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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>
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<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>
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<li>
<p><strong>Puxue Qiao</strong>. Author.
</p>
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<p><strong>Ruqian Lyu</strong>. Author.
</p>
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<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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if (el.id) {
return el.id;
} else {
var anchor = this.generateUniqueId(el);
el.id = anchor;
return anchor;
}
},
createNavList: function() {
return $('<ul class="nav"></ul>');
},
createChildNavList: function($parent) {
var $childList = this.createNavList();
$parent.append($childList);
return $childList;
},
generateNavEl: function(anchor, text) {
var $a = $('<a></a>');
$a.attr('href', '#' + anchor);
$a.text(text);
var $li = $('<li></li>');
$li.append($a);
return $li;
},
generateNavItem: function(headingEl) {
var anchor = this.generateAnchor(headingEl);
var $heading = $(headingEl);
var text = $heading.data('toc-text') || $heading.text();
return this.generateNavEl(anchor, text);
},
// Find the first heading level (`<h1>`, then `<h2>`, etc.) that has more than one element. Defaults to 1 (for `<h1>`).
getTopLevel: function($scope) {
for (var i = 1; i <= 6; i++) {
var $headings = this.findOrFilter($scope, 'h' + i);
if ($headings.length > 1) {
return i;
}
}
return 1;
},
// returns the elements for the top level, and the next below it
getHeadings: function($scope, topLevel) {
var topSelector = 'h' + topLevel;
var secondaryLevel = topLevel + 1;
var secondarySelector = 'h' + secondaryLevel;
return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
},
getNavLevel: function(el) {
return parseInt(el.tagName.charAt(1), 10);
},
populateNav: function($topContext, topLevel, $headings) {
var $context = $topContext;
var $prevNav;
var helpers = this;
$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
$context.append($newNav);
$prevNav = $newNav;
});
},
parseOps: function(arg) {
var opts;
if (arg.jquery) {
opts = {
$nav: arg
};
} else {
opts = arg;
}
opts.$scope = opts.$scope || $(document.body);
return opts;
}
},
// accepts a jQuery object, or an options object
init: function(opts) {
opts = this.helpers.parseOps(opts);
// ensure that the data attribute is in place for styling
opts.$nav.attr('data-toggle', 'toc');
var $topContext = this.helpers.createChildNavList(opts.$nav);
var topLevel = this.helpers.getTopLevel(opts.$scope);
var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
this.helpers.populateNav($topContext, topLevel, $headings);
}
};
$(function() {
$('nav[data-toggle="toc"]').each(function(i, el) {
var $nav = $(el);
Toc.init($nav);
});
});
})();
public/docsearch.css deleted 100644 → 0
+ 0
− 148
View file @ 67959aee
/* Docsearch -------------------------------------------------------------- */
/*
Source: https://github.com/algolia/docsearch/
License: MIT
*/
.algolia-autocomplete {
display: block;
-webkit-box-flex: 1;
-ms-flex: 1;
flex: 1
}
.algolia-autocomplete .ds-dropdown-menu {
width: 100%;
min-width: none;
max-width: none;
padding: .75rem 0;
background-color: #fff;
background-clip: padding-box;
border: 1px solid rgba(0, 0, 0, .1);
box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
}
@media (min-width:768px) {
.algolia-autocomplete .ds-dropdown-menu {
width: 175%
}
}
.algolia-autocomplete .ds-dropdown-menu::before {
display: none
}
.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
padding: 0;
background-color: rgb(255,255,255);
border: 0;
max-height: 80vh;
}
.algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
margin-top: 0
}
.algolia-autocomplete .algolia-docsearch-suggestion {
padding: 0;
overflow: visible
}
.algolia-autocomplete .algolia-docsearch-suggestion--category-header {
padding: .125rem 1rem;
margin-top: 0;
font-size: 1.3em;
font-weight: 500;
color: #00008B;
border-bottom: 0
}
.algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
float: none;
padding-top: 0
}
.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
float: none;
width: auto;
padding: 0;
text-align: left
}
.algolia-autocomplete .algolia-docsearch-suggestion--content {
float: none;
width: auto;
padding: 0
}
.algolia-autocomplete .algolia-docsearch-suggestion--content::before {
display: none
}
.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
padding-top: .75rem;
margin-top: .75rem;
border-top: 1px solid rgba(0, 0, 0, .1)
}
.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
display: block;
padding: .1rem 1rem;
margin-bottom: 0.1;
font-size: 1.0em;
font-weight: 400
/* display: none */
}
.algolia-autocomplete .algolia-docsearch-suggestion--title {
display: block;
padding: .25rem 1rem;
margin-bottom: 0;
font-size: 0.9em;
font-weight: 400
}
.algolia-autocomplete .algolia-docsearch-suggestion--text {
padding: 0 1rem .5rem;
margin-top: -.25rem;
font-size: 0.8em;
font-weight: 400;
line-height: 1.25
}
.algolia-autocomplete .algolia-docsearch-footer {
width: 110px;
height: 20px;
z-index: 3;
margin-top: 10.66667px;
float: right;
font-size: 0;
line-height: 0;
}
.algolia-autocomplete .algolia-docsearch-footer--logo {
background-image: url("data:image/svg+xml;utf8,<svg viewBox='0 0 130 18' xmlns='http://www.w3.org/2000/svg'><defs><linearGradient x1='-36.868%' y1='134.936%' x2='129.432%' y2='-27.7%' id='a'><stop stop-color='%2300AEFF' offset='0%'/><stop stop-color='%233369E7' offset='100%'/></linearGradient></defs><g fill='none' fill-rule='evenodd'><path d='M59.399.022h13.299a2.372 2.372 0 0 1 2.377 2.364V15.62a2.372 2.372 0 0 1-2.377 2.364H59.399a2.372 2.372 0 0 1-2.377-2.364V2.381A2.368 2.368 0 0 1 59.399.022z' fill='url(%23a)'/><path d='M66.257 4.56c-2.815 0-5.1 2.272-5.1 5.078 0 2.806 2.284 5.072 5.1 5.072 2.815 0 5.1-2.272 5.1-5.078 0-2.806-2.279-5.072-5.1-5.072zm0 8.652c-1.983 0-3.593-1.602-3.593-3.574 0-1.972 1.61-3.574 3.593-3.574 1.983 0 3.593 1.602 3.593 3.574a3.582 3.582 0 0 1-3.593 3.574zm0-6.418v2.664c0 .076.082.131.153.093l2.377-1.226c.055-.027.071-.093.044-.147a2.96 2.96 0 0 0-2.465-1.487c-.055 0-.11.044-.11.104l.001-.001zm-3.33-1.956l-.312-.311a.783.783 0 0 0-1.106 0l-.372.37a.773.773 0 0 0 0 1.101l.307.305c.049.049.121.038.164-.011.181-.245.378-.479.597-.697.225-.223.455-.42.707-.599.055-.033.06-.109.016-.158h-.001zm5.001-.806v-.616a.781.781 0 0 0-.783-.779h-1.824a.78.78 0 0 0-.783.779v.632c0 .071.066.12.137.104a5.736 5.736 0 0 1 1.588-.223c.52 0 1.035.071 1.534.207a.106.106 0 0 0 .131-.104z' fill='%23FFF'/><path d='M102.162 13.762c0 1.455-.372 2.517-1.123 3.193-.75.676-1.895 1.013-3.44 1.013-.564 0-1.736-.109-2.673-.316l.345-1.689c.783.163 1.819.207 2.361.207.86 0 1.473-.174 1.84-.523.367-.349.548-.866.548-1.553v-.349a6.374 6.374 0 0 1-.838.316 4.151 4.151 0 0 1-1.194.158 4.515 4.515 0 0 1-1.616-.278 3.385 3.385 0 0 1-1.254-.817 3.744 3.744 0 0 1-.811-1.351c-.192-.539-.29-1.504-.29-2.212 0-.665.104-1.498.307-2.054a3.925 3.925 0 0 1 .904-1.433 4.124 4.124 0 0 1 1.441-.926 5.31 5.31 0 0 1 1.945-.365c.696 0 1.337.087 1.961.191a15.86 15.86 0 0 1 1.588.332v8.456h-.001zm-5.954-4.206c0 .893.197 1.885.592 2.299.394.414.904.621 1.528.621.34 0 .663-.049.964-.142a2.75 2.75 0 0 0 .734-.332v-5.29a8.531 8.531 0 0 0-1.413-.18c-.778-.022-1.369.294-1.786.801-.411.507-.619 1.395-.619 2.223zm16.12 0c0 .719-.104 1.264-.318 1.858a4.389 4.389 0 0 1-.904 1.52c-.389.42-.854.746-1.402.975-.548.229-1.391.36-1.813.36-.422-.005-1.26-.125-1.802-.36a4.088 4.088 0 0 1-1.397-.975 4.486 4.486 0 0 1-.909-1.52 5.037 5.037 0 0 1-.329-1.858c0-.719.099-1.411.318-1.999.219-.588.526-1.09.92-1.509.394-.42.865-.741 1.402-.97a4.547 4.547 0 0 1 1.786-.338 4.69 4.69 0 0 1 1.791.338c.548.229 1.019.55 1.402.97.389.42.69.921.909 1.509.23.588.345 1.28.345 1.999h.001zm-2.191.005c0-.921-.203-1.689-.597-2.223-.394-.539-.948-.806-1.654-.806-.707 0-1.26.267-1.654.806-.394.539-.586 1.302-.586 2.223 0 .932.197 1.558.592 2.098.394.545.948.812 1.654.812.707 0 1.26-.272 1.654-.812.394-.545.592-1.166.592-2.098h-.001zm6.962 4.707c-3.511.016-3.511-2.822-3.511-3.274L113.583.926l2.142-.338v10.003c0 .256 0 1.88 1.375 1.885v1.792h-.001zm3.774 0h-2.153V5.072l2.153-.338v9.534zm-1.079-10.542c.718 0 1.304-.578 1.304-1.291 0-.714-.581-1.291-1.304-1.291-.723 0-1.304.578-1.304 1.291 0 .714.586 1.291 1.304 1.291zm6.431 1.013c.707 0 1.304.087 1.786.262.482.174.871.42 1.156.73.285.311.488.735.608 1.182.126.447.186.937.186 1.476v5.481a25.24 25.24 0 0 1-1.495.251c-.668.098-1.419.147-2.251.147a6.829 6.829 0 0 1-1.517-.158 3.213 3.213 0 0 1-1.178-.507 2.455 2.455 0 0 1-.761-.904c-.181-.37-.274-.893-.274-1.438 0-.523.104-.855.307-1.215.208-.36.487-.654.838-.883a3.609 3.609 0 0 1 1.227-.49 7.073 7.073 0 0 1 2.202-.103c.263.027.537.076.833.147v-.349c0-.245-.027-.479-.088-.697a1.486 1.486 0 0 0-.307-.583c-.148-.169-.34-.3-.581-.392a2.536 2.536 0 0 0-.915-.163c-.493 0-.942.06-1.353.131-.411.071-.75.153-1.008.245l-.257-1.749c.268-.093.668-.185 1.183-.278a9.335 9.335 0 0 1 1.66-.142l-.001-.001zm.181 7.731c.657 0 1.145-.038 1.484-.104v-2.168a5.097 5.097 0 0 0-1.978-.104c-.241.033-.46.098-.652.191a1.167 1.167 0 0 0-.466.392c-.121.169-.175.267-.175.523 0 .501.175.79.493.981.323.196.75.289 1.293.289h.001zM84.109 4.794c.707 0 1.304.087 1.786.262.482.174.871.42 1.156.73.29.316.487.735.608 1.182.126.447.186.937.186 1.476v5.481a25.24 25.24 0 0 1-1.495.251c-.668.098-1.419.147-2.251.147a6.829 6.829 0 0 1-1.517-.158 3.213 3.213 0 0 1-1.178-.507 2.455 2.455 0 0 1-.761-.904c-.181-.37-.274-.893-.274-1.438 0-.523.104-.855.307-1.215.208-.36.487-.654.838-.883a3.609 3.609 0 0 1 1.227-.49 7.073 7.073 0 0 1 2.202-.103c.257.027.537.076.833.147v-.349c0-.245-.027-.479-.088-.697a1.486 1.486 0 0 0-.307-.583c-.148-.169-.34-.3-.581-.392a2.536 2.536 0 0 0-.915-.163c-.493 0-.942.06-1.353.131-.411.071-.75.153-1.008.245l-.257-1.749c.268-.093.668-.185 1.183-.278a8.89 8.89 0 0 1 1.66-.142l-.001-.001zm.186 7.736c.657 0 1.145-.038 1.484-.104v-2.168a5.097 5.097 0 0 0-1.978-.104c-.241.033-.46.098-.652.191a1.167 1.167 0 0 0-.466.392c-.121.169-.175.267-.175.523 0 .501.175.79.493.981.318.191.75.289 1.293.289h.001zm8.682 1.738c-3.511.016-3.511-2.822-3.511-3.274L89.461.926l2.142-.338v10.003c0 .256 0 1.88 1.375 1.885v1.792h-.001z' fill='%23182359'/><path d='M5.027 11.025c0 .698-.252 1.246-.757 1.644-.505.397-1.201.596-2.089.596-.888 0-1.615-.138-2.181-.414v-1.214c.358.168.739.301 1.141.397.403.097.778.145 1.125.145.508 0 .884-.097 1.125-.29a.945.945 0 0 0 .363-.779.978.978 0 0 0-.333-.747c-.222-.204-.68-.446-1.375-.725-.716-.29-1.221-.621-1.515-.994-.294-.372-.44-.82-.44-1.343 0-.655.233-1.171.698-1.547.466-.376 1.09-.564 1.875-.564.752 0 1.5.165 2.245.494l-.408 1.047c-.698-.294-1.321-.44-1.869-.44-.415 0-.73.09-.945.271a.89.89 0 0 0-.322.717c0 .204.043.379.129.524.086.145.227.282.424.411.197.129.551.299 1.063.51.577.24.999.464 1.268.671.269.208.466.442.591.704.125.261.188.569.188.924l-.001.002zm3.98 2.24c-.924 0-1.646-.269-2.167-.808-.521-.539-.782-1.281-.782-2.226 0-.97.242-1.733.725-2.288.483-.555 1.148-.833 1.993-.833.784 0 1.404.238 1.858.714.455.476.682 1.132.682 1.966v.682H7.357c.018.577.174 1.02.467 1.329.294.31.707.465 1.241.465.351 0 .678-.033.98-.099a5.1 5.1 0 0 0 .975-.33v1.026a3.865 3.865 0 0 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1.047h.064c.197-.354.454-.636.771-.843a1.83 1.83 0 0 1 1.023-.312h.001zm4.125 6.155c-.899 0-1.582-.262-2.049-.787-.467-.525-.701-1.277-.701-2.259 0-.999.244-1.767.733-2.304.489-.537 1.195-.806 2.119-.806.627 0 1.191.116 1.692.349l-.381 1.015c-.534-.208-.974-.312-1.321-.312-1.028 0-1.542.682-1.542 2.046 0 .666.128 1.166.384 1.501.256.335.631.502 1.125.502a3.23 3.23 0 0 0 1.595-.419v1.101a2.53 2.53 0 0 1-.722.285 4.356 4.356 0 0 1-.932.086v.002zm8.277-.107h-1.268V9.506c0-.458-.092-.8-.277-1.026-.184-.226-.477-.338-.878-.338-.53 0-.919.158-1.168.475-.249.317-.373.848-.373 1.593v2.949h-1.262V4.801h1.262v2.122c0 .34-.021.704-.064 1.09h.081a1.76 1.76 0 0 1 .717-.666c.306-.158.663-.236 1.072-.236 1.439 0 2.159.725 2.159 2.175v3.873l-.001-.001zm7.649-6.048c.741 0 1.319.269 1.732.806.414.537.62 1.291.62 2.261 0 .974-.209 1.732-.628 2.275-.419.542-1.001.814-1.746.814-.752 0-1.336-.27-1.751-.811h-.086l-.231.704h-.945V4.801h1.262v1.987l-.021.655-.032.553h.054c.401-.591.992-.886 1.772-.886zm-.328 1.031c-.508 0-.875.149-1.098.448-.224.299-.339.799-.346 1.501v.086c0 .723.115 1.247.344 1.571.229.324.603.486 1.123.486.448 0 .787-.177 1.018-.532.231-.354.346-.867.346-1.536 0-1.35-.462-2.025-1.386-2.025l-.001.001zm3.244-.924h1.375l1.209 3.368c.183.48.304.931.365 1.354h.043c.032-.197.091-.436.177-.717.086-.281.541-1.616 1.364-4.004h1.364l-2.541 6.73c-.462 1.235-1.232 1.853-2.31 1.853-.279 0-.551-.03-.816-.091v-.999c.19.043.406.064.65.064.609 0 1.037-.353 1.284-1.058l.22-.559-2.385-5.941h.001z' fill='%231D3657'/></g></svg>");
background-repeat: no-repeat;
background-position: 50%;
background-size: 100%;
overflow: hidden;
text-indent: -9000px;
width: 100%;
height: 100%;
display: block;
transform: translate(-8px);
}
.algolia-autocomplete .algolia-docsearch-suggestion--highlight {
color: #FF8C00;
background: rgba(232, 189, 54, 0.1)
}
.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
}
.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
background-color: rgba(192, 192, 192, .15)
}
public/docsearch.js deleted 100644 → 0
+ 0
− 85
View file @ 67959aee
$(function() {
// register a handler to move the focus to the search bar
// upon pressing shift + "/" (i.e. "?")
$(document).on('keydown', function(e) {
if (e.shiftKey && e.keyCode == 191) {
e.preventDefault();
$("#search-input").focus();
}
});
$(document).ready(function() {
// do keyword highlighting
/* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
var mark = function() {
var referrer = document.URL ;
var paramKey = "q" ;
if (referrer.indexOf("?") !== -1) {
var qs = referrer.substr(referrer.indexOf('?') + 1);
var qs_noanchor = qs.split('#')[0];
var qsa = qs_noanchor.split('&');
var keyword = "";
for (var i = 0; i < qsa.length; i++) {
var currentParam = qsa[i].split('=');
if (currentParam.length !== 2) {
continue;
}
if (currentParam[0] == paramKey) {
keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
}
}
if (keyword !== "") {
$(".contents").unmark({
done: function() {
$(".contents").mark(keyword);
}
});
}
}
};
mark();
});
});
/* Search term highlighting ------------------------------*/
function matchedWords(hit) {
var words = [];
var hierarchy = hit._highlightResult.hierarchy;
// loop to fetch from lvl0, lvl1, etc.
for (var idx in hierarchy) {
words = words.concat(hierarchy[idx].matchedWords);
}
var content = hit._highlightResult.content;
if (content) {
words = words.concat(content.matchedWords);
}
// return unique words
var words_uniq = [...new Set(words)];
return words_uniq;
}
function updateHitURL(hit) {
var words = matchedWords(hit);
var url = "";
if (hit.anchor) {
url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
} else {
url = hit.url + '?q=' + escape(words.join(" "));
}
return url;
}
public/index.html deleted 100644 → 0
+ 0
− 140
View file @ 67959aee
<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Using stochastic individual compartment models (ICMs) to simulate COVID-19 spread • sirplus</title>
<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/cosmo/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous">
<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css">
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<script src="pkgdown.js"></script><meta property="og:title" content="Using stochastic individual compartment models (ICMs) to simulate COVID-19 spread">
<meta property="og:description" content="sirplus is a package for the modeling of COVID-19 spread with extensions to the classical Susceptible-Infectious-Recovered (SIR) model, using
stochastic individual compartment models (ICMs). It provides a simple interface
for creating experiments to demonstrate how factors like social-distancing and
epidemiological parameters will change the curve of an epidemic's trajectory. ">
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