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@ -7,7 +7,7 @@
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@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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reference/age.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -111,16 +111,16 @@
<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 1965-12-05 59 59.20548 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.96986 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 75 75.29863 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 78 78.01096 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.99726 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 37 37.10685 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.47945 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 47 47.06301 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.67397 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.52603 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 59 59.21644 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.98082 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 75 75.30959 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 78 78.02192 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 85 85.00822 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 37 37.11781 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.49041 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 47 47.07397 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.68493 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.53699 13</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

2
reference/age_groups.html
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@ -7,7 +7,7 @@
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reference/antibiogram.html
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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
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@ -7,7 +7,7 @@
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reference/antimicrobial_selectors.html
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@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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reference/as.mic.html
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@ -7,7 +7,7 @@
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@ -83,7 +83,7 @@
<dt id="arg-mic-range">mic_range<a class="anchor" aria-label="anchor" href="#arg-mic-range"></a></dt>
<dd><p>a manual range to limit the MIC values, e.g., <code>mic_range = c(0.001, 32)</code>. Use <code>NA</code> to prevent a limit on one side, e.g., <code>mic_range = c(NA, 32)</code>.</p></dd>
<dd><p>a manual range to rescale the MIC values, e.g., <code>mic_range = c(0.001, 32)</code>. Use <code>NA</code> to prevent rescaling on one side, e.g., <code>mic_range = c(NA, 32)</code>.</p></dd>
<dt id="arg-as-mic">as.mic<a class="anchor" aria-label="anchor" href="#arg-as-mic"></a></dt>

2
reference/as.mo.html
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@ -7,7 +7,7 @@
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reference/as.sir.html
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@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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@ -782,16 +782,16 @@ 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: 57 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</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;chr&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;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-02-18 <span style="color: #949494;">08:45:38</span> 4 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-02-18 <span style="color: #949494;">08:45:44</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-02-18 <span style="color: #949494;">08:45:44</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-02-18 <span style="color: #949494;">08:45:45</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-02-18 <span style="color: #949494;">08:45:45</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-02-18 <span style="color: #949494;">08:45:38</span> 3 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-02-18 <span style="color: #949494;">08:45:44</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-02-18 <span style="color: #949494;">08:45:44</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-02-18 <span style="color: #949494;">08:45:45</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-02-18 <span style="color: #949494;">08:45:45</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-02-22 <span style="color: #949494;">20:31:37</span> 4 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-02-22 <span style="color: #949494;">20:31:43</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-02-22 <span style="color: #949494;">20:31:44</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-02-22 <span style="color: #949494;">20:31:44</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-02-22 <span style="color: #949494;">20:31:45</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-02-22 <span style="color: #949494;">20:31:37</span> 3 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-02-22 <span style="color: #949494;">20:31:43</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-02-22 <span style="color: #949494;">20:31:44</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-02-22 <span style="color: #949494;">20:31:44</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-02-22 <span style="color: #949494;">20:31:45</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;chr&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>

2
reference/atc_online.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/av_from_text.html
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@ -7,7 +7,7 @@
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reference/av_property.html
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@ -7,7 +7,7 @@
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reference/availability.html
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@ -7,7 +7,7 @@
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reference/bug_drug_combinations.html
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@ -7,7 +7,7 @@
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reference/clinical_breakpoints.html
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@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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reference/count.html
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@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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reference/custom_eucast_rules.html
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@ -7,7 +7,7 @@
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reference/dosage.html
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@ -7,7 +7,7 @@
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reference/eucast_rules.html
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@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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reference/example_isolates.html
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@ -7,7 +7,7 @@
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reference/example_isolates_unclean.html
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@ -7,7 +7,7 @@
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reference/export_ncbi_biosample.html
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@ -7,7 +7,7 @@
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reference/first_isolate.html
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@ -9,7 +9,7 @@
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reference/g.test.html
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@ -7,7 +7,7 @@
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reference/get_episode.html
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@ -7,7 +7,7 @@
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reference/ggplot_pca.html
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@ -7,7 +7,7 @@
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reference/ggplot_sir.html
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@ -7,7 +7,7 @@
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reference/guess_ab_col.html
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@ -7,7 +7,7 @@
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reference/index.html
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@ -7,7 +7,7 @@
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reference/intrinsic_resistant.html
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@ -7,7 +7,7 @@
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reference/italicise_taxonomy.html
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@ -7,7 +7,7 @@
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reference/join.html
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@ -7,7 +7,7 @@
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reference/key_antimicrobials.html
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@ -7,7 +7,7 @@
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reference/kurtosis.html
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reference/microorganisms.html
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@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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@ -7,7 +7,7 @@
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reference/mo_property.html
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@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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38
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@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<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="">2.1.1.9152</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9153</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">
@ -156,7 +156,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<dt id="arg-mic-range">mic_range<a class="anchor" aria-label="anchor" href="#arg-mic-range"></a></dt>
<dd><p>a manual range to limit the MIC values, e.g., <code>mic_range = c(0.001, 32)</code>. Use <code>NA</code> to prevent a limit on one side, e.g., <code>mic_range = c(NA, 32)</code>.</p></dd>
<dd><p>A manual range to rescale the MIC values (using <code><a href="as.mic.html">rescale_mic()</a></code>), e.g., <code>mic_range = c(0.001, 32)</code>. Use <code>NA</code> to prevent rescaling on one side, e.g., <code>mic_range = c(NA, 32)</code>. <strong>Note:</strong> This rescales values but does not filter them - use the ggplot2 <code>limits</code> argument separately to exclude values from the plot.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
@ -332,25 +332,25 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic()"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in if (!is.na(mic_range[1]) &amp;&amp; mic_range[1] &lt; lims[1]) { lims[1] &lt;- mic_range[1]}:</span> missing value where TRUE/FALSE needed</span>
<span class="r-plt img"><img src="plot-8.png" alt="" width="700" height="433"></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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span>keep_operators <span class="op">=</span> <span class="st">"all"</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() keeping all operators"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in if (!is.na(mic_range[1]) &amp;&amp; mic_range[1] &lt; lims[1]) { lims[1] &lt;- mic_range[1]}:</span> missing value where TRUE/FALSE needed</span>
<span class="r-plt img"><img src="plot-9.png" alt="" width="700" height="433"></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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span>mic_range <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="fl">1</span>, <span class="fl">16</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() using a manual 'within' range"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-8.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-10.png" alt="" width="700" height="433"></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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">mic_plot</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_x_mic</span><span class="op">(</span>mic_range <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="fl">0.032</span>, <span class="fl">256</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() using a manual 'outside' range"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-9.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-11.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Plotting using scale_y_mic() -----------------------------------------</span></span></span>
@ -364,7 +364,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span>linetype <span class="op">=</span> <span class="fl">2</span>, colour <span class="op">=</span> <span class="st">"grey"</span>, fill <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_y_mic</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in if (!is.na(mic_range[1]) &amp;&amp; mic_range[1] &lt; lims[1]) { lims[1] &lt;- mic_range[1]}:</span> missing value where TRUE/FALSE needed</span>
<span class="r-plt img"><img src="plot-12.png" alt="" width="700" height="433"></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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</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>mic <span class="op">=</span> <span class="va">some_mic_values</span>,</span></span>
<span class="r-in"><span> group <span class="op">=</span> <span class="va">some_groups</span><span class="op">)</span>,</span></span>
@ -373,7 +373,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span>linetype <span class="op">=</span> <span class="fl">2</span>, colour <span class="op">=</span> <span class="st">"grey"</span>, fill <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_y_mic</span><span class="op">(</span>mic_range <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="cn">NA</span>, <span class="fl">2</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-10.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-13.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Plotting using scale_fill_mic() -----------------------------------------</span></span></span>
@ -387,7 +387,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_col</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_fill_mic</span><span class="op">(</span>mic_range <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="fl">0.5</span>, <span class="fl">16</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-11.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-14.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Plotting using scale_x_sir() -----------------------------------------</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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@ -397,7 +397,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_col</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_x_sir</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-12.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-15.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Plotting using scale_y_mic() and scale_colour_sir() ------------------</span></span></span>
@ -421,36 +421,36 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Interpreting MIC values: '</span><span style="color: #0000BB; font-weight: bold;">cipro</span><span style="color: #0000BB;">' (CIP, ciprofloxacin), </span><span style="color: #0000BB; font-weight: bold;">EUCAST 2024</span><span style="color: #0000BB;">...</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #FFFF87;"> NOTE </span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808;"> • Multiple breakpoints available for </span><span style="color: #080808; font-weight: bold;">ciprofloxacin (CIP)</span><span style="color: #080808;"> in </span><span style="color: #080808; font-style: italic;">Escherichia coli</span><span style="color: #080808;"> - assuming body site 'Non-meningitis'.</span></span>
<span class="r-plt img"><img src="plot-13.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-16.png" alt="" width="700" height="433"></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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># and now with our MIC and SIR scale functions:</span></span></span>
<span class="r-in"><span> <span class="va">plain</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_y_mic</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_colour_sir</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in if (!is.na(mic_range[1]) &amp;&amp; mic_range[1] &lt; lims[1]) { lims[1] &lt;- mic_range[1]}:</span> missing value where TRUE/FALSE needed</span>
<span class="r-plt img"><img src="plot-17.png" alt="" width="700" height="433"></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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="va">plain</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_y_mic</span><span class="op">(</span>mic_range <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="fl">0.005</span>, <span class="fl">32</span><span class="op">)</span>, name <span class="op">=</span> <span class="st">"Our MICs!"</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">scale_colour_sir</span><span class="op">(</span>language <span class="op">=</span> <span class="st">"nl"</span>, eucast_I <span class="op">=</span> <span class="cn">FALSE</span>,</span></span>
<span class="r-in"><span> name <span class="op">=</span> <span class="st">"In Dutch!"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-14.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-18.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Plotting using ggplot2's autoplot() ----------------------------------</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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><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">some_mic_values</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-15.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-19.png" alt="" width="700" height="433"></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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><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">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-16.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-20.png" alt="" width="700" height="433"></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://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><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">some_sir_values</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-17.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-21.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Plotting using scale_y_percent() -------------------------------------</span></span></span>
@ -471,9 +471,9 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<span class="r-in"><span> limits <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="fl">0</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
<span class="r-in"><span> <span class="fu">theme_sir</span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-plt img"><img src="plot-18.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-19.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-20.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-22.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-23.png" alt="" width="700" height="433"></span>
<span class="r-plt img"><img src="plot-24.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>

2
reference/proportion.html
View File

@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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="">2.1.1.9152</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9153</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">

36
reference/random.html
View File

@ -7,7 +7,7 @@
<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="">2.1.1.9152</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9153</small>
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@ -99,43 +99,43 @@
<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] 2 &lt;=0.001 0.005 0.0625 &lt;=0.001 &lt;=0.001 2 256 128 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.005 0.002 1 0.002 32 16 64 0.005 0.005 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.025 32 0.5 0.25 0.005 8 256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.001 0.005 0.0625 0.001 0.001 2 &gt;=256 128 0.005 0.002 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 1 0.002 32 16 64 0.005 0.005 0.025 32 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.25 0.005 8 &gt;=256 0.01 </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] 36 16 6 43 36 42 50 43 45 25 34 37 9 25 46 39 43 45 47 17 9 22 45 14 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 16 6 43 36 43 50 45 43 25 34 37 9 25 46 39 40 45 47 17 9 22 45 14 47 41</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 S R S S S R R I S R S S I S R S R I I R I I R I</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] S S S R R I S R S S I S R S R I I R I I R I S S S</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] 128 0.125 4 0.01 256 0.25 0.25 1 0.002 0.25 2 0.005</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.001 64 0.001 0.025 0.025 64 128 0.5 16 2 0.001 0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.125 4 0.01 &gt;=256 0.25 0.25 1 0.002 0.25 2 0.005 0.001</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 64 0.001 0.025 0.025 64 128 0.5 16 2 0.001 0.125 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.025</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 16 8 2 8 8 1 1 8 16 &lt;=0.5 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 4 4 8 2 16 4 2 8 &lt;=0.5 1 16 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] &gt;=32 16 8 2 8 8 1 1 8 &gt;=32 16 &lt;=0.5</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 2 &gt;=32 4 &gt;=32 &gt;=32 &gt;=32 4 8 2 16 4 &gt;=32 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 2 </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 2 1 0.25 0.5 0.5 0.125 0.5 0.25 2 1 0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.25 &gt;=4 0.5 2 1 &gt;=4 0.5 0.125 0.125 2 0.5 0.125</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2 0.125 0.125 0.25 1 1 0.0625 0.5 1 0.5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 4 0.125 0.25 0.25 0.0625 4 0.25 0.125 4 1 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 4 0.5 0.0625 4 0.125 </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] 11 30 36 43 35 14 24 8 38 10 10 15 31 49 13 24 43 49 19 47 10 36 15 48 14</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 47 49 10 40 23 16 20 34 45 8 42 10 20 11 30 36 40 35 14 24 8 38 10 10 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">"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 11 15 17 14 16 17 17 17 11 12 12 12 14 16 15 11 13 11 11 14 14 13 11 17</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 14 12 14 11 13 15 13 11 17 15 14 13 11 15 17 14 16 17 17 17 11 12 12 12 14</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] 18 27 15 25 16 21 15 24 23 22 22 15 23 25 23 24 15 15 26 23 27 18 22 24 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 27 15 17 23 23 18 18 17 15 18 27 15 25 16 21 15 24 23 22 22 15 23 25 23 24</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -9,7 +9,7 @@ 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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9152</small>
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@ -89,7 +89,7 @@ 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] -0.02681013</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.0199978</span>
</code></pre></div>
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