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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>
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reference/AMR-options.html
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@ -7,7 +7,7 @@
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reference/AMR.html
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@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
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reference/WHOCC.html
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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reference/ab_from_text.html
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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2
reference/add_custom_antimicrobials.html
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@ -7,7 +7,7 @@
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2
reference/add_custom_microorganisms.html
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@ -7,7 +7,7 @@
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2
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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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>
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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="">2.1.1.9257</small>
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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="">2.1.1.9257</small>
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2
reference/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="">2.1.1.9257</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>
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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="">2.1.1.9257</small>
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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>
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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>
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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="">2.1.1.9257</small>
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48
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="">2.1.1.9257</small>
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@ -212,7 +212,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<dt id="arg-parallel">parallel<a class="anchor" aria-label="anchor" href="#arg-parallel"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. This requires no additional packages, as the used <code>parallel</code> package is part of base <span style="R">R</span>.</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. This requires no additional packages, as the used <code>parallel</code> package is part of base <span style="R">R</span>. On Windows and on <span style="R">R</span> &lt; 4.0.0 <code><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">parallel::parLapply()</a></code> will be used; in all other cases the most efficient <code><a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply()</a></code> will be used.</p></dd>
<dt id="arg-max-cores">max_cores<a class="anchor" aria-label="anchor" href="#arg-max-cores"></a></dt>
@ -489,20 +489,20 @@ 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: 14 × 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> 2025-04-27 <span style="color: #949494;">08:06:50</span> 1 DISK ampicillin Strep pn… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-04-27 <span style="color: #949494;">08:06:50</span> 1 DISK AMP Escheric… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-04-27 <span style="color: #949494;">15:58:30</span> 1 DISK ampicillin Strep pn… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-04-27 <span style="color: #949494;">15:58:30</span> 1 DISK AMP Escheric… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-04-27 <span style="color: #949494;">08:06:50</span> 1 DISK GEN Escheric… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-04-27 <span style="color: #949494;">08:06:51</span> 1 DISK TOB Escheric… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-04-27 <span style="color: #949494;">08:06:51</span> 1 MIC AMX B_STRPT_… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-04-27 <span style="color: #949494;">08:06:52</span> 1 MIC AMX B_STRPT_… human 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-04-27 <span style="color: #949494;">08:06:52</span> 2 MIC AMX B_STRPT_… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-04-27 <span style="color: #949494;">08:06:52</span> 3 MIC AMX B_STRPT_… human 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-04-27 <span style="color: #949494;">08:06:52</span> 4 MIC AMX B_STRPT_… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2025-04-27 <span style="color: #949494;">08:06:58</span> 1 MIC amoxicillin Escheric… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2025-04-27 <span style="color: #949494;">08:06:58</span> 1 MIC cipro Escheric… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2025-04-27 <span style="color: #949494;">08:06:58</span> 1 DISK tobra Escheric… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">14</span> 2025-04-27 <span style="color: #949494;">08:06:58</span> 1 DISK genta Escheric… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-04-27 <span style="color: #949494;">15:58:30</span> 1 DISK GEN Escheric… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-04-27 <span style="color: #949494;">15:58:31</span> 1 DISK TOB Escheric… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-04-27 <span style="color: #949494;">15:58:31</span> 1 MIC AMX B_STRPT_… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-04-27 <span style="color: #949494;">15:58:32</span> 1 MIC AMX B_STRPT_… human 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-04-27 <span style="color: #949494;">15:58:32</span> 2 MIC AMX B_STRPT_… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-04-27 <span style="color: #949494;">15:58:32</span> 3 MIC AMX B_STRPT_… human 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-04-27 <span style="color: #949494;">15:58:32</span> 4 MIC AMX B_STRPT_… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2025-04-27 <span style="color: #949494;">15:58:38</span> 1 MIC amoxicillin Escheric… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2025-04-27 <span style="color: #949494;">15:58:38</span> 1 MIC cipro Escheric… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2025-04-27 <span style="color: #949494;">15:58:38</span> 1 DISK tobra Escheric… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">14</span> 2025-04-27 <span style="color: #949494;">15:58:38</span> 1 DISK genta Escheric… 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>
@ -683,16 +683,16 @@ 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: 114 × 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> 2025-04-27 <span style="color: #949494;">08:06:50</span> 1 DISK ampicillin Strep pneu human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-04-27 <span style="color: #949494;">08:06:50</span> 1 DISK AMP Escherich… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-04-27 <span style="color: #949494;">15:58:30</span> 1 DISK ampicillin Strep pneu human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-04-27 <span style="color: #949494;">15:58:30</span> 1 DISK AMP Escherich… human 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-04-27 <span style="color: #949494;">08:06:50</span> 1 DISK GEN Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-04-27 <span style="color: #949494;">08:06:51</span> 1 DISK TOB Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-04-27 <span style="color: #949494;">08:06:51</span> 1 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-04-27 <span style="color: #949494;">08:06:52</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-04-27 <span style="color: #949494;">08:06:52</span> 2 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-04-27 <span style="color: #949494;">08:06:52</span> 3 MIC AMX B_STRPT_P… human 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-04-27 <span style="color: #949494;">08:06:52</span> 4 MIC AMX B_STRPT_P… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-04-27 <span style="color: #949494;">15:58:30</span> 1 DISK GEN Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-04-27 <span style="color: #949494;">15:58:31</span> 1 DISK TOB Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-04-27 <span style="color: #949494;">15:58:31</span> 1 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-04-27 <span style="color: #949494;">15:58:32</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-04-27 <span style="color: #949494;">15:58:32</span> 2 MIC AMX B_STRPT_P… human 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-04-27 <span style="color: #949494;">15:58:32</span> 3 MIC AMX B_STRPT_P… human 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-04-27 <span style="color: #949494;">15:58:32</span> 4 MIC AMX B_STRPT_P… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 104 more rows</span></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>

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reference/atc_online.html
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@ -7,7 +7,7 @@
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reference/availability.html
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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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@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@ -7,7 +7,7 @@
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@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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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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@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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reference/plot.html
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@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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reference/proportion.html
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@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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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
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reference/skewness.html
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@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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reference/top_n_microorganisms.html
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reference/translate.html
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