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Built site for AMR: 1.8.2.9139@c2cfc5e
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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="">1.8.2.9138</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9139</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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@@ -195,7 +195,7 @@
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<dt>antibiotics</dt>
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<dd><p>vector of column names, or (any combinations of) <a href="antibiotic_class_selectors.html">antibiotic selectors</a> such as <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> or <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code>. For combination antibiograms, this can also be column names separated with <code>"+"</code>, such as "TZP+TOB" given that the data set contains columns "TZP" and "TOB". See <em>Examples</em>.</p></dd>
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<dd><p>vector of any antibiotic name or code (will be evaluated with <code><a href="as.ab.html">as.ab()</a></code>, column name of <code>x</code>, or (any combinations of) <a href="antibiotic_class_selectors.html">antibiotic selectors</a> such as <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> or <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code>. For combination antibiograms, this can also be set to values separated with <code>"+"</code>, such as "TZP+TOB" or "cipro + genta", given that columns resembling such antibiotics exist in <code>x</code>. See <em>Examples</em>.</p></dd>
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<dt>mo_transform</dt>
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@@ -404,15 +404,24 @@
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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></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> [1] 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 4</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` TZP `TZP + GEN` `TZP + TOB`</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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693) 88 99 98</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-1044) 86 98 95</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># names of antibiotics do not need to resemble columns exactly:</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="op">)</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">"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></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> [1] 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 3</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` Ciprofloxacin `Ciprofloxacin & Gentamicin`</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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Gram-negative (684-694) 91 99</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Gram-positive (724-847) 77 93</span>
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<span class="r-in"><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="co"># Syndromic antibiogram ------------------------------------------------</span></span></span>
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@@ -478,7 +487,13 @@
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<span class="r-in"><span> <span class="st">"WISCA Group 1"</span>, <span class="st">"WISCA Group 2"</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="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 6</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `Syndromic Group` `Pathogen (N min-max)` AMC `AMC + CIP` TZP `TZP + TOB`</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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> WISCA Group 1 Gram-negative (261-285) 76 95 89 99</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> WISCA Group 2 Gram-negative (380-442) 76 98 88 98</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> WISCA Group 1 Gram-positive (123-406) 76 89 81 95</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> WISCA Group 2 Gram-positive (222-732) 76 89 88 95</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># Print the output for R Markdown / Quarto -----------------------------</span></span></span>
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<span class="r-in"><span></span></span>
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@@ -514,18 +529,16 @@
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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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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in ggplot2::autoplot(ab1):</span> Objects of class <span style="color: #0000BB;"><numeric></span> are not supported by autoplot.</span>
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<span class="r-err co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> have you loaded the required package?</span>
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<span class="r-plt img"><img src="antibiogram-1.png" alt="" width="700" height="433"></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">ab2</span><span class="op">)</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-err co"><span class="r-pr">#></span> <span class="error">Error in ggplot2::autoplot(ab2):</span> Objects of class <span style="color: #0000BB;"><numeric></span> are not supported by autoplot.</span>
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<span class="r-err co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> have you loaded the required package?</span>
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<span class="r-plt img"><img src="antibiogram-2.png" alt="" width="700" height="433"></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">ab1</span><span class="op">)</span></span></span>
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<span class="r-plt img"><img src="antibiogram-1.png" alt="" width="700" height="433"></span>
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<span class="r-plt img"><img src="antibiogram-3.png" alt="" width="700" height="433"></span>
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<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">ab2</span><span class="op">)</span></span></span>
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<span class="r-plt img"><img src="antibiogram-2.png" alt="" width="700" height="433"></span>
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<span class="r-plt img"><img src="antibiogram-4.png" alt="" width="700" height="433"></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># }</span></span></span>
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</code></pre></div>
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