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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -205,16 +205,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1966-05-28 56 56.74247 33</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-06-27 54 54.66027 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1969-08-07 53 53.54795 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1979-02-13 44 44.02740 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1987-09-25 35 35.41370 12</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-02-07 74 74.04384 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1950-11-07 72 72.29589 49</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1983-09-03 39 39.47397 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1941-03-04 81 81.97534 58</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1968-03-30 54 54.90411 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1970-09-03 52 52.47671 29</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1961-08-15 61 61.52877 38</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1975-10-03 47 47.39452 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1963-12-22 59 59.17534 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1957-11-01 65 65.31507 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1964-09-04 58 58.47397 35</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1973-11-09 49 49.29315 26</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1945-07-01 77 77.65205 54</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1993-11-25 29 29.24932 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1965-10-15 57 57.36164 34</span>
</code></pre></div>
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@ -171,7 +171,8 @@
<span><span class="co"># S3 method for antibiogram</span></span>
<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">object</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">knit_print.antibiogram</span><span class="op">(</span></span>
<span><span class="co"># S3 method for antibiogram</span></span>
<span><span class="fu">knit_print</span><span class="op">(</span></span>
<span> <span class="va">x</span>,</span>
<span> italicise <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> na <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">"knitr.kable.NA"</span>, default <span class="op">=</span> <span class="st">""</span><span class="op">)</span>,</span>
@ -253,7 +254,7 @@
<dt>italicise</dt>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the microorganism names in the <a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr</a> table should be made italic, using <code><a href="italicise_taxonomy.html">italicise_taxonomy()</a></code>. This only works when the output format is markdown, such as in HTML output.</p></dd>
<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the microorganism names in the <a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr</a> table should be made italic, using <code><a href="italicise_taxonomy.html">italicise_taxonomy()</a></code>.</p></dd>
<dt>na</dt>
@ -264,6 +265,10 @@
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>This function returns a table with values between 0 and 100 for <em>susceptibility</em>, not resistance.</p>
<p><strong>Remember that you should filter your data to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href="first_isolate.html">first_isolate()</a></code> to determine them in your data set with one of the four available algorithms.</p>
<p>All types of antibiograms as listed below can be plotted (using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">ggplot2::autoplot()</a></code> or base <span style="R">R</span> <code><a href="plot.html">plot()</a></code>/<code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code>). The <code>antibiogram</code> object can also be used directly in R Markdown / Quarto (i.e., <code>knitr</code>) for reports. In this case, <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code> will be applied automatically and microorganism names will even be printed in italics at default (see argument <code>italicise</code>). You can also use functions from specific 'table reporting' packages to transform the output of <code>antibiogram()</code> to your needs, e.g. with <code>as_flextable()</code> or <code>gt()</code>.</p><div class="section">
<h3 id="antibiogram-types">Antibiogram Types<a class="anchor" aria-label="anchor" href="#antibiogram-types"></a></h3>
<p>There are four antibiogram types, as proposed by Klinker <em>et al.</em> (2021, <a href="https://doi.org/10.1177/20499361211011373" class="external-link">doi:10.1177/20499361211011373</a>
), and they are all supported by <code>antibiogram()</code>:</p><ol><li><p><strong>Traditional Antibiogram</strong></p>
<p>Case example: Susceptibility of <em>Pseudomonas aeruginosa</em> to piperacillin/tazobactam (TZP)</p>
@ -292,8 +297,7 @@
<span> <span class="va">.</span><span class="op">$</span><span class="va">gender</span> <span class="op">==</span> <span class="st">"Male"</span> <span class="op">&amp;</span></span>
<span> <span class="va">.</span><span class="op">$</span><span class="va">condition</span> <span class="op">==</span> <span class="st">"Heart Disease"</span>,</span>
<span> <span class="st">"Study Group"</span>, <span class="st">"Control Group"</span><span class="op">)</span><span class="op">)</span></span></code></pre><p></p></div></li>
</ol><p>All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">ggplot2::autoplot()</a></code> or base <span style="R">R</span> <code><a href="plot.html">plot()</a></code>/<code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code>) or directly used into R Markdown / Quarto formats for reports (in the last case, <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code> will be applied automatically). Use functions from specific 'table reporting' packages to transform the output of <code>antibiogram()</code> to your needs, e.g. <code>flextable::as_flextable()</code> or <code>gt::gt()</code>.</p>
<p>Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the <code>only_all_tested</code> argument (default is <code>FALSE</code>). See this example for two antibiotics, Drug A and Drug B, about how <code>antibiogram()</code> works to calculate the %SI:</p>
</ol><p>Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the <code>only_all_tested</code> argument (default is <code>FALSE</code>). See this example for two antibiotics, Drug A and Drug B, about how <code>antibiogram()</code> works to calculate the %SI:</p>
<p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> only_all_tested <span class="ot">=</span> <span class="cn">FALSE</span> only_all_tested <span class="ot">=</span> <span class="cn">TRUE</span></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> <span class="sc">-----------------------</span> <span class="sc">-----------------------</span></span>
@ -310,6 +314,8 @@
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a> R <span class="sc">&lt;</span><span class="cn">NA</span><span class="sc">&gt;</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a> <span class="er">&lt;</span><span class="cn">NA</span><span class="sc">&gt;</span> <span class="er">&lt;</span><span class="cn">NA</span><span class="sc">&gt;</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span> <span class="sc">-</span></span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span></code></pre><p></p></div>
</div>
</div>
<div class="section level2">
@ -487,6 +493,7 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> WISCA Group 1 Gram-positive (123-406) 76 89 81 95</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> WISCA Group 2 Gram-positive (222-732) 76 89 88 95</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Print the output for R Markdown / Quarto -----------------------------</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">ureido</span> <span class="op">&lt;-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
@ -499,7 +506,7 @@
<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">"knitr"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu">knitr</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/knit_print.html" class="external-link">knit_print</a></span><span class="op">(</span><span class="va">ureido</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "\n\n| Pathogen (N) | Piperacillin/tazobactam|\n|:----------------------|-----------------------:|\n| CoNS (33) | 30|\n| *E. coli* (416) | 94|\n| *K. pneumoniae* (53) | 89|\n| *S. pneumoniae* (112) | 100|"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "\n\n|Pathogen (N) | Piperacillin/tazobactam|\n|:---------------------|-----------------------:|\n|CoNS (33) | 30|\n|*E. coli* (416) | 94|\n|*K. pneumoniae* (53) | 89|\n|*S. pneumoniae* (112) | 100|"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> attr(,"class")</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "knit_asis"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> attr(,"knit_cacheable")</span>

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2
reference/as.mic.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/as.mo.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
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22
reference/as.sir.html
View File

@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
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@ -534,16 +534,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 17</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_input ab_guid…¹ mo_in…² mo_guideline guide…³</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-23 <span style="color: #949494;">15:33:48</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-02-23 <span style="color: #949494;">15:33:47</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-02-23 <span style="color: #949494;">15:33:47</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-02-23 <span style="color: #949494;">15:33:47</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-02-23 <span style="color: #949494;">15:33:41</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-23 <span style="color: #949494;">15:33:41</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-23 <span style="color: #949494;">15:33:41</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-23 <span style="color: #949494;">15:33:41</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-23 <span style="color: #949494;">15:33:41</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-23 <span style="color: #949494;">15:33:41</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-24 <span style="color: #949494;">08:48:44</span> 1 TOB TOB Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-02-24 <span style="color: #949494;">08:48:43</span> 1 GEN GEN Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-02-24 <span style="color: #949494;">08:48:43</span> 1 CIP CIP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-02-24 <span style="color: #949494;">08:48:43</span> 1 AMP AMP Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-02-24 <span style="color: #949494;">08:48:37</span> 1 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-24 <span style="color: #949494;">08:48:37</span> 2 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-24 <span style="color: #949494;">08:48:37</span> 3 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-24 <span style="color: #949494;">08:48:37</span> 4 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-24 <span style="color: #949494;">08:48:37</span> 5 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-24 <span style="color: #949494;">08:48:37</span> 6 CIP CIP B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 10 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># input &lt;dbl&gt;, outcome &lt;sir&gt;, breakpoint_S_R &lt;chr&gt;, ab_considered &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># mo_considered &lt;lgl&gt;, breakpoint_S &lt;lgl&gt;, breakpoint_R &lt;lgl&gt;,</span></span>

2
reference/atc_online.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
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reference/av_from_text.html
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@ -10,7 +10,7 @@
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reference/av_property.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/availability.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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4
reference/bug_drug_combinations.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
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@ -226,7 +226,7 @@
</div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>The function <code><a href="https://rdrr.io/r/base/format.html" class="external-link">format()</a></code> calculates the resistance per bug-drug combination. Use <code>combine_SI = TRUE</code> (default) to test R vs. S+I and <code>combine_SI = FALSE</code> to test R+I vs. S.</p>
<p>The function <code><a href="https://rdrr.io/r/base/format.html" class="external-link">format()</a></code> calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use <code>combine_SI = TRUE</code> (default) to test R vs. S+I and <code>combine_SI = FALSE</code> to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code>.</p>
</div>
<div class="section level2">

2
reference/clinical_breakpoints.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/count.html
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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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reference/custom_eucast_rules.html
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@ -10,7 +10,7 @@
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reference/dosage.html
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@ -10,7 +10,7 @@
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reference/eucast_rules.html
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@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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reference/example_isolates.html
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@ -10,7 +10,7 @@
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reference/example_isolates_unclean.html
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@ -10,7 +10,7 @@
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reference/first_isolate.html
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@ -12,7 +12,7 @@
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reference/g.test.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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106
reference/get_episode.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -192,27 +192,27 @@
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 35 40 37 41 12 38 37 11 46 3 25 20 29 7 46 15 30 29 16 26 44 22 20 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 25 45 2 38 18 44 39 4 28 9 20 6 27 31 34 22 18 11 45 4 17 24 32 48 5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 34 36 12 47 37 29 2 39 11 29 27 45 35 27 45 23 22 25 7 37 17 40 46 9 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 12 42 21 10 15 14 25 44 25 8 12 26 33 43 45 41 19 33 4 32 6 13 1 18 9</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 42 21 14 39 21 36 28 23 18 43 10 36 41 37 1 39 7 13 36 7 40 29 42 25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 10 30 18 38 35 10 19 6 16 8 28 13 10 11 45 40 32 5 5 31 9 24 22 26 41</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 20 39 17 43 11 11 27 8 12 28 20 1 43 8 33 44 22 17 27 15 16 35 18 42 22</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 34 13 35 11 31 2 17 4 29 43 10 20 22 21 3 34 26 8 44 13 12 6 27 44 7</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] FALSE TRUE TRUE TRUE FALSE TRUE TRUE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE FALSE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] TRUE FALSE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] FALSE FALSE FALSE FALSE</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2003-01-25 088256 73 F ICU B_STPHY_HMNS R NA R R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-21 955940 82 F Clinical B_PSDMN_AERG R NA NA R </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;,</span></span>
@ -247,19 +247,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [98]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [91]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 004531 2013-12-02 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 023456 2012-11-24 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 005088 2007-08-22 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 021648 2004-08-21 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 067927 2002-02-14 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 088256 2003-01-25 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 092034 2006-06-12 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 0F9638 2014-09-22 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 114570 2003-04-22 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 119392 2010-11-01 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 151041 2006-02-09 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1710B8 2008-01-22 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 077922 2009-08-24 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 078381 2014-06-28 A FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 078381 2014-08-17 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 083080 2010-02-25 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 092034 2016-08-07 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 0E2483 2007-05-29 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 0F9638 2014-09-22 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -273,19 +273,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [90]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2013-12-02 004531 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2012-11-24 023456 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2007-08-22 005088 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2004-08-21 021648 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU 2002-02-14 067927 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU 2003-01-25 088256 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2006-06-12 092034 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2014-09-22 0F9638 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2003-04-22 114570 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2010-11-01 119392 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2006-02-09 151041 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2008-01-22 1710B8 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2009-08-24 077922 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2014-06-28 078381 1 FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU 2014-08-17 078381 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2010-02-25 083080 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2016-08-07 092034 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2007-05-29 0E2483 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2014-09-22 0F9638 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -301,9 +301,9 @@
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 55 12 36 42</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 30 11 21 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 10 7 10 10</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 58 12 36 45</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 28 10 23 28</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 4 3 4 4</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@ -332,19 +332,19 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 4F6B71 B_STRPT_GRPB Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 516F62 B_GRNLC_ADCN ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> A76045 B_STPHY_EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 414858 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 329C35 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> D27987 B_ENTRBC_CLOC ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 590035 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 960698 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 151041 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 987C84 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [97]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 895298 B_ESCHR_COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> D08278 B_ESCHR_COLI Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 445249 B_STPHY_CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 968584 B_PSDMN_AERG Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 976813 B_STPHY_AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> AB0003 B_STRPT Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 715822 B_STPHY_EPDR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 387C40 B_KLBSL_PNMN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B13757 B_STPHY_EPDR Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 005088 B_SLMNL_ENTR Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

2
reference/ggplot_pca.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/ggplot_sir.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/guess_ab_col.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

4
reference/index.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -256,7 +256,7 @@
<dl><dt>
<code><a href="antibiogram.html">antibiogram()</a></code> <code><a href="antibiogram.html">plot(<i>&lt;antibiogram&gt;</i>)</a></code> <code><a href="antibiogram.html">autoplot(<i>&lt;antibiogram&gt;</i>)</a></code> <code><a href="antibiogram.html">knit_print.antibiogram()</a></code>
<code><a href="antibiogram.html">antibiogram()</a></code> <code><a href="antibiogram.html">plot(<i>&lt;antibiogram&gt;</i>)</a></code> <code><a href="antibiogram.html">autoplot(<i>&lt;antibiogram&gt;</i>)</a></code> <code><a href="antibiogram.html">knit_print(<i>&lt;antibiogram&gt;</i>)</a></code>
</dt>
<dd>Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA)</dd>
</dl><dl><dt>

2
reference/intrinsic_resistant.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/italicise_taxonomy.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/join.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/key_antimicrobials.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

6
reference/kurtosis.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -182,9 +182,9 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.027456</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.990683</span>
<span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.06012916</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.00935699</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
reference/like.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/mdro.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

71
reference/mean_amr_distance.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -201,30 +201,29 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">sir</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R I R S R R I S S</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I I S I S I I I I S</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.7745967 1.1618950 -0.7745967 1.1618950 -0.7745967 1.1618950</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 1.1618950 -0.7745967 -0.7745967 -0.7745967</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">mic</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 128 0.125 0.025 1 1 8 0.125 &lt;=0.01 1 0.0625</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 256 16 0.025 8 0.001 128 0.001 0.005 0.025 0.025</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.0067688 -0.4415318 -1.0100096 0.2929584 0.2929584 1.0274486</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4415318 -1.3336573 0.2929584 -0.6863619</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.4628662 0.8866012 -0.4563741 0.7425349 -1.1253971 1.3187999</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.1253971 -0.7908856 -0.4563741 -0.4563741</span>
<span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
<span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.0067688 -0.4415318 -1.0100096 0.2929584 0.2929584 1.0274486</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.4415318 -1.3336573 0.2929584 -0.6863619</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.4628662 0.8866012 -0.4563741 0.7425349 -1.1253971 1.3187999</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -1.1253971 -0.7908856 -0.4563741 -0.4563741</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">disk</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 19 33 9 33 40 43 40 7 39 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 50 32 24 26 49 40 9 34 41 14</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.8390265 0.1649368 -1.5561432 0.1649368 0.6669185 0.8820535</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] 0.6669185 -1.6995665 0.5952068 0.9537652</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1.311234687 0.007244391 -0.572306852 -0.427419042 1.238790782</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] 0.586795633 -1.658965433 0.152132201 0.659239539 -1.296745906</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@ -234,22 +233,22 @@
<span class="r-in"><span> tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">y</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A R 20 1 &gt;=16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 17 &gt;=16 &lt;=0.25</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C I 22 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D R 18 &gt;=16 0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E S 25 8 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F I 18 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 28 4 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H R 19 &gt;=16 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I R 21 1 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J I 18 8 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 A I 21 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B S 24 0.5 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 C R 29 0.5 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 D I 29 &gt;=4 4</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E I 31 2 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 F R 24 0.5 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 20 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 H S 23 0.5 8</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 19 1 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 J S 21 2 16</span>
<span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.210274980 -0.189659861 -0.361042252 0.008770745 0.395772293</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] -0.660927881 0.080327628 0.590266790 0.025640147 -0.099422589</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.3578553 -0.2633009 0.2567155 0.7156924 0.4223198 0.1444269</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [7] -0.6445214 -0.1375992 -0.5188196 0.3829419</span>
<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
<span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@ -265,17 +264,17 @@
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and "tobr"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C I 22 2 2 -0.361042252 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 B R 17 &gt;=16 &lt;=0.25 -0.189659861 0.1713824</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J I 18 8 8 -0.099422589 0.2616197</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 F I 18 1 4 -0.660927881 0.2998856</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 D R 18 &gt;=16 0.5 0.008770745 0.3698130</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 I R 21 1 4 0.025640147 0.3866824</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 G I 28 4 1 0.080327628 0.4413699</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 A R 20 1 &gt;=16 0.210274980 0.5713172</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 E S 25 8 8 0.395772293 0.7568145</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 H R 19 &gt;=16 8 0.590266790 0.9513090</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> id amox cipr gent tobr amr_distance check_id_C</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 C R 29 0.5 1 0.2567155 0.0000000</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 F R 24 0.5 2 0.1444269 0.1122886</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 J S 21 2 16 0.3829419 0.1262264</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 E I 31 2 2 0.4223198 0.1656043</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 H S 23 0.5 8 -0.1375992 0.3943147</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 D I 29 &gt;=4 4 0.7156924 0.4589769</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 B S 24 0.5 4 -0.2633009 0.5200164</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 A I 21 2 1 -0.3578553 0.6145708</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 I I 19 1 2 -0.5188196 0.7755351</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 G I 20 1 1 -0.6445214 0.9012368</span>
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># support for groups</span></span></span>
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>

2
reference/microorganisms.codes.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/microorganisms.html
View File

@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9142</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9143</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/mo_matching_score.html
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@ -10,7 +10,7 @@
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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@ -193,42 +193,44 @@
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.025 16 2 64 0.5 0.01 8 2 16 0.025 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.125 0.002 0.001 16 0.0625 1 0.001 0.001 0.0625 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.025 0.001 64 32 64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 8 0.002 0.005 0.125 &gt;=256 16 32 &gt;=256 0.025 0.125 &gt;=256 0.005</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] &gt;=256 &gt;=256 &gt;=256 0.025 16 1 0.125 128 8 0.001 128 0.005</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 64 </span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 26 50 43 50 14 13 12 7 15 49 10 6 48 40 38 45 43 50 36 45 36 29 27 37 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 49 42 10 37 12 22 29 28 11 50 44 39 14 41 6 16 47 46 43 38 24 15 42 45 38</span>
<span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] R I S I R R R S I S S R R I S I R S I R I I R R I</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] I R I S I I R I R R I R I I I S I I R I I S R R I</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &lt;=0.001 &gt;=64 4 0.01 4 16 0.0625 &lt;=0.001 &gt;=64 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.001 0.005 0.002 0.01 &lt;=0.001 0.0625 2 0.0625 &lt;=0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 2 1 0.025 8 0.0625 &gt;=64 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 1 64 8 0.025 0.001 0.001 2 0.5 16 0.005 32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.125 1 32 0.25 0.125 0.002 2 0.5 4 0.125 0.01 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.001</span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.5 0.5 4 &gt;=32 4 1 2 4 4 2 0.5 1 2 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 1 &gt;=32 &gt;=32 0.5 8 0.5 2 0.5 4 &gt;=32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 4 1 &gt;=16 4 &gt;=16 1 &lt;=0.5 2 &gt;=16 &lt;=0.5 &lt;=0.5 &gt;=16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 8 4 8 &gt;=16 2 &lt;=0.5 &lt;=0.5 1 &gt;=16 2 1 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 1 </span>
<span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 0.0625 0.0625 0.125 0.25 2 0.0625 0.0625 0.125 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.0625 0.125 0.125 4 0.0625 4 0.125 0.25 0.5 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.0625 0.0625 0.5 0.125 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1 8 0.5 0.25 4 &gt;=16 8 0.25 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [9] &lt;=0.0625 0.125 1 8 &gt;=16 &gt;=16 &gt;=16 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [17] 4 0.5 &lt;=0.0625 0.5 2 2 0.125 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 8 </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 40 12 48 48 41 39 44 22 46 45 19 9 37 49 50 18 9 42 14 16 50 39 14 45 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 30 23 42 49 27 45 39 9 28 12 43 30 29 49 45 25 13 46 41 47 10 26 37 14 27</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 13 13 17 14 17 12 11 11 14 17 15 15 14 15 13 13 15 11 11 17 12 12 14 13 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 11 14 16 14 14 14 17 13 15 17 13 13 15 11 13 14 13 14 12 13 11 12 15 14 15</span>
<span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 25 23 24 18 15 27 25 17 24 18 17 15 16 21 27 16 24 20 17 23 25 22 19 23 24</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 22 20 21 17 20 27 17 24 17 25 27 18 27 25 16 21 25 20 19 27 15 17 20 24 20</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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reference/resistance_predict.html
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@ -10,7 +10,7 @@
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reference/skewness.html
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@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -181,7 +181,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01690184</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.003828091</span>
</code></pre></div>
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