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Built site for AMR@2.1.1.9163: 07efc29
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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9160</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9163</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -430,7 +430,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"atc"</span>,</span></span>
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<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></span>
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<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 5</span></span>
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@ -444,7 +445,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
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<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span></span></span>
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<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"name"</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 5 × 3</span></span>
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<span class="r-out co"><span class="r-pr">#></span> Pathogen Imipenem Meropenem </span>
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@ -463,7 +465,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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<span class="r-in"><span><span class="co"># combined antibiotics yield higher empiric coverage</span></span></span>
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<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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<span class="r-in"><span> antibiotics <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">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></span>
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<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 4</span></span>
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<span class="r-out co"><span class="r-pr">#></span> Pathogen Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³</span>
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<span class="r-out co"><span class="r-pr">#></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;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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@ -480,7 +483,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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<span class="r-in"><span> antibiotics <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">"Cipro"</span>, <span class="st">"cipro + genta"</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span></span>
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<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
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<span class="r-in"><span> sep <span class="op">=</span> <span class="st">" & "</span><span class="op">)</span></span></span>
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<span class="r-in"><span> sep <span class="op">=</span> <span class="st">" & "</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 3</span></span>
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<span class="r-out co"><span class="r-pr">#></span> Pathogen Ciprofloxacin `Ciprofloxacin & Gentamicin`</span>
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<span class="r-out co"><span class="r-pr">#></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;"><chr></span> </span>
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@ -495,7 +499,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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<span class="r-in"><span><span class="co"># the data set could contain a filter for e.g. respiratory specimens</span></span></span>
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<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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<span class="r-in"><span> antibiotics <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="fu"><a href="antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span></span>
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<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
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@ -532,7 +537,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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<span class="r-in"><span> syndromic_group <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">ex1</span><span class="op">$</span><span class="va">ward</span> <span class="op">==</span> <span class="st">"ICU"</span>,</span></span>
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<span class="r-in"><span> <span class="st">"UCI"</span>, <span class="st">"No UCI"</span></span></span>
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<span class="r-in"><span> <span class="op">)</span>,</span></span>
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<span class="r-in"><span> language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span></span></span>
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<span class="r-in"><span> language <span class="op">=</span> <span class="st">"es"</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># An Antibiogram (non-WISCA / 95% CI): 2 × 5</span></span>
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@ -550,7 +556,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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<span class="r-in"><span> antibiotics <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">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span>,</span></span>
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<span class="r-in"><span> wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-in"><span> wisca <span class="op">=</span> <span class="cn">TRUE</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># An Antibiogram (WISCA / 95% CI): 3 × 4</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `Syndromic Group` `Piperacillin/tazobactam` Piperacillin/tazobactam + Gentam…¹</span>
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<span class="r-out co"><span class="r-pr">#></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;"><chr></span> </span>
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@ -568,7 +575,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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<span class="r-in"><span><span class="va">ureido</span> <span class="op"><-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_selectors.html">ureidopenicillins</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span>,</span></span>
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<span class="r-in"><span> wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-in"><span> wisca <span class="op">=</span> <span class="cn">TRUE</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">ureidopenicillins()</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">' (piperacillin/tazobactam)</span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># in an Rmd file, you would just need to return `ureido` in a chunk,</span></span></span>
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@ -589,11 +597,13 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="va">ab1</span> <span class="op"><-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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<span class="r-in"><span> antibiotics <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">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></span>
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<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="va">ab2</span> <span class="op"><-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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<span class="r-in"><span> antibiotics <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">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span></span>
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<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span></span>
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<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"ggplot2"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="fu">ggplot2</span><span class="fu">::</span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">ab1</span><span class="op">)</span></span></span>
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