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reference/AMR-deprecated.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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reference/AMR-options.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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reference/AMR.html
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@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/WHOCC.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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reference/WHONET.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/ab_from_text.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/ab_property.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/add_custom_antimicrobials.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/add_custom_microorganisms.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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22
reference/age.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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@ -112,16 +112,16 @@
<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 1980-02-27 45 45.41370 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.00548 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 75 75.90137 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 38 38.98356 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 92 92.68767 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.32877 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.09589 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 61 61.86301 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.20000 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 72 72.70137 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 45 45.44110 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.03288 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 75 75.92877 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.01096 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 92 92.71507 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.35616 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.12329 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 61 61.89041 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.22740 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 72 72.72877 47</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 @@
<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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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8
reference/amr-tidymodels.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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@ -176,10 +176,10 @@ may affect the computations for subsequent operations.</p></dd>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: tidymodels</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Attaching packages</span> ────────────────────────────────────── tidymodels 1.3.0 ──</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom </span> 1.0.8 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample </span> 1.3.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials </span> 1.4.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tibble </span> 3.3.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom </span> 1.0.9 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample </span> 1.3.1</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials </span> 1.4.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tibble </span> 3.3.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer </span> 1.0.9 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr </span> 1.3.1</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata </span> 1.4.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune </span> 1.3.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata </span> 1.5.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune </span> 1.3.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip </span> 1.3.2 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows </span> 1.2.0</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr </span> 1.1.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes </span> 1.3.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick </span> 1.3.2</span>

2
reference/antibiogram.html
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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/antimicrobial_selectors.html
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@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/antimicrobials.html
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@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will 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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/as.ab.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/as.av.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/as.disk.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/as.mic.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/as.mo.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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10
reference/as.sir.html
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@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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">
@ -415,10 +415,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</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;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;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-07-28 <span style="color: #949494;">10:29:06</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-07-28 <span style="color: #949494;">10:29:06</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-07-28 <span style="color: #949494;">10:29:07</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-07-28 <span style="color: #949494;">10:29:07</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-08-07 <span style="color: #949494;">14:32:10</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-08-07 <span style="color: #949494;">14:32:10</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-08-07 <span style="color: #949494;">14:32:10</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-08-07 <span style="color: #949494;">14:32:11</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/av_from_text.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</small>
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2
reference/av_property.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/availability.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/bug_drug_combinations.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/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
<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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/count.html
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@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
<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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/custom_eucast_rules.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/custom_mdro_guideline.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/dosage.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/esbl_isolates.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/eucast_rules.html
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@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/example_isolates.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/example_isolates_unclean.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/export_ncbi_biosample.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/first_isolate.html
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@ -9,7 +9,7 @@
<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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/g.test.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/get_episode.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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_pca.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/index.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/intrinsic_resistant.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/kurtosis.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/like.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/mdro.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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">
@ -126,7 +126,7 @@
<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to turn Verbose mode on and off (default is off). In Verbose mode, the function returns a data set with the MDRO results in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.</p></dd>
<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>

2
reference/mean_amr_distance.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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.codes.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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.groups.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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
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@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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_property.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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_source.html
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@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/pca.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/plot.html
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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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/random.html
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@ -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="">3.0.0.9017</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9018</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/resistance_predict.html
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@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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