<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<title>Home</title>
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<link href="site_libs/font-awesome-4.5.0/css/font-awesome.min.css" rel="stylesheet" />
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
}
h2 {
font-size: 30px;
}
h3 {
font-size: 24px;
}
h4 {
font-size: 18px;
}
h5 {
font-size: 16px;
}
h6 {
font-size: 12px;
}
.table th:not([align]) {
text-align: left;
}
</style>
</head>
<body>
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
height: auto;
}
.tabbed-pane {
padding-top: 12px;
}
button.code-folding-btn:focus {
outline: none;
}
</style>
<style type="text/css">
/* padding for bootstrap navbar */
body {
padding-top: 51px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 56px;
margin-top: -56px;
}
.section h2 {
padding-top: 56px;
margin-top: -56px;
}
.section h3 {
padding-top: 56px;
margin-top: -56px;
}
.section h4 {
padding-top: 56px;
margin-top: -56px;
}
.section h5 {
padding-top: 56px;
margin-top: -56px;
}
.section h6 {
padding-top: 56px;
margin-top: -56px;
}
</style>
<script>
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
});
</script>
<div class="container-fluid main-container">
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
</script>
<!-- code folding -->
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">FLASHvestigations</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">Home</a>
</li>
<li>
<a href="about.html">About</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/willwerscheid/FLASHvestigations">
<span class="fa fa-github"></span>
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<!-- Add a small amount of space between sections. -->
<style type="text/css">
div.section {
padding-top: 12px;
}
</style>
<div class="fluid-row" id="header">
<h1 class="title toc-ignore">Home</h1>
</div>
<p><strong>Last updated:</strong> 2018-09-12</p>
<strong>workflowr checks:</strong> <small>(Click a bullet for more information)</small>
<ul>
<li>
<p><details> <summary> <strong style="color:blue;">✔</strong> <strong>R Markdown file:</strong> up-to-date </summary></p>
<p>Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.</p>
</details>
</li>
<li>
<p><details> <summary> <strong style="color:blue;">✔</strong> <strong>Repository version:</strong> <a href="https://github.com/willwerscheid/FLASHvestigations/tree/5e96e40e78b4b1d2fc2ff9306f666b5cc380b556" target="_blank">5e96e40</a> </summary></p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated. <br><br> Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
<pre><code>
Ignored files:
Ignored: .DS_Store
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: docs/.DS_Store
Ignored: docs/figure/.DS_Store
Untracked files:
Untracked: data/greedy19.rds
</code></pre>
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes. </details>
</li>
</ul>
<details> <summary> <small><strong>Expand here to see past versions:</strong></small> </summary>
<ul>
<table style="border-collapse:separate; border-spacing:5px;">
<thead>
<tr>
<th style="text-align:left;">
File
</th>
<th style="text-align:left;">
Version
</th>
<th style="text-align:left;">
Author
</th>
<th style="text-align:left;">
Date
</th>
<th style="text-align:left;">
Message
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/5e96e40e78b4b1d2fc2ff9306f666b5cc380b556/analysis/index.Rmd" target="_blank">5e96e40</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-09-12
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/efbae906de11b0902da3737a7bfd2ac2fb90ac54/docs/index.html" target="_blank">efbae90</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-09-11
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/734b172ca600d856cccc2d491cfeeb2494b28326/analysis/index.Rmd" target="_blank">734b172</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-09-11
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/eb78de4d5291707ed7b792b71bd10842b7182e96/docs/index.html" target="_blank">eb78de4</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-29
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/9302eccd741ccb37f564b7f98e550a2435d6d7ed/analysis/index.Rmd" target="_blank">9302ecc</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-29
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/10a535ba7c2ace3c56df29336db48a80cf347dce/docs/index.html" target="_blank">10a535b</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-29
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/47f0b23591d871b300829348865a1c785c469ac6/analysis/index.Rmd" target="_blank">47f0b23</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-29
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/07ffbc28e4a1a06924be9a71d42a695139644a70/docs/index.html" target="_blank">07ffbc2</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-23
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/c73018d8a14e7bfe2e968dc3d0c0901b9164bfea/analysis/index.Rmd" target="_blank">c73018d</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-23
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/9e39a5fa5e3751c1287ff58c7c90d752b29cb165/docs/index.html" target="_blank">9e39a5f</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-22
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/ac09d4b28c85321b073eb3e4eb4bd7d88a929e3a/analysis/index.Rmd" target="_blank">ac09d4b</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-22
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/b0fbbe0da22eea5350f5aaa812f18f5002676d48/docs/index.html" target="_blank">b0fbbe0</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-22
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/4fe662c9d4c2effbebf9c583c777efa651c1c78e/analysis/index.Rmd" target="_blank">4fe662c</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-22
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/02be9e984146edd47c969ee02968eeda2202c415/docs/index.html" target="_blank">02be9e9</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-17
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/6e0036f138f36d377c707ce6d0c385fbe7ceb6f0/analysis/index.Rmd" target="_blank">6e0036f</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-17
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/a6d55b672bde78a49630438c6479624be9b271f8/docs/index.html" target="_blank">a6d55b6</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-16
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/c972927eeeb4e8ab1f01b6bb563a8f63826a35e4/analysis/index.Rmd" target="_blank">c972927</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-16
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”, “analysis/parallel2.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/10d46c01b3f7d081b2b3a33a398089a79b9ae379/docs/index.html" target="_blank">10d46c0</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-15
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/acd7f0cb823dc52faca461b0305a20efa895fcf4/analysis/index.Rmd" target="_blank">acd7f0c</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-15
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/86ef31aa8de2c09ba247351608e776c485ea708f/docs/index.html" target="_blank">86ef31a</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-12
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/73aa339af4771f929c750b57dc6e376f5262fe01/analysis/index.Rmd" target="_blank">73aa339</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-12
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/5a2e2a9601fa2c67d7858623a8f1a021b7bd6774/docs/index.html" target="_blank">5a2e2a9</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-12
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/6a9bf1c4cb55f106ec6bfa8279041df485958868/analysis/index.Rmd" target="_blank">6a9bf1c</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-12
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”, “analysis/parallel.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/9246c68c81509a23ff8bad9053af3bab2feb9e41/docs/index.html" target="_blank">9246c68</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-12
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/eaba09b9681df28c1319325ecf9f96d390be6a39/analysis/index.Rmd" target="_blank">eaba09b</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-08-12
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”, “analysis/parallel.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/cfa8e839b23324c7f7fed93e572a4a171bd23528/docs/index.html" target="_blank">cfa8e83</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-27
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/f497f36b336da9df75073fe017053b5e3795dd6f/analysis/index.Rmd" target="_blank">f497f36</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-27
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/warmstart2.Rmd”,
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/974e1dbb656dfecae013bdbdcb4909d4e2200051/docs/index.html" target="_blank">974e1db</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-27
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/2d81ef4ca61839fa284040db904acf36f3261e65/analysis/index.Rmd" target="_blank">2d81ef4</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-27
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”, “analysis/init_fn2.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/9fc59e738853b443964d2d9b80ed7ed1b0afd057/docs/index.html" target="_blank">9fc59e7</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-26
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/21cbf89a97a8f9dfa29a08cfbbd09b927d37bdd5/analysis/index.Rmd" target="_blank">21cbf89</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-26
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/8f471cb5154cd24bddbc304744401f0609d0499b/docs/index.html" target="_blank">8f471cb</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-26
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/ff417b60a3d432a0b36a187b0b1594abc58a52a4/analysis/index.Rmd" target="_blank">ff417b6</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-26
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/warmstart.Rmd”, “analysis/index.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/aae4dfcc7a5bca6b9885567d66bc183757fa133a/docs/index.html" target="_blank">aae4dfc</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-25
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/6417d4e9ca3d658552b99b7953213af0612c7bd9/analysis/index.Rmd" target="_blank">6417d4e</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-25
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”, “analysis/init_fn.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/3983695c16a2c5700be77cb42b5825d0ac874598/docs/index.html" target="_blank">3983695</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-25
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/566c2028d736e8ca0d7786a5b3b17b5c46932675/analysis/index.Rmd" target="_blank">566c202</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-25
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/dd91b193f497cdabfcd05b18003620c4e8aa00fe/docs/index.html" target="_blank">dd91b19</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-20
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/032edd6bab4628d200863b6c50aa54a8da204ece/analysis/index.Rmd" target="_blank">032edd6</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-20
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”, “analysis/flash_em.Rmd”,
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/f995dbbc6396ea622eec30cc332a8c89f1a0699d/docs/index.html" target="_blank">f995dbb</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-20
</td>
<td style="text-align:left;">
manual commits to remove licence
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/c9f10b03dedc9390af311c0036ed57736766ca0e/docs/index.html" target="_blank">c9f10b0</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-20
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/4fc94bd76eeb18ead30130cc05641c64986868c5/analysis/index.Rmd" target="_blank">4fc94bd</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-20
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”, “analysis/flash_em.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/1de2af0deb970a80ac248b3911c8316252f3e6a1/docs/index.html" target="_blank">1de2af0</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-20
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/9ac7bb07c1368b96dac32ffc6d9d1c5a3cdf7557/analysis/index.Rmd" target="_blank">9ac7bb0</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-20
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/f98f61fb0ebcafe4be7c87c6fcef483281f30788/docs/index.html" target="_blank">f98f61f</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-20
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/8e383cd7c0eafd626b18c4059861342d9d6bfdb1/analysis/index.Rmd" target="_blank">8e383cd</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-20
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/58b3ea46fa26104117a808989e2d14a9bc899f2d/docs/index.html" target="_blank">58b3ea4</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-19
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/eb264b175eab489dc4f703e4e846ac61cc30b924/analysis/index.Rmd" target="_blank">eb264b1</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-19
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/36a6312262223d1418cb2247125ce9332d39b701/docs/index.html" target="_blank">36a6312</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-19
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/a9f8cc678d25b5ce3e0cbbc0f195eb39809b0bfa/analysis/index.Rmd" target="_blank">a9f8cc6</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-19
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/c420802434b231593bcfeae3f6b10482ca50f108/docs/index.html" target="_blank">c420802</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-17
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/38942eb81dd60bd3d1b10afd2dabc4aad661df0b/analysis/index.Rmd" target="_blank">38942eb</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-17
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/e2e1286424015e8cbed280a8548f5e9b0d6a723b/docs/index.html" target="_blank">e2e1286</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/55f42cad6e56835471c8988e99ce73af56dedb8b/analysis/index.Rmd" target="_blank">55f42ca</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/de8f82306cc8bec7a369010bc572bc2e794b9544/docs/index.html" target="_blank">de8f823</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/f5379fab679055aa1fe5195856876bce376841e0/analysis/index.Rmd" target="_blank">f5379fa</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
wflow_publish(“analysis/index.Rmd”)
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/7db12a1efed12474ff15a3cf6c111dbf946d7107/docs/index.html" target="_blank">7db12a1</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/873da40adfea91a43fd5eaa922c03ad24ab2d77e/docs/index.html" target="_blank">873da40</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-16
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/58e136aec27b1c1414626a3820ac4685c2252dc6/docs/index.html" target="_blank">58e136a</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-15
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/82c7cdd1d6fe660851f65975e7c1fff62ec60737/analysis/index.Rmd" target="_blank">82c7cdd</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-15
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”, “analysis/about.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
html
</td>
<td style="text-align:left;">
<a href="https://cdn.rawgit.com/willwerscheid/FLASHvestigations/76eacb75d7f6a19857f7adfe769a3fd76643e3bb/docs/index.html" target="_blank">76eacb7</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-15
</td>
<td style="text-align:left;">
Build site.
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/f6928cc38fc84fe9d0d5ddcf11d954fba36c6910/analysis/index.Rmd" target="_blank">f6928cc</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-15
</td>
<td style="text-align:left;">
wflow_publish(c(“analysis/index.Rmd”, “analysis/about.Rmd”))
</td>
</tr>
<tr>
<td style="text-align:left;">
Rmd
</td>
<td style="text-align:left;">
<a href="https://github.com/willwerscheid/FLASHvestigations/blob/56d7ded8c6138ce9a71293c5e31a2363fa6f0c75/analysis/index.Rmd" target="_blank">56d7ded</a>
</td>
<td style="text-align:left;">
Jason Willwerscheid
</td>
<td style="text-align:left;">
2018-07-14
</td>
<td style="text-align:left;">
Start workflowr project.
</td>
</tr>
</tbody>
</table>
</ul>
<p></details></p>
<hr />
<div id="in-progress" class="section level2">
<h2>In Progress</h2>
<p>Investigations 8 and 9 implement parallel backfitting updates.</p>
<ul>
<li><p><a href="parallel.html">Investigation 8.</a> Parallelizing the backfitting algorithm shows promise.</p></li>
<li><p><a href="parallel2.html">Investigation 9.</a> An additional trick is needed to parallelize the backfitting updates performed in this <a href="https://willwerscheid.github.io/MASHvFLASH/MASHvFLASHgtex3.html">MASH v FLASH GTEx analysis</a>.</p></li>
</ul>
<p><a href="squarem.html">Investigation 10.</a> SQUAREM does poorly on FLASH backfits. DAAREM (a more recent algorithm by one of the authors of SQUAREM) does better, but offers smaller performance gains than parallelization.</p>
<p><a href="random.html">Investigation 11.</a> The order in which factor/loading pairs are updated (during backfitting) makes some difference, but not much.</p>
<p><a href="arbitraryV.html">Investigation 12.</a> To fit a FLASH model with an arbitrary error covariance matrix, I follow up on a <a href="https://github.com/stephenslab/flashr/issues/17">suggestion</a> by Matthew Stephens.</p>
<p><a href="nonnegative.html">Investigation 13.</a> I use nonnegative priors to obtain a factorization of the GTEx donation matrix.</p>
</div>
<div id="still-relevant" class="section level2">
<h2>Still Relevant</h2>
<p>Notes 1 and 2 and Investigation 4 describe a way to compute the FLASH objective directly (rather than using the indirect method implemented in <code>flashr</code>).</p>
<ul>
<li><p><a href="obj_notes.html">Note 1.</a> Notes on computing the FLASH objective function. I derive an explicit expression for the KL divergence between prior and posterior.</p></li>
<li><p><a href="flash_em.html">Note 2.</a> An alternate algorithm for optimizing the FLASH objective, using the explicit expression derived in the previous note.</p></li>
<li><p><a href="alt_alg.html">Investigation 4.</a> The alternate algorithm agrees with FLASH with respect to both the objective and fit obtained.</p></li>
</ul>
<p>Investigations 5a-b and 13 attempt to determine the best default initialization function.</p>
<ul>
<li><p><a href="init_fn.html">Investigation 5a.</a> An argument for changing the default <code>init_fn</code> to <code>udv_si_svd</code> when there is missing data and <code>udv_svd</code> otherwise. Based on an analysis of GTEx data.</p></li>
<li><p><a href="init_fn2.html">Investigation 5b.</a> More evidence supporting the recommendations in Investigation 5a.</p></li>
<li><p><a href="init_fn3.html">Investigation 13.</a> A counterargument. Results in Investigations 5a-b probably depend on the fact that <span class="math inline">\(n\)</span> is small (<span class="math inline">\(n = 44\)</span>). For large <span class="math inline">\(n\)</span>, setting <code>init_fn</code> to <code>udv_si</code> is best.</p></li>
</ul>
</div>
<div id="archived" class="section level2">
<h2>Archived</h2>
<p>The bug causing the problem described in Investigations 1-3 was fixed in version 0.1-13 of package <code>ebnm</code>.</p>
<ul>
<li><p><a href="objective.html">Investigation 1.</a> The FLASH objective function can behave very erratically.</p></li>
<li><p><a href="objective2.html">Investigation 2.</a> This problem only occurs when using <code>ebnm_pn</code>, not <code>ebnm_ash</code>.</p></li>
<li><p><a href="objective3.html">Investigation 3.</a> The objective can continue to get worse as loadings are repeatedly updated. Nonetheless, convergence takes place (from above!).</p></li>
</ul>
<p>Investigations 6 and 7 deal with warmstarts, which were implemented in version 0.5-14 of <code>flashr</code>.</p>
<ul>
<li><p><a href="warmstart.html">Investigation 6.</a> Poor <code>optim</code> results can produce large decreases in the objective function. We should use warmstarts when <code>ebnm_fn = ebnm_pn</code>.</p></li>
<li><p><a href="warmstart2.html">Investigation 7.</a> The advantages of warmstarts are not nearly as compelling when <code>ebnm_fn = ebnm_ash</code>.</p></li>
</ul>
</div>
<!-- Adjust MathJax settings so that all math formulae are shown using
TeX fonts only; see
http://docs.mathjax.org/en/latest/configuration.html. This will make
the presentation more consistent at the cost of the webpage sometimes
taking slightly longer to load. Note that this only works because the
footer is added to webpages before the MathJax javascript. -->
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
"HTML-CSS": { availableFonts: ["TeX"] }
});
</script>
<hr>
<p>
This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a>
analysis was created with
<a href="https://github.com/jdblischak/workflowr">workflowr</a> 1.0.1
</p>
<hr>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>