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  <main id="main"><div class="page-header">
      <img src="../logo.png" class="logo" alt=""><h1>R journal examples</h1>
            
      
      <small class="dont-index">Source: <a href="https://github.com/giabaio/BCEA/blob/HEAD/vignettes/R_journal_examples.Rmd" class="external-link"><code>vignettes/R_journal_examples.Rmd</code></a></small>
      <div class="d-none name"><code>R_journal_examples.Rmd</code></div>
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<!-- these are taken directly from the BCEA book by G Baio -->
<div class="section level2">
<h2 id="smoking-cessation-example">Smoking cessation example<a class="anchor" aria-label="anchor" href="#smoking-cessation-example"></a>
</h2>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/Smoking.html">data</a></span><span class="op">(</span><span class="va">Smoking</span><span class="op">)</span>

<span class="va">treats</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/Smoking.html">c</a></span><span class="op">(</span><span class="st">"No intervention"</span>, <span class="st">"Self-help"</span>, <span class="st">"Individual counselling"</span>, <span class="st">"Group counselling"</span><span class="op">)</span>
<span class="va">bcea_smoke</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/bcea.html">bcea</a></span><span class="op">(</span><span class="va">e</span>, <span class="va">c</span>, ref <span class="op">=</span> <span class="fl">4</span>, interventions <span class="op">=</span> <span class="va">treats</span>, Kmax <span class="op">=</span> <span class="fl">500</span><span class="op">)</span></code></pre></div>
<p>grid of plots</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span>

<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">bcea_smoke</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-4-1.png" width="960"></p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">bcea_smoke</span>, graph <span class="op">=</span> <span class="st">"ggplot2"</span>, wtp <span class="op">=</span> <span class="fl">250</span>, pos <span class="op">=</span> <span class="cn">TRUE</span>, size <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/element.html" class="external-link">rel</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span>, ICER.size <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-4-2.png" width="960"></p>
<p>individual plots cost-effectiveness plane</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/ceplane.plot.html">ceplane.plot</a></span><span class="op">(</span><span class="va">bcea_smoke</span>, comparison <span class="op">=</span> <span class="fl">2</span>, wtp <span class="op">=</span> <span class="fl">250</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-5-1.png" width="576"></p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/setComparisons.html">setComparisons</a></span><span class="op">(</span><span class="va">bcea_smoke</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/Smoking.html">c</a></span><span class="op">(</span><span class="fl">1</span>,<span class="fl">3</span><span class="op">)</span>

<span class="fu"><a href="../reference/ceplane.plot.html">ceplane.plot</a></span><span class="op">(</span><span class="va">bcea_smoke</span>, wtp <span class="op">=</span> <span class="fl">250</span>, graph <span class="op">=</span> <span class="st">"ggplot2"</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-5-2.png" width="576"></p>
<p>other plots</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/eib.plot.html">eib.plot</a></span><span class="op">(</span><span class="va">bcea_smoke</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-6-1.png" width="576"></p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/contour.html">contour</a></span><span class="op">(</span><span class="va">bcea_smoke</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-6-2.png" width="576"></p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/ceac.plot.html">ceac.plot</a></span><span class="op">(</span><span class="va">bcea_smoke</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-6-3.png" width="576"></p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/ib.plot.html">ib.plot</a></span><span class="op">(</span><span class="va">bcea_smoke</span><span class="op">)</span>
<span class="co">#&gt; NB: k (wtp) is defined in the interval [0 - 500]</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-6-4.png" width="576"></p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R">
<span class="fu"><a href="../reference/ceef.plot.html">ceef.plot</a></span><span class="op">(</span><span class="va">bcea_smoke</span><span class="op">)</span>
<span class="co">#&gt; </span>
<span class="co">#&gt; Cost-effectiveness efficiency frontier summary </span>
<span class="co">#&gt; </span>
<span class="co">#&gt; Interventions on the efficiency frontier:</span>
<span class="co">#&gt;                        Effectiveness   Costs Increase slope Increase angle</span>
<span class="co">#&gt; Self-help                    0.48486  94.919         195.77         1.5657</span>
<span class="co">#&gt; Individual counselling       0.72252 143.301         203.57         1.5659</span>
<span class="co">#&gt; </span>
<span class="co">#&gt; Interventions not on the efficiency frontier:</span>
<span class="co">#&gt;                 Effectiveness Costs     Dominance type</span>
<span class="co">#&gt; No intervention             0     0 Extended dominance</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-6-5.png" width="576"></p>
<p>multiple simultaneous comparisons</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">bcea_smoke</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/multi.ce.html">multi.ce</a></span><span class="op">(</span><span class="va">bcea_smoke</span><span class="op">)</span>

<span class="fu"><a href="../reference/ceac.plot.html">ceac.plot</a></span><span class="op">(</span><span class="va">bcea_smoke</span>, pos <span class="op">=</span> <span class="st">"topright"</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-7-1.png" width="576"></p>
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/ceaf.plot.html">ceaf.plot</a></span><span class="op">(</span><span class="va">bcea_smoke</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-7-2.png" width="576"></p>
<p>mixed strategy</p>
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/mixedAn-set.html">mixedAn</a></span><span class="op">(</span><span class="va">bcea_smoke</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/Smoking.html">c</a></span><span class="op">(</span><span class="fl">0.4</span>, <span class="fl">0.3</span>, <span class="fl">0.2</span>, <span class="fl">0.1</span><span class="op">)</span>
<span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">bcea_smoke</span>, wtp <span class="op">=</span> <span class="fl">250</span><span class="op">)</span>
<span class="co">#&gt; </span>
<span class="co">#&gt; Analysis of mixed strategy for willingness to pay parameter k = 250</span>
<span class="co">#&gt; </span>
<span class="co">#&gt; Reference intervention: Group counselling (10.00% market share)</span>
<span class="co">#&gt; Comparator intervention(s): No intervention (40.00% market share)</span>
<span class="co">#&gt;                           : Individual counselling (20.00% market share)</span>
<span class="co">#&gt; </span>
<span class="co">#&gt; Loss in the expected value of information = 34.43</span>
<span class="fu"><a href="../reference/evi.plot.html">evi.plot</a></span><span class="op">(</span><span class="va">bcea_smoke</span>, graph <span class="op">=</span> <span class="st">"ggplot"</span>, pos <span class="op">=</span> <span class="st">"b"</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-8-1.png" width="576"></p>
<p>risk aversion</p>
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">r</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/Smoking.html">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.005</span>, <span class="fl">0.020</span>, <span class="fl">0.035</span><span class="op">)</span>
<span class="fu"><a href="../reference/CEriskav_assign.html">CEriskav</a></span><span class="op">(</span><span class="va">bcea_smoke</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">r</span>

<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">bcea_smoke</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-9-1.png" width="576"><img src="R_journal_examples_files/figure-html/unnamed-chunk-9-2.png" width="576"></p>
</div>
<div class="section level2">
<h2 id="influenza-vaccine-data">Influenza vaccine data<a class="anchor" aria-label="anchor" href="#influenza-vaccine-data"></a>
</h2>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/Smoking.html">data</a></span><span class="op">(</span><span class="va">Vaccine</span><span class="op">)</span>

<span class="va">treats</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/Smoking.html">c</a></span><span class="op">(</span><span class="st">"Status quo"</span>, <span class="st">"Vaccination"</span><span class="op">)</span>
<span class="va">bcea_vacc</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/bcea.html">bcea</a></span><span class="op">(</span><span class="va">e</span>, <span class="va">c</span>, ref <span class="op">=</span> <span class="fl">2</span>, interventions <span class="op">=</span> <span class="va">treats</span><span class="op">)</span></code></pre></div>
<p>grid of plots</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">bcea_vacc</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-11-1.png" width="960"></p>
<p>summary output</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">bcea_vacc</span>, wtp <span class="op">=</span> <span class="fl">10000</span><span class="op">)</span>
<span class="co">#&gt; </span>
<span class="co">#&gt; Cost-effectiveness analysis summary </span>
<span class="co">#&gt; </span>
<span class="co">#&gt; Reference intervention:  Vaccination</span>
<span class="co">#&gt; Comparator intervention: Status quo</span>
<span class="co">#&gt; </span>
<span class="co">#&gt; Optimal decision: choose Status quo for k &lt; 20100 and Vaccination for k &gt;= 20100</span>
<span class="co">#&gt; </span>
<span class="co">#&gt; </span>
<span class="co">#&gt; Analysis for willingness to pay parameter k = 10000</span>
<span class="co">#&gt; </span>
<span class="co">#&gt;             Expected utility</span>
<span class="co">#&gt; Status quo           -36.054</span>
<span class="co">#&gt; Vaccination          -34.826</span>
<span class="co">#&gt; </span>
<span class="co">#&gt;                              EIB  CEAC  ICER</span>
<span class="co">#&gt; Vaccination vs Status quo 1.2284 0.529 20098</span>
<span class="co">#&gt; </span>
<span class="co">#&gt; Optimal intervention (max expected utility) for k = 10000: Status quo</span>
<span class="co">#&gt;            </span>
<span class="co">#&gt; EVPI 3.0287</span>
<span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu"><a href="../reference/sim_table.html">sim_table</a></span><span class="op">(</span><span class="va">bcea_vacc</span>, wtp <span class="op">=</span> <span class="fl">25000</span><span class="op">)</span><span class="op">$</span><span class="va">Table</span><span class="op">)</span>
<span class="co">#&gt;          U1        U2        U*      IB2_1       OL         VI</span>
<span class="co">#&gt; 1 -36.57582 -38.71760 -36.57582 -2.1417866 2.141787  -1.135907</span>
<span class="co">#&gt; 2 -27.92514 -27.67448 -27.67448  0.2506573 0.000000   7.765431</span>
<span class="co">#&gt; 3 -28.03024 -33.37394 -28.03024 -5.3436963 5.343696   7.409665</span>
<span class="co">#&gt; 4 -53.28408 -47.13734 -47.13734  6.1467384 0.000000 -11.697432</span>
<span class="co">#&gt; 5 -43.58389 -40.40469 -40.40469  3.1791976 0.000000  -4.964782</span>
<span class="co">#&gt; 6 -42.37456 -33.08547 -33.08547  9.2890987 0.000000   2.354444</span></code></pre></div>
<p>risk aversion</p>
<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">r</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/Smoking.html">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.005</span>, <span class="fl">0.020</span>, <span class="fl">0.035</span><span class="op">)</span>
<span class="fu"><a href="../reference/CEriskav_assign.html">CEriskav</a></span><span class="op">(</span><span class="va">bcea_vacc</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="va">r</span>

<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">bcea_vacc</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-13-1.png" width="576"><img src="R_journal_examples_files/figure-html/unnamed-chunk-13-2.png" width="576"></p>
<p>value of information</p>
<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="../reference/evi.plot.html">evi.plot</a></span><span class="op">(</span><span class="va">bcea_vacc</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-14-1.png" width="576"></p>
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">inp</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/createInputs.html">createInputs</a></span><span class="op">(</span><span class="va">vaccine_mat</span>, print_is_linear_comb <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>
<span class="fu"><a href="../reference/info.rank.html">info.rank</a></span><span class="op">(</span><span class="va">bcea_vacc</span>, <span class="va">inp</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-15-1.png" width="576"></p>
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">EVPPI</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/evppi.html">evppi</a></span><span class="op">(</span><span class="va">bcea_vacc</span>, <span class="fu"><a href="../reference/Smoking.html">c</a></span><span class="op">(</span><span class="st">"beta.1."</span>, <span class="st">"beta.2."</span><span class="op">)</span>, <span class="va">inp</span><span class="op">$</span><span class="va">mat</span><span class="op">)</span>
<span class="co">#&gt; [1] "method: GAM" "method: GAM"</span>
<span class="co">#&gt; </span>
<span class="co">#&gt; Calculating fitted values for the GAM regression </span>
<span class="co">#&gt; </span>
<span class="co">#&gt; Calculating fitted values for the GAM regression </span>
<span class="co">#&gt; Calculating EVPPI</span>
<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">EVPPI</span><span class="op">)</span></code></pre></div>
<p><img src="R_journal_examples_files/figure-html/unnamed-chunk-16-1.png" width="576"></p>
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