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Built site for AMR: 1.8.2.9114@bc434db
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@@ -10,7 +10,7 @@
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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="">1.8.2.9111</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9114</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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@@ -160,7 +160,7 @@
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<span> add_ab_group <span class="op">=</span> <span class="cn">TRUE</span>,</span>
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<span> remove_intrinsic_resistant <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> decimal.mark <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"OutDec"</span><span class="op">)</span>,</span>
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<span> big.mark <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">decimal.mark</span> <span class="op">==</span> <span class="st">","</span>, <span class="st">" "</span>, <span class="st">","</span><span class="op">)</span>,</span>
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<span> big.mark <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">decimal.mark</span> <span class="op">==</span> <span class="st">","</span>, <span class="st">"."</span>, <span class="st">","</span><span class="op">)</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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</div>
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@@ -231,8 +231,7 @@
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="co">#' # example_isolates is a data set available in the AMR package.</span></span></span>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># example_isolates is a data set available in the AMR package.</span></span></span>
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<span class="r-in"><span><span class="co"># run ?example_isolates for more info.</span></span></span>
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<span class="r-in"><span><span class="va">example_isolates</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
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@@ -256,7 +255,19 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <sir>, COL <sir>, MUP <sir>, RIF <sir></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"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
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<span class="r-in"><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="va">x</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;"># A tibble: 6 × 6</span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo ab S I R total</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;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> (unknown species) AMC 15 0 0 15</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> (unknown species) AMK 0 0 0 0</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> (unknown species) AMP 15 0 1 16</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> (unknown species) AMX 15 0 1 16</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> (unknown species) AZM 3 0 3 6</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">6</span> (unknown species) CAZ 0 0 0 0</span>
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<span class="r-msg co"><span class="r-pr">#></span> Use 'format()' on this result to get a publishable/printable format.</span>
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<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">x</span>, translate_ab <span class="op">=</span> <span class="st">"name (atc)"</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;"># A tibble: 39 × 12</span></span>
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<span class="r-out co"><span class="r-pr">#></span> Group Drug CoNS E. co…¹ E. fa…² K. pn…³ P. ae…⁴ P. mi…⁵ S. au…⁶ S. ep…⁷</span>
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@@ -280,7 +291,7 @@
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<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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<span class="r-in"><span> FUN <span class="op">=</span> <span class="va">mo_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;"># A tibble: 120 × 6</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 80 × 6</span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo ab S I R total</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Gram-negative AMC 463 89 174 726</span>
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@@ -293,7 +304,7 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CIP 610 11 63 684</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Gram-negative CLI 18 1 709 728</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Gram-negative COL 309 0 78 387</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 110 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 70 more rows</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> Use 'format()' on this result to get a publishable/printable format.</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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