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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.5.54">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<meta name="author" content="Shelby Tisdale, Sam Darby">
<title>Physical Activity and Mortality in the NHANES dataset</title>
<style>
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padding: 0 4px; width: 4em;
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pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
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</style>
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<div class="quarto-title">
<h1 class="title">Physical Activity and Mortality in the NHANES dataset</h1>
<p class="subtitle lead">UMN Equitable Data Science in Adolescent Development Hackathon III</p>
</div>
<div class="quarto-title-meta">
<div>
<div class="quarto-title-meta-heading">Author</div>
<div class="quarto-title-meta-contents">
<p>Shelby Tisdale, Sam Darby </p>
</div>
</div>
</div>
</header>
<section id="research-question" class="level1">
<h1>Research Question</h1>
<p>Is there a causal relationship between high physical activity intensity for the day and mortality?</p>
</section>
<section id="data-preparation" class="level1">
<h1>Data Preparation</h1>
<ul>
<li><strong>Eligibility:</strong> All NHANES participants with mortality data</li>
<li><strong>Exposure definition:</strong> Individual had high average physical activity (TMIMS)</li>
<li><strong>Assignment procedures:</strong>
<ul>
<li>Observed: an individual had high avereage physical activity (TMIMS > 16,000), the individual is classified as “exposed”, otherwise “unexposed”</li>
</ul></li>
<li><strong>Outcome definition:</strong> mortality outcome</li>
<li><strong>Causal contrast of interest:</strong> Average treatment effect</li>
<li><strong>Analyis plan:</strong>
<ul>
<li>Prepare data based on eligibility criteria.</li>
<li>Use DAG to determine potential confounders.</li>
<li>Fit a propensity score model to estimate average treatment effect (ATE) of exposure on outcome.</li>
<li>Create a matched dataset using propensity score model, adjusting for confounders.</li>
<li>Build logistic regression model using matched dataset to determine causal effect of exposure on outcomes</li>
</ul></li>
</ul>
<section id="load-data-and-packages" class="level2">
<h2 class="anchored" data-anchor-id="load-data-and-packages">Load Data and Packages</h2>
<div class="cell">
<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">library</span>(tidyverse)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(gt)</span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(gtsummary)</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(tidymodels)</span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(knitr)</span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(halfmoon)</span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(janitor)</span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(ggdag)</span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(dagitty)</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(MatchIt)</span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(WeightIt)</span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(survey)</span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(marginaleffects)</span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a><span class="co"># load data</span></span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a>nhanes <span class="ot"><-</span> <span class="fu">readRDS</span>(<span class="st">"nhanes_fda_with_r.rds"</span>)</span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a>nhanes <span class="ot"><-</span> nhanes[,<span class="dv">1</span><span class="sc">:</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>
<div class="cell">
<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">set.seed</span>(<span class="dv">123</span>)</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="co"># clean data</span></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>nhanes_clean <span class="ot"><-</span> nhanes <span class="sc">|></span></span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(<span class="sc">-</span><span class="fu">c</span>(SEQN, time, CHD, education)) <span class="sc">|></span></span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">drop_na</span>() <span class="sc">|></span></span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">high_activity =</span> <span class="fu">factor</span>(<span class="fu">if_else</span>(TMIMS <span class="sc">>=</span> <span class="dv">16000</span>, <span class="dv">1</span>, <span class="dv">0</span>)))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</div>
<section id="table-1" class="level3">
<h3 class="anchored" data-anchor-id="table-1">Table 1</h3>
<div class="cell">
<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>nhanes_clean <span class="sc">|></span></span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">mortality =</span> <span class="fu">if_else</span>(event <span class="sc">==</span> <span class="dv">1</span>, <span class="st">"Yes"</span>, <span class="st">"No"</span>)) <span class="sc">|></span></span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">high_activity =</span> <span class="fu">if_else</span>(high_activity <span class="sc">==</span> <span class="dv">1</span>, <span class="st">"Yes"</span>, <span class="st">"No"</span>)) <span class="sc">|></span></span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(</span>
<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a> <span class="st">`</span><span class="at">Death</span><span class="st">`</span> <span class="ot">=</span> event,</span>
<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a> <span class="at">Age =</span> age,</span>
<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a> <span class="at">Gender =</span> gender,</span>
<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a> <span class="at">Race =</span> <span class="fu">fct_relevel</span>(race, </span>
<span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(<span class="st">"Non-Hispanic White"</span>, </span>
<span id="cb3-10"><a href="#cb3-10" aria-hidden="true" tabindex="-1"></a> <span class="st">"Non-Hispanic Black"</span>, </span>
<span id="cb3-11"><a href="#cb3-11" aria-hidden="true" tabindex="-1"></a> <span class="st">"Mexican American"</span>,</span>
<span id="cb3-12"><a href="#cb3-12" aria-hidden="true" tabindex="-1"></a> <span class="st">"Non-Hispanic Asian"</span>,</span>
<span id="cb3-13"><a href="#cb3-13" aria-hidden="true" tabindex="-1"></a> <span class="st">"Other Hispanic"</span>,</span>
<span id="cb3-14"><a href="#cb3-14" aria-hidden="true" tabindex="-1"></a> <span class="st">"Other Race"</span>)),</span>
<span id="cb3-15"><a href="#cb3-15" aria-hidden="true" tabindex="-1"></a> <span class="at">high_physical_activity =</span> <span class="fu">ifelse</span>(high_activity <span class="sc">==</span> <span class="dv">1</span>, </span>
<span id="cb3-16"><a href="#cb3-16" aria-hidden="true" tabindex="-1"></a> <span class="st">"High Physical Activity"</span>,</span>
<span id="cb3-17"><a href="#cb3-17" aria-hidden="true" tabindex="-1"></a> <span class="st">"Low/Moderate Physical Activity"</span>)</span>
<span id="cb3-18"><a href="#cb3-18" aria-hidden="true" tabindex="-1"></a>) <span class="sc">|></span></span>
<span id="cb3-19"><a href="#cb3-19" aria-hidden="true" tabindex="-1"></a> <span class="fu">select</span>(Death, Age, Gender, Race, PIR, BMI, high_physical_activity) <span class="sc">|></span></span>
<span id="cb3-20"><a href="#cb3-20" aria-hidden="true" tabindex="-1"></a> <span class="fu">tbl_summary</span>(<span class="at">by=</span>high_physical_activity)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
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<colgroup>
<col style="width: 50%">
<col style="width: 50%">
</colgroup>
<thead>
<tr class="header gt_col_headings">
<th id="<strong>Characteristic</strong>" class="gt_col_heading gt_columns_bottom_border gt_left" data-quarto-table-cell-role="th" scope="col"><strong>Characteristic</strong></th>
<th id="<strong>Low/Moderate Physical Activity</strong>, N = 7,985<span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>1</sup></span>" class="gt_col_heading gt_columns_bottom_border gt_center" data-quarto-table-cell-role="th" scope="col"><strong>Low/Moderate Physical Activity</strong>, N = 7,985<span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>1</sup></span></th>
</tr>
</thead>
<tbody class="gt_table_body">
<tr class="odd">
<td class="gt_row gt_left" headers="label">Death</td>
<td class="gt_row gt_center" headers="stat_1">738 (9.2%)</td>
</tr>
<tr class="even">
<td class="gt_row gt_left" headers="label">Age</td>
<td class="gt_row gt_center" headers="stat_1">49 (33, 63)</td>
</tr>
<tr class="odd">
<td class="gt_row gt_left" headers="label">Gender</td>
<td class="gt_row gt_center" headers="stat_1"><br>
</td>
</tr>
<tr class="even">
<td class="gt_row gt_left" headers="label"> Male</td>
<td class="gt_row gt_center" headers="stat_1">3,829 (48%)</td>
</tr>
<tr class="odd">
<td class="gt_row gt_left" headers="label"> Female</td>
<td class="gt_row gt_center" headers="stat_1">4,156 (52%)</td>
</tr>
<tr class="even">
<td class="gt_row gt_left" headers="label">Race</td>
<td class="gt_row gt_center" headers="stat_1"><br>
</td>
</tr>
<tr class="odd">
<td class="gt_row gt_left" headers="label"> Non-Hispanic White</td>
<td class="gt_row gt_center" headers="stat_1">3,307 (41%)</td>
</tr>
<tr class="even">
<td class="gt_row gt_left" headers="label"> Non-Hispanic Black</td>
<td class="gt_row gt_center" headers="stat_1">1,864 (23%)</td>
</tr>
<tr class="odd">
<td class="gt_row gt_left" headers="label"> Mexican American</td>
<td class="gt_row gt_center" headers="stat_1">924 (12%)</td>
</tr>
<tr class="even">
<td class="gt_row gt_left" headers="label"> Non-Hispanic Asian</td>
<td class="gt_row gt_center" headers="stat_1">884 (11%)</td>
</tr>
<tr class="odd">
<td class="gt_row gt_left" headers="label"> Other Hispanic</td>
<td class="gt_row gt_center" headers="stat_1">766 (9.6%)</td>
</tr>
<tr class="even">
<td class="gt_row gt_left" headers="label"> Other Race</td>
<td class="gt_row gt_center" headers="stat_1">240 (3.0%)</td>
</tr>
<tr class="odd">
<td class="gt_row gt_left" headers="label">PIR</td>
<td class="gt_row gt_center" headers="stat_1">1.97 (1.02, 3.94)</td>
</tr>
<tr class="even">
<td class="gt_row gt_left" headers="label">BMI</td>
<td class="gt_row gt_center" headers="stat_1">28 (24, 33)</td>
</tr>
</tbody><tfoot class="gt_footnotes">
<tr class="odd">
<td colspan="2" class="gt_footnote"><span class="gt_footnote_marks" style="white-space:nowrap;font-style:italic;font-weight:normal;"><sup>1</sup></span> n (%); Median (IQR)</td>
</tr>
</tfoot>
</table>
</div>
</div>
</div>
</section>
</section>
</section>
<section id="determine-confounders" class="level1">
<h1>Determine Confounders</h1>
<div class="cell">
<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="fu">dagify</span>(mortality <span class="sc">~</span> race <span class="sc">+</span> age <span class="sc">+</span> PIR <span class="sc">+</span> gender,</span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a> high_activity <span class="sc">~</span> age <span class="sc">+</span> BMI <span class="sc">+</span> gender,</span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a> <span class="at">exposure =</span> <span class="st">"high_activity"</span>,</span>
<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a> <span class="at">outcome =</span> <span class="st">"mortality"</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>dag {
BMI
PIR
age
gender
high_activity [exposure]
mortality [outcome]
race
BMI -> high_activity
PIR -> mortality
age -> high_activity
age -> mortality
gender -> high_activity
gender -> mortality
race -> mortality
}</code></pre>
</div>
<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>nhanes_dag <span class="ot"><-</span> <span class="fu">dagify</span>(</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a> mortality <span class="sc">~</span> race <span class="sc">+</span> age <span class="sc">+</span> PIR <span class="sc">+</span> gender,</span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a> high_activity <span class="sc">~</span> age <span class="sc">+</span> BMI <span class="sc">+</span> gender,</span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a> <span class="at">exposure =</span> <span class="st">"high_activity"</span>,</span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a> <span class="at">outcome =</span> <span class="st">"mortality"</span>,</span>
<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a> <span class="at">labels =</span> <span class="fu">c</span>(</span>
<span id="cb6-7"><a href="#cb6-7" aria-hidden="true" tabindex="-1"></a> <span class="at">race =</span> <span class="st">"race"</span>,</span>
<span id="cb6-8"><a href="#cb6-8" aria-hidden="true" tabindex="-1"></a> <span class="at">age =</span> <span class="st">"age"</span>,</span>
<span id="cb6-9"><a href="#cb6-9" aria-hidden="true" tabindex="-1"></a> <span class="at">BMI =</span> <span class="st">"BMI"</span>,</span>
<span id="cb6-10"><a href="#cb6-10" aria-hidden="true" tabindex="-1"></a> <span class="at">PIR =</span> <span class="st">"PIR"</span>,</span>
<span id="cb6-11"><a href="#cb6-11" aria-hidden="true" tabindex="-1"></a> <span class="at">gender =</span> <span class="st">"gender"</span>,</span>
<span id="cb6-12"><a href="#cb6-12" aria-hidden="true" tabindex="-1"></a> <span class="at">high_activity =</span> <span class="st">"high activity"</span>,</span>
<span id="cb6-13"><a href="#cb6-13" aria-hidden="true" tabindex="-1"></a> <span class="at">mortality =</span> <span class="st">"mortality"</span></span>
<span id="cb6-14"><a href="#cb6-14" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb6-15"><a href="#cb6-15" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb6-16"><a href="#cb6-16" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb6-17"><a href="#cb6-17" aria-hidden="true" tabindex="-1"></a><span class="fu">ggdag</span>(nhanes_dag, <span class="at">use_labels =</span> <span class="st">"label"</span>, <span class="at">text =</span> <span class="cn">FALSE</span>) <span class="sc">+</span></span>
<span id="cb6-18"><a href="#cb6-18" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_dag</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="nhanes_files/figure-html/determine-confounders-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
<section id="linear-models-to-evaluate-causal-assumptions" class="level3">
<h3 class="anchored" data-anchor-id="linear-models-to-evaluate-causal-assumptions">Linear models to evaluate causal assumptions</h3>
<div class="cell">
<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="fu">summary</span>(<span class="fu">lm</span>(</span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a> TMIMS <span class="sc">~</span> race <span class="sc">+</span> gender <span class="sc">+</span> age <span class="sc">+</span> BMI, <span class="co"># PIR removed</span></span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> nhanes_clean</span>
<span id="cb7-4"><a href="#cb7-4" 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>
Call:
lm(formula = TMIMS ~ race + gender + age + BMI, data = nhanes_clean)
Residuals:
Min 1Q Median 3Q Max
-17257.3 -2367.5 -181.5 2163.2 22171.1
Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) 19685.147 229.014 85.956 < 2e-16 ***
raceOther Hispanic -280.733 175.632 -1.598 0.11
raceNon-Hispanic White -1867.499 134.588 -13.876 < 2e-16 ***
raceNon-Hispanic Black -1526.584 144.681 -10.551 < 2e-16 ***
raceNon-Hispanic Asian -1675.225 171.538 -9.766 < 2e-16 ***
raceOther Race -1964.253 260.013 -7.554 4.67e-14 ***
genderFemale 847.608 80.608 10.515 < 2e-16 ***
age -72.061 2.221 -32.449 < 2e-16 ***
BMI -64.095 5.840 -10.975 < 2e-16 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Residual standard error: 3587 on 7976 degrees of freedom
Multiple R-squared: 0.1785, Adjusted R-squared: 0.1777
F-statistic: 216.7 on 8 and 7976 DF, p-value: < 2.2e-16</code></pre>
</div>
<div class="sourceCode cell-code" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">summary</span>(<span class="fu">glm</span>(</span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a> event <span class="sc">~</span> race <span class="sc">+</span> gender <span class="sc">+</span> age <span class="sc">+</span> PIR, <span class="co"># BMI removed</span></span>
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a> <span class="at">data =</span> nhanes_clean, <span class="at">family =</span> <span class="fu">binomial</span>(<span class="at">link =</span> <span class="st">"logit"</span>)</span>
<span id="cb9-4"><a href="#cb9-4" 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>
Call:
glm(formula = event ~ race + gender + age + PIR, family = binomial(link = "logit"),
data = nhanes_clean)
Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -7.445481 0.280114 -26.580 < 2e-16 ***
raceOther Hispanic -0.124266 0.230074 -0.540 0.589118
raceNon-Hispanic White 0.594720 0.173681 3.424 0.000617 ***
raceNon-Hispanic Black 0.492681 0.182431 2.701 0.006921 **
raceNon-Hispanic Asian -0.270061 0.252193 -1.071 0.284238
raceOther Race 0.750670 0.322420 2.328 0.019900 *
genderFemale -0.351294 0.087209 -4.028 5.62e-05 ***
age 0.092982 0.003582 25.956 < 2e-16 ***
PIR -0.257182 0.029978 -8.579 < 2e-16 ***
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
(Dispersion parameter for binomial family taken to be 1)
Null deviance: 4920.5 on 7984 degrees of freedom
Residual deviance: 3596.0 on 7976 degrees of freedom
AIC: 3614
Number of Fisher Scoring iterations: 7</code></pre>
</div>
</div>
</section>
<section id="visualize-data-and-assumptions" class="level2">
<h2 class="anchored" data-anchor-id="visualize-data-and-assumptions">Visualize Data and Assumptions</h2>
<section id="positivity-assumption" class="level3">
<h3 class="anchored" data-anchor-id="positivity-assumption">Positivity assumption</h3>
<p>Confounding variables: age, gender, race, BMI, PIR</p>
<section id="outcome-variable" class="level4">
<h4 class="anchored" data-anchor-id="outcome-variable">Outcome Variable</h4>
<div class="cell">
<div class="sourceCode cell-code" id="cb11"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>nhanes_clean <span class="sc">|></span> </span>
<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">mortality =</span> <span class="fu">if_else</span>(event <span class="sc">==</span> <span class="dv">1</span>, <span class="st">"Yes"</span>, <span class="st">"No"</span>)) <span class="sc">|></span></span>
<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">high_activity =</span> <span class="fu">if_else</span>(high_activity <span class="sc">==</span> <span class="dv">1</span>, <span class="st">"Yes"</span>, <span class="st">"No"</span>)) <span class="sc">|></span></span>
<span id="cb11-4"><a href="#cb11-4" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> mortality, <span class="at">group =</span> high_activity, <span class="at">fill =</span> high_activity)) <span class="sc">+</span></span>
<span id="cb11-5"><a href="#cb11-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_bar</span>(<span class="at">position =</span> <span class="fu">position_dodge2</span>(<span class="at">width =</span> <span class="fl">0.9</span>, <span class="at">preserve =</span> <span class="st">"single"</span>)) <span class="sc">+</span></span>
<span id="cb11-6"><a href="#cb11-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_minimal</span>() <span class="sc">+</span></span>
<span id="cb11-7"><a href="#cb11-7" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(<span class="at">title =</span> <span class="st">"Mortality status by activity level"</span>,</span>
<span id="cb11-8"><a href="#cb11-8" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> <span class="st">"Mortality"</span>,</span>
<span id="cb11-9"><a href="#cb11-9" aria-hidden="true" tabindex="-1"></a> <span class="at">fill =</span> <span class="st">"High physical activity"</span>,</span>
<span id="cb11-10"><a href="#cb11-10" aria-hidden="true" tabindex="-1"></a> <span class="at">y =</span> <span class="st">"Count"</span>) <span class="sc">+</span></span>
<span id="cb11-11"><a href="#cb11-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_brewer</span>(<span class="at">palette =</span> <span class="st">"Dark2"</span>) <span class="sc">+</span></span>
<span id="cb11-12"><a href="#cb11-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">legend.position =</span> <span class="st">"bottom"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="nhanes_files/figure-html/visualize-confounders-1-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
</section>
<section id="confounding-variables" class="level4">
<h4 class="anchored" data-anchor-id="confounding-variables">Confounding Variables</h4>
<div class="cell">
<div class="sourceCode cell-code" id="cb12"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a>nhanes_clean <span class="sc">|></span> </span>
<span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">mortality =</span> <span class="fu">if_else</span>(event <span class="sc">==</span> <span class="dv">1</span>, <span class="st">"Yes"</span>, <span class="st">"No"</span>)) <span class="sc">|></span></span>
<span id="cb12-3"><a href="#cb12-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">high_activity =</span> <span class="fu">if_else</span>(high_activity <span class="sc">==</span> <span class="dv">1</span>, <span class="st">"Yes"</span>, <span class="st">"No"</span>)) <span class="sc">|></span></span>
<span id="cb12-4"><a href="#cb12-4" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(</span>
<span id="cb12-5"><a href="#cb12-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">aes</span>(</span>
<span id="cb12-6"><a href="#cb12-6" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> age,</span>
<span id="cb12-7"><a href="#cb12-7" aria-hidden="true" tabindex="-1"></a> <span class="at">group =</span> high_activity,</span>
<span id="cb12-8"><a href="#cb12-8" aria-hidden="true" tabindex="-1"></a> <span class="at">fill =</span> high_activity</span>
<span id="cb12-9"><a href="#cb12-9" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb12-10"><a href="#cb12-10" aria-hidden="true" tabindex="-1"></a>) <span class="sc">+</span></span>
<span id="cb12-11"><a href="#cb12-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_mirror_histogram</span>(<span class="at">bins =</span> <span class="dv">20</span>) <span class="sc">+</span></span>
<span id="cb12-12"><a href="#cb12-12" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(</span>
<span id="cb12-13"><a href="#cb12-13" aria-hidden="true" tabindex="-1"></a> <span class="at">fill =</span> <span class="st">"High physical activity"</span>,</span>
<span id="cb12-14"><a href="#cb12-14" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> <span class="st">"Age"</span>,</span>
<span id="cb12-15"><a href="#cb12-15" aria-hidden="true" tabindex="-1"></a> <span class="at">title =</span> <span class="st">"Activity level by age"</span>,</span>
<span id="cb12-16"><a href="#cb12-16" aria-hidden="true" tabindex="-1"></a> <span class="at">y =</span> <span class="st">"Count"</span></span>
<span id="cb12-17"><a href="#cb12-17" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb12-18"><a href="#cb12-18" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_minimal</span>() <span class="sc">+</span></span>
<span id="cb12-19"><a href="#cb12-19" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_brewer</span>(<span class="at">palette =</span> <span class="st">"Dark2"</span>) <span class="sc">+</span></span>
<span id="cb12-20"><a href="#cb12-20" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">legend.position =</span> <span class="st">"bottom"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="nhanes_files/figure-html/unnamed-chunk-7-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
<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>nhanes_clean <span class="sc">|></span> </span>
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">high_activity =</span> <span class="fu">if_else</span>(high_activity <span class="sc">==</span> <span class="dv">1</span>, <span class="st">"Yes"</span>, <span class="st">"No"</span>)) <span class="sc">|></span></span>
<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> gender, <span class="at">group =</span> high_activity, <span class="at">fill =</span> high_activity)) <span class="sc">+</span></span>
<span id="cb13-4"><a href="#cb13-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_bar</span>(<span class="at">position =</span> <span class="fu">position_dodge2</span>(<span class="at">width =</span> <span class="fl">0.9</span>, <span class="at">preserve =</span> <span class="st">"single"</span>)) <span class="sc">+</span></span>
<span id="cb13-5"><a href="#cb13-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_minimal</span>() <span class="sc">+</span></span>
<span id="cb13-6"><a href="#cb13-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(<span class="at">title =</span> <span class="st">"Activity level by gender"</span>,</span>
<span id="cb13-7"><a href="#cb13-7" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> <span class="st">"Gender"</span>,</span>
<span id="cb13-8"><a href="#cb13-8" aria-hidden="true" tabindex="-1"></a> <span class="at">fill =</span> <span class="st">"High physical activity"</span>,</span>
<span id="cb13-9"><a href="#cb13-9" aria-hidden="true" tabindex="-1"></a> <span class="at">y =</span> <span class="st">"Count"</span>) <span class="sc">+</span></span>
<span id="cb13-10"><a href="#cb13-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_brewer</span>(<span class="at">palette =</span> <span class="st">"Dark2"</span>) <span class="sc">+</span></span>
<span id="cb13-11"><a href="#cb13-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">legend.position =</span> <span class="st">"bottom"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="nhanes_files/figure-html/unnamed-chunk-8-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb14"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a>nhanes_clean <span class="sc">|></span></span>
<span id="cb14-2"><a href="#cb14-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">high_activity =</span> <span class="fu">if_else</span>(high_activity <span class="sc">==</span> <span class="dv">1</span>, <span class="st">"Yes"</span>, <span class="st">"No"</span>)) <span class="sc">|></span></span>
<span id="cb14-3"><a href="#cb14-3" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(</span>
<span id="cb14-4"><a href="#cb14-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">aes</span>(</span>
<span id="cb14-5"><a href="#cb14-5" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> PIR,</span>
<span id="cb14-6"><a href="#cb14-6" aria-hidden="true" tabindex="-1"></a> <span class="at">group =</span> high_activity,</span>
<span id="cb14-7"><a href="#cb14-7" aria-hidden="true" tabindex="-1"></a> <span class="at">fill =</span> high_activity</span>
<span id="cb14-8"><a href="#cb14-8" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb14-9"><a href="#cb14-9" aria-hidden="true" tabindex="-1"></a>) <span class="sc">+</span></span>
<span id="cb14-10"><a href="#cb14-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_mirror_histogram</span>(<span class="at">bins =</span> <span class="dv">20</span>) <span class="sc">+</span></span>
<span id="cb14-11"><a href="#cb14-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(</span>
<span id="cb14-12"><a href="#cb14-12" aria-hidden="true" tabindex="-1"></a> <span class="at">fill =</span> <span class="st">"High physical activity"</span>,</span>
<span id="cb14-13"><a href="#cb14-13" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> <span class="st">"PIR"</span>,</span>
<span id="cb14-14"><a href="#cb14-14" aria-hidden="true" tabindex="-1"></a> <span class="at">title =</span> <span class="st">"Activity level by poverty-income ratio"</span>,</span>
<span id="cb14-15"><a href="#cb14-15" aria-hidden="true" tabindex="-1"></a> <span class="at">y =</span> <span class="st">"Count"</span></span>
<span id="cb14-16"><a href="#cb14-16" aria-hidden="true" tabindex="-1"></a> ) <span class="sc">+</span></span>
<span id="cb14-17"><a href="#cb14-17" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_minimal</span>() <span class="sc">+</span></span>
<span id="cb14-18"><a href="#cb14-18" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_brewer</span>(<span class="at">palette =</span> <span class="st">"Dark2"</span>) <span class="sc">+</span></span>
<span id="cb14-19"><a href="#cb14-19" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">legend.position =</span> <span class="st">"bottom"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="nhanes_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="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>nhanes_clean <span class="sc">|></span> </span>
<span id="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">high_activity =</span> <span class="fu">if_else</span>(high_activity <span class="sc">==</span> <span class="dv">1</span>, <span class="st">"Yes"</span>, <span class="st">"No"</span>)) <span class="sc">|></span></span>
<span id="cb15-3"><a href="#cb15-3" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(<span class="fu">aes</span>(<span class="at">x =</span> race, <span class="at">group =</span> high_activity, <span class="at">fill =</span> high_activity)) <span class="sc">+</span></span>
<span id="cb15-4"><a href="#cb15-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_bar</span>(<span class="at">position =</span> <span class="fu">position_dodge2</span>(<span class="at">width =</span> <span class="fl">0.9</span>, <span class="at">preserve =</span> <span class="st">"single"</span>)) <span class="sc">+</span></span>
<span id="cb15-5"><a href="#cb15-5" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme_minimal</span>() <span class="sc">+</span></span>
<span id="cb15-6"><a href="#cb15-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(<span class="at">title =</span> <span class="st">"Activity level by race"</span>,</span>
<span id="cb15-7"><a href="#cb15-7" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> <span class="st">"Race"</span>,</span>
<span id="cb15-8"><a href="#cb15-8" aria-hidden="true" tabindex="-1"></a> <span class="at">fill =</span> <span class="st">"High physical activity"</span>,</span>
<span id="cb15-9"><a href="#cb15-9" aria-hidden="true" tabindex="-1"></a> <span class="at">y =</span> <span class="st">"Count"</span>) <span class="sc">+</span></span>
<span id="cb15-10"><a href="#cb15-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">scale_fill_brewer</span>(<span class="at">palette =</span> <span class="st">"Dark2"</span>) <span class="sc">+</span></span>
<span id="cb15-11"><a href="#cb15-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">theme</span>(<span class="at">legend.position =</span> <span class="st">"bottom"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<div class="cell-output-display">
<div>
<figure class="figure">
<p><img src="nhanes_files/figure-html/unnamed-chunk-10-1.png" class="img-fluid figure-img" width="672"></p>
</figure>
</div>
</div>
</div>
<div class="cell">
<div class="sourceCode cell-code" id="cb16"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a>nhanes_clean <span class="sc">|></span></span>
<span id="cb16-2"><a href="#cb16-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate</span>(<span class="at">high_activity =</span> <span class="fu">if_else</span>(high_activity <span class="sc">==</span> <span class="dv">1</span>, <span class="st">"Yes"</span>, <span class="st">"No"</span>)) <span class="sc">|></span></span>
<span id="cb16-3"><a href="#cb16-3" aria-hidden="true" tabindex="-1"></a><span class="fu">ggplot</span>(</span>
<span id="cb16-4"><a href="#cb16-4" aria-hidden="true" tabindex="-1"></a> <span class="fu">aes</span>(</span>
<span id="cb16-5"><a href="#cb16-5" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> BMI,</span>
<span id="cb16-6"><a href="#cb16-6" aria-hidden="true" tabindex="-1"></a> <span class="at">group =</span> high_activity,</span>
<span id="cb16-7"><a href="#cb16-7" aria-hidden="true" tabindex="-1"></a> <span class="at">fill =</span> high_activity</span>
<span id="cb16-8"><a href="#cb16-8" aria-hidden="true" tabindex="-1"></a> )</span>
<span id="cb16-9"><a href="#cb16-9" aria-hidden="true" tabindex="-1"></a>) <span class="sc">+</span></span>
<span id="cb16-10"><a href="#cb16-10" aria-hidden="true" tabindex="-1"></a> <span class="fu">geom_mirror_histogram</span>(<span class="at">bins =</span> <span class="dv">20</span>) <span class="sc">+</span></span>
<span id="cb16-11"><a href="#cb16-11" aria-hidden="true" tabindex="-1"></a> <span class="fu">labs</span>(</span>
<span id="cb16-12"><a href="#cb16-12" aria-hidden="true" tabindex="-1"></a> <span class="at">fill =</span> <span class="st">"High physical activity"</span>,</span>
<span id="cb16-13"><a href="#cb16-13" aria-hidden="true" tabindex="-1"></a> <span class="at">x =</span> <span class="st">"BMI"</span>,</span>
<span id="cb16-14"><a href="#cb16-14" aria-hidden="true" tabindex="-1"></a> <span class="at">title =</span> <span class="st">"Activity level by BMI"</span>,</span>