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update ordinal response plots, recompile website
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@margoal1
margoal1 committed Mar 2, 2022
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196 changes: 85 additions & 111 deletions Adverse_Events.html
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<!DOCTYPE html>

<html xmlns="http://www.w3.org/1999/xhtml">
<html>

<head>

<meta charset="utf-8" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />

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<title>Safety Plots</title>

<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/bootstrap.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>
<style>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;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
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<span class=visible-md-block> </span>
<span class=visible-lg-block> </span>

<style type="text/css">code{white-space: pre;}</style>


<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>

<style type="text/css">code{white-space: pre;}</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
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<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>




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margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
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summary {
display: list-item;
}
pre code {
padding: 0;
}
</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;
}
.dropdown-submenu {
position: relative;
}
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margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
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}
</style>

<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
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var menuAnchor = $('a[href="' + href + '"]');

// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');

// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');

// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>

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max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
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border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}

.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
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}
}

@media print {
.toc-content {
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
float: right;
}
}

.toc-content {
padding-left: 30px;
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<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
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</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
Data Checking
Data

<span class="caret"></span>
</a>
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<p/>
<p class="warning"> Dear Internet Explorer user: Please ensure compatibility view settings are turned OFF in order to view this website propertly. For best results, use Chrome. <br/>
<p/>
<![endif]-->
<![endif]-->

<div class="fluid-row" id="header">

<div class="btn-group pull-right">
<button type="button" class="btn btn-default btn-xs dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>
<ul class="dropdown-menu" style="min-width: 50px;">
<div id="header">

<div class="btn-group pull-right float-right">
<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>
<ul class="dropdown-menu dropdown-menu-right" style="min-width: 50px;">
<li><a id="rmd-show-all-code" href="#">Show All Code</a></li>
<li><a id="rmd-hide-all-code" href="#">Hide All Code</a></li>
</ul>
Expand Down Expand Up @@ -891,7 +870,7 @@ <h2>Oncology individual plots of percent change from baseline, including dosing
<div id="r-session-info" class="section level2">
<h2>R Session Info</h2>
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>## R version 3.6.1 (2019-07-05)
<pre><code>## R version 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Red Hat Enterprise Linux
##
Expand All @@ -904,41 +883,33 @@ <h2>R Session Info</h2>
## Sample: Rounding
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] zoo_1.8-6 xgxr_1.0.7 gridExtra_2.3 tidyr_1.0.0 dplyr_0.8.3
## [6] ggplot2_3.2.1
## [1] zoo_1.8-9 xgxr_1.1.1 gridExtra_2.3 tidyr_1.1.3 dplyr_1.0.7 ggplot2_3.3.5
##
## loaded via a namespace (and not attached):
## [1] rstan_2.19.2 tidyselect_0.2.5 xfun_0.10
## [4] purrr_0.3.3 pander_0.6.3 reshape2_1.4.3
## [7] lattice_0.20-38 colorspace_1.4-1 vctrs_0.2.0
## [10] htmltools_0.4.0 stats4_3.6.1 loo_2.1.0
## [13] yaml_2.2.0 rlang_0.4.1 pkgbuild_1.0.6
## [16] pillar_1.4.2 glue_1.3.1 withr_2.1.2
## [19] RColorBrewer_1.1-2 matrixStats_0.55.0 binom_1.1-1
## [22] lifecycle_0.1.0 plyr_1.8.4 stringr_1.4.0
## [25] munsell_0.5.0 gtable_0.3.0 codetools_0.2-16
## [28] evaluate_0.14 labeling_0.3 inline_0.3.15
## [31] knitr_1.25 callr_3.3.2 ps_1.3.0
## [34] parallel_3.6.1 Rcpp_1.0.3 scales_1.0.0
## [37] backports_1.1.5 StanHeaders_2.19.0 png_0.1-7
## [40] digest_0.6.22 stringi_1.4.3 processx_3.4.1
## [43] grid_3.6.1 cli_1.1.0 tools_3.6.1
## [46] magrittr_1.5 lazyeval_0.2.2 tibble_2.1.3
## [49] crayon_1.3.4 pkgconfig_2.0.3 zeallot_0.1.0
## [52] rsconnect_0.8.15 prettyunits_1.0.2 assertthat_0.2.1
## [55] rmarkdown_1.16 rstudioapi_0.10 R6_2.4.0
## [58] compiler_3.6.1</code></pre>
## [1] nlme_3.1-152 bitops_1.0-7 RColorBrewer_1.1-2 Deriv_4.1.3 tools_4.1.0 backports_1.2.1
## [7] bslib_0.2.5.1 utf8_1.2.2 R6_2.5.1 rpart_4.1-15 Hmisc_4.5-0 DBI_1.1.1
## [13] mgcv_1.8-35 colorspace_2.0-2 nnet_7.3-16 withr_2.4.2 tidyselect_1.1.1 Exact_2.1
## [19] compiler_4.1.0 cli_3.0.1 htmlTable_2.2.1 binom_1.1-1 expm_0.999-6 labeling_0.4.2
## [25] sass_0.4.0 scales_1.1.1 checkmate_2.0.0 mvtnorm_1.1-2 readr_2.0.1 proxy_0.4-26
## [31] stringr_1.4.0 digest_0.6.27 foreign_0.8-81 rmarkdown_2.11 base64enc_0.1-3 jpeg_0.1-9
## [37] pkgconfig_2.0.3 htmltools_0.5.1.1 highr_0.9 htmlwidgets_1.5.3 rlang_0.4.11 rstudioapi_0.13
## [43] jquerylib_0.1.4 generics_0.1.0 farver_2.1.0 jsonlite_1.7.2 RCurl_1.98-1.4 magrittr_2.0.1
## [49] Formula_1.2-4 Matrix_1.3-3 Rcpp_1.0.7 DescTools_0.99.42 munsell_0.5.0 fansi_0.5.0
## [55] lifecycle_1.0.0 stringi_1.7.3 yaml_2.2.1 MASS_7.3-54 rootSolve_1.8.2.2 plyr_1.8.6
## [61] grid_4.1.0 crayon_1.4.1 lmom_2.8 lattice_0.20-44 splines_4.1.0 pander_0.6.4
## [67] hms_1.1.0 knitr_1.33 pillar_1.6.2 boot_1.3-28 gld_2.6.2 codetools_0.2-18
## [73] glue_1.4.2 evaluate_0.14 latticeExtra_0.6-29 data.table_1.14.0 png_0.1-7 vctrs_0.3.8
## [79] tzdb_0.1.2 gtable_0.3.0 purrr_0.3.4 assertthat_0.2.1 xfun_0.25 e1071_1.7-8
## [85] rsconnect_0.8.24 class_7.3-19 survival_3.2-11 minpack.lm_1.2-1 tibble_3.1.3 cluster_2.1.2
## [91] ellipsis_0.3.2</code></pre>
</div>


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// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.header').parent('thead').parent('table').addClass('table table-condensed');
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
Expand All @@ -970,7 +941,7 @@ <h2>R Session Info</h2>

$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
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<script>
$(document).ready(function () {

// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')

// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')
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theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_').toLowerCase();
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
},
ignoreSelector: ".toc-ignore",
scrollTo: 0
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