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<h2 id="toc-title">Table of contents</h2>
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<ul>
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<li><a href="#title" id="toc-title" class="nav-link active" data-scroll-target="#title"><span class="header-section-number">1</span> Title</a></li>
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<li><a href="#table-of-contents" id="toc-table-of-contents" class="nav-link" data-scroll-target="#table-of-contents"><span class="header-section-number">2</span> Table of Contents</a></li>
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<li><a href="#introduction" id="toc-introduction" class="nav-link" data-scroll-target="#introduction"><span class="header-section-number">3</span> Introduction</a></li>
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<li><a href="#method-result" id="toc-method-result" class="nav-link" data-scroll-target="#method-result"><span class="header-section-number">4</span> Method & Result</a>
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<ul class="collapse">
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<li><a href="#identify-predictors-m" id="toc-identify-predictors-m" class="nav-link" data-scroll-target="#identify-predictors-m"><span class="header-section-number">4.1</span> Identify Predictors (M)</a></li>
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<li><a href="#table-l" id="toc-table-l" class="nav-link" data-scroll-target="#table-l"><span class="header-section-number">4.2</span> Table (L)</a></li>
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</ul></li>
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<li><a href="#table-1-by-transplant-type" id="toc-table-1-by-transplant-type" class="nav-link" data-scroll-target="#table-1-by-transplant-type"><span class="header-section-number">5</span> Table 1: By Transplant Type</a>
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<ul class="collapse">
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<li><a href="#transplant-type-vs-sex" id="toc-transplant-type-vs-sex" class="nav-link" data-scroll-target="#transplant-type-vs-sex"><span class="header-section-number">5.1</span> Transplant Type vs Sex</a></li>
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<li><a href="#transplant-type-vs-recipient-age" id="toc-transplant-type-vs-recipient-age" class="nav-link" data-scroll-target="#transplant-type-vs-recipient-age"><span class="header-section-number">5.2</span> Transplant Type vs Recipient Age</a></li>
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</ul></li>
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<li><a href="#table-1-by-transplant-type-1" id="toc-table-1-by-transplant-type-1" class="nav-link" data-scroll-target="#table-1-by-transplant-type-1"><span class="header-section-number">6</span> Table 1: By Transplant Type</a>
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<ul class="collapse">
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<li><a href="#transplant-type-vs-hla-match" id="toc-transplant-type-vs-hla-match" class="nav-link" data-scroll-target="#transplant-type-vs-hla-match"><span class="header-section-number">6.1</span> Transplant Type vs HLA Match</a></li>
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<li><a href="#transplant-type-vs-donor-age" id="toc-transplant-type-vs-donor-age" class="nav-link" data-scroll-target="#transplant-type-vs-donor-age"><span class="header-section-number">6.2</span> Transplant Type vs Donor Age</a></li>
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||
</ul></li>
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<li><a href="#overall-survival" id="toc-overall-survival" class="nav-link" data-scroll-target="#overall-survival"><span class="header-section-number">7</span> Overall Survival</a></li>
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||
<li><a href="#hazard-by-transplant-type" id="toc-hazard-by-transplant-type" class="nav-link" data-scroll-target="#hazard-by-transplant-type"><span class="header-section-number">8</span> Hazard by Transplant Type</a>
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||
<ul class="collapse">
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||
<li><a href="#death-distribution" id="toc-death-distribution" class="nav-link" data-scroll-target="#death-distribution"><span class="header-section-number">8.1</span> Death distribution</a></li>
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||
</ul></li>
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||
<li><a href="#hazard-rate-by-transplant-type" id="toc-hazard-rate-by-transplant-type" class="nav-link" data-scroll-target="#hazard-rate-by-transplant-type"><span class="header-section-number">9</span> Hazard Rate by Transplant Type</a></li>
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||
<li><a href="#cox-model-transplant-type" id="toc-cox-model-transplant-type" class="nav-link" data-scroll-target="#cox-model-transplant-type"><span class="header-section-number">10</span> Cox Model: Transplant Type</a></li>
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||
<li><a href="#cox-model-age-recipient-continuous" id="toc-cox-model-age-recipient-continuous" class="nav-link" data-scroll-target="#cox-model-age-recipient-continuous"><span class="header-section-number">11</span> Cox Model: Age Recipient (Continuous)</a></li>
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||
<li><a href="#cox-model-age-recipient-categorical" id="toc-cox-model-age-recipient-categorical" class="nav-link" data-scroll-target="#cox-model-age-recipient-categorical"><span class="header-section-number">12</span> Cox Model: Age Recipient (Categorical)</a></li>
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||
<li><a href="#cox-model-age-recipient-categorical-1" id="toc-cox-model-age-recipient-categorical-1" class="nav-link" data-scroll-target="#cox-model-age-recipient-categorical-1"><span class="header-section-number">13</span> Cox Model: Age Recipient (Categorical)</a></li>
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||
<li><a href="#identifying-predictors" id="toc-identifying-predictors" class="nav-link" data-scroll-target="#identifying-predictors"><span class="header-section-number">14</span> Identifying Predictors</a>
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<ul class="collapse">
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||
<li><a href="#start-with-nothing" id="toc-start-with-nothing" class="nav-link" data-scroll-target="#start-with-nothing"><span class="header-section-number">14.1</span> Start with nothing</a></li>
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||
<li><a href="#tx.type" id="toc-tx.type" class="nav-link" data-scroll-target="#tx.type"><span class="header-section-number">14.2</span> <code>tx.type</code> + ?</a></li>
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||
<li><a href="#tx.type-age.rec" id="toc-tx.type-age.rec" class="nav-link" data-scroll-target="#tx.type-age.rec"><span class="header-section-number">14.3</span> <code>tx.type</code> + <code>age.rec</code> + ?</a></li>
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<li><a href="#tx.type-age.rec-age.donor" id="toc-tx.type-age.rec-age.donor" class="nav-link" data-scroll-target="#tx.type-age.rec-age.donor"><span class="header-section-number">14.4</span> <code>tx.type</code> + <code>age.rec</code> + <code>age.donor</code> + ?</a></li>
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<li><a href="#tx.type-age.rec-age.donor-year" id="toc-tx.type-age.rec-age.donor-year" class="nav-link" data-scroll-target="#tx.type-age.rec-age.donor-year"><span class="header-section-number">14.5</span> <code>tx.type</code> + <code>age.rec</code> + <code>age.donor</code> + <code>year</code> + ?</a></li>
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||
<li><a href="#tx.type-age.rec-age.donor-year-hla.match" id="toc-tx.type-age.rec-age.donor-year-hla.match" class="nav-link" data-scroll-target="#tx.type-age.rec-age.donor-year-hla.match"><span class="header-section-number">14.6</span> <code>tx.type</code> + <code>age.rec</code> + <code>age.donor</code> + <code>year</code> + <code>hla.match</code> + ?</a></li>
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||
</ul></li>
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||
<li><a href="#full-model" id="toc-full-model" class="nav-link" data-scroll-target="#full-model"><span class="header-section-number">15</span> Full Model</a></li>
|
||
<li><a href="#proportional-hazards-assumption" id="toc-proportional-hazards-assumption" class="nav-link" data-scroll-target="#proportional-hazards-assumption"><span class="header-section-number">16</span> Proportional hazards assumption</a>
|
||
<ul class="collapse">
|
||
<li><a href="#what-happened-to-year" id="toc-what-happened-to-year" class="nav-link" data-scroll-target="#what-happened-to-year"><span class="header-section-number">16.1</span> What happened to <code>year</code>?</a></li>
|
||
<li><a href="#without-year" id="toc-without-year" class="nav-link" data-scroll-target="#without-year"><span class="header-section-number">16.2</span> Without <code>year</code></a></li>
|
||
</ul></li>
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<li><a href="#old" id="toc-old" class="nav-link" data-scroll-target="#old"><span class="header-section-number">17</span> Old</a>
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<ul class="collapse">
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<li><a href="#death-censored" id="toc-death-censored" class="nav-link" data-scroll-target="#death-censored"><span class="header-section-number">17.1</span> Death & Censored</a></li>
|
||
<li><a href="#cox-model---age-as-a-continuous-variable" id="toc-cox-model---age-as-a-continuous-variable" class="nav-link" data-scroll-target="#cox-model---age-as-a-continuous-variable"><span class="header-section-number">17.2</span> Cox Model - Age as a Continuous Variable</a></li>
|
||
<li><a href="#cox-model---age-as-a-categorical-variable" id="toc-cox-model---age-as-a-categorical-variable" class="nav-link" data-scroll-target="#cox-model---age-as-a-categorical-variable"><span class="header-section-number">17.3</span> Cox Model - Age as a Categorical Variable</a></li>
|
||
<li><a href="#table-1-l" id="toc-table-1-l" class="nav-link" data-scroll-target="#table-1-l"><span class="header-section-number">17.4</span> Table 1 (L)</a>
|
||
<ul class="collapse">
|
||
<li><a href="#hla-match-hla.match" id="toc-hla-match-hla.match" class="nav-link" data-scroll-target="#hla-match-hla.match"><span class="header-section-number">17.4.1</span> HLA match <code>hla.match</code></a></li>
|
||
<li><a href="#donor-age-age.donor" id="toc-donor-age-age.donor" class="nav-link" data-scroll-target="#donor-age-age.donor"><span class="header-section-number">17.4.2</span> Donor age <code>age.donor</code></a></li>
|
||
<li><a href="#recipient-age-age.rec" id="toc-recipient-age-age.rec" class="nav-link" data-scroll-target="#recipient-age-age.rec"><span class="header-section-number">17.4.3</span> Recipient Age <code>age.rec</code></a></li>
|
||
<li><a href="#cold-ischemia-time-cold.isc" id="toc-cold-ischemia-time-cold.isc" class="nav-link" data-scroll-target="#cold-ischemia-time-cold.isc"><span class="header-section-number">17.4.4</span> Cold Ischemia Time <code>cold.isc</code></a></li>
|
||
<li><a href="#transplant-type-tx.type" id="toc-transplant-type-tx.type" class="nav-link" data-scroll-target="#transplant-type-tx.type"><span class="header-section-number">17.4.5</span> Transplant Type <code>tx.type</code></a></li>
|
||
<li><a href="#year-year" id="toc-year-year" class="nav-link" data-scroll-target="#year-year"><span class="header-section-number">17.4.6</span> Year <code>year</code></a></li>
|
||
</ul></li>
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||
<li><a href="#kaplan-meier" id="toc-kaplan-meier" class="nav-link" data-scroll-target="#kaplan-meier"><span class="header-section-number">17.5</span> Kaplan-Meier</a>
|
||
<ul class="collapse">
|
||
<li><a href="#overall-l" id="toc-overall-l" class="nav-link" data-scroll-target="#overall-l"><span class="header-section-number">17.5.1</span> Overall (L)</a></li>
|
||
<li><a href="#tx.type-m" id="toc-tx.type-m" class="nav-link" data-scroll-target="#tx.type-m"><span class="header-section-number">17.5.2</span> <code>tx.type</code> (M)</a></li>
|
||
</ul></li>
|
||
<li><a href="#cox-model" id="toc-cox-model" class="nav-link" data-scroll-target="#cox-model"><span class="header-section-number">17.6</span> Cox Model</a>
|
||
<ul class="collapse">
|
||
<li><a href="#death-distribution-1" id="toc-death-distribution-1" class="nav-link" data-scroll-target="#death-distribution-1"><span class="header-section-number">17.6.1</span> <code>death</code> Distribution (?)</a></li>
|
||
<li><a href="#overall-l-1" id="toc-overall-l-1" class="nav-link" data-scroll-target="#overall-l-1"><span class="header-section-number">17.6.2</span> Overall (L)</a></li>
|
||
<li><a href="#tx.type-m-1" id="toc-tx.type-m-1" class="nav-link" data-scroll-target="#tx.type-m-1"><span class="header-section-number">17.6.3</span> <code>tx.type</code> (M)</a></li>
|
||
<li><a href="#age-continuous-l" id="toc-age-continuous-l" class="nav-link" data-scroll-target="#age-continuous-l"><span class="header-section-number">17.6.4</span> <code>age</code> (continuous) (L)</a></li>
|
||
<li><a href="#age-categorical-m" id="toc-age-categorical-m" class="nav-link" data-scroll-target="#age-categorical-m"><span class="header-section-number">17.6.5</span> <code>age</code> (categorical) (M)</a></li>
|
||
<li><a href="#full-model-l" id="toc-full-model-l" class="nav-link" data-scroll-target="#full-model-l"><span class="header-section-number">17.6.6</span> Full model (L)</a></li>
|
||
<li><a href="#discussion-include-year-or-not" id="toc-discussion-include-year-or-not" class="nav-link" data-scroll-target="#discussion-include-year-or-not"><span class="header-section-number">17.6.7</span> Discussion: include <code>year</code> or not?</a></li>
|
||
</ul></li>
|
||
<li><a href="#assumption-testing" id="toc-assumption-testing" class="nav-link" data-scroll-target="#assumption-testing"><span class="header-section-number">17.7</span> Assumption Testing</a></li>
|
||
<li><a href="#challenges-in-survival-analysis-l" id="toc-challenges-in-survival-analysis-l" class="nav-link" data-scroll-target="#challenges-in-survival-analysis-l"><span class="header-section-number">17.8</span> Challenges in Survival Analysis (L)</a></li>
|
||
</ul></li>
|
||
</ul>
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</nav>
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</div>
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<main class="content" id="quarto-document-content">
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<header id="title-block-header" class="quarto-title-block default">
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<div class="quarto-title">
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<h1 class="title">Slides</h1>
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</div>
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</header>
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<section id="title" class="level1" data-number="1">
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<h1 data-number="1"><span class="header-section-number">1</span> Title</h1>
|
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</section>
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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" class="level1" data-number="3">
|
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<h1 data-number="3"><span class="header-section-number">3</span> Introduction</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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</ul>
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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><span class="fu">nrow</span>(dat)</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>[1] 9775</code></pre>
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</div>
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<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">range</span>(dat<span class="sc">$</span>year)</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">
|
||
<pre><code>[1] 1990 2002</code></pre>
|
||
</div>
|
||
</div>
|
||
<ul>
|
||
<li>Covariates</li>
|
||
<li>Outcome</li>
|
||
</ul>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>[1] "hla.match" "age.donor" "age.rec" "cold.isc" "death" "year"
|
||
[7] "sex" "tx.type" "follow.up"</code></pre>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="table-l" class="level2" data-number="4.2">
|
||
<h2 data-number="4.2" class="anchored" data-anchor-id="table-l"><span class="header-section-number">4.2</span> Table (L)</h2>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div id="ifllbkegxd" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
|
||
<style>#ifllbkegxd 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;
|
||
}
|
||
|
||
#ifllbkegxd thead, #ifllbkegxd tbody, #ifllbkegxd tfoot, #ifllbkegxd tr, #ifllbkegxd td, #ifllbkegxd th {
|
||
border-style: none;
|
||
}
|
||
|
||
#ifllbkegxd p {
|
||
margin: 0;
|
||
padding: 0;
|
||
}
|
||
|
||
#ifllbkegxd .gt_table {
|
||
display: table;
|
||
border-collapse: collapse;
|
||
line-height: normal;
|
||
margin-left: auto;
|
||
margin-right: auto;
|
||
color: #333333;
|
||
font-size: 18px;
|
||
font-weight: normal;
|
||
font-style: normal;
|
||
background-color: #F8EFCB;
|
||
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;
|
||
}
|
||
|
||
#ifllbkegxd .gt_caption {
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
}
|
||
|
||
#ifllbkegxd .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: #F8EFCB;
|
||
border-bottom-width: 0;
|
||
}
|
||
|
||
#ifllbkegxd .gt_subtitle {
|
||
color: #333333;
|
||
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|
||
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|
||
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|
||
padding-bottom: 5px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-top-color: #F8EFCB;
|
||
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|
||
}
|
||
|
||
#ifllbkegxd .gt_heading {
|
||
background-color: #F8EFCB;
|
||
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|
||
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|
||
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|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
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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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|
||
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|
||
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|
||
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;
|
||
}
|
||
|
||
#ifllbkegxd .gt_col_heading {
|
||
color: #333333;
|
||
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|
||
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|
||
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|
||
text-transform: inherit;
|
||
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|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
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|
||
padding-top: 5px;
|
||
padding-bottom: 6px;
|
||
padding-left: 5px;
|
||
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|
||
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|
||
}
|
||
|
||
#ifllbkegxd .gt_column_spanner_outer {
|
||
color: #333333;
|
||
background-color: #F8EFCB;
|
||
font-size: 100%;
|
||
font-weight: bold;
|
||
text-transform: inherit;
|
||
padding-top: 0;
|
||
padding-bottom: 0;
|
||
padding-left: 4px;
|
||
padding-right: 4px;
|
||
}
|
||
|
||
#ifllbkegxd .gt_column_spanner_outer:first-child {
|
||
padding-left: 0;
|
||
}
|
||
|
||
#ifllbkegxd .gt_column_spanner_outer:last-child {
|
||
padding-right: 0;
|
||
}
|
||
|
||
#ifllbkegxd .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%;
|
||
}
|
||
|
||
#ifllbkegxd .gt_spanner_row {
|
||
border-bottom-style: hidden;
|
||
}
|
||
|
||
#ifllbkegxd .gt_group_heading {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
color: #333333;
|
||
background-color: #F8EFCB;
|
||
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;
|
||
}
|
||
|
||
#ifllbkegxd .gt_empty_group_heading {
|
||
padding: 0.5px;
|
||
color: #333333;
|
||
background-color: #F8EFCB;
|
||
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;
|
||
}
|
||
|
||
#ifllbkegxd .gt_from_md > :first-child {
|
||
margin-top: 0;
|
||
}
|
||
|
||
#ifllbkegxd .gt_from_md > :last-child {
|
||
margin-bottom: 0;
|
||
}
|
||
|
||
#ifllbkegxd .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;
|
||
}
|
||
|
||
#ifllbkegxd .gt_stub {
|
||
color: #333333;
|
||
background-color: #F8EFCB;
|
||
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;
|
||
}
|
||
|
||
#ifllbkegxd .gt_stub_row_group {
|
||
color: #333333;
|
||
background-color: #F8EFCB;
|
||
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;
|
||
}
|
||
|
||
#ifllbkegxd .gt_row_group_first td {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#ifllbkegxd .gt_row_group_first th {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#ifllbkegxd .gt_summary_row {
|
||
color: #333333;
|
||
background-color: #F8EFCB;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#ifllbkegxd .gt_first_summary_row {
|
||
border-top-style: solid;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#ifllbkegxd .gt_first_summary_row.thick {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#ifllbkegxd .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;
|
||
}
|
||
|
||
#ifllbkegxd .gt_grand_summary_row {
|
||
color: #333333;
|
||
background-color: #F8EFCB;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
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|
||
}
|
||
|
||
#ifllbkegxd .gt_first_grand_summary_row {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
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|
||
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|
||
border-top-style: double;
|
||
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|
||
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|
||
}
|
||
|
||
#ifllbkegxd .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;
|
||
}
|
||
|
||
#ifllbkegxd .gt_striped {
|
||
background-color: #EFE6D0;
|
||
}
|
||
|
||
#ifllbkegxd .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;
|
||
}
|
||
|
||
#ifllbkegxd .gt_footnotes {
|
||
color: #333333;
|
||
background-color: #F8EFCB;
|
||
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;
|
||
}
|
||
|
||
#ifllbkegxd .gt_footnote {
|
||
margin: 0px;
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#ifllbkegxd .gt_sourcenotes {
|
||
color: #333333;
|
||
background-color: #F8EFCB;
|
||
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;
|
||
}
|
||
|
||
#ifllbkegxd .gt_sourcenote {
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#ifllbkegxd .gt_left {
|
||
text-align: left;
|
||
}
|
||
|
||
#ifllbkegxd .gt_center {
|
||
text-align: center;
|
||
}
|
||
|
||
#ifllbkegxd .gt_right {
|
||
text-align: right;
|
||
font-variant-numeric: tabular-nums;
|
||
}
|
||
|
||
#ifllbkegxd .gt_font_normal {
|
||
font-weight: normal;
|
||
}
|
||
|
||
#ifllbkegxd .gt_font_bold {
|
||
font-weight: bold;
|
||
}
|
||
|
||
#ifllbkegxd .gt_font_italic {
|
||
font-style: italic;
|
||
}
|
||
|
||
#ifllbkegxd .gt_super {
|
||
font-size: 65%;
|
||
}
|
||
|
||
#ifllbkegxd .gt_footnote_marks {
|
||
font-size: 75%;
|
||
vertical-align: 0.4em;
|
||
position: initial;
|
||
}
|
||
|
||
#ifllbkegxd .gt_asterisk {
|
||
font-size: 100%;
|
||
vertical-align: 0;
|
||
}
|
||
|
||
#ifllbkegxd .gt_indent_1 {
|
||
text-indent: 5px;
|
||
}
|
||
|
||
#ifllbkegxd .gt_indent_2 {
|
||
text-indent: 10px;
|
||
}
|
||
|
||
#ifllbkegxd .gt_indent_3 {
|
||
text-indent: 15px;
|
||
}
|
||
|
||
#ifllbkegxd .gt_indent_4 {
|
||
text-indent: 20px;
|
||
}
|
||
|
||
#ifllbkegxd .gt_indent_5 {
|
||
text-indent: 25px;
|
||
}
|
||
|
||
#ifllbkegxd .katex-display {
|
||
display: inline-flex !important;
|
||
margin-bottom: 0.75em !important;
|
||
}
|
||
|
||
#ifllbkegxd 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" style="background-color: #A83262; color: #FFFFFF; font-weight: bold" 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" style="background-color: #A83262; color: #FFFFFF; font-weight: bold" 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" style="background-color: #A83262; color: #FFFFFF; font-weight: bold" 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" style="background-color: #A83262; color: #FFFFFF; font-weight: bold" 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" style="background-color: #F8EFCB; color: #2F2F2F">Sex, n(%)</td>
|
||
<td class="gt_row gt_center" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F"><br>
|
||
</td>
|
||
<td class="gt_row gt_center" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F"><br>
|
||
</td>
|
||
<td class="gt_row gt_center" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F"><br>
|
||
</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left gt_striped" headers="label" style="background-color: #F8EFCB; color: #2F2F2F"> Female</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">4,014 (41%)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">2,105 (41%)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">1,909 (41%)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label" style="background-color: #F8EFCB; color: #2F2F2F"> Male</td>
|
||
<td class="gt_row gt_center" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">5,761 (59%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">3,043 (59%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">2,718 (59%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left gt_striped" headers="label" style="background-color: #F8EFCB; color: #2F2F2F">Recipient age, median (IQR)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">13 (8, 16)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">13 (7, 16)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">14 (9, 16)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label" style="background-color: #F8EFCB; color: #2F2F2F"> Unknown</td>
|
||
<td class="gt_row gt_center" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">9</td>
|
||
<td class="gt_row gt_center" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">7</td>
|
||
<td class="gt_row gt_center" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">2</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left gt_striped" headers="label" style="background-color: #F8EFCB; color: #2F2F2F">Donor age, median (IQR)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">33 (21, 41)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">37 (31, 42)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">22 (15, 37)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label" style="background-color: #F8EFCB; color: #2F2F2F"> Unknown</td>
|
||
<td class="gt_row gt_center" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">113</td>
|
||
<td class="gt_row gt_center" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">112</td>
|
||
<td class="gt_row gt_center" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">1</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left gt_striped" headers="label" style="background-color: #F8EFCB; color: #2F2F2F">HLA matches, n(%)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F"><br>
|
||
</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F"><br>
|
||
</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F"><br>
|
||
</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label" style="background-color: #F8EFCB; color: #2F2F2F"> 0</td>
|
||
<td class="gt_row gt_center" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">784 (8.2%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">125 (2.5%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">659 (14%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left gt_striped" headers="label" style="background-color: #F8EFCB; color: #2F2F2F"> 1</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">1,504 (16%)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">160 (3.2%)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">1,344 (29%)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label" style="background-color: #F8EFCB; color: #2F2F2F"> 2</td>
|
||
<td class="gt_row gt_center" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">1,553 (16%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">228 (4.6%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">1,325 (29%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left gt_striped" headers="label" style="background-color: #F8EFCB; color: #2F2F2F"> 3</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">3,778 (40%)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">3,039 (61%)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">739 (16%)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label" style="background-color: #F8EFCB; color: #2F2F2F"> 4</td>
|
||
<td class="gt_row gt_center" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">1,278 (13%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">1,007 (20%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">271 (5.9%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left gt_striped" headers="label" style="background-color: #F8EFCB; color: #2F2F2F"> 5</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">365 (3.8%)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">241 (4.9%)</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">124 (2.7%)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label" style="background-color: #F8EFCB; color: #2F2F2F"> 6</td>
|
||
<td class="gt_row gt_center" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">279 (2.9%)</td>
|
||
<td class="gt_row gt_center" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">153 (3.1%)</td>
|
||
<td class="gt_row gt_center" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">126 (2.7%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left gt_striped" headers="label" style="background-color: #F8EFCB; color: #2F2F2F"> Unknown</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">234</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">195</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">39</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_left" headers="label" style="background-color: #F8EFCB; color: #2F2F2F">Cold ischemic time (hours), median (IQR)</td>
|
||
<td class="gt_row gt_center" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">7 (1, 19)</td>
|
||
<td class="gt_row gt_center" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">1 (0, 1)</td>
|
||
<td class="gt_row gt_center" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">19 (13, 25)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_left gt_striped" headers="label" style="background-color: #F8EFCB; color: #2F2F2F"> Unknown</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_0" style="background-color: #F8EFCB; color: #2F2F2F">2,250</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_1" style="background-color: #F8EFCB; color: #2F2F2F">1,490</td>
|
||
<td class="gt_row gt_center gt_striped" headers="stat_2" style="background-color: #F8EFCB; color: #2F2F2F">760</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</section>
|
||
<section id="table-1-by-transplant-type" class="level1" data-number="5">
|
||
<h1 data-number="5"><span class="header-section-number">5</span> Table 1: By Transplant Type</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>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>
|
||
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
|
||
58 290 227 156 161 151 155 167 202 218 218 250 287 330 357 420 466 508 520 </code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>
|
||
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
|
||
35 104 154 121 118 135 147 166 169 170 212 193 254 314 328 454 469 565 517 </code></pre>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</section>
|
||
<section id="table-1-by-transplant-type-1" class="level1" data-number="6">
|
||
<h1 data-number="6"><span class="header-section-number">6</span> Table 1: By Transplant Type</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-11-1.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-12-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</section>
|
||
<section id="overall-survival" class="level1" data-number="7">
|
||
<h1 data-number="7"><span class="header-section-number">7</span> Overall Survival</h1>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-14-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div id="aajxcexzuu" 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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|
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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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}
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|
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#aajxcexzuu .gt_last_grand_summary_row_top {
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}
|
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}
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color: #333333;
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#aajxcexzuu .gt_footnote {
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margin: 0px;
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|
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|
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}
|
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|
||
#aajxcexzuu .gt_sourcenotes {
|
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color: #333333;
|
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background-color: #FFF4CC;
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|
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|
||
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|
||
}
|
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|
||
#aajxcexzuu .gt_sourcenote {
|
||
font-size: 90%;
|
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padding-top: 4px;
|
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padding-bottom: 4px;
|
||
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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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|
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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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|
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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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}
|
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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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|
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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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|
||
#aajxcexzuu .katex-display {
|
||
display: inline-flex !important;
|
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margin-bottom: 0.75em !important;
|
||
}
|
||
|
||
#aajxcexzuu 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="5" 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>
|
||
<th id="lower" 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">Upper 95% CI</th>
|
||
<th id="upper" 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">Lower 95% CI</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>
|
||
<td class="gt_row gt_right" headers="lower" style="background-color: #FFF4CC">0.999</td>
|
||
<td class="gt_row gt_right" headers="upper" 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>
|
||
<td class="gt_row gt_right gt_striped" headers="lower" style="background-color: #FFF4CC">0.964</td>
|
||
<td class="gt_row gt_right gt_striped" headers="upper" style="background-color: #FFF4CC">0.971</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>
|
||
<td class="gt_row gt_right" headers="lower" style="background-color: #FFF4CC">0.948</td>
|
||
<td class="gt_row gt_right" headers="upper" style="background-color: #FFF4CC">0.958</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>
|
||
<td class="gt_row gt_right gt_striped" headers="lower" style="background-color: #FFF4CC">0.931</td>
|
||
<td class="gt_row gt_right gt_striped" headers="upper" style="background-color: #FFF4CC">0.944</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>
|
||
<td class="gt_row gt_right" headers="lower" style="background-color: #FFF4CC">0.910</td>
|
||
<td class="gt_row gt_right" headers="upper" style="background-color: #FFF4CC">0.928</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>
|
||
<td class="gt_row gt_right gt_striped" headers="lower" style="background-color: #FFF4CC">0.888</td>
|
||
<td class="gt_row gt_right gt_striped" headers="upper" style="background-color: #FFF4CC">0.913</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>
|
||
<td class="gt_row gt_right" headers="lower" style="background-color: #FFF4CC">0.871</td>
|
||
<td class="gt_row gt_right" headers="upper" style="background-color: #FFF4CC">0.905</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="hazard-by-transplant-type" class="level1" data-number="8">
|
||
<h1 data-number="8"><span class="header-section-number">8</span> Hazard by Transplant Type</h1>
|
||
<section id="death-distribution" class="level2" data-number="8.1">
|
||
<h2 data-number="8.1" class="anchored" data-anchor-id="death-distribution"><span class="header-section-number">8.1</span> Death distribution</h2>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> total first.1.total first.1.ratio first.5.total first.5.ratio
|
||
1 465 216 46.45161 390 83.87097</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-18-1.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-19-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</section>
|
||
<section id="hazard-rate-by-transplant-type" class="level1" data-number="9">
|
||
<h1 data-number="9"><span class="header-section-number">9</span> Hazard Rate by Transplant Type</h1>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-21-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div id="gmxfdrxnqo" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
|
||
<style>#gmxfdrxnqo 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;
|
||
}
|
||
|
||
#gmxfdrxnqo thead, #gmxfdrxnqo tbody, #gmxfdrxnqo tfoot, #gmxfdrxnqo tr, #gmxfdrxnqo td, #gmxfdrxnqo th {
|
||
border-style: none;
|
||
}
|
||
|
||
#gmxfdrxnqo p {
|
||
margin: 0;
|
||
padding: 0;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_table {
|
||
display: table;
|
||
border-collapse: collapse;
|
||
line-height: normal;
|
||
margin-left: auto;
|
||
margin-right: auto;
|
||
color: #333333;
|
||
font-size: 18px;
|
||
font-weight: normal;
|
||
font-style: normal;
|
||
background-color: #FFF2CC;
|
||
width: auto;
|
||
border-top-style: solid;
|
||
border-top-width: 2px;
|
||
border-top-color: #5B5FE0;
|
||
border-right-style: none;
|
||
border-right-width: 2px;
|
||
border-right-color: #D3D3D3;
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #5B5FE0;
|
||
border-left-style: none;
|
||
border-left-width: 2px;
|
||
border-left-color: #D3D3D3;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_caption {
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_title {
|
||
color: #333333;
|
||
font-size: 22px;
|
||
font-weight: initial;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
border-bottom-color: #FFF2CC;
|
||
border-bottom-width: 0;
|
||
}
|
||
|
||
#gmxfdrxnqo .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: #FFF2CC;
|
||
border-top-width: 0;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_heading {
|
||
background-color: #FFF2CC;
|
||
text-align: center;
|
||
border-bottom-color: #FFF2CC;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_bottom_border {
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#gmxfdrxnqo .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: #5B5FE0;
|
||
border-left-style: none;
|
||
border-left-width: 1px;
|
||
border-left-color: #D3D3D3;
|
||
border-right-style: none;
|
||
border-right-width: 1px;
|
||
border-right-color: #D3D3D3;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_col_heading {
|
||
color: #333333;
|
||
background-color: #FFF2CC;
|
||
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;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_column_spanner_outer {
|
||
color: #333333;
|
||
background-color: #FFF2CC;
|
||
font-size: 100%;
|
||
font-weight: bold;
|
||
text-transform: inherit;
|
||
padding-top: 0;
|
||
padding-bottom: 0;
|
||
padding-left: 4px;
|
||
padding-right: 4px;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_column_spanner_outer:first-child {
|
||
padding-left: 0;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_column_spanner_outer:last-child {
|
||
padding-right: 0;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_column_spanner {
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #5B5FE0;
|
||
vertical-align: bottom;
|
||
padding-top: 5px;
|
||
padding-bottom: 5px;
|
||
overflow-x: hidden;
|
||
display: inline-block;
|
||
width: 100%;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_spanner_row {
|
||
border-bottom-style: hidden;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_group_heading {
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
color: #333333;
|
||
background-color: #FFF2CC;
|
||
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;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_empty_group_heading {
|
||
padding: 0.5px;
|
||
color: #333333;
|
||
background-color: #FFF2CC;
|
||
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;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_from_md > :first-child {
|
||
margin-top: 0;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_from_md > :last-child {
|
||
margin-bottom: 0;
|
||
}
|
||
|
||
#gmxfdrxnqo .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;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_stub {
|
||
color: #333333;
|
||
background-color: #FFF2CC;
|
||
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;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_stub_row_group {
|
||
color: #333333;
|
||
background-color: #FFF2CC;
|
||
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;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_row_group_first td {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_row_group_first th {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_summary_row {
|
||
color: #333333;
|
||
background-color: #FFF2CC;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_first_summary_row {
|
||
border-top-style: solid;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_first_summary_row.thick {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#gmxfdrxnqo .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;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_grand_summary_row {
|
||
color: #333333;
|
||
background-color: #FFF2CC;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#gmxfdrxnqo .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;
|
||
}
|
||
|
||
#gmxfdrxnqo .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;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_striped {
|
||
background-color: #F6E7B8;
|
||
}
|
||
|
||
#gmxfdrxnqo .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;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_footnotes {
|
||
color: #333333;
|
||
background-color: #FFF2CC;
|
||
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;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_footnote {
|
||
margin: 0px;
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_sourcenotes {
|
||
color: #333333;
|
||
background-color: #FFF2CC;
|
||
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;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_sourcenote {
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_left {
|
||
text-align: left;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_center {
|
||
text-align: center;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_right {
|
||
text-align: right;
|
||
font-variant-numeric: tabular-nums;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_font_normal {
|
||
font-weight: normal;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_font_bold {
|
||
font-weight: bold;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_font_italic {
|
||
font-style: italic;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_super {
|
||
font-size: 65%;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_footnote_marks {
|
||
font-size: 75%;
|
||
vertical-align: 0.4em;
|
||
position: initial;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_asterisk {
|
||
font-size: 100%;
|
||
vertical-align: 0;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_indent_1 {
|
||
text-indent: 5px;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_indent_2 {
|
||
text-indent: 10px;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_indent_3 {
|
||
text-indent: 15px;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_indent_4 {
|
||
text-indent: 20px;
|
||
}
|
||
|
||
#gmxfdrxnqo .gt_indent_5 {
|
||
text-indent: 25px;
|
||
}
|
||
|
||
#gmxfdrxnqo .katex-display {
|
||
display: inline-flex !important;
|
||
margin-bottom: 0.75em !important;
|
||
}
|
||
|
||
#gmxfdrxnqo 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" style="color: #5B5FE0; font-size: 22px; font-weight: bold">Estimated Hazard Rate by Transplant Type</th>
|
||
</tr>
|
||
<tr class="gt_col_headings even">
|
||
<th id="fu.interval" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" style="background-color: #5B5FE0; color: #FFFFFF; font-weight: bold" scope="col">Follow-up Interval</th>
|
||
<th id="Deceased" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" style="background-color: #5B5FE0; color: #FFFFFF; font-weight: bold" scope="col">Deceased</th>
|
||
<th id="Living" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" style="background-color: #5B5FE0; color: #FFFFFF; font-weight: bold" scope="col">Living</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody class="gt_table_body">
|
||
<tr class="odd">
|
||
<td class="gt_row gt_center" headers="fu.interval" style="background-color: #FFF2CC; color: #2F2F2F">1/3</td>
|
||
<td class="gt_row gt_center" headers="Deceased" style="background-color: #FFF2CC; color: #2F2F2F">0.010</td>
|
||
<td class="gt_row gt_center" headers="Living" style="background-color: #FFF2CC; color: #2F2F2F">0.022</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_center gt_striped" headers="fu.interval" style="background-color: #FFF2CC; color: #2F2F2F">2/3</td>
|
||
<td class="gt_row gt_center gt_striped" headers="Deceased" style="background-color: #FFF2CC; color: #2F2F2F">0.003</td>
|
||
<td class="gt_row gt_center gt_striped" headers="Living" style="background-color: #FFF2CC; color: #2F2F2F">0.006</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_center" headers="fu.interval" style="background-color: #FFF2CC; color: #2F2F2F">1</td>
|
||
<td class="gt_row gt_center" headers="Deceased" style="background-color: #FFF2CC; color: #2F2F2F">0.003</td>
|
||
<td class="gt_row gt_center" headers="Living" style="background-color: #FFF2CC; color: #2F2F2F">0.004</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_center gt_striped" headers="fu.interval" style="background-color: #FFF2CC; color: #2F2F2F">2</td>
|
||
<td class="gt_row gt_center gt_striped" headers="Deceased" style="background-color: #FFF2CC; color: #2F2F2F">0.006</td>
|
||
<td class="gt_row gt_center gt_striped" headers="Living" style="background-color: #FFF2CC; color: #2F2F2F">0.011</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_center" headers="fu.interval" style="background-color: #FFF2CC; color: #2F2F2F">3</td>
|
||
<td class="gt_row gt_center" headers="Deceased" style="background-color: #FFF2CC; color: #2F2F2F">0.005</td>
|
||
<td class="gt_row gt_center" headers="Living" style="background-color: #FFF2CC; color: #2F2F2F">0.008</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td class="gt_row gt_center gt_striped" headers="fu.interval" style="background-color: #FFF2CC; color: #2F2F2F">4</td>
|
||
<td class="gt_row gt_center gt_striped" headers="Deceased" style="background-color: #FFF2CC; color: #2F2F2F">0.006</td>
|
||
<td class="gt_row gt_center gt_striped" headers="Living" style="background-color: #FFF2CC; color: #2F2F2F">0.010</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td class="gt_row gt_center" headers="fu.interval" style="background-color: #FFF2CC; color: #2F2F2F">5</td>
|
||
<td class="gt_row gt_center" headers="Deceased" style="background-color: #FFF2CC; color: #2F2F2F">0.005</td>
|
||
<td class="gt_row gt_center" headers="Living" style="background-color: #FFF2CC; color: #2F2F2F">0.011</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="cox-model-transplant-type" class="level1" data-number="10">
|
||
<h1 data-number="10"><span class="header-section-number">10</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-25-1.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="11">
|
||
<h1 data-number="11"><span class="header-section-number">11</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-29-1.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="12">
|
||
<h1 data-number="12"><span class="header-section-number">12</span> Cox Model: Age Recipient (Categorical)</h1>
|
||
<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>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="cb15"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb15-1"><a href="#cb15-1" 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="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a> <span class="at">type =</span> <span class="st">"response"</span>)</span>
|
||
<span id="cb15-3"><a href="#cb15-3" 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-35-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="cox-model-age-recipient-categorical-1" class="level1" data-number="13">
|
||
<h1 data-number="13"><span class="header-section-number">13</span> Cox Model: Age Recipient (Categorical)</h1>
|
||
<div class="cell">
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-36-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="identifying-predictors" class="level1" data-number="14">
|
||
<h1 data-number="14"><span class="header-section-number">14</span> Identifying Predictors</h1>
|
||
<section id="start-with-nothing" class="level2" data-number="14.1">
|
||
<h2 data-number="14.1" class="anchored" data-anchor-id="start-with-nothing"><span class="header-section-number">14.1</span> Start with nothing</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb17"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb17-1"><a href="#cb17-1" aria-hidden="true" tabindex="-1"></a>old.vars <span class="ot"><-</span> <span class="fu">c</span>()</span>
|
||
<span id="cb17-2"><a href="#cb17-2" 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="cb20"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb20-1"><a href="#cb20-1" 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="cb23"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb23-1"><a href="#cb23-1" 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="cb26"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb26-1"><a href="#cb26-1" 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 class="sourceCode cell-code" id="cb29"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb29-1"><a href="#cb29-1" 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.match1 -0.07016 0.93225 0.17301 -0.405 0.6851
|
||
hla.match2 -0.36381 0.69503 0.17922 -2.030 0.0424
|
||
hla.match3 -0.76176 0.46684 0.16442 -4.633 3.60e-06
|
||
hla.match4 -0.89933 0.40684 0.20835 -4.317 1.59e-05
|
||
hla.match5 -0.59727 0.55031 0.28740 -2.078 0.0377
|
||
hla.match6 -0.66377 0.51491 0.31171 -2.129 0.0332
|
||
|
||
Likelihood ratio test=47.36 on 6 df, p=1.584e-08
|
||
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 0.1644258 1 0.685114</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb32"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb32-1"><a href="#cb32-1" 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="cb35"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb35-1"><a href="#cb35-1" 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>
|
||
</section>
|
||
<section id="tx.type" class="level2" data-number="14.2">
|
||
<h2 data-number="14.2" class="anchored" data-anchor-id="tx.type"><span class="header-section-number">14.2</span> <code>tx.type</code> + ?</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb38"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb38-1"><a href="#cb38-1" 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="cb38-2"><a href="#cb38-2" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb38-3"><a href="#cb38-3" 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="cb41"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb41-1"><a href="#cb41-1" 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="cb44"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb44-1"><a href="#cb44-1" 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 class="sourceCode cell-code" id="cb47"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb47-1"><a href="#cb47-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"hla.match"</span>, <span class="dv">2</span><span class="sc">:</span><span class="dv">7</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 0.39047 1.47768 0.12688 3.078 0.00209
|
||
hla.match1 -0.08836 0.91543 0.17308 -0.510 0.60970
|
||
hla.match2 -0.36329 0.69539 0.17919 -2.027 0.04263
|
||
hla.match3 -0.50800 0.60170 0.18299 -2.776 0.00550
|
||
hla.match4 -0.65400 0.51996 0.22221 -2.943 0.00325
|
||
hla.match5 -0.39435 0.67412 0.29410 -1.341 0.17997
|
||
hla.match6 -0.51481 0.59761 0.31489 -1.635 0.10208
|
||
|
||
Likelihood ratio test=56.78 on 7 df, p=6.605e-10
|
||
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 14.7018 6 0.02270728</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb50"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb50-1"><a href="#cb50-1" 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="cb53"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb53-1"><a href="#cb53-1" 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>
|
||
<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="14.3">
|
||
<h2 data-number="14.3" class="anchored" data-anchor-id="tx.type-age.rec"><span class="header-section-number">14.3</span> <code>tx.type</code> + <code>age.rec</code> + ?</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb56"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb56-1"><a href="#cb56-1" 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="cb56-2"><a href="#cb56-2" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb56-3"><a href="#cb56-3" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"age.donor"</span>, <span class="dv">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="cb59"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb59-1"><a href="#cb59-1" 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 class="sourceCode cell-code" id="cb62"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb62-1"><a href="#cb62-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"hla.match"</span>, <span class="dv">3</span><span class="sc">:</span><span class="dv">8</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 0.439788 1.552378 0.129107 3.406 0.000658
|
||
age.rec -0.048395 0.952758 0.008687 -5.571 2.53e-08
|
||
hla.match1 -0.065986 0.936144 0.173137 -0.381 0.703116
|
||
hla.match2 -0.339580 0.712069 0.179741 -1.889 0.058856
|
||
hla.match3 -0.479802 0.618906 0.184469 -2.601 0.009295
|
||
hla.match4 -0.617490 0.539296 0.223835 -2.759 0.005803
|
||
hla.match5 -0.362744 0.695764 0.294632 -1.231 0.218257
|
||
hla.match6 -0.410614 0.663243 0.315392 -1.302 0.192946
|
||
|
||
Likelihood ratio test=86.59 on 8 df, p=2.288e-15
|
||
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 13.1233 6 0.04111916</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb65"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb65-1"><a href="#cb65-1" 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="cb68"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb68-1"><a href="#cb68-1" 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>
|
||
<p><code>age.donor</code> has the smallest <span class="math inline">\(p\)</span>-value</p>
|
||
</section>
|
||
<section id="tx.type-age.rec-age.donor" class="level2" data-number="14.4">
|
||
<h2 data-number="14.4" class="anchored" data-anchor-id="tx.type-age.rec-age.donor"><span class="header-section-number">14.4</span> <code>tx.type</code> + <code>age.rec</code> + <code>age.donor</code> + ?</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb71"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb71-1"><a href="#cb71-1" 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">"age.donor"</span>)</span>
|
||
<span id="cb71-2"><a href="#cb71-2" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb71-3"><a href="#cb71-3" 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 0.571096 1.770207 0.107278 5.324 1.02e-07
|
||
age.rec -0.044243 0.956721 0.008718 -5.075 3.87e-07
|
||
age.donor -0.009313 0.990730 0.003793 -2.456 0.0141
|
||
year -0.031516 0.968975 0.015475 -2.037 0.0417
|
||
|
||
Likelihood ratio test=87.47 on 4 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 4.14746 1 0.04169701</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb74"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb74-1"><a href="#cb74-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"hla.match"</span>, <span class="dv">4</span><span class="sc">:</span><span class="dv">9</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 0.343744 1.410218 0.135594 2.535 0.01124
|
||
age.rec -0.044106 0.956853 0.008869 -4.973 6.6e-07
|
||
age.donor -0.008401 0.991634 0.003842 -2.187 0.02878
|
||
hla.match1 -0.060302 0.941480 0.173155 -0.348 0.72765
|
||
hla.match2 -0.319994 0.726153 0.179955 -1.778 0.07537
|
||
hla.match3 -0.457366 0.632949 0.185204 -2.470 0.01353
|
||
hla.match4 -0.580080 0.559853 0.224649 -2.582 0.00982
|
||
hla.match5 -0.327698 0.720580 0.295711 -1.108 0.26779
|
||
hla.match6 -0.399931 0.670366 0.316127 -1.265 0.20584
|
||
|
||
Likelihood ratio test=89.74 on 9 df, p=1.834e-15
|
||
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 11.68364 6 0.06941019</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb77"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb77-1"><a href="#cb77-1" 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 0.574554 1.776338 0.107419 5.349 8.86e-08
|
||
age.rec -0.045101 0.955901 0.008757 -5.150 2.60e-07
|
||
age.donor -0.009501 0.990544 0.003799 -2.501 0.0124
|
||
sexMale -0.127413 0.880370 0.094265 -1.352 0.1765
|
||
|
||
Likelihood ratio test=85.12 on 4 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 1.826933 1 0.1764903</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb80"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb80-1"><a href="#cb80-1" 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 0.475677 1.609104 0.178023 2.672 0.00754
|
||
age.rec -0.023171 0.977095 0.010194 -2.273 0.02303
|
||
age.donor -0.004841 0.995171 0.004205 -1.151 0.24970
|
||
cold.isc 0.003780 1.003787 0.006755 0.559 0.57583
|
||
|
||
Likelihood ratio test=36.13 on 4 df, p=2.722e-07
|
||
n= 7480, number of events= 356
|
||
(2295 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 0.3130214 1 0.575832</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-age.donor-year" class="level2" data-number="14.5">
|
||
<h2 data-number="14.5" class="anchored" data-anchor-id="tx.type-age.rec-age.donor-year"><span class="header-section-number">14.5</span> <code>tx.type</code> + <code>age.rec</code> + <code>age.donor</code> + <code>year</code> + ?</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb83"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb83-1"><a href="#cb83-1" 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">"age.donor"</span>, <span class="st">"year"</span>)</span>
|
||
<span id="cb83-2"><a href="#cb83-2" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb83-3"><a href="#cb83-3" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"hla.match"</span>, <span class="dv">5</span><span class="sc">:</span><span class="dv">10</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 0.330259 1.391328 0.135752 2.433 0.01498
|
||
age.rec -0.044176 0.956785 0.008869 -4.981 6.32e-07
|
||
age.donor -0.007886 0.992145 0.003836 -2.056 0.03978
|
||
year -0.034415 0.966170 0.015880 -2.167 0.03022
|
||
hla.match1 -0.087933 0.915822 0.173602 -0.507 0.61249
|
||
hla.match2 -0.352526 0.702910 0.180569 -1.952 0.05090
|
||
hla.match3 -0.504964 0.603527 0.186678 -2.705 0.00683
|
||
hla.match4 -0.625722 0.534875 0.225828 -2.771 0.00559
|
||
hla.match5 -0.364687 0.694414 0.296524 -1.230 0.21874
|
||
hla.match6 -0.456586 0.633442 0.317208 -1.439 0.15004
|
||
|
||
Likelihood ratio test=94.45 on 10 df, p=6.975e-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 13.08326 6 0.0417326</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb86"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb86-1"><a href="#cb86-1" 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 0.574624 1.776462 0.107327 5.354 8.60e-08
|
||
age.rec -0.045294 0.955716 0.008759 -5.171 2.33e-07
|
||
age.donor -0.009119 0.990922 0.003795 -2.403 0.0163
|
||
year -0.031699 0.968798 0.015475 -2.048 0.0405
|
||
sexMale -0.129147 0.878844 0.094284 -1.370 0.1708
|
||
|
||
Likelihood ratio test=89.33 on 5 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 1.876286 1 0.1707569</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb89"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb89-1"><a href="#cb89-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"cold.isc"</span>, <span class="dv">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 0.509289 1.664108 0.179269 2.841 0.0045
|
||
age.rec -0.023037 0.977226 0.010191 -2.261 0.0238
|
||
age.donor -0.004381 0.995629 0.004202 -1.043 0.2971
|
||
year -0.036400 0.964254 0.018995 -1.916 0.0553
|
||
cold.isc 0.002027 1.002029 0.006812 0.298 0.7660
|
||
|
||
Likelihood ratio test=39.84 on 5 df, p=1.608e-07
|
||
n= 7480, number of events= 356
|
||
(2295 observations deleted due to missingness)</code></pre>
|
||
</div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code> Wald df p
|
||
1 0.0885476 1 0.7660318</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-age.donor-year-hla.match" class="level2" data-number="14.6">
|
||
<h2 data-number="14.6" class="anchored" data-anchor-id="tx.type-age.rec-age.donor-year-hla.match"><span class="header-section-number">14.6</span> <code>tx.type</code> + <code>age.rec</code> + <code>age.donor</code> + <code>year</code> + <code>hla.match</code> + ?</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb92"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb92-1"><a href="#cb92-1" 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">"age.donor"</span>, <span class="st">"year"</span>, <span class="st">"hla.match"</span>)</span>
|
||
<span id="cb92-2"><a href="#cb92-2" aria-hidden="true" tabindex="-1"></a></span>
|
||
<span id="cb92-3"><a href="#cb92-3" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"sex"</span>, <span class="dv">11</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 0.334671 1.397480 0.135776 2.465 0.01371
|
||
age.rec -0.044917 0.956077 0.008908 -5.043 4.59e-07
|
||
age.donor -0.007753 0.992277 0.003838 -2.020 0.04341
|
||
year -0.034523 0.966066 0.015880 -2.174 0.02970
|
||
hla.match1 -0.088750 0.915074 0.173601 -0.511 0.60919
|
||
hla.match2 -0.350775 0.704142 0.180587 -1.942 0.05209
|
||
hla.match3 -0.501788 0.605447 0.186640 -2.689 0.00718
|
||
hla.match4 -0.624023 0.535784 0.225726 -2.765 0.00570
|
||
hla.match5 -0.361475 0.696648 0.296530 -1.219 0.22284
|
||
hla.match6 -0.450811 0.637111 0.317311 -1.421 0.15540
|
||
sexMale -0.092818 0.911359 0.095967 -0.967 0.33345
|
||
|
||
Likelihood ratio test=95.39 on 11 df, p=1.457e-15
|
||
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 0.9354639 1 0.3334471</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb95"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb95-1"><a href="#cb95-1" aria-hidden="true" tabindex="-1"></a><span class="fu">test.new.var</span>(old.vars, <span class="st">"cold.isc"</span>, <span class="dv">11</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 0.310337 1.363884 0.201059 1.544 0.1227
|
||
age.rec -0.021521 0.978709 0.010287 -2.092 0.0364
|
||
age.donor -0.002701 0.997303 0.004215 -0.641 0.5216
|
||
year -0.038176 0.962544 0.019265 -1.982 0.0475
|
||
hla.match1 0.070810 1.073377 0.218390 0.324 0.7458
|
||
hla.match2 -0.100219 0.904639 0.221242 -0.453 0.6506
|
||
hla.match3 -0.285575 0.751582 0.227967 -1.253 0.2103
|
||
hla.match4 -0.314582 0.730094 0.262605 -1.198 0.2309
|
||
hla.match5 -0.132791 0.875648 0.351300 -0.378 0.7054
|
||
hla.match6 -0.279719 0.755996 0.359291 -0.779 0.4363
|
||
cold.isc 0.002472 1.002475 0.006832 0.362 0.7175
|
||
|
||
Likelihood ratio test=40.14 on 11 df, p=3.39e-05
|
||
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 0.1308801 1 0.7175212</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="15">
|
||
<h1 data-number="15"><span class="header-section-number">15</span> Full Model</h1>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>Call:
|
||
coxph(formula = surv.full, data = dat, method = "breslow")
|
||
|
||
n= 9433, number of events= 449
|
||
(342 observations deleted due to missingness)
|
||
|
||
coef exp(coef) se(coef) z Pr(>|z|)
|
||
tx.typeLiving 0.330259 1.391328 0.135752 2.433 0.01498 *
|
||
age.rec -0.044176 0.956785 0.008869 -4.981 6.32e-07 ***
|
||
age.donor -0.007886 0.992145 0.003836 -2.056 0.03978 *
|
||
year -0.034415 0.966170 0.015880 -2.167 0.03022 *
|
||
hla.match1 -0.087933 0.915822 0.173602 -0.507 0.61249
|
||
hla.match2 -0.352526 0.702910 0.180569 -1.952 0.05090 .
|
||
hla.match3 -0.504964 0.603527 0.186678 -2.705 0.00683 **
|
||
hla.match4 -0.625722 0.534875 0.225828 -2.771 0.00559 **
|
||
hla.match5 -0.364687 0.694414 0.296524 -1.230 0.21874
|
||
hla.match6 -0.456586 0.633442 0.317208 -1.439 0.15004
|
||
---
|
||
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
|
||
|
||
exp(coef) exp(-coef) lower .95 upper .95
|
||
tx.typeLiving 1.3913 0.7187 1.0663 1.8154
|
||
age.rec 0.9568 1.0452 0.9403 0.9736
|
||
age.donor 0.9921 1.0079 0.9847 0.9996
|
||
year 0.9662 1.0350 0.9366 0.9967
|
||
hla.match1 0.9158 1.0919 0.6517 1.2870
|
||
hla.match2 0.7029 1.4227 0.4934 1.0014
|
||
hla.match3 0.6035 1.6569 0.4186 0.8702
|
||
hla.match4 0.5349 1.8696 0.3436 0.8327
|
||
hla.match5 0.6944 1.4401 0.3883 1.2417
|
||
hla.match6 0.6334 1.5787 0.3402 1.1795
|
||
|
||
Concordance= 0.644 (se = 0.015 )
|
||
Likelihood ratio test= 94.45 on 10 df, p=7e-16
|
||
Wald test = 96.48 on 10 df, p=3e-16
|
||
Score (logrank) test = 99.11 on 10 df, p=<2e-16</code></pre>
|
||
</div>
|
||
</div>
|
||
<div class="cell">
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>[1] 1</code></pre>
|
||
</div>
|
||
<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="576"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="proportional-hazards-assumption" class="level1" data-number="16">
|
||
<h1 data-number="16"><span class="header-section-number">16</span> Proportional hazards assumption</h1>
|
||
<div class="cell">
|
||
<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 0.330259 1.391328 0.135752 2.433 0.01498
|
||
age.rec -0.044176 0.956785 0.008869 -4.981 6.32e-07
|
||
age.donor -0.007886 0.992145 0.003836 -2.056 0.03978
|
||
year -0.034415 0.966170 0.015880 -2.167 0.03022
|
||
hla.match1 -0.087933 0.915822 0.173602 -0.507 0.61249
|
||
hla.match2 -0.352526 0.702910 0.180569 -1.952 0.05090
|
||
hla.match3 -0.504964 0.603527 0.186678 -2.705 0.00683
|
||
hla.match4 -0.625722 0.534875 0.225828 -2.771 0.00559
|
||
hla.match5 -0.364687 0.694414 0.296524 -1.230 0.21874
|
||
hla.match6 -0.456586 0.633442 0.317208 -1.439 0.15004
|
||
|
||
Likelihood ratio test=94.45 on 10 df, p=6.975e-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> chisq df p
|
||
tx.type 2.46 1 0.11651
|
||
age.rec 36.40 1 1.6e-09
|
||
age.donor 10.84 1 0.00099
|
||
year 4.00 1 0.04537
|
||
hla.match 12.87 6 0.04507
|
||
GLOBAL 56.91 10 1.4e-08</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-47-1.png" class="img-fluid figure-img" width="1440"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-47-2.png" class="img-fluid figure-img" width="1440"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-47-3.png" class="img-fluid figure-img" width="1440"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-47-4.png" class="img-fluid figure-img" width="1440"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-47-5.png" class="img-fluid figure-img" width="1440"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
<section id="what-happened-to-year" class="level2" data-number="16.1">
|
||
<h2 data-number="16.1" class="anchored" data-anchor-id="what-happened-to-year"><span class="header-section-number">16.1</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-48-1.png" class="img-fluid figure-img" width="960"></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-49-1.png" class="img-fluid figure-img" width="960"></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>
|
||
<p>Probabily want to omit it</p>
|
||
</section>
|
||
<section id="without-year" class="level2" data-number="16.2">
|
||
<h2 data-number="16.2" class="anchored" data-anchor-id="without-year"><span class="header-section-number">16.2</span> Without <code>year</code></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.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 0.343744 1.410218 0.135594 2.535 0.01124
|
||
age.rec -0.044106 0.956853 0.008869 -4.973 6.6e-07
|
||
hla.match1 -0.060302 0.941480 0.173155 -0.348 0.72765
|
||
hla.match2 -0.319994 0.726153 0.179955 -1.778 0.07537
|
||
hla.match3 -0.457366 0.632949 0.185204 -2.470 0.01353
|
||
hla.match4 -0.580080 0.559853 0.224649 -2.582 0.00982
|
||
hla.match5 -0.327698 0.720580 0.295711 -1.108 0.26779
|
||
hla.match6 -0.399931 0.670366 0.316127 -1.265 0.20584
|
||
age.donor -0.008401 0.991634 0.003842 -2.187 0.02878
|
||
|
||
Likelihood ratio test=89.74 on 9 df, p=1.834e-15
|
||
n= 9433, number of events= 449
|
||
(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-53-1.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># A tibble: 19 × 8
|
||
term estimate std.error statistic p.value conf.low conf.high model
|
||
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <chr>
|
||
1 Living donor 1.39 0.136 2.43 1.50e-2 1.07 1.82 Full…
|
||
2 Recipient age 0.957 0.00887 -4.98 6.32e-7 0.940 0.974 Full…
|
||
3 Donor age 0.992 0.00384 -2.06 3.98e-2 0.985 1.000 Full…
|
||
4 Transplant year 0.966 0.0159 -2.17 3.02e-2 0.937 0.997 Full…
|
||
5 hla.match1 0.916 0.174 -0.507 6.12e-1 0.652 1.29 Full…
|
||
6 hla.match2 0.703 0.181 -1.95 5.09e-2 0.493 1.00 Full…
|
||
7 hla.match3 0.604 0.187 -2.71 6.83e-3 0.419 0.870 Full…
|
||
8 hla.match4 0.535 0.226 -2.77 5.59e-3 0.344 0.833 Full…
|
||
9 hla.match5 0.694 0.297 -1.23 2.19e-1 0.388 1.24 Full…
|
||
10 hla.match6 0.633 0.317 -1.44 1.50e-1 0.340 1.18 Full…
|
||
11 Living donor 1.41 0.136 2.54 1.12e-2 1.08 1.84 Mode…
|
||
12 Recipient age 0.957 0.00887 -4.97 6.60e-7 0.940 0.974 Mode…
|
||
13 hla.match1 0.941 0.173 -0.348 7.28e-1 0.671 1.32 Mode…
|
||
14 hla.match2 0.726 0.180 -1.78 7.54e-2 0.510 1.03 Mode…
|
||
15 hla.match3 0.633 0.185 -2.47 1.35e-2 0.440 0.910 Mode…
|
||
16 hla.match4 0.560 0.225 -2.58 9.82e-3 0.360 0.870 Mode…
|
||
17 hla.match5 0.721 0.296 -1.11 2.68e-1 0.404 1.29 Mode…
|
||
18 hla.match6 0.670 0.316 -1.27 2.06e-1 0.361 1.25 Mode…
|
||
19 Donor age 0.992 0.00384 -2.19 2.88e-2 0.984 0.999 Mode…</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="576"></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="17">
|
||
<h1 data-number="17"><span class="header-section-number">17</span> Old</h1>
|
||
<details>
|
||
<section id="death-censored" class="level2" data-number="17.1">
|
||
<h2 data-number="17.1" class="anchored" data-anchor-id="death-censored"><span class="header-section-number">17.1</span> Death & Censored</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb105"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb105-1"><a href="#cb105-1" aria-hidden="true" tabindex="-1"></a>dat <span class="sc">|></span></span>
|
||
<span id="cb105-2"><a href="#cb105-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">group_by</span>(death) <span class="sc">|></span></span>
|
||
<span id="cb105-3"><a href="#cb105-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">summarise</span>(</span>
|
||
<span id="cb105-4"><a href="#cb105-4" aria-hidden="true" tabindex="-1"></a> <span class="at">n =</span> <span class="fu">n</span>(),</span>
|
||
<span id="cb105-5"><a href="#cb105-5" 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="cb105-6"><a href="#cb105-6" 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-58-1.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-59-1.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="17.2">
|
||
<h2 data-number="17.2" class="anchored" data-anchor-id="cox-model---age-as-a-continuous-variable"><span class="header-section-number">17.2</span> Cox Model - Age as a Continuous Variable</h2>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb109"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb109-1"><a href="#cb109-1" 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="cb109-2"><a href="#cb109-2" 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="17.3">
|
||
<h2 data-number="17.3" class="anchored" data-anchor-id="cox-model---age-as-a-categorical-variable"><span class="header-section-number">17.3</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 0.11643
|
||
age.rec 36.41 1 1.6e-09
|
||
hla.match 12.88 6 0.04498
|
||
age.donor 10.85 1 0.00099
|
||
year 4.01 1 0.04535
|
||
GLOBAL 56.93 10 1.4e-08</code></pre>
|
||
</div>
|
||
<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="960"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-63-2.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-63-3.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-63-4.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-63-5.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-63-6.png" class="img-fluid figure-img" width="960"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="table-1-l" class="level2" data-number="17.4">
|
||
<h2 data-number="17.4" class="anchored" data-anchor-id="table-1-l"><span class="header-section-number">17.4</span> Table 1 (L)</h2>
|
||
<section id="hla-match-hla.match" class="level3" data-number="17.4.1">
|
||
<h3 data-number="17.4.1" class="anchored" data-anchor-id="hla-match-hla.match"><span class="header-section-number">17.4.1</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-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="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="17.4.2">
|
||
<h3 data-number="17.4.2" class="anchored" data-anchor-id="donor-age-age.donor"><span class="header-section-number">17.4.2</span> Donor age <code>age.donor</code></h3>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb113"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb113-1"><a href="#cb113-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mean</span>(dat<span class="sc">$</span>age.donor, <span class="at">na.rm =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>[1] 31.29952</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb115"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb115-1"><a href="#cb115-1" aria-hidden="true" tabindex="-1"></a><span class="fu">median</span>(dat<span class="sc">$</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-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="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-70-1.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-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="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="17.4.3">
|
||
<h3 data-number="17.4.3" class="anchored" data-anchor-id="recipient-age-age.rec"><span class="header-section-number">17.4.3</span> Recipient Age <code>age.rec</code></h3>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb117"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb117-1"><a href="#cb117-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mean</span>(dat<span class="sc">$</span>age.rec, <span class="at">na.rm =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>[1] 11.64653</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb119"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb119-1"><a href="#cb119-1" aria-hidden="true" tabindex="-1"></a><span class="fu">median</span>(dat<span class="sc">$</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-74-1.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-75-1.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-76-1.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-77-1.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-78-1.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="17.4.4">
|
||
<h3 data-number="17.4.4" class="anchored" data-anchor-id="cold-ischemia-time-cold.isc"><span class="header-section-number">17.4.4</span> Cold Ischemia Time <code>cold.isc</code></h3>
|
||
<div class="cell">
|
||
<div class="sourceCode cell-code" id="cb121"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb121-1"><a href="#cb121-1" aria-hidden="true" tabindex="-1"></a><span class="fu">mean</span>(dat<span class="sc">$</span>cold.isc, <span class="at">na.rm =</span> <span class="cn">TRUE</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
|
||
<div class="cell-output cell-output-stdout">
|
||
<pre><code>[1] 10.85967</code></pre>
|
||
</div>
|
||
<div class="sourceCode cell-code" id="cb123"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb123-1"><a href="#cb123-1" aria-hidden="true" tabindex="-1"></a><span class="fu">median</span>(dat<span class="sc">$</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-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 id="transplant-type-tx.type" class="level3" data-number="17.4.5">
|
||
<h3 data-number="17.4.5" class="anchored" data-anchor-id="transplant-type-tx.type"><span class="header-section-number">17.4.5</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="cb126"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb126-1"><a href="#cb126-1" 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-85-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="year-year" class="level3" data-number="17.4.6">
|
||
<h3 data-number="17.4.6" class="anchored" data-anchor-id="year-year"><span class="header-section-number">17.4.6</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-87-1.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-88-1.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-89-1.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-90-1.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-91-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</section>
|
||
<section id="kaplan-meier" class="level2" data-number="17.5">
|
||
<h2 data-number="17.5" class="anchored" data-anchor-id="kaplan-meier"><span class="header-section-number">17.5</span> Kaplan-Meier</h2>
|
||
<section id="overall-l" class="level3" data-number="17.5.1">
|
||
<h3 data-number="17.5.1" class="anchored" data-anchor-id="overall-l"><span class="header-section-number">17.5.1</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-93-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="tx.type-m" class="level3" data-number="17.5.2">
|
||
<h3 data-number="17.5.2" class="anchored" data-anchor-id="tx.type-m"><span class="header-section-number">17.5.2</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-94-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
</section>
|
||
<section id="cox-model" class="level2" data-number="17.6">
|
||
<h2 data-number="17.6" class="anchored" data-anchor-id="cox-model"><span class="header-section-number">17.6</span> Cox Model</h2>
|
||
<section id="death-distribution-1" class="level3" data-number="17.6.1">
|
||
<h3 data-number="17.6.1" class="anchored" data-anchor-id="death-distribution-1"><span class="header-section-number">17.6.1</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-98-1.png" class="img-fluid figure-img" width="672"></p>
|
||
</figure>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="overall-l-1" class="level3" data-number="17.6.2">
|
||
<h3 data-number="17.6.2" class="anchored" data-anchor-id="overall-l-1"><span class="header-section-number">17.6.2</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="17.6.3">
|
||
<h3 data-number="17.6.3" class="anchored" data-anchor-id="tx.type-m-1"><span class="header-section-number">17.6.3</span> <code>tx.type</code> (M)</h3>
|
||
</section>
|
||
<section id="age-continuous-l" class="level3" data-number="17.6.4">
|
||
<h3 data-number="17.6.4" class="anchored" data-anchor-id="age-continuous-l"><span class="header-section-number">17.6.4</span> <code>age</code> (continuous) (L)</h3>
|
||
</section>
|
||
<section id="age-categorical-m" class="level3" data-number="17.6.5">
|
||
<h3 data-number="17.6.5" class="anchored" data-anchor-id="age-categorical-m"><span class="header-section-number">17.6.5</span> <code>age</code> (categorical) (M)</h3>
|
||
</section>
|
||
<section id="full-model-l" class="level3" data-number="17.6.6">
|
||
<h3 data-number="17.6.6" class="anchored" data-anchor-id="full-model-l"><span class="header-section-number">17.6.6</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.match1 -0.08845 0.91535 0.17308 -0.511 0.60933
|
||
hla.match2 -0.36340 0.69531 0.17919 -2.028 0.04256 *
|
||
hla.match3 -0.50810 0.60164 0.18298 -2.777 0.00549 **
|
||
hla.match4 -0.65410 0.51991 0.22221 -2.944 0.00324 **
|
||
hla.match5 -0.39445 0.67405 0.29410 -1.341 0.17985
|
||
hla.match6 -0.51491 0.59755 0.31489 -1.635 0.10201
|
||
tx.typeLiving 0.39049 1.47771 0.12688 3.078 0.00209 **
|
||
---
|
||
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
|
||
|
||
exp(coef) exp(-coef) lower .95 upper .95
|
||
hla.match1 0.9153 1.0925 0.6520 1.2850
|
||
hla.match2 0.6953 1.4382 0.4894 0.9879
|
||
hla.match3 0.6016 1.6621 0.4203 0.8612
|
||
hla.match4 0.5199 1.9234 0.3363 0.8037
|
||
hla.match5 0.6740 1.4836 0.3787 1.1996
|
||
hla.match6 0.5976 1.6735 0.3224 1.1077
|
||
tx.typeLiving 1.4777 0.6767 1.1524 1.8949
|
||
|
||
Concordance= 0.613 (se = 0.014 )
|
||
Likelihood ratio test= 56.79 on 7 df, p=7e-10
|
||
Wald test = 57.08 on 7 df, p=6e-10
|
||
Score (logrank) test = 59.51 on 7 df, p=2e-10</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.match1 0.8094 2.2467 0.8165 0.991 0.3215
|
||
hla.match2 1.1371 3.1176 0.7530 1.510 0.1311
|
||
hla.match3 0.4217 1.5245 0.7140 0.591 0.5548
|
||
hla.match4 0.1094 1.1156 0.7341 0.149 0.8816
|
||
hla.match5 0.4754 1.6087 0.7820 0.608 0.5432
|
||
hla.match6 0.5836 1.7925 0.8021 0.728 0.4669
|
||
tx.typeLiving 1.3801 3.9752 0.7218 1.912 0.0559 .
|
||
hla.match1:tx.typeLiving -0.9614 0.3823 0.8355 -1.151 0.2498
|
||
hla.match2:tx.typeLiving -1.6578 0.1905 0.7762 -2.136 0.0327 *
|
||
hla.match3:tx.typeLiving -1.0096 0.3644 0.7461 -1.353 0.1760
|
||
hla.match4:tx.typeLiving -0.5175 0.5960 0.7863 -0.658 0.5105
|
||
hla.match5:tx.typeLiving -0.8601 0.4231 0.8805 -0.977 0.3286
|
||
hla.match6:tx.typeLiving -1.3342 0.2634 0.9113 -1.464 0.1432
|
||
---
|
||
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
|
||
|
||
exp(coef) exp(-coef) lower .95 upper .95
|
||
hla.match1 2.2467 0.4451 0.45341 11.1322
|
||
hla.match2 3.1176 0.3208 0.71257 13.6400
|
||
hla.match3 1.5245 0.6559 0.37617 6.1787
|
||
hla.match4 1.1156 0.8964 0.26460 4.7032
|
||
hla.match5 1.6087 0.6216 0.34737 7.4498
|
||
hla.match6 1.7925 0.5579 0.37212 8.6342
|
||
tx.typeLiving 3.9752 0.2516 0.96600 16.3580
|
||
hla.match1:tx.typeLiving 0.3823 2.6155 0.07435 1.9662
|
||
hla.match2:tx.typeLiving 0.1905 5.2480 0.04162 0.8723
|
||
hla.match3:tx.typeLiving 0.3644 2.7444 0.08443 1.5726
|
||
hla.match4:tx.typeLiving 0.5960 1.6778 0.12763 2.7836
|
||
hla.match5:tx.typeLiving 0.4231 2.3635 0.07533 2.3763
|
||
hla.match6:tx.typeLiving 0.2634 3.7971 0.04414 1.5712
|
||
|
||
Concordance= 0.615 (se = 0.014 )
|
||
Likelihood ratio test= 66.78 on 13 df, p=3e-09
|
||
Wald test = 65.9 on 13 df, p=5e-09
|
||
Score (logrank) test = 69.92 on 13 df, p=8e-10</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 -3848.5
|
||
2 -3843.5 9.9891 6 0.1251</code></pre>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<section id="discussion-include-year-or-not" class="level3" data-number="17.6.7">
|
||
<h3 data-number="17.6.7" class="anchored" data-anchor-id="discussion-include-year-or-not"><span class="header-section-number">17.6.7</span> Discussion: include <code>year</code> or not?</h3>
|
||
</section>
|
||
</section>
|
||
<section id="assumption-testing" class="level2" data-number="17.7">
|
||
<h2 data-number="17.7" class="anchored" data-anchor-id="assumption-testing"><span class="header-section-number">17.7</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">
|
||
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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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|
||
<td class="gt_row gt_center" headers="transplant">2000</td>
|
||
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|
||
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|
||
<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>
|
||
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|
||
<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>
|
||
</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>
|
||
</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>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
</div>
|
||
</div>
|
||
<div class="cell-output-display">
|
||
<div>
|
||
<figure class="figure">
|
||
<p><img src="slides_files/figure-html/unnamed-chunk-102-1.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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|
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|
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#cxfgwdyrjq .gt_stub {
|
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#cxfgwdyrjq .gt_stub_row_group {
|
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#cxfgwdyrjq .gt_first_summary_row {
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}
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|
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|
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#cxfgwdyrjq .gt_footnote {
|
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|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#cxfgwdyrjq .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;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_sourcenote {
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_left {
|
||
text-align: left;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_center {
|
||
text-align: center;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_right {
|
||
text-align: right;
|
||
font-variant-numeric: tabular-nums;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_font_normal {
|
||
font-weight: normal;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_font_bold {
|
||
font-weight: bold;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_font_italic {
|
||
font-style: italic;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_super {
|
||
font-size: 65%;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_footnote_marks {
|
||
font-size: 75%;
|
||
vertical-align: 0.4em;
|
||
position: initial;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_asterisk {
|
||
font-size: 100%;
|
||
vertical-align: 0;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_indent_1 {
|
||
text-indent: 5px;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_indent_2 {
|
||
text-indent: 10px;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_indent_3 {
|
||
text-indent: 15px;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_indent_4 {
|
||
text-indent: 20px;
|
||
}
|
||
|
||
#cxfgwdyrjq .gt_indent_5 {
|
||
text-indent: 25px;
|
||
}
|
||
|
||
#cxfgwdyrjq .katex-display {
|
||
display: inline-flex !important;
|
||
margin-bottom: 0.75em !important;
|
||
}
|
||
|
||
#cxfgwdyrjq 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-104-1.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="vzbrnozhhi" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
|
||
<style>#vzbrnozhhi 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;
|
||
}
|
||
|
||
#vzbrnozhhi thead, #vzbrnozhhi tbody, #vzbrnozhhi tfoot, #vzbrnozhhi tr, #vzbrnozhhi td, #vzbrnozhhi th {
|
||
border-style: none;
|
||
}
|
||
|
||
#vzbrnozhhi p {
|
||
margin: 0;
|
||
padding: 0;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_caption {
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_bottom_border {
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_column_spanner_outer:first-child {
|
||
padding-left: 0;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_column_spanner_outer:last-child {
|
||
padding-right: 0;
|
||
}
|
||
|
||
#vzbrnozhhi .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%;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_spanner_row {
|
||
border-bottom-style: hidden;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_from_md > :first-child {
|
||
margin-top: 0;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_from_md > :last-child {
|
||
margin-bottom: 0;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_row_group_first td {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_row_group_first th {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_summary_row {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_first_summary_row {
|
||
border-top-style: solid;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_first_summary_row.thick {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_grand_summary_row {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_striped {
|
||
background-color: rgba(128, 128, 128, 0.05);
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_footnote {
|
||
margin: 0px;
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#vzbrnozhhi .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;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_sourcenote {
|
||
font-size: 90%;
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_left {
|
||
text-align: left;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_center {
|
||
text-align: center;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_right {
|
||
text-align: right;
|
||
font-variant-numeric: tabular-nums;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_font_normal {
|
||
font-weight: normal;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_font_bold {
|
||
font-weight: bold;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_font_italic {
|
||
font-style: italic;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_super {
|
||
font-size: 65%;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_footnote_marks {
|
||
font-size: 75%;
|
||
vertical-align: 0.4em;
|
||
position: initial;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_asterisk {
|
||
font-size: 100%;
|
||
vertical-align: 0;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_indent_1 {
|
||
text-indent: 5px;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_indent_2 {
|
||
text-indent: 10px;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_indent_3 {
|
||
text-indent: 15px;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_indent_4 {
|
||
text-indent: 20px;
|
||
}
|
||
|
||
#vzbrnozhhi .gt_indent_5 {
|
||
text-indent: 25px;
|
||
}
|
||
|
||
#vzbrnozhhi .katex-display {
|
||
display: inline-flex !important;
|
||
margin-bottom: 0.75em !important;
|
||
}
|
||
|
||
#vzbrnozhhi 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-107-1.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-107-2.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="hlvzyseljj" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
|
||
<style>#hlvzyseljj 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;
|
||
}
|
||
|
||
#hlvzyseljj thead, #hlvzyseljj tbody, #hlvzyseljj tfoot, #hlvzyseljj tr, #hlvzyseljj td, #hlvzyseljj th {
|
||
border-style: none;
|
||
}
|
||
|
||
#hlvzyseljj p {
|
||
margin: 0;
|
||
padding: 0;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .gt_caption {
|
||
padding-top: 4px;
|
||
padding-bottom: 4px;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .gt_bottom_border {
|
||
border-bottom-style: solid;
|
||
border-bottom-width: 2px;
|
||
border-bottom-color: #D3D3D3;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .gt_column_spanner_outer:first-child {
|
||
padding-left: 0;
|
||
}
|
||
|
||
#hlvzyseljj .gt_column_spanner_outer:last-child {
|
||
padding-right: 0;
|
||
}
|
||
|
||
#hlvzyseljj .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%;
|
||
}
|
||
|
||
#hlvzyseljj .gt_spanner_row {
|
||
border-bottom-style: hidden;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .gt_from_md > :first-child {
|
||
margin-top: 0;
|
||
}
|
||
|
||
#hlvzyseljj .gt_from_md > :last-child {
|
||
margin-bottom: 0;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .gt_row_group_first td {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#hlvzyseljj .gt_row_group_first th {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#hlvzyseljj .gt_summary_row {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#hlvzyseljj .gt_first_summary_row {
|
||
border-top-style: solid;
|
||
border-top-color: #D3D3D3;
|
||
}
|
||
|
||
#hlvzyseljj .gt_first_summary_row.thick {
|
||
border-top-width: 2px;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .gt_grand_summary_row {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
|
||
text-transform: inherit;
|
||
padding-top: 8px;
|
||
padding-bottom: 8px;
|
||
padding-left: 5px;
|
||
padding-right: 5px;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .gt_striped {
|
||
background-color: rgba(128, 128, 128, 0.05);
|
||
}
|
||
|
||
#hlvzyseljj .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;
|
||
}
|
||
|
||
#hlvzyseljj .gt_footnotes {
|
||
color: #333333;
|
||
background-color: #FFFFFF;
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#hlvzyseljj div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after {
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<div>
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|
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|
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|
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|
||
</div>
|
||
<hr>
|
||
<p>How many patients are right censored?</p>
|
||
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|
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<div class="cell-output-display">
|
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<div>
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|
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</div>
|
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</div>
|
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</section>
|
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<section id="challenges-in-survival-analysis-l" class="level2" data-number="17.8">
|
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<h2 data-number="17.8" class="anchored" data-anchor-id="challenges-in-survival-analysis-l"><span class="header-section-number">17.8</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>
|
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<li>Patients not dead before 2000 are not included in the dataset.</li>
|
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</ul></li>
|
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</ul>
|
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</section></details>
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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> |