='co'># S3 method for seiqhrf</span>
-<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>object</th>
- <td><p>seiqhrf object, returned by <code><a href='seiqhrf.html'>seiqhrf</a></code>.</p></td>
- </tr>
- <tr>
- <th>...</th>
- <td><p>Additional parameters.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>A list of compartments, each compartment is a list of three:</p><ul>
-<li><p><code>mean</code>: (t-dimensional vector) Mean of simulated counts of the compartment;</p></li>
-<li><p><code>sd</code>: (t-dimensional vector) Standard deviation of simulated counts of the compartment;</p></li>
-<li><p><code>CI</code>: (t by 2 matrix) 95% confidence intervals of simulated counts of the compartment (assumed Gaussian),</p></li>
-<li><p><code>qntCI</code>: (t by 2 matrix) 95% quantile confidence intervals,</p></li>
-</ul><p>where t is the total number of time points in the simulation (i.e. object$nstep).</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
- </nav>
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diff --git a/public/reference/vary_param.html b/public/reference/vary_param.html
deleted file mode 100644
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- <h1>Generating time-dependent parameters</h1>
-
- <div class="hidden name"><code>vary_param.Rd</code></div>
- </div>
-
- <div class="ref-description">
- <p>Function to generate parameter values for the time range of the simulation
-that can change over time.</p>
- </div>
-
- <pre class="usage"><span class='fu'>vary_param</span>(<span class='kw'>nstep</span> <span class='kw'>=</span> <span class='no'>nstep</span>, <span class='kw'>vals</span> <span class='kw'>=</span> <span class='no'>vals</span>, <span class='kw'>timing</span> <span class='kw'>=</span> <span class='no'>timing</span>)</pre>
-
- <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
- <table class="ref-arguments">
- <colgroup><col class="name" /><col class="desc" /></colgroup>
- <tr>
- <th>nstep</th>
- <td><p>Number of time steps to generate parameter values for.</p></td>
- </tr>
- <tr>
- <th>vals</th>
- <td><p>List of parameter values to include over the nsteps.</p></td>
- </tr>
- <tr>
- <th>timing</th>
- <td><p>List of the step numbers at which to start changes, with the
-last number reflecting when to hit the last parameter value in vals.</p></td>
- </tr>
- </table>
-
- <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
-
- <p>list of parameter values for length t</p>
-
- </div>
- <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
- <nav id="toc" data-toggle="toc" class="sticky-top">
- <h2 data-toc-skip>Contents</h2>
- </nav>
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