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<h1 class="title">Slides</h1>
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Warning
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<p>There are 25 repondents with <code>follow.up = 0</code>, 21 of which with <code>death = 0</code> and other 4 with <code>death = 1</code>.</p>
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<div class="cell">
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<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>dat[dat<span class="sc">$</span>follow.up <span class="sc">==</span> <span class="dv">0</span>, ] <span class="sc">|></span></span>
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<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(death) <span class="sc">|></span></span>
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<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarise</span>(<span class="at">n =</span> <span class="fu">n</span>())</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<div class="cell-output cell-output-stdout">
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<pre><code># A tibble: 2 × 2
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death n
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<int> <int>
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1 0 21
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2 1 4</code></pre>
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</div>
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<p>Reasons to omit them, that is, have <code>dat <- dat[dat$follow.up > 0,]</code> at the very beginning:</p>
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<ul>
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<li>If <code>death = 1</code>, transplant failed. They shouldn’t be included in the research question “survival rate of a <em>successful</em> tranplant”.</li>
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<li>If <code>death = 0</code>, transplant was successful, but they were immediately removed from populatoin at risk, contributiong nothing to the analysis.</li>
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</ul>
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<h1 data-number="1"><span class="header-section-number">1</span> Title</h1>
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<section id="table-of-contents" class="level1" data-number="2">
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<h1 data-number="2"><span class="header-section-number">2</span> Table of Contents (?)</h1>
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</section>
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<section id="introduction-m" class="level1" data-number="3">
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<h1 data-number="3"><span class="header-section-number">3</span> Introduction (M)</h1>
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</section>
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<section id="method-result" class="level1" data-number="4">
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<h1 data-number="4"><span class="header-section-number">4</span> Method & Result</h1>
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<section id="identify-predictors-m" class="level2" data-number="4.1">
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<h2 data-number="4.1" class="anchored" data-anchor-id="identify-predictors-m"><span class="header-section-number">4.1</span> Identify Predictors (M)</h2>
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<ul>
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<li>Data source</li>
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<li>Study population</li>
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<div class="cell">
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<pre><code>[1] 9775</code></pre>
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<ul>
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<li>Covariates</li>
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<li>Outcome</li>
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</ul>
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<div class="cell">
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<div class="cell-output cell-output-stdout">
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<pre><code>[1] "hla.match" "age.donor" "age.rec" "cold.isc" "death" "year"
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[7] "sex" "tx.type" "follow.up"</code></pre>
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#qsvenzfqqw .gt_row_group_first th {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_summary_row {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_first_summary_row {
|
||
border-top-style: solid;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_first_summary_row.thick {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_last_summary_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_grand_summary_row {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_first_grand_summary_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-top-style: double;
|
||
border-top-width: 6px;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_last_grand_summary_row_top {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-style: double;
|
||
border-bottom-width: 6px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_striped {
|
||
background-color: rgba(128, 128, 128, 0.05);
|
||
}
|
||
|
||
#qsvenzfqqw .gt_table_body {
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_footnotes {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
border-bottom-style: none;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_footnote {
|
||
margin: 0px;
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_sourcenotes {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
border-bottom-style: none;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_sourcenote {
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_left {
|
||
text-align: left;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_center {
|
||
text-align: center;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_right {
|
||
text-align: right;
|
||
font-variant-numeric: tabular-nums;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_font_normal {
|
||
font-weight: normal;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_font_bold {
|
||
font-weight: bold;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_font_italic {
|
||
font-style: italic;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_super {
|
||
font-size: 65%;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_footnote_marks {
|
||
font-size: 75%;
|
||
vertical-align: 0.4em;
|
||
position: initial;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_asterisk {
|
||
font-size: 100%;
|
||
vertical-align: 0;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_indent_1 {
|
||
text-indent: 5px;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_indent_2 {
|
||
text-indent: 10px;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_indent_3 {
|
||
text-indent: 15px;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_indent_4 {
|
||
text-indent: 20px;
|
||
}
|
||
|
||
#qsvenzfqqw .gt_indent_5 {
|
||
text-indent: 25px;
|
||
}
|
||
|
||
#qsvenzfqqw .katex-display {
|
||
display: inline-flex !important;
|
||
margin-bottom: 0.75em !important;
|
||
}
|
||
|
||
#qsvenzfqqw div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after {
|
||
height: 0px !important;
|
||
}
|
||
</style>
|
||
|
||
<table class="gt_table caption-top table table-sm table-striped small" data-quarto-postprocess="true" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
|
||
<colgroup>
|
||
<col style="width: 25%">
|
||
<col style="width: 25%">
|
||
<col style="width: 25%">
|
||
<col style="width: 25%">
|
||
</colgroup>
|
||
<thead>
|
||
<tr class="gt_col_headings header">
|
||
<th id="label" class="gt_col_heading gt_columns_bottom_border gt_left" data-quarto-table-cell-role="th" scope="col"><strong>Characteristic</strong></th>
|
||
<th id="stat_0" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col"><strong>Overall</strong><br>
|
||
N = 9,775</th>
|
||
<th id="stat_1" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col"><strong>Cadaveric</strong><br>
|
||
N = 5,148</th>
|
||
<th id="stat_2" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col"><strong>Living</strong><br>
|
||
N = 4,627</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody class="gt_table_body">
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label">Sex, n(%)</td>
|
||
<td class="gt_row gt_center" headers="stat_0"><br>
|
||
</td>
|
||
<td class="gt_row gt_center" headers="stat_1"><br>
|
||
</td>
|
||
<td class="gt_row gt_center" headers="stat_2"><br>
|
||
</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left" headers="label"> Female</td>
|
||
<td class="gt_row gt_center" headers="stat_0">4,014 (41%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1">2,105 (41%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2">1,909 (41%)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label"> Male</td>
|
||
<td class="gt_row gt_center" headers="stat_0">5,761 (59%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1">3,043 (59%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2">2,718 (59%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left" headers="label">Recipient age, median (IQR)</td>
|
||
<td class="gt_row gt_center" headers="stat_0">13 (8, 16)</td>
|
||
<td class="gt_row gt_center" headers="stat_1">13 (7, 16)</td>
|
||
<td class="gt_row gt_center" headers="stat_2">14 (9, 16)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label"> Unknown</td>
|
||
<td class="gt_row gt_center" headers="stat_0">9</td>
|
||
<td class="gt_row gt_center" headers="stat_1">7</td>
|
||
<td class="gt_row gt_center" headers="stat_2">2</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left" headers="label">Donor age, median (IQR)</td>
|
||
<td class="gt_row gt_center" headers="stat_0">33 (21, 41)</td>
|
||
<td class="gt_row gt_center" headers="stat_1">37 (31, 42)</td>
|
||
<td class="gt_row gt_center" headers="stat_2">22 (15, 37)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label"> Unknown</td>
|
||
<td class="gt_row gt_center" headers="stat_0">113</td>
|
||
<td class="gt_row gt_center" headers="stat_1">112</td>
|
||
<td class="gt_row gt_center" headers="stat_2">1</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left" headers="label">HLA matches, n(%)</td>
|
||
<td class="gt_row gt_center" headers="stat_0"><br>
|
||
</td>
|
||
<td class="gt_row gt_center" headers="stat_1"><br>
|
||
</td>
|
||
<td class="gt_row gt_center" headers="stat_2"><br>
|
||
</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label"> 0</td>
|
||
<td class="gt_row gt_center" headers="stat_0">784 (8.2%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1">125 (2.5%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2">659 (14%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left" headers="label"> 1</td>
|
||
<td class="gt_row gt_center" headers="stat_0">1,504 (16%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1">160 (3.2%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2">1,344 (29%)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label"> 2</td>
|
||
<td class="gt_row gt_center" headers="stat_0">1,553 (16%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1">228 (4.6%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2">1,325 (29%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left" headers="label"> 3</td>
|
||
<td class="gt_row gt_center" headers="stat_0">3,778 (40%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1">3,039 (61%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2">739 (16%)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label"> 4</td>
|
||
<td class="gt_row gt_center" headers="stat_0">1,278 (13%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1">1,007 (20%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2">271 (5.9%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left" headers="label"> 5</td>
|
||
<td class="gt_row gt_center" headers="stat_0">365 (3.8%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1">241 (4.9%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2">124 (2.7%)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label"> 6</td>
|
||
<td class="gt_row gt_center" headers="stat_0">279 (2.9%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1">153 (3.1%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2">126 (2.7%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left" headers="label"> Unknown</td>
|
||
<td class="gt_row gt_center" headers="stat_0">234</td>
|
||
<td class="gt_row gt_center" headers="stat_1">195</td>
|
||
<td class="gt_row gt_center" headers="stat_2">39</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label">Cold ischemic time (hours), median (IQR),</td>
|
||
<td class="gt_row gt_center" headers="stat_0">7 (1, 19)</td>
|
||
<td class="gt_row gt_center" headers="stat_1">1 (0, 1)</td>
|
||
<td class="gt_row gt_center" headers="stat_2">19 (13, 25)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left" headers="label"> Unknown</td>
|
||
<td class="gt_row gt_center" headers="stat_0">2,250</td>
|
||
<td class="gt_row gt_center" headers="stat_1">1,490</td>
|
||
<td class="gt_row gt_center" headers="stat_2">760</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</section>
|
||
<section id="elementary-analysis-transplant-type-l" class="level1" data-number="5">
|
||
<h1 data-number="5"><span class="header-section-number">5</span> Elementary Analysis: Transplant Type (L)</h1>
|
||
<section id="transplant-type-vs-sex" class="level2" data-number="5.1">
|
||
<h2 data-number="5.1" class="anchored" data-anchor-id="transplant-type-vs-sex"><span class="header-section-number">5.1</span> Transplant Type vs Sex</h2>
|
||
<p><code>sex</code> are similar across <code>tx.type</code></p>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-8-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="transplant-type-vs-recipient-age" class="level2" data-number="5.2">
|
||
<h2 data-number="5.2" class="anchored" data-anchor-id="transplant-type-vs-recipient-age"><span class="header-section-number">5.2</span> Transplant Type vs Recipient Age</h2>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-9-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</section>
|
||
<section id="elementary-analysis-transplant-type-cont." class="level1" data-number="6">
|
||
<h1 data-number="6"><span class="header-section-number">6</span> Elementary Analysis: Transplant Type (Cont.)</h1>
|
||
<section id="transplant-type-vs-hla-match" class="level2" data-number="6.1">
|
||
<h2 data-number="6.1" class="anchored" data-anchor-id="transplant-type-vs-hla-match"><span class="header-section-number">6.1</span> Transplant Type vs HLA Match</h2>
|
||
<p>Living donors have less <code>hla.match</code> then cadaveric donors.</p>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-10-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="transplant-type-vs-donor-age" class="level2" data-number="6.2">
|
||
<h2 data-number="6.2" class="anchored" data-anchor-id="transplant-type-vs-donor-age"><span class="header-section-number">6.2</span> Transplant Type vs Donor Age</h2>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-11-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</section>
|
||
<section id="overall-kaplan-meier-curve" class="level1" data-number="7">
|
||
<h1 data-number="7"><span class="header-section-number">7</span> Overall Kaplan-Meier Curve</h1>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-13-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div id="ghhayaugts" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
|
||
<style>#ghhayaugts table {
|
||
font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';
|
||
-webkit-font-smoothing: antialiased;
|
||
-moz-osx-font-smoothing: grayscale;
|
||
}
|
||
|
||
#ghhayaugts thead, #ghhayaugts tbody, #ghhayaugts tfoot, #ghhayaugts tr, #ghhayaugts td, #ghhayaugts th {
|
||
border-style: none;
|
||
}
|
||
|
||
#ghhayaugts p {
|
||
margin: 0;
|
||
padding: 0;
|
||
}
|
||
|
||
#ghhayaugts .gt_table {
|
||
display: table;
|
||
border-collapse: collapse;
|
||
line-height: normal;
|
||
margin-left: auto;
|
||
margin-right: auto;
|
||
color: #333333;
|
||
font-size: 15px;
|
||
font-weight: normal;
|
||
font-style: normal;
|
||
background-color: #FFFFFF;
|
||
width: auto;
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #A8A8A8;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #A8A8A8;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
}
|
||
|
||
#ghhayaugts .gt_caption {
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
}
|
||
|
||
#ghhayaugts .gt_title {
|
||
color: #333333;
|
||
font-size: 20px;
|
||
font-weight: initial;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-color: #FFFFFF;
|
||
border-bottom-width: 0;
|
||
}
|
||
|
||
#ghhayaugts .gt_subtitle {
|
||
color: #333333;
|
||
font-size: 85%;
|
||
font-weight: initial;
|
||
padding-top: 3px;
|
||
padding-bottom: 5px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-top-color: #FFFFFF;
|
||
border-top-width: 0;
|
||
}
|
||
|
||
#ghhayaugts .gt_heading {
|
||
background-color: #FFFFFF;
|
||
text-align: center;
|
||
border-bottom-color: #FFFFFF;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#ghhayaugts .gt_bottom_border {
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#ghhayaugts .gt_col_headings {
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#ghhayaugts .gt_col_heading {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: bold;
|
||
text-transform: inherit;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
vertical-align: bottom;
|
||
padding-top: 5px;
|
||
padding-bottom: 6px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
overflow-x: hidden;
|
||
}
|
||
|
||
#ghhayaugts .gt_column_spanner_outer {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: bold;
|
||
text-transform: inherit;
|
||
padding-top: 0;
|
||
padding-bottom: 0;
|
||
padding-left: 4px;
|
||
padding-right: 4px;
|
||
}
|
||
|
||
#ghhayaugts .gt_column_spanner_outer:first-child {
|
||
padding-left: 0;
|
||
}
|
||
|
||
#ghhayaugts .gt_column_spanner_outer:last-child {
|
||
padding-right: 0;
|
||
}
|
||
|
||
#ghhayaugts .gt_column_spanner {
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
vertical-align: bottom;
|
||
padding-top: 5px;
|
||
padding-bottom: 5px;
|
||
overflow-x: hidden;
|
||
display: inline-block;
|
||
width: 100%;
|
||
}
|
||
|
||
#ghhayaugts .gt_spanner_row {
|
||
border-bottom-style: hidden;
|
||
}
|
||
|
||
#ghhayaugts .gt_group_heading {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
text-transform: inherit;
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
vertical-align: middle;
|
||
text-align: left;
|
||
}
|
||
|
||
#ghhayaugts .gt_empty_group_heading {
|
||
padding: 0.5px;
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
vertical-align: middle;
|
||
}
|
||
|
||
#ghhayaugts .gt_from_md > :first-child {
|
||
margin-top: 0;
|
||
}
|
||
|
||
#ghhayaugts .gt_from_md > :last-child {
|
||
margin-bottom: 0;
|
||
}
|
||
|
||
#ghhayaugts .gt_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
margin: 10px;
|
||
border-top-style: solid;
|
||
border-top-width: 1px;
|
||
border-top-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
vertical-align: middle;
|
||
overflow-x: hidden;
|
||
}
|
||
|
||
#ghhayaugts .gt_stub {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
text-transform: inherit;
|
||
border-right-style: solid;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#ghhayaugts .gt_stub_row_group {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
text-transform: inherit;
|
||
border-right-style: solid;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
vertical-align: top;
|
||
}
|
||
|
||
#ghhayaugts .gt_row_group_first td {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#ghhayaugts .gt_row_group_first th {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#ghhayaugts .gt_summary_row {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#ghhayaugts .gt_first_summary_row {
|
||
border-top-style: solid;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#ghhayaugts .gt_first_summary_row.thick {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#ghhayaugts .gt_last_summary_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#ghhayaugts .gt_grand_summary_row {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#ghhayaugts .gt_first_grand_summary_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-top-style: double;
|
||
border-top-width: 6px;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#ghhayaugts .gt_last_grand_summary_row_top {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-style: double;
|
||
border-bottom-width: 6px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#ghhayaugts .gt_striped {
|
||
background-color: rgba(128, 128, 128, 0.05);
|
||
}
|
||
|
||
#ghhayaugts .gt_table_body {
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#ghhayaugts .gt_footnotes {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
border-bottom-style: none;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#ghhayaugts .gt_footnote {
|
||
margin: 0px;
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#ghhayaugts .gt_sourcenotes {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
border-bottom-style: none;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#ghhayaugts .gt_sourcenote {
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#ghhayaugts .gt_left {
|
||
text-align: left;
|
||
}
|
||
|
||
#ghhayaugts .gt_center {
|
||
text-align: center;
|
||
}
|
||
|
||
#ghhayaugts .gt_right {
|
||
text-align: right;
|
||
font-variant-numeric: tabular-nums;
|
||
}
|
||
|
||
#ghhayaugts .gt_font_normal {
|
||
font-weight: normal;
|
||
}
|
||
|
||
#ghhayaugts .gt_font_bold {
|
||
font-weight: bold;
|
||
}
|
||
|
||
#ghhayaugts .gt_font_italic {
|
||
font-style: italic;
|
||
}
|
||
|
||
#ghhayaugts .gt_super {
|
||
font-size: 65%;
|
||
}
|
||
|
||
#ghhayaugts .gt_footnote_marks {
|
||
font-size: 75%;
|
||
vertical-align: 0.4em;
|
||
position: initial;
|
||
}
|
||
|
||
#ghhayaugts .gt_asterisk {
|
||
font-size: 100%;
|
||
vertical-align: 0;
|
||
}
|
||
|
||
#ghhayaugts .gt_indent_1 {
|
||
text-indent: 5px;
|
||
}
|
||
|
||
#ghhayaugts .gt_indent_2 {
|
||
text-indent: 10px;
|
||
}
|
||
|
||
#ghhayaugts .gt_indent_3 {
|
||
text-indent: 15px;
|
||
}
|
||
|
||
#ghhayaugts .gt_indent_4 {
|
||
text-indent: 20px;
|
||
}
|
||
|
||
#ghhayaugts .gt_indent_5 {
|
||
text-indent: 25px;
|
||
}
|
||
|
||
#ghhayaugts .katex-display {
|
||
display: inline-flex !important;
|
||
margin-bottom: 0.75em !important;
|
||
}
|
||
|
||
#ghhayaugts div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after {
|
||
height: 0px !important;
|
||
}
|
||
</style>
|
||
|
||
<table class="gt_table caption-top table table-sm table-striped small" data-quarto-postprocess="true" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
|
||
<thead>
|
||
<tr class="gt_heading header">
|
||
<th colspan="3" class="gt_heading gt_title gt_font_normal gt_bottom_border">Overall Kaplan-Meier Survival Summary</th>
|
||
</tr>
|
||
<tr class="gt_col_headings even">
|
||
<th id="time" class="gt_col_heading gt_columns_bottom_border gt_right" data-quarto-table-cell-role="th" scope="col">Follow-up Time</th>
|
||
<th id="n.risk" class="gt_col_heading gt_columns_bottom_border gt_right" data-quarto-table-cell-role="th" scope="col">Number at Risk</th>
|
||
<th id="surv" class="gt_col_heading gt_columns_bottom_border gt_right" data-quarto-table-cell-role="th" scope="col">Survival Probability</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody class="gt_table_body">
|
||
<tr class="odd">
|
||
<td class="gt_row gt_right" headers="time">0</td>
|
||
<td class="gt_row gt_right" headers="n.risk">9775</td>
|
||
<td class="gt_row gt_right" headers="surv">1.000</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_right" headers="time">2</td>
|
||
<td class="gt_row gt_right" headers="n.risk">6451</td>
|
||
<td class="gt_row gt_right" headers="surv">0.968</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_right" headers="time">4</td>
|
||
<td class="gt_row gt_right" headers="n.risk">4150</td>
|
||
<td class="gt_row gt_right" headers="surv">0.953</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_right" headers="time">6</td>
|
||
<td class="gt_row gt_right" headers="n.risk">2398</td>
|
||
<td class="gt_row gt_right" headers="surv">0.937</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_right" headers="time">8</td>
|
||
<td class="gt_row gt_right" headers="n.risk">1197</td>
|
||
<td class="gt_row gt_right" headers="surv">0.919</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_right" headers="time">10</td>
|
||
<td class="gt_row gt_right" headers="n.risk">492</td>
|
||
<td class="gt_row gt_right" headers="surv">0.901</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_right" headers="time">12</td>
|
||
<td class="gt_row gt_right" headers="n.risk">48</td>
|
||
<td class="gt_row gt_right" headers="surv">0.888</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div id="npikqhagsh" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
|
||
<style>#npikqhagsh table {
|
||
font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';
|
||
-webkit-font-smoothing: antialiased;
|
||
-moz-osx-font-smoothing: grayscale;
|
||
}
|
||
|
||
#npikqhagsh thead, #npikqhagsh tbody, #npikqhagsh tfoot, #npikqhagsh tr, #npikqhagsh td, #npikqhagsh th {
|
||
border-style: none;
|
||
}
|
||
|
||
#npikqhagsh p {
|
||
margin: 0;
|
||
padding: 0;
|
||
}
|
||
|
||
#npikqhagsh .gt_table {
|
||
display: table;
|
||
border-collapse: collapse;
|
||
line-height: normal;
|
||
margin-left: auto;
|
||
margin-right: auto;
|
||
color: #333333;
|
||
font-size: 16px;
|
||
font-weight: normal;
|
||
font-style: normal;
|
||
background-color: #FFF4CC;
|
||
width: auto;
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #A83262;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #A83262;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
}
|
||
|
||
#npikqhagsh .gt_caption {
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
}
|
||
|
||
#npikqhagsh .gt_title {
|
||
color: #333333;
|
||
font-size: 18px;
|
||
font-weight: initial;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-color: #FFF4CC;
|
||
border-bottom-width: 0;
|
||
}
|
||
|
||
#npikqhagsh .gt_subtitle {
|
||
color: #333333;
|
||
font-size: 85%;
|
||
font-weight: initial;
|
||
padding-top: 3px;
|
||
padding-bottom: 5px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-top-color: #FFF4CC;
|
||
border-top-width: 0;
|
||
}
|
||
|
||
#npikqhagsh .gt_heading {
|
||
background-color: #FFF4CC;
|
||
text-align: center;
|
||
border-bottom-color: #FFF4CC;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#npikqhagsh .gt_bottom_border {
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#npikqhagsh .gt_col_headings {
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #A83262;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#npikqhagsh .gt_col_heading {
|
||
color: #333333;
|
||
background-color: #FFF4CC;
|
||
font-size: 100%;
|
||
font-weight: normal;
|
||
text-transform: inherit;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
vertical-align: bottom;
|
||
padding-top: 5px;
|
||
padding-bottom: 6px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
overflow-x: hidden;
|
||
}
|
||
|
||
#npikqhagsh .gt_column_spanner_outer {
|
||
color: #333333;
|
||
background-color: #FFF4CC;
|
||
font-size: 100%;
|
||
font-weight: normal;
|
||
text-transform: inherit;
|
||
padding-top: 0;
|
||
padding-bottom: 0;
|
||
padding-left: 4px;
|
||
padding-right: 4px;
|
||
}
|
||
|
||
#npikqhagsh .gt_column_spanner_outer:first-child {
|
||
padding-left: 0;
|
||
}
|
||
|
||
#npikqhagsh .gt_column_spanner_outer:last-child {
|
||
padding-right: 0;
|
||
}
|
||
|
||
#npikqhagsh .gt_column_spanner {
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #A83262;
|
||
vertical-align: bottom;
|
||
padding-top: 5px;
|
||
padding-bottom: 5px;
|
||
overflow-x: hidden;
|
||
display: inline-block;
|
||
width: 100%;
|
||
}
|
||
|
||
#npikqhagsh .gt_spanner_row {
|
||
border-bottom-style: hidden;
|
||
}
|
||
|
||
#npikqhagsh .gt_group_heading {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
color: #333333;
|
||
background-color: #FFF4CC;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
text-transform: inherit;
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
vertical-align: middle;
|
||
text-align: left;
|
||
}
|
||
|
||
#npikqhagsh .gt_empty_group_heading {
|
||
padding: 0.5px;
|
||
color: #333333;
|
||
background-color: #FFF4CC;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
vertical-align: middle;
|
||
}
|
||
|
||
#npikqhagsh .gt_from_md > :first-child {
|
||
margin-top: 0;
|
||
}
|
||
|
||
#npikqhagsh .gt_from_md > :last-child {
|
||
margin-bottom: 0;
|
||
}
|
||
|
||
#npikqhagsh .gt_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
margin: 10px;
|
||
border-top-style: solid;
|
||
border-top-width: 1px;
|
||
border-top-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
vertical-align: middle;
|
||
overflow-x: hidden;
|
||
}
|
||
|
||
#npikqhagsh .gt_stub {
|
||
color: #333333;
|
||
background-color: #FFF4CC;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
text-transform: inherit;
|
||
border-right-style: solid;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#npikqhagsh .gt_stub_row_group {
|
||
color: #333333;
|
||
background-color: #FFF4CC;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
text-transform: inherit;
|
||
border-right-style: solid;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
vertical-align: top;
|
||
}
|
||
|
||
#npikqhagsh .gt_row_group_first td {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#npikqhagsh .gt_row_group_first th {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#npikqhagsh .gt_summary_row {
|
||
color: #333333;
|
||
background-color: #FFF4CC;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#npikqhagsh .gt_first_summary_row {
|
||
border-top-style: solid;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#npikqhagsh .gt_first_summary_row.thick {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#npikqhagsh .gt_last_summary_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#npikqhagsh .gt_grand_summary_row {
|
||
color: #333333;
|
||
background-color: #FFF4CC;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#npikqhagsh .gt_first_grand_summary_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-top-style: double;
|
||
border-top-width: 6px;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#npikqhagsh .gt_last_grand_summary_row_top {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-style: double;
|
||
border-bottom-width: 6px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#npikqhagsh .gt_striped {
|
||
background-color: #F6E8C3;
|
||
}
|
||
|
||
#npikqhagsh .gt_table_body {
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#npikqhagsh .gt_footnotes {
|
||
color: #333333;
|
||
background-color: #FFF4CC;
|
||
border-bottom-style: none;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#npikqhagsh .gt_footnote {
|
||
margin: 0px;
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#npikqhagsh .gt_sourcenotes {
|
||
color: #333333;
|
||
background-color: #FFF4CC;
|
||
border-bottom-style: none;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#npikqhagsh .gt_sourcenote {
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#npikqhagsh .gt_left {
|
||
text-align: left;
|
||
}
|
||
|
||
#npikqhagsh .gt_center {
|
||
text-align: center;
|
||
}
|
||
|
||
#npikqhagsh .gt_right {
|
||
text-align: right;
|
||
font-variant-numeric: tabular-nums;
|
||
}
|
||
|
||
#npikqhagsh .gt_font_normal {
|
||
font-weight: normal;
|
||
}
|
||
|
||
#npikqhagsh .gt_font_bold {
|
||
font-weight: bold;
|
||
}
|
||
|
||
#npikqhagsh .gt_font_italic {
|
||
font-style: italic;
|
||
}
|
||
|
||
#npikqhagsh .gt_super {
|
||
font-size: 65%;
|
||
}
|
||
|
||
#npikqhagsh .gt_footnote_marks {
|
||
font-size: 75%;
|
||
vertical-align: 0.4em;
|
||
position: initial;
|
||
}
|
||
|
||
#npikqhagsh .gt_asterisk {
|
||
font-size: 100%;
|
||
vertical-align: 0;
|
||
}
|
||
|
||
#npikqhagsh .gt_indent_1 {
|
||
text-indent: 5px;
|
||
}
|
||
|
||
#npikqhagsh .gt_indent_2 {
|
||
text-indent: 10px;
|
||
}
|
||
|
||
#npikqhagsh .gt_indent_3 {
|
||
text-indent: 15px;
|
||
}
|
||
|
||
#npikqhagsh .gt_indent_4 {
|
||
text-indent: 20px;
|
||
}
|
||
|
||
#npikqhagsh .gt_indent_5 {
|
||
text-indent: 25px;
|
||
}
|
||
|
||
#npikqhagsh .katex-display {
|
||
display: inline-flex !important;
|
||
margin-bottom: 0.75em !important;
|
||
}
|
||
|
||
#npikqhagsh div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after {
|
||
height: 0px !important;
|
||
}
|
||
</style>
|
||
|
||
<table class="gt_table caption-top table table-sm table-striped small" data-quarto-postprocess="true" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
|
||
<thead>
|
||
<tr class="gt_heading header">
|
||
<th colspan="3" class="gt_heading gt_title gt_font_normal gt_bottom_border">Overall Kaplan-Meier Survival Summary</th>
|
||
</tr>
|
||
<tr class="gt_col_headings even">
|
||
<th id="time" class="gt_col_heading gt_columns_bottom_border gt_right" data-quarto-table-cell-role="th" style="background-color: #A83262; color: #FFFFFF; font-weight: bold" scope="col">Follow-up Time</th>
|
||
<th id="n.risk" class="gt_col_heading gt_columns_bottom_border gt_right" data-quarto-table-cell-role="th" style="background-color: #A83262; color: #FFFFFF; font-weight: bold" scope="col">Number at Risk</th>
|
||
<th id="surv" class="gt_col_heading gt_columns_bottom_border gt_right" data-quarto-table-cell-role="th" style="background-color: #A83262; color: #FFFFFF; font-weight: bold" scope="col">Survival Probability</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody class="gt_table_body">
|
||
<tr class="odd">
|
||
<td class="gt_row gt_right" headers="time" style="background-color: #FFF4CC">0</td>
|
||
<td class="gt_row gt_right" headers="n.risk" style="background-color: #FFF4CC">9775</td>
|
||
<td class="gt_row gt_right" headers="surv" style="background-color: #FFF4CC">1.000</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_right gt_striped" headers="time" style="background-color: #FFF4CC">2</td>
|
||
<td class="gt_row gt_right gt_striped" headers="n.risk" style="background-color: #FFF4CC">6451</td>
|
||
<td class="gt_row gt_right gt_striped" headers="surv" style="background-color: #FFF4CC">0.968</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_right" headers="time" style="background-color: #FFF4CC">4</td>
|
||
<td class="gt_row gt_right" headers="n.risk" style="background-color: #FFF4CC">4150</td>
|
||
<td class="gt_row gt_right" headers="surv" style="background-color: #FFF4CC">0.953</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_right gt_striped" headers="time" style="background-color: #FFF4CC">6</td>
|
||
<td class="gt_row gt_right gt_striped" headers="n.risk" style="background-color: #FFF4CC">2398</td>
|
||
<td class="gt_row gt_right gt_striped" headers="surv" style="background-color: #FFF4CC">0.937</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_right" headers="time" style="background-color: #FFF4CC">8</td>
|
||
<td class="gt_row gt_right" headers="n.risk" style="background-color: #FFF4CC">1197</td>
|
||
<td class="gt_row gt_right" headers="surv" style="background-color: #FFF4CC">0.919</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_right gt_striped" headers="time" style="background-color: #FFF4CC">10</td>
|
||
<td class="gt_row gt_right gt_striped" headers="n.risk" style="background-color: #FFF4CC">492</td>
|
||
<td class="gt_row gt_right gt_striped" headers="surv" style="background-color: #FFF4CC">0.901</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_right" headers="time" style="background-color: #FFF4CC">12</td>
|
||
<td class="gt_row gt_right" headers="n.risk" style="background-color: #FFF4CC">48</td>
|
||
<td class="gt_row gt_right" headers="surv" style="background-color: #FFF4CC">0.888</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="cox-model-with-intervals" class="level1" data-number="8">
|
||
<h1 data-number="8"><span class="header-section-number">8</span> Cox Model (with intervals?)</h1>
|
||
</section>
|
||
<section id="cox-model-transplant-type" class="level1" data-number="9">
|
||
<h1 data-number="9"><span class="header-section-number">9</span> Cox Model: Transplant Type</h1>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = Surv(follow.up, death) ~ tx.type, data = dat)
|
||
|
||
n= 9775, number of events= 465
|
||
|
||
coef exp(coef) se(coef) z Pr(>|z|)
|
||
tx.typeLiving 0.64469 1.90539 0.09558 6.745 1.53e-11 ***
|
||
---
|
||
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
|
||
|
||
exp(coef) exp(-coef) lower .95 upper .95
|
||
tx.typeLiving 1.905 0.5248 1.58 2.298
|
||
|
||
Concordance= 0.586 (se = 0.012 )
|
||
Likelihood ratio test= 47.1 on 1 df, p=7e-12
|
||
Wald test = 45.5 on 1 df, p=2e-11
|
||
Score (logrank) test = 47.09 on 1 df, p=7e-12</code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-19-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call: survfit(formula = Surv(follow.up, death) ~ tx.type, data = dat)
|
||
|
||
tx.type=Cadaveric
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 5148 0 1.000 0.00000 1.000 1.000
|
||
4 2297 130 0.967 0.00294 0.961 0.973
|
||
8 711 34 0.943 0.00514 0.933 0.953
|
||
12 27 13 0.908 0.01135 0.886 0.931
|
||
|
||
tx.type=Living
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 4627 4 0.999 0.000432 0.998 1.000
|
||
4 1853 225 0.937 0.004212 0.928 0.945
|
||
8 486 52 0.891 0.007720 0.876 0.906
|
||
12 21 7 0.864 0.013257 0.838 0.890</code></pre>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="cox-model-age-recipient-continuous" class="level1" data-number="10">
|
||
<h1 data-number="10"><span class="header-section-number">10</span> Cox Model: Age Recipient (Continuous)</h1>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = Surv(follow.up, death) ~ age.rec, data = dat)
|
||
|
||
n= 9766, number of events= 464
|
||
(9 observations deleted due to missingness)
|
||
|
||
coef exp(coef) se(coef) z Pr(>|z|)
|
||
age.rec -0.042550 0.958342 0.008434 -5.045 4.53e-07 ***
|
||
---
|
||
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
|
||
|
||
exp(coef) exp(-coef) lower .95 upper .95
|
||
age.rec 0.9583 1.043 0.9426 0.9743
|
||
|
||
Concordance= 0.586 (se = 0.016 )
|
||
Likelihood ratio test= 24.81 on 1 df, p=6e-07
|
||
Wald test = 25.45 on 1 df, p=5e-07
|
||
Score (logrank) test = 25.75 on 1 df, p=4e-07</code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-23-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<details>
|
||
<summary>
|
||
View life table
|
||
</summary>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call: survfit(formula = Surv(follow.up, death) ~ age.rec, data = dat)
|
||
|
||
9 observations deleted due to missingness
|
||
age.rec=0
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 93 1 0.989 0.0107 0.969 1.00
|
||
4 34 17 0.784 0.0460 0.699 0.88
|
||
8 13 0 0.784 0.0460 0.699 0.88
|
||
|
||
age.rec=1
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 394 0 1.000 0.0000 1.000 1.000
|
||
4 158 32 0.900 0.0173 0.866 0.934
|
||
8 60 3 0.876 0.0217 0.835 0.920
|
||
12 1 0 0.876 0.0217 0.835 0.920
|
||
|
||
age.rec=2
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 381 0 1.000 0.0000 1.000 1.000
|
||
4 161 26 0.917 0.0160 0.886 0.949
|
||
8 73 2 0.899 0.0204 0.859 0.939
|
||
12 1 2 0.860 0.0336 0.797 0.929
|
||
|
||
age.rec=3
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 277 0 1.000 0.0000 1.000 1.000
|
||
4 130 15 0.938 0.0157 0.907 0.969
|
||
8 44 2 0.915 0.0223 0.872 0.960
|
||
|
||
age.rec=4
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 279 0 1.000 0.0000 1.000 1.000
|
||
4 129 14 0.942 0.0151 0.913 0.972
|
||
8 44 5 0.895 0.0257 0.846 0.947
|
||
12 1 0 0.895 0.0257 0.846 0.947
|
||
|
||
age.rec=5
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 286 0 1.000 0.0000 1.000 1.000
|
||
4 133 10 0.955 0.0141 0.928 0.983
|
||
8 49 3 0.920 0.0251 0.872 0.971
|
||
12 4 1 0.898 0.0330 0.835 0.965
|
||
|
||
age.rec=6
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 302 0 1.000 0.0000 1.000 1.000
|
||
4 140 10 0.961 0.0123 0.937 0.985
|
||
8 53 0 0.961 0.0123 0.937 0.985
|
||
12 2 0 0.961 0.0123 0.937 0.985
|
||
|
||
age.rec=7
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 333 0 1.000 0.0000 1.000 1.000
|
||
4 162 14 0.948 0.0140 0.921 0.976
|
||
8 62 2 0.932 0.0177 0.898 0.967
|
||
12 3 2 0.859 0.0546 0.759 0.973
|
||
|
||
age.rec=8
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 371 0 1.000 0.0000 1.000 1.000
|
||
4 183 12 0.964 0.0102 0.944 0.984
|
||
8 72 3 0.935 0.0199 0.897 0.975
|
||
12 1 3 0.869 0.0416 0.791 0.954
|
||
|
||
age.rec=9
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 388 0 1.000 0.0000 1.000 1.000
|
||
4 171 12 0.953 0.0137 0.927 0.980
|
||
8 63 7 0.891 0.0268 0.840 0.945
|
||
12 5 0 0.891 0.0268 0.840 0.945
|
||
|
||
age.rec=10
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 430 1 0.998 0.00232 0.993 1.000
|
||
4 203 7 0.976 0.00876 0.959 0.993
|
||
8 69 4 0.943 0.01874 0.907 0.981
|
||
12 3 2 0.846 0.06716 0.725 0.989
|
||
|
||
age.rec=11
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 443 0 1.000 0.0000 1.000 1.000
|
||
4 198 8 0.976 0.0087 0.959 0.993
|
||
8 63 6 0.921 0.0242 0.875 0.970
|
||
12 4 1 0.881 0.0455 0.796 0.975
|
||
|
||
age.rec=12
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 541 1 0.998 0.00185 0.995 1.000
|
||
4 246 15 0.963 0.00943 0.944 0.981
|
||
8 69 5 0.933 0.01684 0.900 0.966
|
||
12 2 1 0.904 0.03300 0.841 0.971
|
||
|
||
age.rec=13
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 644 0 1.000 0.00000 1.000 1.000
|
||
4 282 22 0.954 0.00981 0.935 0.974
|
||
8 57 4 0.922 0.02042 0.883 0.963
|
||
12 4 2 0.872 0.04013 0.796 0.954
|
||
|
||
age.rec=14
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 685 0 1.000 0.00000 1.000 1.000
|
||
4 303 15 0.971 0.00753 0.957 0.986
|
||
8 59 4 0.945 0.01537 0.916 0.976
|
||
12 2 1 0.909 0.03860 0.837 0.988
|
||
|
||
age.rec=15
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 874 1 0.999 0.00114 0.997 1.000
|
||
4 336 36 0.945 0.00910 0.927 0.963
|
||
8 66 6 0.918 0.01432 0.890 0.946
|
||
12 3 0 0.918 0.01432 0.890 0.946
|
||
|
||
age.rec=16
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 935 0 1.000 0.0000 1.000 1.000
|
||
4 375 29 0.956 0.0082 0.941 0.973
|
||
8 86 8 0.924 0.0145 0.896 0.953
|
||
12 4 0 0.924 0.0145 0.896 0.953
|
||
|
||
age.rec=17
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 1073 0 1.000 0.00000 1.000 1.000
|
||
4 410 28 0.961 0.00753 0.946 0.976
|
||
8 90 16 0.889 0.02020 0.850 0.929
|
||
12 1 2 0.854 0.03175 0.794 0.918
|
||
|
||
age.rec=18
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
0 1037 0 1.000 0.00000 1.000 1.000
|
||
4 395 32 0.955 0.00802 0.940 0.971
|
||
8 104 6 0.931 0.01309 0.906 0.957
|
||
12 7 2 0.905 0.02210 0.863 0.949</code></pre>
|
||
</div>
|
||
</div>
|
||
</details>
|
||
</section>
|
||
<section id="cox-model-age-recipient-categorical" class="level1" data-number="11">
|
||
<h1 data-number="11"><span class="header-section-number">11</span> Cox Model: Age Recipient (Categorical)</h1>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>cox.age.rec.group</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = Surv(follow.up, death) ~ age.rec.group, data = dat.age.rec.group)
|
||
|
||
coef exp(coef) se(coef) z p
|
||
age.rec.group2-5 -0.5947 0.5517 0.1767 -3.366 0.000764
|
||
age.rec.group6-10 -1.0578 0.3472 0.1776 -5.956 2.59e-09
|
||
age.rec.group11-18 -1.0192 0.3609 0.1513 -6.736 1.63e-11
|
||
|
||
Likelihood ratio test=44.93 on 3 df, p=9.559e-10
|
||
n= 9766, number of events= 464
|
||
(9 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>eme.age.rec.group <span class="ot"><-</span> <span class="fu">emmeans</span>(cox.age.rec.group, pairwise <span class="sc">~</span> age.rec.group,</span>
|
||
<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a> <span class="at">type =</span> <span class="st">"response"</span>)</span>
|
||
<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a>eme.age.rec.group</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>$emmeans
|
||
age.rec.group response SE df asymp.LCL asymp.UCL
|
||
0-1 1.000 0.0000 Inf 1.000 1.000
|
||
2-5 0.552 0.0975 Inf 0.390 0.780
|
||
6-10 0.347 0.0617 Inf 0.245 0.492
|
||
11-18 0.361 0.0546 Inf 0.268 0.485
|
||
|
||
Confidence level used: 0.95
|
||
Intervals are back-transformed from the log scale
|
||
|
||
$contrasts
|
||
contrast ratio SE df null z.ratio p.value
|
||
(0-1) / (2-5) 1.813 0.320 Inf 1 3.366 0.0043
|
||
(0-1) / (6-10) 2.880 0.511 Inf 1 5.956 <.0001
|
||
(0-1) / (11-18) 2.771 0.419 Inf 1 6.736 <.0001
|
||
(2-5) / (6-10) 1.589 0.251 Inf 1 2.928 0.0179
|
||
(2-5) / (11-18) 1.529 0.196 Inf 1 3.314 0.0051
|
||
(6-10) / (11-18) 0.962 0.124 Inf 1 -0.298 0.9908
|
||
|
||
P value adjustment: tukey method for comparing a family of 4 estimates
|
||
Tests are performed on the log scale </code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-29-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-30-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="identifying-predictors" class="level1" data-number="12">
|
||
<h1 data-number="12"><span class="header-section-number">12</span> Identifying Predictors</h1>
|
||
<section id="start-with-nothing" class="level2" data-number="12.1">
|
||
<h2 data-number="12.1" class="anchored" data-anchor-id="start-with-nothing"><span class="header-section-number">12.1</span> Start with nothing</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb13"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a>old.vars <span class="ot"><-</span> <span class="fu">c</span>()</span>
|
||
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"tx.type"</span>, <span class="dv">1</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.64466 1.90534 0.09558 6.745 1.53e-11
|
||
|
||
Likelihood ratio test=47.1 on 1 df, p=6.742e-12
|
||
n= 9775, number of events= 465 </code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 45.49594 1 1.529554e-11</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb16"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"hla.match"</span>, <span class="dv">1</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
hla.match -0.2096 0.8109 0.0351 -5.972 2.34e-09
|
||
|
||
Likelihood ratio test=35.87 on 1 df, p=2.112e-09
|
||
n= 9541, number of events= 451
|
||
(234 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 35.6703 1 2.336993e-09</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb19"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb19-1"><a href="#cb19-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"age.donor"</span>, <span class="dv">1</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
age.donor -0.021738 0.978497 0.003467 -6.269 3.62e-10
|
||
|
||
Likelihood ratio test=38.96 on 1 df, p=4.319e-10
|
||
n= 9662, number of events= 464
|
||
(113 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 39.30567 1 3.62387e-10</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb22"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb22-1"><a href="#cb22-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"age.rec"</span>, <span class="dv">1</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
age.rec -0.042545 0.958348 0.008434 -5.045 4.54e-07
|
||
|
||
Likelihood ratio test=24.8 on 1 df, p=6.362e-07
|
||
n= 9766, number of events= 464
|
||
(9 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 25.44856 1 4.543371e-07</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb25"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb25-1"><a href="#cb25-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"cold.isc"</span>, <span class="dv">1</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
cold.isc 0.019094 1.019278 0.004052 4.712 2.45e-06
|
||
|
||
Likelihood ratio test=20.88 on 1 df, p=4.888e-06
|
||
n= 7525, number of events= 357
|
||
(2250 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 22.20574 1 2.449402e-06</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb28"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb28-1"><a href="#cb28-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"sex"</span>, <span class="dv">1</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
sexMale -0.08422 0.91923 0.09374 -0.898 0.369
|
||
|
||
Likelihood ratio test=0.8 on 1 df, p=0.37
|
||
n= 9775, number of events= 465 </code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 0.8072063 1 0.3689475</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb31"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb31-1"><a href="#cb31-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"year"</span>, <span class="dv">1</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
year -0.03667 0.96399 0.01550 -2.366 0.018
|
||
|
||
Likelihood ratio test=5.62 on 1 df, p=0.0178
|
||
n= 9775, number of events= 465 </code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 5.595603 1 0.01800561</code></pre>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="tx.type" class="level2" data-number="12.2">
|
||
<h2 data-number="12.2" class="anchored" data-anchor-id="tx.type"><span class="header-section-number">12.2</span> <code>tx.type</code> + ?</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb34"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb34-1"><a href="#cb34-1" aria-hidden="true" tabindex="-1"></a>old.vars <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"tx.type"</span>)</span>
|
||
<span id="cb34-2"><a href="#cb34-2" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb34-3"><a href="#cb34-3" aria-hidden="true" tabindex="-1"></a><span class="co"># test.new.var(old.vars, "hla.match", 2:7)</span></span>
|
||
<span id="cb34-4"><a href="#cb34-4" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"hla.match"</span>, <span class="dv">2</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.45336 1.57359 0.11146 4.068 4.75e-05
|
||
hla.match -0.12459 0.88286 0.03959 -3.147 0.00165
|
||
|
||
Likelihood ratio test=52.43 on 2 df, p=4.122e-12
|
||
n= 9541, number of events= 451
|
||
(234 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 9.905243 1 0.001648086</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb37"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb37-1"><a href="#cb37-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"age.donor"</span>, <span class="dv">2</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.478191 1.613154 0.106660 4.483 7.35e-06
|
||
age.donor -0.013523 0.986568 0.003745 -3.611 0.000305
|
||
|
||
Likelihood ratio test=59.05 on 2 df, p=1.506e-13
|
||
n= 9662, number of events= 464
|
||
(113 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 13.0412 1 0.0003047131</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb40"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb40-1"><a href="#cb40-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"age.rec"</span>, <span class="dv">2</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.693775 2.001255 0.096157 7.215 5.39e-13
|
||
age.rec -0.049081 0.952104 0.008536 -5.750 8.92e-09
|
||
|
||
Likelihood ratio test=78.72 on 2 df, p=< 2.2e-16
|
||
n= 9766, number of events= 464
|
||
(9 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 33.06396 1 8.917646e-09</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb43"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb43-1"><a href="#cb43-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"cold.isc"</span>, <span class="dv">2</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.477550 1.612119 0.171044 2.792 0.00524
|
||
cold.isc 0.004924 1.004937 0.006728 0.732 0.46420
|
||
|
||
Likelihood ratio test=28.72 on 2 df, p=5.811e-07
|
||
n= 7525, number of events= 357
|
||
(2250 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 0.5357515 1 0.4641988</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb46"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb46-1"><a href="#cb46-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"sex"</span>, <span class="dv">2</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.64499 1.90597 0.09558 6.748 1.5e-11
|
||
sexMale -0.08657 0.91707 0.09374 -0.924 0.356
|
||
|
||
Likelihood ratio test=47.95 on 2 df, p=3.87e-11
|
||
n= 9775, number of events= 465 </code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 0.8528929 1 0.3557352</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb49"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb49-1"><a href="#cb49-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"year"</span>, <span class="dv">2</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.63806 1.89281 0.09563 6.672 2.52e-11
|
||
year -0.03310 0.96744 0.01548 -2.138 0.0325
|
||
|
||
Likelihood ratio test=51.69 on 2 df, p=5.967e-12
|
||
n= 9775, number of events= 465 </code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 4.573044 1 0.0324788</code></pre>
|
||
</div>
|
||
</div>
|
||
<p><code>age.rec</code> has the smallest <span class="math inline">\(p\)</span>-value</p>
|
||
</section>
|
||
<section id="tx.type-age.rec" class="level2" data-number="12.3">
|
||
<h2 data-number="12.3" class="anchored" data-anchor-id="tx.type-age.rec"><span class="header-section-number">12.3</span> <code>tx.type</code> + <code>age.rec</code> + ?</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb52"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb52-1"><a href="#cb52-1" aria-hidden="true" tabindex="-1"></a>old.vars <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"tx.type"</span>, <span class="st">"age.rec"</span>)</span>
|
||
<span id="cb52-2"><a href="#cb52-2" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb52-3"><a href="#cb52-3" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"hla.match"</span>, <span class="dv">3</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.512664 1.669733 0.112875 4.542 5.58e-06
|
||
age.rec -0.048268 0.952878 0.008688 -5.556 2.77e-08
|
||
hla.match -0.113954 0.892299 0.039929 -2.854 0.00432
|
||
|
||
Likelihood ratio test=81.92 on 3 df, p=< 2.2e-16
|
||
n= 9535, number of events= 450
|
||
(240 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 8.144605 1 0.004318947</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb55"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb55-1"><a href="#cb55-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"age.donor"</span>, <span class="dv">3</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.571325 1.770611 0.107377 5.321 1.03e-07
|
||
age.rec -0.044085 0.956872 0.008718 -5.057 4.26e-07
|
||
age.donor -0.009688 0.990359 0.003797 -2.551 0.0107
|
||
|
||
Likelihood ratio test=83.3 on 3 df, p=< 2.2e-16
|
||
n= 9655, number of events= 463
|
||
(120 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 6.508773 1 0.01073435</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb58"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb58-1"><a href="#cb58-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"cold.isc"</span>, <span class="dv">3</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.489852 1.632075 0.170731 2.869 0.00412
|
||
age.rec -0.025545 0.974779 0.010019 -2.550 0.01078
|
||
cold.isc 0.005637 1.005653 0.006709 0.840 0.40085
|
||
|
||
Likelihood ratio test=35.04 on 3 df, p=1.194e-07
|
||
n= 7519, number of events= 357
|
||
(2256 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 0.705761 1 0.4008547</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb61"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb61-1"><a href="#cb61-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"sex"</span>, <span class="dv">3</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.695122 2.003953 0.096164 7.229 4.88e-13
|
||
age.rec -0.050004 0.951226 0.008569 -5.835 5.37e-09
|
||
sexMale -0.130416 0.877730 0.094113 -1.386 0.166
|
||
|
||
Likelihood ratio test=80.63 on 3 df, p=< 2.2e-16
|
||
n= 9766, number of events= 464
|
||
(9 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 1.920263 1 0.1658277</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb64"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb64-1"><a href="#cb64-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"year"</span>, <span class="dv">3</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.687661 1.989059 0.096215 7.147 8.86e-13
|
||
age.rec -0.049029 0.952153 0.008537 -5.743 9.30e-09
|
||
year -0.033478 0.967076 0.015475 -2.163 0.0305
|
||
|
||
Likelihood ratio test=83.42 on 3 df, p=< 2.2e-16
|
||
n= 9766, number of events= 464
|
||
(9 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 4.680122 1 0.03051359</code></pre>
|
||
</div>
|
||
</div>
|
||
<p><code>hla.match</code> has the smallest <span class="math inline">\(p\)</span>-value</p>
|
||
</section>
|
||
<section id="tx.type-age.rec-hla.match" class="level2" data-number="12.4">
|
||
<h2 data-number="12.4" class="anchored" data-anchor-id="tx.type-age.rec-hla.match"><span class="header-section-number">12.4</span> <code>tx.type</code> + <code>age.rec</code> + <code>hla.match</code> + ?</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb67"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb67-1"><a href="#cb67-1" aria-hidden="true" tabindex="-1"></a>old.vars <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"tx.type"</span>, <span class="st">"age.rec"</span>, <span class="st">"hla.match"</span>)</span>
|
||
<span id="cb67-2"><a href="#cb67-2" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb67-3"><a href="#cb67-3" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"age.donor"</span>, <span class="dv">4</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.408204 1.504113 0.121727 3.353 0.000798
|
||
age.rec -0.043716 0.957225 0.008875 -4.926 8.39e-07
|
||
hla.match -0.107306 0.898251 0.040127 -2.674 0.007491
|
||
age.donor -0.008810 0.991229 0.003859 -2.283 0.022443
|
||
|
||
Likelihood ratio test=85.46 on 4 df, p=< 2.2e-16
|
||
n= 9433, number of events= 449
|
||
(342 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 5.211086 1 0.02244331</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb70"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb70-1"><a href="#cb70-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"cold.isc"</span>, <span class="dv">4</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.349594 1.418492 0.182948 1.911 0.0560
|
||
age.rec -0.023299 0.976970 0.010119 -2.302 0.0213
|
||
hla.match -0.071073 0.931394 0.044036 -1.614 0.1065
|
||
cold.isc 0.006428 1.006449 0.006717 0.957 0.3386
|
||
|
||
Likelihood ratio test=33.68 on 4 df, p=8.682e-07
|
||
n= 7381, number of events= 352
|
||
(2394 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 0.9158816 1 0.3385587</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb73"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb73-1"><a href="#cb73-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"sex"</span>, <span class="dv">4</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.515100 1.673806 0.112902 4.562 5.06e-06
|
||
age.rec -0.048944 0.952234 0.008721 -5.612 2.00e-08
|
||
hla.match -0.112940 0.893204 0.039936 -2.828 0.00468
|
||
sexMale -0.094882 0.909480 0.095783 -0.991 0.32188
|
||
|
||
Likelihood ratio test=82.9 on 4 df, p=< 2.2e-16
|
||
n= 9535, number of events= 450
|
||
(240 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 0.9812753 1 0.3218842</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb76"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb76-1"><a href="#cb76-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"year"</span>, <span class="dv">4</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.494911 1.640353 0.113403 4.364 1.28e-05
|
||
age.rec -0.048129 0.953011 0.008689 -5.539 3.04e-08
|
||
hla.match -0.122559 0.884654 0.040341 -3.038 0.00238
|
||
year -0.035190 0.965422 0.015831 -2.223 0.02622
|
||
|
||
Likelihood ratio test=86.88 on 4 df, p=< 2.2e-16
|
||
n= 9535, number of events= 450
|
||
(240 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 4.941346 1 0.02622161</code></pre>
|
||
</div>
|
||
</div>
|
||
<p><code>age.donor</code> has the smallest <span class="math inline">\(p\)</span>-value</p>
|
||
</section>
|
||
<section id="tx.type-age.rec-hla.match-age.donor" class="level2" data-number="12.5">
|
||
<h2 data-number="12.5" class="anchored" data-anchor-id="tx.type-age.rec-hla.match-age.donor"><span class="header-section-number">12.5</span> <code>tx.type</code> + <code>age.rec</code> + <code>hla.match</code> + <code>age.donor</code> + ?</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb79"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb79-1"><a href="#cb79-1" aria-hidden="true" tabindex="-1"></a>old.vars <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"tx.type"</span>, <span class="st">"age.rec"</span>, <span class="st">"hla.match"</span>, <span class="st">"age.donor"</span>)</span>
|
||
<span id="cb79-2"><a href="#cb79-2" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb79-3"><a href="#cb79-3" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"cold.isc"</span>, <span class="dv">5</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.355582 1.427011 0.188970 1.882 0.0599
|
||
age.rec -0.021491 0.978738 0.010298 -2.087 0.0369
|
||
hla.match -0.067709 0.934532 0.044223 -1.531 0.1257
|
||
age.donor -0.003508 0.996499 0.004230 -0.829 0.4069
|
||
cold.isc 0.004519 1.004530 0.006774 0.667 0.5047
|
||
|
||
Likelihood ratio test=34.04 on 5 df, p=2.333e-06
|
||
n= 7347, number of events= 351
|
||
(2428 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 0.445129 1 0.5046572</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb82"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb82-1"><a href="#cb82-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"sex"</span>, <span class="dv">5</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.411943 1.509748 0.121783 3.383 0.000718
|
||
age.rec -0.044462 0.956512 0.008914 -4.988 6.1e-07
|
||
hla.match -0.106379 0.899084 0.040136 -2.650 0.008038
|
||
age.donor -0.008675 0.991362 0.003862 -2.246 0.024677
|
||
sexMale -0.092710 0.911458 0.095941 -0.966 0.333885
|
||
|
||
Likelihood ratio test=86.39 on 5 df, p=< 2.2e-16
|
||
n= 9433, number of events= 449
|
||
(342 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 0.9337712 1 0.3338849</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb85"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb85-1"><a href="#cb85-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"year"</span>, <span class="dv">5</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.397903 1.488700 0.121903 3.264 0.00110
|
||
age.rec -0.043831 0.957116 0.008875 -4.939 7.87e-07
|
||
hla.match -0.115648 0.890789 0.040537 -2.853 0.00433
|
||
age.donor -0.008325 0.991709 0.003854 -2.160 0.03078
|
||
year -0.033109 0.967433 0.015844 -2.090 0.03664
|
||
|
||
Likelihood ratio test=89.84 on 5 df, p=< 2.2e-16
|
||
n= 9433, number of events= 449
|
||
(342 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 4.367128 1 0.0366387</code></pre>
|
||
</div>
|
||
</div>
|
||
<p><code>year</code> has the smallest <span class="math inline">\(p\)</span>-value</p>
|
||
</section>
|
||
<section id="tx.type-age.rec-hla.match-age.donor-year" class="level2" data-number="12.6">
|
||
<h2 data-number="12.6" class="anchored" data-anchor-id="tx.type-age.rec-hla.match-age.donor-year"><span class="header-section-number">12.6</span> <code>tx.type</code> + <code>age.rec</code> + <code>hla.match</code> + <code>age.donor</code> + <code>year</code></h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb88"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb88-1"><a href="#cb88-1" aria-hidden="true" tabindex="-1"></a>old.vars <span class="ot"><-</span> <span class="fu">c</span>(<span class="st">"tx.type"</span>, <span class="st">"age.rec"</span>, <span class="st">"hla.match"</span>, <span class="st">"age.donor"</span>, <span class="st">"year"</span>)</span>
|
||
<span id="cb88-2"><a href="#cb88-2" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb88-3"><a href="#cb88-3" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"cold.isc"</span>, <span class="dv">6</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.381855 1.464999 0.189901 2.011 0.0443
|
||
age.rec -0.021369 0.978857 0.010295 -2.076 0.0379
|
||
hla.match -0.073960 0.928708 0.044568 -1.660 0.0970
|
||
age.donor -0.002981 0.997024 0.004226 -0.705 0.4806
|
||
year -0.037375 0.963315 0.019227 -1.944 0.0519
|
||
cold.isc 0.002743 1.002747 0.006825 0.402 0.6878
|
||
|
||
Likelihood ratio test=37.86 on 6 df, p=1.195e-06
|
||
n= 7347, number of events= 351
|
||
(2428 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 0.1615171 1 0.6877636</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb91"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb91-1"><a href="#cb91-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"sex"</span>, <span class="dv">6</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = new.surv, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.401829 1.494556 0.121963 3.295 0.000985
|
||
age.rec -0.044602 0.956378 0.008916 -5.003 5.66e-07
|
||
hla.match -0.114750 0.891589 0.040546 -2.830 0.004653
|
||
age.donor -0.008185 0.991848 0.003857 -2.122 0.033833
|
||
year -0.033222 0.967324 0.015844 -2.097 0.036011
|
||
sexMale -0.094191 0.910109 0.095956 -0.982 0.326293
|
||
|
||
Likelihood ratio test=90.8 on 6 df, p=< 2.2e-16
|
||
n= 9433, number of events= 449
|
||
(342 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 0.9635531 1 0.3262933</code></pre>
|
||
</div>
|
||
</div>
|
||
<p>Neither has <span class="math inline">\(p\)</span>-value less than 0.05. Stop.</p>
|
||
</section>
|
||
</section>
|
||
<section id="full-model" class="level1" data-number="13">
|
||
<h1 data-number="13"><span class="header-section-number">13</span> Full Model</h1>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb94"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb94-1"><a href="#cb94-1" aria-hidden="true" tabindex="-1"></a>cox.full</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = surv.full, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.0734859 1.0762534 0.0253724 2.896 0.00378
|
||
age.rec 0.0154431 1.0155630 0.0020497 7.534 4.9e-14
|
||
hla.match -0.0210826 0.9791381 0.0086077 -2.449 0.01431
|
||
age.donor -0.0009874 0.9990131 0.0008841 -1.117 0.26405
|
||
year 0.4429003 1.5572171 0.0057586 76.910 < 2e-16
|
||
|
||
Likelihood ratio test=8440 on 5 df, p=< 2.2e-16
|
||
n= 9433, number of events= 9433
|
||
(342 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-40-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<section id="what-happened-to-year" class="level2" data-number="13.1">
|
||
<h2 data-number="13.1" class="anchored" data-anchor-id="what-happened-to-year"><span class="header-section-number">13.1</span> What happened to <code>year</code>?</h2>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-41-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-42-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<p>Probabily want to omit it</p>
|
||
</section>
|
||
<section id="without-year" class="level2" data-number="13.2">
|
||
<h2 data-number="13.2" class="anchored" data-anchor-id="without-year"><span class="header-section-number">13.2</span> Without <code>year</code></h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb96"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb96-1"><a href="#cb96-1" aria-hidden="true" tabindex="-1"></a>cox.full<span class="fl">.1</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = surv.full.1, data = dat, method = "breslow")
|
||
|
||
coef exp(coef) se(coef) z p
|
||
tx.typeLiving 0.0037484 1.0037554 0.0254736 0.147 0.8830
|
||
age.rec 0.0139177 1.0140150 0.0020498 6.790 1.12e-11
|
||
hla.match -0.0854685 0.9180821 0.0089546 -9.545 < 2e-16
|
||
age.donor 0.0023071 1.0023098 0.0008657 2.665 0.0077
|
||
|
||
Likelihood ratio test=172.9 on 4 df, p=< 2.2e-16
|
||
n= 9433, number of events= 9433
|
||
(342 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-45-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<hr>
|
||
<p>TODO: write a more generic function (UPDATE: FAILED)</p>
|
||
<details>
|
||
</details>
|
||
<hr>
|
||
</section>
|
||
</section>
|
||
<section id="old" class="level1" data-number="14">
|
||
<h1 data-number="14"><span class="header-section-number">14</span> Old</h1>
|
||
<details>
|
||
<section id="death-censored" class="level2" data-number="14.1">
|
||
<h2 data-number="14.1" class="anchored" data-anchor-id="death-censored"><span class="header-section-number">14.1</span> Death & Censored</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb98"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb98-1"><a href="#cb98-1" aria-hidden="true" tabindex="-1"></a>dat <span class="sc">|></span></span>
|
||
<span id="cb98-2"><a href="#cb98-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(death) <span class="sc">|></span></span>
|
||
<span id="cb98-3"><a href="#cb98-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarise</span>(</span>
|
||
<span id="cb98-4"><a href="#cb98-4" aria-hidden="true" tabindex="-1"></a> <span class="at">n =</span> <span class="fu">n</span>(),</span>
|
||
<span id="cb98-5"><a href="#cb98-5" aria-hidden="true" tabindex="-1"></a> <span class="at">percentage =</span> <span class="fu">n</span>() <span class="sc">/</span> <span class="fu">nrow</span>(dat) <span class="sc">*</span> <span class="dv">100</span></span>
|
||
<span id="cb98-6"><a href="#cb98-6" aria-hidden="true" tabindex="-1"></a> )</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code># A tibble: 2 × 3
|
||
death n percentage
|
||
<int> <int> <dbl>
|
||
1 0 9310 95.2
|
||
2 1 465 4.76</code></pre>
|
||
</div>
|
||
</div>
|
||
<p>Most of the patients (95.24%) were censored.</p>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-49-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-50-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> hla.match age.donor age.rec cold.isc death year sex tx.type follow.up
|
||
1 2 25 15 6 0 2002 Female Living 0
|
||
2 1 42 10 11 1 1999 Female Living 0
|
||
3 1 9 14 8 0 2002 Male Living 0
|
||
4 0 35 12 26 0 2002 Male Living 0
|
||
5 2 17 12 28 1 1997 Male Living 0
|
||
6 3 44 13 1 0 2002 Male Cadaveric 0
|
||
7 1 34 12 1 0 2002 Male Cadaveric 0
|
||
8 4 38 11 2 0 2002 Female Cadaveric 0
|
||
9 0 23 10 6 0 2002 Female Living 0
|
||
10 3 26 1 1 0 2002 Male Cadaveric 0
|
||
11 NA 42 18 NA 0 2002 Male Cadaveric 0
|
||
12 4 39 9 NA 0 2002 Female Cadaveric 0
|
||
13 3 34 13 NA 0 2002 Male Cadaveric 0
|
||
14 3 NA 14 2 0 2002 Female Cadaveric 0
|
||
15 3 40 17 1 0 2002 Female Cadaveric 0
|
||
16 3 22 14 2 0 2002 Female Cadaveric 0
|
||
17 0 17 17 12 0 2002 Male Living 0
|
||
18 3 NA 7 NA 0 2002 Male Cadaveric 0
|
||
19 0 4 0 NA 1 2001 Female Living 0
|
||
20 4 NA NA 1 0 2002 Female Cadaveric 0
|
||
21 3 42 18 1 0 2002 Male Cadaveric 0
|
||
22 1 19 15 21 1 1994 Male Living 0
|
||
23 3 44 10 NA 0 2002 Male Cadaveric 0
|
||
24 0 13 14 NA 0 2001 Male Living 0
|
||
25 1 NA 6 1 0 2002 Male Cadaveric 0</code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> hla.match age.donor age.rec cold.isc death year sex tx.type follow.up
|
||
1 2 25 15 6 0 2002 Female Living 0
|
||
2 1 42 10 11 1 1999 Female Living 0
|
||
3 1 9 14 8 0 2002 Male Living 0
|
||
4 0 35 12 26 0 2002 Male Living 0
|
||
5 2 17 12 28 1 1997 Male Living 0
|
||
6 3 44 13 1 0 2002 Male Cadaveric 0</code></pre>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="cox-model---age-as-a-continuous-variable" class="level2" data-number="14.2">
|
||
<h2 data-number="14.2" class="anchored" data-anchor-id="cox-model---age-as-a-continuous-variable"><span class="header-section-number">14.2</span> Cox Model - Age as a Continuous Variable</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb102"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb102-1"><a href="#cb102-1" aria-hidden="true" tabindex="-1"></a>cox.age.rec <span class="ot"><-</span> <span class="fu">coxph</span>(<span class="fu">Surv</span>(follow.up, death) <span class="sc">~</span> age.rec, <span class="at">data =</span> dat)</span>
|
||
<span id="cb102-2"><a href="#cb102-2" aria-hidden="true" tabindex="-1"></a>cox.age.rec <span class="sc">|></span> <span class="fu">summary</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = Surv(follow.up, death) ~ age.rec, data = dat)
|
||
|
||
n= 9766, number of events= 464
|
||
(9 observations deleted due to missingness)
|
||
|
||
coef exp(coef) se(coef) z Pr(>|z|)
|
||
age.rec -0.042550 0.958342 0.008434 -5.045 4.53e-07 ***
|
||
---
|
||
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
|
||
|
||
exp(coef) exp(-coef) lower .95 upper .95
|
||
age.rec 0.9583 1.043 0.9426 0.9743
|
||
|
||
Concordance= 0.586 (se = 0.016 )
|
||
Likelihood ratio test= 24.81 on 1 df, p=6e-07
|
||
Wald test = 25.45 on 1 df, p=5e-07
|
||
Score (logrank) test = 25.75 on 1 df, p=4e-07</code></pre>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="cox-model---age-as-a-categorical-variable" class="level2" data-number="14.3">
|
||
<h2 data-number="14.3" class="anchored" data-anchor-id="cox-model---age-as-a-categorical-variable"><span class="header-section-number">14.3</span> Cox Model - Age as a Categorical Variable</h2>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> chisq df p
|
||
tx.type 2.46 1 0.11654
|
||
age.rec 36.09 1 1.9e-09
|
||
hla.match 8.63 1 0.00331
|
||
age.donor 10.88 1 0.00097
|
||
year 3.96 1 0.04666
|
||
GLOBAL 52.00 5 5.4e-10</code></pre>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-54-1.png" class="img-fluid figure-img" width="960"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-54-2.png" class="img-fluid figure-img" width="960"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-54-3.png" class="img-fluid figure-img" width="960"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-54-4.png" class="img-fluid figure-img" width="960"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-54-5.png" class="img-fluid figure-img" width="960"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-54-6.png" class="img-fluid figure-img" width="960"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="table-1-l" class="level2" data-number="14.4">
|
||
<h2 data-number="14.4" class="anchored" data-anchor-id="table-1-l"><span class="header-section-number">14.4</span> Table 1 (L)</h2>
|
||
<section id="hla-match-hla.match" class="level3" data-number="14.4.1">
|
||
<h3 data-number="14.4.1" class="anchored" data-anchor-id="hla-match-hla.match"><span class="header-section-number">14.4.1</span> HLA match <code>hla.match</code></h3>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>
|
||
0 1 2 3 4 5 6 <NA>
|
||
784 1504 1553 3778 1278 365 279 234 </code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-56-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-57-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="callout callout-style-default callout-warning callout-titled">
|
||
<div class="callout-header d-flex align-content-center">
|
||
<div class="callout-icon-container">
|
||
<i class="callout-icon"></i>
|
||
</div>
|
||
<div class="callout-title-container flex-fill">
|
||
Warning
|
||
</div>
|
||
</div>
|
||
<div class="callout-body-container callout-body">
|
||
<p>TODO: change to percentage within each <code>tx.type</code></p>
|
||
</div>
|
||
</div>
|
||
<div class="callout callout-style-default callout-note callout-titled">
|
||
<div class="callout-header d-flex align-content-center">
|
||
<div class="callout-icon-container">
|
||
<i class="callout-icon"></i>
|
||
</div>
|
||
<div class="callout-title-container flex-fill">
|
||
Note
|
||
</div>
|
||
</div>
|
||
<div class="callout-body-container callout-body">
|
||
<p>Living donors have less <code>hla.match</code> then cadaveric donors</p>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="donor-age-age.donor" class="level3" data-number="14.4.2">
|
||
<h3 data-number="14.4.2" class="anchored" data-anchor-id="donor-age-age.donor"><span class="header-section-number">14.4.2</span> Donor age <code>age.donor</code></h3>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb106"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb106-1"><a href="#cb106-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mean</span>(dat<span class="sc">$</span>age.donor, <span class="at">na.rm =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>[1] 31.29952</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb108"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb108-1"><a href="#cb108-1" aria-hidden="true" tabindex="-1"></a><span class="fu">median</span>(dat<span class="sc">$</span>age.donor, <span class="at">na.rm =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>[1] 33</code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-59-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-60-1.png" class="img-fluid figure-img" width="768"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-61-1.png" class="img-fluid figure-img" width="768"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-62-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-63-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="callout callout-style-default callout-note callout-titled">
|
||
<div class="callout-header d-flex align-content-center">
|
||
<div class="callout-icon-container">
|
||
<i class="callout-icon"></i>
|
||
</div>
|
||
<div class="callout-title-container flex-fill">
|
||
Note
|
||
</div>
|
||
</div>
|
||
<div class="callout-body-container callout-body">
|
||
<p>There is age difference between different <code>tx.type</code></p>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="recipient-age-age.rec" class="level3" data-number="14.4.3">
|
||
<h3 data-number="14.4.3" class="anchored" data-anchor-id="recipient-age-age.rec"><span class="header-section-number">14.4.3</span> Recipient Age <code>age.rec</code></h3>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb110"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb110-1"><a href="#cb110-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mean</span>(dat<span class="sc">$</span>age.rec, <span class="at">na.rm =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>[1] 11.64653</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb112"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb112-1"><a href="#cb112-1" aria-hidden="true" tabindex="-1"></a><span class="fu">median</span>(dat<span class="sc">$</span>age.rec, <span class="at">na.rm =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>[1] 13</code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-65-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-66-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-67-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-68-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-69-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="cold-ischemia-time-cold.isc" class="level3" data-number="14.4.4">
|
||
<h3 data-number="14.4.4" class="anchored" data-anchor-id="cold-ischemia-time-cold.isc"><span class="header-section-number">14.4.4</span> Cold Ischemia Time <code>cold.isc</code></h3>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb114"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb114-1"><a href="#cb114-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mean</span>(dat<span class="sc">$</span>cold.isc, <span class="at">na.rm =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>[1] 10.85967</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb116"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb116-1"><a href="#cb116-1" aria-hidden="true" tabindex="-1"></a><span class="fu">median</span>(dat<span class="sc">$</span>cold.isc, <span class="at">na.rm =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>[1] 7</code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-71-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-72-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-73-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="transplant-type-tx.type" class="level3" data-number="14.4.5">
|
||
<h3 data-number="14.4.5" class="anchored" data-anchor-id="transplant-type-tx.type"><span class="header-section-number">14.4.5</span> Transplant Type <code>tx.type</code></h3>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>
|
||
Cadaveric Living <NA>
|
||
5148 4627 0 </code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb119"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb119-1"><a href="#cb119-1" aria-hidden="true" tabindex="-1"></a>dat<span class="sc">$</span>tx.type <span class="sc">|></span> <span class="fu">table</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>
|
||
Cadaveric Living
|
||
5148 4627 </code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-76-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="year-year" class="level3" data-number="14.4.6">
|
||
<h3 data-number="14.4.6" class="anchored" data-anchor-id="year-year"><span class="header-section-number">14.4.6</span> Year <code>year</code></h3>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>
|
||
1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002
|
||
728 734 666 736 787 813 789 745 740 842 706 834 655 </code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-78-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-79-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-80-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-81-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-82-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</section>
|
||
<section id="kaplan-meier" class="level2" data-number="14.5">
|
||
<h2 data-number="14.5" class="anchored" data-anchor-id="kaplan-meier"><span class="header-section-number">14.5</span> Kaplan-Meier</h2>
|
||
<section id="overall-l" class="level3" data-number="14.5.1">
|
||
<h3 data-number="14.5.1" class="anchored" data-anchor-id="overall-l"><span class="header-section-number">14.5.1</span> Overall (L)</h3>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call: survfit(formula = Surv(follow.up, death) ~ 1, data = dat)
|
||
|
||
time n.risk n.event survival std.err lower 95% CI upper 95% CI
|
||
4 4150 359 0.953 0.00252 0.948 0.958
|
||
8 1197 86 0.919 0.00449 0.910 0.928
|
||
12 48 20 0.888 0.00867 0.871 0.905</code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-84-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="tx.type-m" class="level3" data-number="14.5.2">
|
||
<h3 data-number="14.5.2" class="anchored" data-anchor-id="tx.type-m"><span class="header-section-number">14.5.2</span> <code>tx.type</code> (M)</h3>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-85-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</section>
|
||
<section id="cox-model" class="level2" data-number="14.6">
|
||
<h2 data-number="14.6" class="anchored" data-anchor-id="cox-model"><span class="header-section-number">14.6</span> Cox Model</h2>
|
||
<section id="death-distribution" class="level3" data-number="14.6.1">
|
||
<h3 data-number="14.6.1" class="anchored" data-anchor-id="death-distribution"><span class="header-section-number">14.6.1</span> <code>death</code> Distribution (?)</h3>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-89-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="overall-l-1" class="level3" data-number="14.6.2">
|
||
<h3 data-number="14.6.2" class="anchored" data-anchor-id="overall-l-1"><span class="header-section-number">14.6.2</span> Overall (L)</h3>
|
||
<div class="callout callout-style-default callout-note callout-titled">
|
||
<div class="callout-header d-flex align-content-center">
|
||
<div class="callout-icon-container">
|
||
<i class="callout-icon"></i>
|
||
</div>
|
||
<div class="callout-title-container flex-fill">
|
||
Note
|
||
</div>
|
||
</div>
|
||
<div class="callout-body-container callout-body">
|
||
<p>skip overall, jump directly to <code>tx.type</code></p>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code># A tibble: 7 × 5
|
||
fu.interval n.censored n.event n.at.risk hazard.rate
|
||
<dbl> <int> <int> <dbl> <dbl>
|
||
1 0.333 830 152 9775 0.0155
|
||
2 0.667 491 37 8793 0.00421
|
||
3 1 613 27 8265 0.00327
|
||
4 2 1164 62 7625 0.00813
|
||
5 3 1143 41 6399 0.00641
|
||
6 4 1053 40 5215 0.00767
|
||
7 5 919 31 4122 0.00752</code></pre>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="tx.type-m-1" class="level3" data-number="14.6.3">
|
||
<h3 data-number="14.6.3" class="anchored" data-anchor-id="tx.type-m-1"><span class="header-section-number">14.6.3</span> <code>tx.type</code> (M)</h3>
|
||
</section>
|
||
<section id="age-continuous-l" class="level3" data-number="14.6.4">
|
||
<h3 data-number="14.6.4" class="anchored" data-anchor-id="age-continuous-l"><span class="header-section-number">14.6.4</span> <code>age</code> (continuous) (L)</h3>
|
||
</section>
|
||
<section id="age-categorical-m" class="level3" data-number="14.6.5">
|
||
<h3 data-number="14.6.5" class="anchored" data-anchor-id="age-categorical-m"><span class="header-section-number">14.6.5</span> <code>age</code> (categorical) (M)</h3>
|
||
</section>
|
||
<section id="full-model-l" class="level3" data-number="14.6.6">
|
||
<h3 data-number="14.6.6" class="anchored" data-anchor-id="full-model-l"><span class="header-section-number">14.6.6</span> Full model (L)</h3>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = Surv(follow.up, death) ~ hla.match + tx.type,
|
||
data = dat)
|
||
|
||
n= 9541, number of events= 451
|
||
(234 observations deleted due to missingness)
|
||
|
||
coef exp(coef) se(coef) z Pr(>|z|)
|
||
hla.match -0.12460 0.88285 0.03959 -3.148 0.00165 **
|
||
tx.typeLiving 0.45336 1.57359 0.11146 4.068 4.75e-05 ***
|
||
---
|
||
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
|
||
|
||
exp(coef) exp(-coef) lower .95 upper .95
|
||
hla.match 0.8828 1.1327 0.8169 0.9541
|
||
tx.typeLiving 1.5736 0.6355 1.2648 1.9578
|
||
|
||
Concordance= 0.611 (se = 0.014 )
|
||
Likelihood ratio test= 52.43 on 2 df, p=4e-12
|
||
Wald test = 51.54 on 2 df, p=6e-12
|
||
Score (logrank) test = 53.06 on 2 df, p=3e-12</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = Surv(follow.up, death) ~ hla.match * tx.type,
|
||
data = dat)
|
||
|
||
n= 9541, number of events= 451
|
||
(234 observations deleted due to missingness)
|
||
|
||
coef exp(coef) se(coef) z Pr(>|z|)
|
||
hla.match -0.08577 0.91780 0.07828 -1.096 0.2732
|
||
tx.typeLiving 0.59989 1.82192 0.27919 2.149 0.0317 *
|
||
hla.match:tx.typeLiving -0.05232 0.94902 0.09086 -0.576 0.5647
|
||
---
|
||
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
|
||
|
||
exp(coef) exp(-coef) lower .95 upper .95
|
||
hla.match 0.9178 1.0896 0.7873 1.070
|
||
tx.typeLiving 1.8219 0.5489 1.0541 3.149
|
||
hla.match:tx.typeLiving 0.9490 1.0537 0.7942 1.134
|
||
|
||
Concordance= 0.611 (se = 0.014 )
|
||
Likelihood ratio test= 52.77 on 3 df, p=2e-11
|
||
Wald test = 52.64 on 3 df, p=2e-11
|
||
Score (logrank) test = 54.76 on 3 df, p=8e-12</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Analysis of Deviance Table
|
||
Cox model: response is Surv(follow.up, death)
|
||
Model 1: ~ hla.match + tx.type
|
||
Model 2: ~ hla.match * tx.type
|
||
loglik Chisq Df Pr(>|Chi|)
|
||
1 -3850.6
|
||
2 -3850.5 0.3327 1 0.5641</code></pre>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="discussion-include-year-or-not" class="level3" data-number="14.6.7">
|
||
<h3 data-number="14.6.7" class="anchored" data-anchor-id="discussion-include-year-or-not"><span class="header-section-number">14.6.7</span> Discussion: include <code>year</code> or not?</h3>
|
||
</section>
|
||
</section>
|
||
<section id="assumption-testing" class="level2" data-number="14.7">
|
||
<h2 data-number="14.7" class="anchored" data-anchor-id="assumption-testing"><span class="header-section-number">14.7</span> Assumption Testing</h2>
|
||
<p>## Why Survival Analysis (L)</p>
|
||
<p>Motivation: study the distribution of time to event <span class="math inline">\(T\)</span>.</p>
|
||
<p>Example: time of death after kidney transplant.</p>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div id="xzadzxkzsi" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
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|
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|
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|
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|
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|
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|
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<thead>
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|
||
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|
||
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|
||
<th id="death" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col">Death</th>
|
||
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|
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|
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|
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|
||
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|
||
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|
||
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|
||
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|
||
<tr class="even">
|
||
<td class="gt_row gt_center" headers="id">2</td>
|
||
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|
||
<td class="gt_row gt_center" headers="death">2009</td>
|
||
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|
||
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|
||
<td class="gt_row gt_center" headers="id">3</td>
|
||
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|
||
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|
||
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|
||
<tr class="even">
|
||
<td class="gt_row gt_center" headers="id">4</td>
|
||
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|
||
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|
||
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|
||
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|
||
<td class="gt_row gt_center" headers="id">5</td>
|
||
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|
||
<td class="gt_row gt_center" headers="death">2016</td>
|
||
</tr>
|
||
</tbody>
|
||
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|
||
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-93-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<hr>
|
||
<p>We then calculate time to death for each respondents.</p>
|
||
<p>With this, all we need is to fit a linear model <code>t ~ X</code> or <code>log(t) ~ X</code></p>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
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<div id="dxcaywasew" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
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|
||
margin: 10px;
|
||
border-top-style: solid;
|
||
border-top-width: 1px;
|
||
border-top-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
vertical-align: middle;
|
||
overflow-x: hidden;
|
||
}
|
||
|
||
#dxcaywasew .gt_stub {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
text-transform: inherit;
|
||
border-right-style: solid;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#dxcaywasew .gt_stub_row_group {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
text-transform: inherit;
|
||
border-right-style: solid;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
vertical-align: top;
|
||
}
|
||
|
||
#dxcaywasew .gt_row_group_first td {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#dxcaywasew .gt_row_group_first th {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#dxcaywasew .gt_summary_row {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#dxcaywasew .gt_first_summary_row {
|
||
border-top-style: solid;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#dxcaywasew .gt_first_summary_row.thick {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#dxcaywasew .gt_last_summary_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#dxcaywasew .gt_grand_summary_row {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#dxcaywasew .gt_first_grand_summary_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-top-style: double;
|
||
border-top-width: 6px;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#dxcaywasew .gt_last_grand_summary_row_top {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-style: double;
|
||
border-bottom-width: 6px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#dxcaywasew .gt_striped {
|
||
background-color: rgba(128, 128, 128, 0.05);
|
||
}
|
||
|
||
#dxcaywasew .gt_table_body {
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#dxcaywasew .gt_footnotes {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
border-bottom-style: none;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#dxcaywasew .gt_footnote {
|
||
margin: 0px;
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#dxcaywasew .gt_sourcenotes {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
border-bottom-style: none;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#dxcaywasew .gt_sourcenote {
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#dxcaywasew .gt_left {
|
||
text-align: left;
|
||
}
|
||
|
||
#dxcaywasew .gt_center {
|
||
text-align: center;
|
||
}
|
||
|
||
#dxcaywasew .gt_right {
|
||
text-align: right;
|
||
font-variant-numeric: tabular-nums;
|
||
}
|
||
|
||
#dxcaywasew .gt_font_normal {
|
||
font-weight: normal;
|
||
}
|
||
|
||
#dxcaywasew .gt_font_bold {
|
||
font-weight: bold;
|
||
}
|
||
|
||
#dxcaywasew .gt_font_italic {
|
||
font-style: italic;
|
||
}
|
||
|
||
#dxcaywasew .gt_super {
|
||
font-size: 65%;
|
||
}
|
||
|
||
#dxcaywasew .gt_footnote_marks {
|
||
font-size: 75%;
|
||
vertical-align: 0.4em;
|
||
position: initial;
|
||
}
|
||
|
||
#dxcaywasew .gt_asterisk {
|
||
font-size: 100%;
|
||
vertical-align: 0;
|
||
}
|
||
|
||
#dxcaywasew .gt_indent_1 {
|
||
text-indent: 5px;
|
||
}
|
||
|
||
#dxcaywasew .gt_indent_2 {
|
||
text-indent: 10px;
|
||
}
|
||
|
||
#dxcaywasew .gt_indent_3 {
|
||
text-indent: 15px;
|
||
}
|
||
|
||
#dxcaywasew .gt_indent_4 {
|
||
text-indent: 20px;
|
||
}
|
||
|
||
#dxcaywasew .gt_indent_5 {
|
||
text-indent: 25px;
|
||
}
|
||
|
||
#dxcaywasew .katex-display {
|
||
display: inline-flex !important;
|
||
margin-bottom: 0.75em !important;
|
||
}
|
||
|
||
#dxcaywasew div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after {
|
||
height: 0px !important;
|
||
}
|
||
</style>
|
||
|
||
<table class="gt_table caption-top table table-sm table-striped small" data-quarto-postprocess="true" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
|
||
<thead>
|
||
<tr class="gt_col_headings header">
|
||
<th id="id" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col">ID</th>
|
||
<th id="transplant" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col">Transplant</th>
|
||
<th id="death" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col">Death</th>
|
||
<th id="t" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col">Time to death</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody class="gt_table_body">
|
||
<tr class="odd">
|
||
<td class="gt_row gt_center" headers="id">1</td>
|
||
<td class="gt_row gt_center" headers="transplant">2000</td>
|
||
<td class="gt_row gt_center" headers="death">2005</td>
|
||
<td class="gt_row gt_center" headers="t">5</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_center" headers="id">2</td>
|
||
<td class="gt_row gt_center" headers="transplant">2000</td>
|
||
<td class="gt_row gt_center" headers="death">2009</td>
|
||
<td class="gt_row gt_center" headers="t">9</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_center" headers="id">3</td>
|
||
<td class="gt_row gt_center" headers="transplant">2001</td>
|
||
<td class="gt_row gt_center" headers="death">2005</td>
|
||
<td class="gt_row gt_center" headers="t">4</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_center" headers="id">4</td>
|
||
<td class="gt_row gt_center" headers="transplant">2003</td>
|
||
<td class="gt_row gt_center" headers="death">2004</td>
|
||
<td class="gt_row gt_center" headers="t">1</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_center" headers="id">5</td>
|
||
<td class="gt_row gt_center" headers="transplant">2004</td>
|
||
<td class="gt_row gt_center" headers="death">2016</td>
|
||
<td class="gt_row gt_center" headers="t">12</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-95-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<hr>
|
||
<p>What if we do not know when exactly some respondents die?</p>
|
||
<p>Scenario 1: the study ends at the year 2008?</p>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div id="rrfvqewnmz" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
|
||
<style>#rrfvqewnmz table {
|
||
font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';
|
||
-webkit-font-smoothing: antialiased;
|
||
-moz-osx-font-smoothing: grayscale;
|
||
}
|
||
|
||
#rrfvqewnmz thead, #rrfvqewnmz tbody, #rrfvqewnmz tfoot, #rrfvqewnmz tr, #rrfvqewnmz td, #rrfvqewnmz th {
|
||
border-style: none;
|
||
}
|
||
|
||
#rrfvqewnmz p {
|
||
margin: 0;
|
||
padding: 0;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_table {
|
||
display: table;
|
||
border-collapse: collapse;
|
||
line-height: normal;
|
||
margin-left: auto;
|
||
margin-right: auto;
|
||
color: #333333;
|
||
font-size: 16px;
|
||
font-weight: normal;
|
||
font-style: normal;
|
||
background-color: #FFFFFF;
|
||
width: auto;
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #A8A8A8;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #A8A8A8;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_caption {
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_title {
|
||
color: #333333;
|
||
font-size: 125%;
|
||
font-weight: initial;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-color: #FFFFFF;
|
||
border-bottom-width: 0;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_subtitle {
|
||
color: #333333;
|
||
font-size: 85%;
|
||
font-weight: initial;
|
||
padding-top: 3px;
|
||
padding-bottom: 5px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-top-color: #FFFFFF;
|
||
border-top-width: 0;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_heading {
|
||
background-color: #FFFFFF;
|
||
text-align: center;
|
||
border-bottom-color: #FFFFFF;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_bottom_border {
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_col_headings {
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_col_heading {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: normal;
|
||
text-transform: inherit;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
vertical-align: bottom;
|
||
padding-top: 5px;
|
||
padding-bottom: 6px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
overflow-x: hidden;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_column_spanner_outer {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: normal;
|
||
text-transform: inherit;
|
||
padding-top: 0;
|
||
padding-bottom: 0;
|
||
padding-left: 4px;
|
||
padding-right: 4px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_column_spanner_outer:first-child {
|
||
padding-left: 0;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_column_spanner_outer:last-child {
|
||
padding-right: 0;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_column_spanner {
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
vertical-align: bottom;
|
||
padding-top: 5px;
|
||
padding-bottom: 5px;
|
||
overflow-x: hidden;
|
||
display: inline-block;
|
||
width: 100%;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_spanner_row {
|
||
border-bottom-style: hidden;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_group_heading {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
text-transform: inherit;
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
vertical-align: middle;
|
||
text-align: left;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_empty_group_heading {
|
||
padding: 0.5px;
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
vertical-align: middle;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_from_md > :first-child {
|
||
margin-top: 0;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_from_md > :last-child {
|
||
margin-bottom: 0;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
margin: 10px;
|
||
border-top-style: solid;
|
||
border-top-width: 1px;
|
||
border-top-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
vertical-align: middle;
|
||
overflow-x: hidden;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_stub {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
text-transform: inherit;
|
||
border-right-style: solid;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_stub_row_group {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
text-transform: inherit;
|
||
border-right-style: solid;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
vertical-align: top;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_row_group_first td {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_row_group_first th {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_summary_row {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_first_summary_row {
|
||
border-top-style: solid;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_first_summary_row.thick {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_last_summary_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_grand_summary_row {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_first_grand_summary_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-top-style: double;
|
||
border-top-width: 6px;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_last_grand_summary_row_top {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-style: double;
|
||
border-bottom-width: 6px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_striped {
|
||
background-color: rgba(128, 128, 128, 0.05);
|
||
}
|
||
|
||
#rrfvqewnmz .gt_table_body {
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_footnotes {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
border-bottom-style: none;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_footnote {
|
||
margin: 0px;
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_sourcenotes {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
border-bottom-style: none;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_sourcenote {
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_left {
|
||
text-align: left;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_center {
|
||
text-align: center;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_right {
|
||
text-align: right;
|
||
font-variant-numeric: tabular-nums;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_font_normal {
|
||
font-weight: normal;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_font_bold {
|
||
font-weight: bold;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_font_italic {
|
||
font-style: italic;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_super {
|
||
font-size: 65%;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_footnote_marks {
|
||
font-size: 75%;
|
||
vertical-align: 0.4em;
|
||
position: initial;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_asterisk {
|
||
font-size: 100%;
|
||
vertical-align: 0;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_indent_1 {
|
||
text-indent: 5px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_indent_2 {
|
||
text-indent: 10px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_indent_3 {
|
||
text-indent: 15px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_indent_4 {
|
||
text-indent: 20px;
|
||
}
|
||
|
||
#rrfvqewnmz .gt_indent_5 {
|
||
text-indent: 25px;
|
||
}
|
||
|
||
#rrfvqewnmz .katex-display {
|
||
display: inline-flex !important;
|
||
margin-bottom: 0.75em !important;
|
||
}
|
||
|
||
#rrfvqewnmz div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after {
|
||
height: 0px !important;
|
||
}
|
||
</style>
|
||
|
||
<table class="gt_table caption-top table table-sm table-striped small" data-quarto-postprocess="true" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
|
||
<thead>
|
||
<tr class="gt_col_headings header">
|
||
<th id="id" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col">ID</th>
|
||
<th id="transplant" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col">Transplant</th>
|
||
<th id="death_censored_txt" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col">Death</th>
|
||
<th id="t_1_txt" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col">Time to death</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody class="gt_table_body">
|
||
<tr class="odd">
|
||
<td class="gt_row gt_center" headers="id">1</td>
|
||
<td class="gt_row gt_center" headers="transplant">2000</td>
|
||
<td class="gt_row gt_center" headers="death_censored_txt">2005</td>
|
||
<td class="gt_row gt_center" headers="t_1_txt">5</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_center" headers="id">2</td>
|
||
<td class="gt_row gt_center" headers="transplant">2000</td>
|
||
<td class="gt_row gt_center" headers="death_censored_txt">> 2008</td>
|
||
<td class="gt_row gt_center" headers="t_1_txt">> 8</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_center" headers="id">3</td>
|
||
<td class="gt_row gt_center" headers="transplant">2001</td>
|
||
<td class="gt_row gt_center" headers="death_censored_txt">2005</td>
|
||
<td class="gt_row gt_center" headers="t_1_txt">4</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_center" headers="id">4</td>
|
||
<td class="gt_row gt_center" headers="transplant">2003</td>
|
||
<td class="gt_row gt_center" headers="death_censored_txt">2004</td>
|
||
<td class="gt_row gt_center" headers="t_1_txt">1</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_center" headers="id">5</td>
|
||
<td class="gt_row gt_center" headers="transplant">2004</td>
|
||
<td class="gt_row gt_center" headers="death_censored_txt">> 2008</td>
|
||
<td class="gt_row gt_center" headers="t_1_txt">> 4</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-98-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-98-2.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<p><strong>Right Censoring</strong>: only observe the event (death) if it occurs before a certain time (2008).</p>
|
||
<hr>
|
||
<p>Scenario 2: respondent 3 move away; loss follow up</p>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div id="jhpcdeabse" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
|
||
<style>#jhpcdeabse table {
|
||
font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';
|
||
-webkit-font-smoothing: antialiased;
|
||
-moz-osx-font-smoothing: grayscale;
|
||
}
|
||
|
||
#jhpcdeabse thead, #jhpcdeabse tbody, #jhpcdeabse tfoot, #jhpcdeabse tr, #jhpcdeabse td, #jhpcdeabse th {
|
||
border-style: none;
|
||
}
|
||
|
||
#jhpcdeabse p {
|
||
margin: 0;
|
||
padding: 0;
|
||
}
|
||
|
||
#jhpcdeabse .gt_table {
|
||
display: table;
|
||
border-collapse: collapse;
|
||
line-height: normal;
|
||
margin-left: auto;
|
||
margin-right: auto;
|
||
color: #333333;
|
||
font-size: 16px;
|
||
font-weight: normal;
|
||
font-style: normal;
|
||
background-color: #FFFFFF;
|
||
width: auto;
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #A8A8A8;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #A8A8A8;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
}
|
||
|
||
#jhpcdeabse .gt_caption {
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
}
|
||
|
||
#jhpcdeabse .gt_title {
|
||
color: #333333;
|
||
font-size: 125%;
|
||
font-weight: initial;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-color: #FFFFFF;
|
||
border-bottom-width: 0;
|
||
}
|
||
|
||
#jhpcdeabse .gt_subtitle {
|
||
color: #333333;
|
||
font-size: 85%;
|
||
font-weight: initial;
|
||
padding-top: 3px;
|
||
padding-bottom: 5px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-top-color: #FFFFFF;
|
||
border-top-width: 0;
|
||
}
|
||
|
||
#jhpcdeabse .gt_heading {
|
||
background-color: #FFFFFF;
|
||
text-align: center;
|
||
border-bottom-color: #FFFFFF;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#jhpcdeabse .gt_bottom_border {
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#jhpcdeabse .gt_col_headings {
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#jhpcdeabse .gt_col_heading {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: normal;
|
||
text-transform: inherit;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
vertical-align: bottom;
|
||
padding-top: 5px;
|
||
padding-bottom: 6px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
overflow-x: hidden;
|
||
}
|
||
|
||
#jhpcdeabse .gt_column_spanner_outer {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: normal;
|
||
text-transform: inherit;
|
||
padding-top: 0;
|
||
padding-bottom: 0;
|
||
padding-left: 4px;
|
||
padding-right: 4px;
|
||
}
|
||
|
||
#jhpcdeabse .gt_column_spanner_outer:first-child {
|
||
padding-left: 0;
|
||
}
|
||
|
||
#jhpcdeabse .gt_column_spanner_outer:last-child {
|
||
padding-right: 0;
|
||
}
|
||
|
||
#jhpcdeabse .gt_column_spanner {
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
vertical-align: bottom;
|
||
padding-top: 5px;
|
||
padding-bottom: 5px;
|
||
overflow-x: hidden;
|
||
display: inline-block;
|
||
width: 100%;
|
||
}
|
||
|
||
#jhpcdeabse .gt_spanner_row {
|
||
border-bottom-style: hidden;
|
||
}
|
||
|
||
#jhpcdeabse .gt_group_heading {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
text-transform: inherit;
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
vertical-align: middle;
|
||
text-align: left;
|
||
}
|
||
|
||
#jhpcdeabse .gt_empty_group_heading {
|
||
padding: 0.5px;
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
font-size: 100%;
|
||
font-weight: initial;
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
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|
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||
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|
||
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<th id="t_1_txt" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col">Time to death</th>
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|
||
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|
||
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|
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|
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|
||
<td class="gt_row gt_center" headers="transplant">2000</td>
|
||
<td class="gt_row gt_center" headers="death_censored_txt">> 2008</td>
|
||
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|
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|
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|
||
<td class="gt_row gt_center" headers="death_censored_txt">> 2005</td>
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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<p><img src="slides_files/figure-html/unnamed-chunk-100-2.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
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|
||
</div>
|
||
</div>
|
||
<hr>
|
||
<p>How many patients are right censored?</p>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
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<div>
|
||
<figure class="figure">
|
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<p><img src="slides_files/figure-html/unnamed-chunk-101-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
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|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="challenges-in-survival-analysis-l" class="level2" data-number="14.8">
|
||
<h2 data-number="14.8" class="anchored" data-anchor-id="challenges-in-survival-analysis-l"><span class="header-section-number">14.8</span> Challenges in Survival Analysis (L)</h2>
|
||
<ul>
|
||
<li><strong>Right Censoring</strong>: only observe the event if it occurs before a certain time.</li>
|
||
<li><strong>Left Censoring</strong>: event has occurred prior to the start of a research
|
||
<ul>
|
||
<li>Follow up every 3 years.</li>
|
||
<li>Event has occurred -> event happened sometime before follow up.</li>
|
||
</ul></li>
|
||
<li><strong>Left Truncation</strong>: delayed entry; respondents are included only if they survived long enough.
|
||
<ul>
|
||
<li>Start follow up with patients 100 days after the transplant</li>
|
||
<li>Patients dies within 100 day wouldn’t be included in the dataset</li>
|
||
</ul></li>
|
||
<li><strong>Right Truncation</strong>: respondents are included only if they have already experienced the event.
|
||
<ul>
|
||
<li>Retrospective analysis from deceased patients between 1990 and 2000.</li>
|
||
<li>Patients not dead before 2000 are not included in the dataset.</li>
|
||
</ul></li>
|
||
</ul>
|
||
</section></details>
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|
||
}
|
||
}
|
||
stripColumnClz(note)
|
||
if (id === null || id.startsWith('sec-')) {
|
||
// Special case sections, only their first couple elements
|
||
const container = document.createElement("div");
|
||
if (note.children && note.children.length > 2) {
|
||
container.appendChild(note.children[0].cloneNode(true));
|
||
for (let i = 1; i < note.children.length; i++) {
|
||
const child = note.children[i];
|
||
if (child.tagName === "P" && child.innerText === "") {
|
||
continue;
|
||
} else {
|
||
container.appendChild(child.cloneNode(true));
|
||
break;
|
||
}
|
||
}
|
||
if (window.Quarto?.typesetMath) {
|
||
window.Quarto.typesetMath(container);
|
||
}
|
||
return container.innerHTML
|
||
} else {
|
||
if (window.Quarto?.typesetMath) {
|
||
window.Quarto.typesetMath(note);
|
||
}
|
||
return note.innerHTML;
|
||
}
|
||
} else {
|
||
// Remove any anchor links if they are present
|
||
const anchorLink = note.querySelector('a.anchorjs-link');
|
||
if (anchorLink) {
|
||
anchorLink.remove();
|
||
}
|
||
if (window.Quarto?.typesetMath) {
|
||
window.Quarto.typesetMath(note);
|
||
}
|
||
if (note.classList.contains("callout")) {
|
||
return note.outerHTML;
|
||
} else {
|
||
return note.innerHTML;
|
||
}
|
||
}
|
||
}
|
||
for (var i=0; i<xrefs.length; i++) {
|
||
const xref = xrefs[i];
|
||
tippyHover(xref, undefined, function(instance) {
|
||
instance.disable();
|
||
let url = xref.getAttribute('href');
|
||
let hash = undefined;
|
||
if (url.startsWith('#')) {
|
||
hash = url;
|
||
} else {
|
||
try { hash = new URL(url).hash; } catch {}
|
||
}
|
||
if (hash) {
|
||
const id = hash.replace(/^#\/?/, "");
|
||
const note = window.document.getElementById(id);
|
||
if (note !== null) {
|
||
try {
|
||
const html = processXRef(id, note.cloneNode(true));
|
||
instance.setContent(html);
|
||
} finally {
|
||
instance.enable();
|
||
instance.show();
|
||
}
|
||
} else {
|
||
// See if we can fetch this
|
||
fetch(url.split('#')[0])
|
||
.then(res => res.text())
|
||
.then(html => {
|
||
const parser = new DOMParser();
|
||
const htmlDoc = parser.parseFromString(html, "text/html");
|
||
const note = htmlDoc.getElementById(id);
|
||
if (note !== null) {
|
||
const html = processXRef(id, note);
|
||
instance.setContent(html);
|
||
}
|
||
}).finally(() => {
|
||
instance.enable();
|
||
instance.show();
|
||
});
|
||
}
|
||
} else {
|
||
// See if we can fetch a full url (with no hash to target)
|
||
// This is a special case and we should probably do some content thinning / targeting
|
||
fetch(url)
|
||
.then(res => res.text())
|
||
.then(html => {
|
||
const parser = new DOMParser();
|
||
const htmlDoc = parser.parseFromString(html, "text/html");
|
||
const note = htmlDoc.querySelector('main.content');
|
||
if (note !== null) {
|
||
// This should only happen for chapter cross references
|
||
// (since there is no id in the URL)
|
||
// remove the first header
|
||
if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
|
||
note.children[0].remove();
|
||
}
|
||
const html = processXRef(null, note);
|
||
instance.setContent(html);
|
||
}
|
||
}).finally(() => {
|
||
instance.enable();
|
||
instance.show();
|
||
});
|
||
}
|
||
}, function(instance) {
|
||
});
|
||
}
|
||
let selectedAnnoteEl;
|
||
const selectorForAnnotation = ( cell, annotation) => {
|
||
let cellAttr = 'data-code-cell="' + cell + '"';
|
||
let lineAttr = 'data-code-annotation="' + annotation + '"';
|
||
const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
|
||
return selector;
|
||
}
|
||
const selectCodeLines = (annoteEl) => {
|
||
const doc = window.document;
|
||
const targetCell = annoteEl.getAttribute("data-target-cell");
|
||
const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
|
||
const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
|
||
const lines = annoteSpan.getAttribute("data-code-lines").split(",");
|
||
const lineIds = lines.map((line) => {
|
||
return targetCell + "-" + line;
|
||
})
|
||
let top = null;
|
||
let height = null;
|
||
let parent = null;
|
||
if (lineIds.length > 0) {
|
||
//compute the position of the single el (top and bottom and make a div)
|
||
const el = window.document.getElementById(lineIds[0]);
|
||
top = el.offsetTop;
|
||
height = el.offsetHeight;
|
||
parent = el.parentElement.parentElement;
|
||
if (lineIds.length > 1) {
|
||
const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
|
||
const bottom = lastEl.offsetTop + lastEl.offsetHeight;
|
||
height = bottom - top;
|
||
}
|
||
if (top !== null && height !== null && parent !== null) {
|
||
// cook up a div (if necessary) and position it
|
||
let div = window.document.getElementById("code-annotation-line-highlight");
|
||
if (div === null) {
|
||
div = window.document.createElement("div");
|
||
div.setAttribute("id", "code-annotation-line-highlight");
|
||
div.style.position = 'absolute';
|
||
parent.appendChild(div);
|
||
}
|
||
div.style.top = top - 2 + "px";
|
||
div.style.height = height + 4 + "px";
|
||
div.style.left = 0;
|
||
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
|
||
if (gutterDiv === null) {
|
||
gutterDiv = window.document.createElement("div");
|
||
gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
|
||
gutterDiv.style.position = 'absolute';
|
||
const codeCell = window.document.getElementById(targetCell);
|
||
const gutter = codeCell.querySelector('.code-annotation-gutter');
|
||
gutter.appendChild(gutterDiv);
|
||
}
|
||
gutterDiv.style.top = top - 2 + "px";
|
||
gutterDiv.style.height = height + 4 + "px";
|
||
}
|
||
selectedAnnoteEl = annoteEl;
|
||
}
|
||
};
|
||
const unselectCodeLines = () => {
|
||
const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
|
||
elementsIds.forEach((elId) => {
|
||
const div = window.document.getElementById(elId);
|
||
if (div) {
|
||
div.remove();
|
||
}
|
||
});
|
||
selectedAnnoteEl = undefined;
|
||
};
|
||
// Handle positioning of the toggle
|
||
window.addEventListener(
|
||
"resize",
|
||
throttle(() => {
|
||
elRect = undefined;
|
||
if (selectedAnnoteEl) {
|
||
selectCodeLines(selectedAnnoteEl);
|
||
}
|
||
}, 10)
|
||
);
|
||
function throttle(fn, ms) {
|
||
let throttle = false;
|
||
let timer;
|
||
return (...args) => {
|
||
if(!throttle) { // first call gets through
|
||
fn.apply(this, args);
|
||
throttle = true;
|
||
} else { // all the others get throttled
|
||
if(timer) clearTimeout(timer); // cancel #2
|
||
timer = setTimeout(() => {
|
||
fn.apply(this, args);
|
||
timer = throttle = false;
|
||
}, ms);
|
||
}
|
||
};
|
||
}
|
||
// Attach click handler to the DT
|
||
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
|
||
for (const annoteDlNode of annoteDls) {
|
||
annoteDlNode.addEventListener('click', (event) => {
|
||
const clickedEl = event.target;
|
||
if (clickedEl !== selectedAnnoteEl) {
|
||
unselectCodeLines();
|
||
const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
|
||
if (activeEl) {
|
||
activeEl.classList.remove('code-annotation-active');
|
||
}
|
||
selectCodeLines(clickedEl);
|
||
clickedEl.classList.add('code-annotation-active');
|
||
} else {
|
||
// Unselect the line
|
||
unselectCodeLines();
|
||
clickedEl.classList.remove('code-annotation-active');
|
||
}
|
||
});
|
||
}
|
||
const findCites = (el) => {
|
||
const parentEl = el.parentElement;
|
||
if (parentEl) {
|
||
const cites = parentEl.dataset.cites;
|
||
if (cites) {
|
||
return {
|
||
el,
|
||
cites: cites.split(' ')
|
||
};
|
||
} else {
|
||
return findCites(el.parentElement)
|
||
}
|
||
} else {
|
||
return undefined;
|
||
}
|
||
};
|
||
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
|
||
for (var i=0; i<bibliorefs.length; i++) {
|
||
const ref = bibliorefs[i];
|
||
const citeInfo = findCites(ref);
|
||
if (citeInfo) {
|
||
tippyHover(citeInfo.el, function() {
|
||
var popup = window.document.createElement('div');
|
||
citeInfo.cites.forEach(function(cite) {
|
||
var citeDiv = window.document.createElement('div');
|
||
citeDiv.classList.add('hanging-indent');
|
||
citeDiv.classList.add('csl-entry');
|
||
var biblioDiv = window.document.getElementById('ref-' + cite);
|
||
if (biblioDiv) {
|
||
citeDiv.innerHTML = biblioDiv.innerHTML;
|
||
}
|
||
popup.appendChild(citeDiv);
|
||
});
|
||
return popup.innerHTML;
|
||
});
|
||
}
|
||
}
|
||
});
|
||
</script>
|
||
</div> <!-- /content -->
|
||
|
||
|
||
|
||
|
||
</body></html> |