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<img src="../logo.svg" class="logo" alt=""><h1>Estimating Empirical Coverage with WISCA</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/WISCA.Rmd" class="external-link"><code>vignettes/WISCA.Rmd</code></a></small>
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<div class="d-none name"><code>WISCA.Rmd</code></div>
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<blockquote>
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<p>This explainer was largely written by our <a href="https://chat.amr-for-r.org" class="external-link">AMR for R Assistant</a>, a ChatGPT
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manually-trained model able to answer any question about the
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<code>AMR</code> package.</p>
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</blockquote>
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<div class="section level2">
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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<p>Clinical guidelines for empirical antimicrobial therapy require
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<em>probabilistic reasoning</em>: what is the chance that a regimen will
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cover the likely infecting organisms, before culture results are
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available?</p>
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<p>This is the purpose of <strong>WISCA</strong>, or
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<strong>Weighted-Incidence Syndromic Combination
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Antibiogram</strong>.</p>
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<p>WISCA is a Bayesian approach that integrates:</p>
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<ul>
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<li>
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<strong>Pathogen prevalence</strong> (how often each species causes
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the syndrome),</li>
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<li>
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<strong>Regimen susceptibility</strong> (how often a regimen works
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<em>if</em> the pathogen is known),</li>
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</ul>
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<p>to estimate the <strong>overall empirical coverage</strong> of
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antimicrobial regimens, with quantified uncertainty.</p>
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<p>This vignette explains how WISCA works, why it is useful, and how to
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apply it using the <code>AMR</code> package.</p>
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</div>
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<div class="section level2">
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<h2 id="why-traditional-antibiograms-fall-short">Why traditional antibiograms fall short<a class="anchor" aria-label="anchor" href="#why-traditional-antibiograms-fall-short"></a>
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</h2>
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<p>A standard antibiogram gives you:</p>
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<pre><code>Species → Antibiotic → Susceptibility %</code></pre>
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<p>But clinicians don’t know the species <em>a priori</em>. They need to
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choose a regimen that covers the <strong>likely pathogens</strong>,
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without knowing which one is present.</p>
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<p>Traditional antibiograms calculate the susceptibility % as just the
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number of resistant isolates divided by the total number of tested
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isolates. Therefore, traditional antibiograms:</p>
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<ul>
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<li>Fragment information by organism,</li>
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<li>Do not weight by real-world prevalence,</li>
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<li>Do not account for combination therapy or sample size,</li>
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<li>Do not provide uncertainty.</li>
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</ul>
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</div>
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<div class="section level2">
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<h2 id="the-idea-of-wisca">The idea of WISCA<a class="anchor" aria-label="anchor" href="#the-idea-of-wisca"></a>
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</h2>
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<p>WISCA asks:</p>
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<blockquote>
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<p>“What is the <strong>probability</strong> that this regimen
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<strong>will cover</strong> the pathogen, given the syndrome?”</p>
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</blockquote>
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<p>This means combining two things:</p>
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<ul>
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<li>
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<strong>Incidence</strong> of each pathogen in the syndrome,</li>
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<li>
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<strong>Susceptibility</strong> of each pathogen to the
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regimen.</li>
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</ul>
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<p>We can write this as:</p>
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<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Coverage</mtext><mo>=</mo><munder><mo>∑</mo><mi>i</mi></munder><mrow><mo stretchy="true" form="prefix">(</mo><msub><mtext mathvariant="normal">Incidence</mtext><mi>i</mi></msub><mo>×</mo><msub><mtext mathvariant="normal">Susceptibility</mtext><mi>i</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\text{Coverage} = \sum_i (\text{Incidence}_i \times \text{Susceptibility}_i)</annotation></semantics></math></p>
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<p>For example, suppose:</p>
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<ul>
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<li>
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<em>E. coli</em> causes 60% of cases, and 90% of <em>E. coli</em>
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are susceptible to a drug.</li>
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<li>
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<em>Klebsiella</em> causes 40% of cases, and 70% of
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<em>Klebsiella</em> are susceptible.</li>
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</ul>
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<p>Then:</p>
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<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Coverage</mtext><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>0.6</mn><mo>×</mo><mn>0.9</mn><mo stretchy="true" form="postfix">)</mo></mrow><mo>+</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>0.4</mn><mo>×</mo><mn>0.7</mn><mo stretchy="true" form="postfix">)</mo></mrow><mo>=</mo><mn>0.82</mn></mrow><annotation encoding="application/x-tex">\text{Coverage} = (0.6 \times 0.9) + (0.4 \times 0.7) = 0.82</annotation></semantics></math></p>
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<p>But in real data, incidence and susceptibility are <strong>estimated
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from samples</strong>, so they carry uncertainty. WISCA models this
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<strong>probabilistically</strong>, using conjugate Bayesian
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distributions.</p>
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</div>
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<div class="section level2">
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<h2 id="the-bayesian-engine-behind-wisca">The Bayesian engine behind WISCA<a class="anchor" aria-label="anchor" href="#the-bayesian-engine-behind-wisca"></a>
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</h2>
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<div class="section level3">
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<h3 id="pathogen-incidence">Pathogen incidence<a class="anchor" aria-label="anchor" href="#pathogen-incidence"></a>
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</h3>
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<p>Let:</p>
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<ul>
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<li>
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<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>K</mi><annotation encoding="application/x-tex">K</annotation></semantics></math>
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be the number of pathogens,</li>
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<li>
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<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>α</mi><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>,</mo><mn>1</mn><mo>,</mo><mi>…</mi><mo>,</mo><mn>1</mn><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\alpha = (1, 1, \ldots, 1)</annotation></semantics></math>
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be a <strong>Dirichlet</strong> prior (uniform),</li>
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<li>
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<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>n</mi><mo>=</mo><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>n</mi><mn>1</mn></msub><mo>,</mo><mi>…</mi><mo>,</mo><msub><mi>n</mi><mi>K</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">n = (n_1, \ldots, n_K)</annotation></semantics></math>
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be the observed counts per species.</li>
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</ul>
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<p>Then the posterior incidence is:</p>
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<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>p</mi><mo>∼</mo><mtext mathvariant="normal">Dirichlet</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mn>1</mn></msub><mo>+</mo><msub><mi>n</mi><mn>1</mn></msub><mo>,</mo><mi>…</mi><mo>,</mo><msub><mi>α</mi><mi>K</mi></msub><mo>+</mo><msub><mi>n</mi><mi>K</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">p \sim \text{Dirichlet}(\alpha_1 + n_1, \ldots, \alpha_K + n_K)</annotation></semantics></math></p>
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<p>To simulate from this, we use:</p>
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<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>x</mi><mi>i</mi></msub><mo>∼</mo><mtext mathvariant="normal">Gamma</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mi>i</mi></msub><mo>+</mo><msub><mi>n</mi><mi>i</mi></msub><mo>,</mo><mspace width="0.222em"></mspace><mn>1</mn><mo stretchy="true" form="postfix">)</mo></mrow><mo>,</mo><mspace width="1.0em"></mspace><msub><mi>p</mi><mi>i</mi></msub><mo>=</mo><mfrac><msub><mi>x</mi><mi>i</mi></msub><mrow><munderover><mo>∑</mo><mrow><mi>j</mi><mo>=</mo><mn>1</mn></mrow><mi>K</mi></munderover><msub><mi>x</mi><mi>j</mi></msub></mrow></mfrac></mrow><annotation encoding="application/x-tex">x_i \sim \text{Gamma}(\alpha_i + n_i,\ 1), \quad p_i = \frac{x_i}{\sum_{j=1}^{K} x_j}</annotation></semantics></math></p>
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</div>
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<div class="section level3">
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<h3 id="susceptibility">Susceptibility<a class="anchor" aria-label="anchor" href="#susceptibility"></a>
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</h3>
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<p>Each pathogen–regimen pair has a prior and data:</p>
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<ul>
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<li>Prior:
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<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Beta</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mn>0</mn></msub><mo>,</mo><msub><mi>β</mi><mn>0</mn></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\text{Beta}(\alpha_0, \beta_0)</annotation></semantics></math>,
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with default
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<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>α</mi><mn>0</mn></msub><mo>=</mo><msub><mi>β</mi><mn>0</mn></msub><mo>=</mo><mn>1</mn></mrow><annotation encoding="application/x-tex">\alpha_0 = \beta_0 = 1</annotation></semantics></math>
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</li>
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<li>Data:
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<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>S</mi><annotation encoding="application/x-tex">S</annotation></semantics></math>
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susceptible out of
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<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>N</mi><annotation encoding="application/x-tex">N</annotation></semantics></math>
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tested</li>
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</ul>
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<p>The
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<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mi>S</mi><annotation encoding="application/x-tex">S</annotation></semantics></math>
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category could also include values SDD (susceptible, dose-dependent) and
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I (intermediate [CLSI], or susceptible, increased exposure
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[EUCAST]).</p>
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<p>Then the posterior is:</p>
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<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>θ</mi><mo>∼</mo><mtext mathvariant="normal">Beta</mtext><mrow><mo stretchy="true" form="prefix">(</mo><msub><mi>α</mi><mn>0</mn></msub><mo>+</mo><mi>S</mi><mo>,</mo><mspace width="0.222em"></mspace><msub><mi>β</mi><mn>0</mn></msub><mo>+</mo><mi>N</mi><mo>−</mo><mi>S</mi><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\theta \sim \text{Beta}(\alpha_0 + S,\ \beta_0 + N - S)</annotation></semantics></math></p>
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</div>
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<div class="section level3">
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<h3 id="final-coverage-estimate">Final coverage estimate<a class="anchor" aria-label="anchor" href="#final-coverage-estimate"></a>
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</h3>
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<p>Putting it together:</p>
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<ol style="list-style-type: decimal">
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<li>Simulate pathogen incidence:
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<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mi>𝐩</mi><mo>∼</mo><mtext mathvariant="normal">Dirichlet</mtext></mrow><annotation encoding="application/x-tex">\boldsymbol{p} \sim \text{Dirichlet}</annotation></semantics></math>
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</li>
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<li>Simulate susceptibility:
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<math display="inline" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><msub><mi>θ</mi><mi>i</mi></msub><mo>∼</mo><mtext mathvariant="normal">Beta</mtext><mrow><mo stretchy="true" form="prefix">(</mo><mn>1</mn><mo>+</mo><msub><mi>S</mi><mi>i</mi></msub><mo>,</mo><mspace width="0.222em"></mspace><mn>1</mn><mo>+</mo><msub><mi>R</mi><mi>i</mi></msub><mo stretchy="true" form="postfix">)</mo></mrow></mrow><annotation encoding="application/x-tex">\theta_i \sim \text{Beta}(1 + S_i,\ 1 + R_i)</annotation></semantics></math>
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</li>
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<li>Combine:</li>
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</ol>
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<p><math display="block" xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext mathvariant="normal">Coverage</mtext><mo>=</mo><munderover><mo>∑</mo><mrow><mi>i</mi><mo>=</mo><mn>1</mn></mrow><mi>K</mi></munderover><msub><mi>p</mi><mi>i</mi></msub><mo>⋅</mo><msub><mi>θ</mi><mi>i</mi></msub></mrow><annotation encoding="application/x-tex">\text{Coverage} = \sum_{i=1}^{K} p_i \cdot \theta_i</annotation></semantics></math></p>
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<p>Repeat this simulation (e.g. 1000×) and summarise:</p>
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<ul>
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<li>
|
||
<strong>Mean</strong> = expected coverage</li>
|
||
<li>
|
||
<strong>Quantiles</strong> = credible interval</li>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="practical-use-in-the-amr-package">Practical use in the <code>AMR</code> package<a class="anchor" aria-label="anchor" href="#practical-use-in-the-amr-package"></a>
|
||
</h2>
|
||
<div class="section level3">
|
||
<h3 id="prepare-data-and-simulate-synthetic-syndrome">Prepare data and simulate synthetic syndrome<a class="anchor" aria-label="anchor" href="#prepare-data-and-simulate-synthetic-syndrome"></a>
|
||
</h3>
|
||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><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://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
|
||
<span><span class="va">data</span> <span class="op"><-</span> <span class="va">example_isolates</span></span>
|
||
<span></span>
|
||
<span><span class="co"># Structure of our data</span></span>
|
||
<span><span class="va">data</span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
|
||
<span><span class="co">#> date patient age gender ward mo PEN OXA FLC AMX </span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># ℹ 1,990 more rows</span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,</span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,</span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …</span></span></span>
|
||
<span></span>
|
||
<span><span class="co"># Add a fake syndrome column</span></span>
|
||
<span><span class="va">data</span><span class="op">$</span><span class="va">syndrome</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">data</span><span class="op">$</span><span class="va">mo</span> <span class="op"><a href="../reference/like.html">%like%</a></span> <span class="st">"coli"</span>, <span class="st">"UTI"</span>, <span class="st">"No UTI"</span><span class="op">)</span></span></code></pre></div>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="basic-wisca-antibiogram">Basic WISCA antibiogram<a class="anchor" aria-label="anchor" href="#basic-wisca-antibiogram"></a>
|
||
</h3>
|
||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
|
||
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"CIP"</span>, <span class="st">"GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
|
||
<table class="table">
|
||
<thead><tr class="header">
|
||
<th align="left">Amoxicillin/clavulanic acid</th>
|
||
<th align="left">Ciprofloxacin</th>
|
||
<th align="left">Gentamicin</th>
|
||
</tr></thead>
|
||
<tbody><tr class="odd">
|
||
<td align="left">73.7% (71.7-75.8%)</td>
|
||
<td align="left">77% (74.3-79.4%)</td>
|
||
<td align="left">72.8% (70.7-74.8%)</td>
|
||
</tr></tbody>
|
||
</table>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="use-combination-regimens">Use combination regimens<a class="anchor" aria-label="anchor" href="#use-combination-regimens"></a>
|
||
</h3>
|
||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
|
||
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="24%">
|
||
<col width="38%">
|
||
<col width="36%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="left">Amoxicillin/clavulanic acid</th>
|
||
<th align="left">Amoxicillin/clavulanic acid + Ciprofloxacin</th>
|
||
<th align="left">Amoxicillin/clavulanic acid + Gentamicin</th>
|
||
</tr></thead>
|
||
<tbody><tr class="odd">
|
||
<td align="left">73.8% (71.8-75.7%)</td>
|
||
<td align="left">87.5% (85.9-89%)</td>
|
||
<td align="left">89.7% (88.2-91.1%)</td>
|
||
</tr></tbody>
|
||
</table>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="stratify-by-syndrome">Stratify by syndrome<a class="anchor" aria-label="anchor" href="#stratify-by-syndrome"></a>
|
||
</h3>
|
||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
|
||
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span>
|
||
<span> syndromic_group <span class="op">=</span> <span class="st">"syndrome"</span><span class="op">)</span></span></code></pre></div>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="12%">
|
||
<col width="21%">
|
||
<col width="34%">
|
||
<col width="31%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="left">Syndromic Group</th>
|
||
<th align="left">Amoxicillin/clavulanic acid</th>
|
||
<th align="left">Amoxicillin/clavulanic acid + Ciprofloxacin</th>
|
||
<th align="left">Amoxicillin/clavulanic acid + Gentamicin</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="left">No UTI</td>
|
||
<td align="left">70.1% (67.8-72.3%)</td>
|
||
<td align="left">85.2% (83.1-87.2%)</td>
|
||
<td align="left">87.1% (85.3-88.7%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">UTI</td>
|
||
<td align="left">80.9% (77.7-83.8%)</td>
|
||
<td align="left">88.2% (85.7-90.5%)</td>
|
||
<td align="left">90.9% (88.7-93%)</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>The <code>AMR</code> package is available in 20 languages, which can
|
||
all be used for the <code><a href="../reference/antibiogram.html">wisca()</a></code> function too:</p>
|
||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">data</span>,</span>
|
||
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC + CIP"</span>, <span class="st">"AMC + GEN"</span><span class="op">)</span>,</span>
|
||
<span> syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/grep.html" class="external-link">gsub</a></span><span class="op">(</span><span class="st">"UTI"</span>, <span class="st">"UCI"</span>, <span class="va">data</span><span class="op">$</span><span class="va">syndrome</span><span class="op">)</span>,</span>
|
||
<span> language <span class="op">=</span> <span class="st">"Spanish"</span><span class="op">)</span></span></code></pre></div>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="12%">
|
||
<col width="21%">
|
||
<col width="34%">
|
||
<col width="31%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="left">Grupo sindrómico</th>
|
||
<th align="left">Amoxicilina/ácido clavulánico</th>
|
||
<th align="left">Amoxicilina/ácido clavulánico + Ciprofloxacina</th>
|
||
<th align="left">Amoxicilina/ácido clavulánico + Gentamicina</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="left">No UCI</td>
|
||
<td align="left">70% (67.8-72.4%)</td>
|
||
<td align="left">85.3% (83.3-87.2%)</td>
|
||
<td align="left">87% (85.3-88.8%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">UCI</td>
|
||
<td align="left">80.9% (77.7-83.9%)</td>
|
||
<td align="left">88.2% (85.5-90.6%)</td>
|
||
<td align="left">90.9% (88.7-93%)</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="sensible-defaults-which-can-be-customised">Sensible defaults, which can be customised<a class="anchor" aria-label="anchor" href="#sensible-defaults-which-can-be-customised"></a>
|
||
</h2>
|
||
<ul>
|
||
<li>
|
||
<code>simulations = 1000</code>: number of Monte Carlo draws</li>
|
||
<li>
|
||
<code>conf_interval = 0.95</code>: coverage interval width</li>
|
||
<li>
|
||
<code>combine_SI = TRUE</code>: count “I” and “SDD” as
|
||
susceptible</li>
|
||
</ul>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="limitations">Limitations<a class="anchor" aria-label="anchor" href="#limitations"></a>
|
||
</h2>
|
||
<ul>
|
||
<li>It assumes your data are representative</li>
|
||
<li>No adjustment for patient-level covariates, although these could be
|
||
passed onto the <code>syndromic_group</code> argument</li>
|
||
<li>WISCA does not model resistance over time, you might want to use
|
||
<code>tidymodels</code> for that, for which we <a href="https://amr-for-r.org/articles/AMR_with_tidymodels.html">wrote a
|
||
basic introduction</a>
|
||
</li>
|
||
</ul>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
|
||
</h2>
|
||
<p>WISCA enables:</p>
|
||
<ul>
|
||
<li>Empirical regimen comparison,</li>
|
||
<li>Syndrome-specific coverage estimation,</li>
|
||
<li>Fully probabilistic interpretation.</li>
|
||
</ul>
|
||
<p>It is available in the <code>AMR</code> package via either:</p>
|
||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span><span class="va">...</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">...</span>, wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="reference">Reference<a class="anchor" aria-label="anchor" href="#reference"></a>
|
||
</h2>
|
||
<p>Bielicki, JA, et al. (2016). <em>Selecting appropriate empirical
|
||
antibiotic regimens for paediatric bloodstream infections: application
|
||
of a Bayesian decision model to local and pooled antimicrobial
|
||
resistance surveillance data.</em> <strong>J Antimicrob
|
||
Chemother</strong>. 71(3):794-802. <a href="https://doi.org/10.1093/jac/dkv397" class="external-link uri">https://doi.org/10.1093/jac/dkv397</a></p>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||
</nav></aside>
|
||
</div>
|
||
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown-footer-right">
|
||
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
|
||
</div>
|
||
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