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reference/AMR-deprecated.html
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<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="">2.1.1.9275</small>
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reference/AMR-options.html
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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
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reference/WHOCC.html
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reference/ab_from_text.html
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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="">2.1.1.9275</small>
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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="">2.1.1.9275</small>
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reference/age.html
+11 -11
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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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</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 1999-06-30 25 25.86849 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.28493 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.43562 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.20000 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.52877 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.24110 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.22740 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.33699 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.70959 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.29315 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 25 25.87397 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 57 57.29041 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 59 59.44110 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 45 45.20548 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 75 75.53425 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 78 78.24658 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 85 85.23288 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 37 37.34247 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 27 27.71507 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 47 47.29863 21</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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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
<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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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reference/antimicrobial_selectors.html
+2 -2
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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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</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">
@@ -164,7 +164,7 @@ my_data_with_all_these_columns %&amp;gt;%
<dl><dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns of class <code>sir</code> must be selected (default is <code>FALSE</code>), see <code><a href="as.sir.html">as.sir()</a></code>.</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antimicrobial columns must be included that were transformed to class <a href="as.sir.html">sir</a> on beforehand. Defaults to <code>FALSE</code>.</p></dd>
<dt id="arg-only-treatable">only_treatable<a class="anchor" aria-label="anchor" href="#arg-only-treatable"></a></dt>
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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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reference/as.ab.html
+1 -1
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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="">2.1.1.9275</small>
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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="">2.1.1.9275</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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9275</small>
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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="">2.1.1.9275</small>
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reference/as.mo.html
+1 -1
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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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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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="">2.1.1.9275</small>
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@@ -414,10 +414,10 @@ 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> 2025-05-13 <span style="color: #949494;">17:02:01</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> 2025-05-13 <span style="color: #949494;">17:02:01</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> 2025-05-13 <span style="color: #949494;">17:02:01</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> 2025-05-13 <span style="color: #949494;">17:02:02</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> 2025-05-15 <span style="color: #949494;">08:46:28</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> 2025-05-15 <span style="color: #949494;">08:46:28</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> 2025-05-15 <span style="color: #949494;">08:46:28</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> 2025-05-15 <span style="color: #949494;">08:46:28</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>
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="">2.1.1.9275</small>
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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="">2.1.1.9275</small>
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reference/av_property.html
+1 -1
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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="">2.1.1.9275</small>
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reference/availability.html
+1 -1
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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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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reference/bug_drug_combinations.html
+1 -1
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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="">2.1.1.9275</small>
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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
+1 -1
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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/dosage.html
+1 -1
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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="">2.1.1.9275</small>
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reference/eucast_rules.html
+5 -6
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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="">2.1.1.9275</small>
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@@ -62,7 +62,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<span> rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_eucastrules"</span>, default <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"breakpoints"</span>,</span>
<span> <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, version_breakpoints <span class="op">=</span> <span class="fl">15</span>,</span>
<span> version_expected_phenotypes <span class="op">=</span> <span class="fl">1.2</span>, version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span>
<span> ampc_cephalosporin_resistance <span class="op">=</span> <span class="cn">NA</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> ampc_cephalosporin_resistance <span class="op">=</span> <span class="cn">NA</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
<span> custom_rules <span class="op">=</span> <span class="cn">NULL</span>, overwrite <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="va">ab</span>, administration <span class="op">=</span> <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">15</span><span class="op">)</span></span></code></pre></div>
@@ -122,7 +122,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antimicrobial columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>).</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antimicrobial columns must be included that were transformed to class <a href="as.sir.html">sir</a> on beforehand. Defaults to <code>FALSE</code> if no columns of <code>x</code> have a class <a href="as.sir.html">sir</a>.</p></dd>
<dt id="arg-custom-rules">custom_rules<a class="anchor" aria-label="anchor" href="#arg-custom-rules"></a></dt>
@@ -178,9 +178,8 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<h2 id="antimicrobials">Antimicrobials<a class="anchor" aria-label="anchor" href="#antimicrobials"></a></h2>
<p>To define antimicrobials column names, leave as it is to determine it automatically with <code><a href="guess_ab_col.html">guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antimicrobials are eligible for the functions <code>eucast_rules()</code> and <code><a href="mdro.html">mdro()</a></code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href="https://atcddd.fhi.no/atc/structure_and_principles/" class="external-link">ATC code</a>)', sorted alphabetically:</p>
<p>Amikacin (<code>AMK</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01GB06&amp;showdescription=no" class="external-link">J01GB06</a>), amoxicillin (<code>AMX</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&amp;showdescription=no" class="external-link">J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&amp;showdescription=no" class="external-link">J01CR02</a>), amoxicillin/sulbactam (<code>AXS</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&amp;showdescription=no" class="external-link">J01CR02</a>), ampicillin (<code>AMP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA01&amp;showdescription=no" class="external-link">J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CR01&amp;showdescription=no" class="external-link">J01CR01</a>), apramycin (<code>APR</code>, <a href="https://atcddd.fhi.no/atcvet/atcvet_index/?code=QA07AA92&amp;showdescription=no" class="external-link">QA07AA92</a>), arbekacin (<code>ARB</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01GB12&amp;showdescription=no" class="external-link">J01GB12</a>), aspoxicillin (<code>APX</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA19&amp;showdescription=no" class="external-link">J01CA19</a>), azidocillin (<code>AZD</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE04&amp;showdescription=no" class="external-link">J01CE04</a>), azithromycin (<code>AZM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01FA10&amp;showdescription=no" class="external-link">J01FA10</a>), azlocillin (<code>AZL</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA09&amp;showdescription=no" class="external-link">J01CA09</a>), aztreonam (<code>ATM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF01&amp;showdescription=no" class="external-link">J01DF01</a>), aztreonam/avibactam (<code>AZA</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&amp;showdescription=no" class="external-link">J01DF51</a>), aztreonam/nacubactam (<code>ANC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&amp;showdescription=no" class="external-link">J01DF51</a>), bacampicillin (<code>BAM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA06&amp;showdescription=no" class="external-link">J01CA06</a>), bekanamycin (<code>BEK</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01GB13&amp;showdescription=no" class="external-link">J01GB13</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE08&amp;showdescription=no" class="external-link">J01CE08</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE10&amp;showdescription=no" class="external-link">J01CE10</a>), benzylpenicillin (<code>PEN</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE01&amp;showdescription=no" class="external-link">J01CE01</a>), besifloxacin (<code>BES</code>, <a href="https://atcddd.fhi.no/atcvet/atcvet_index/?code=QS01AE08&amp;showdescription=no" class="external-link">QS01AE08</a>), biapenem (<code>BIA</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&amp;showdescription=no" class="external-link">J01DH05</a>), bleomycin (<code>BLM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=L01DC01&amp;showdescription=no" class="external-link">L01DC01</a>), brodimoprim (<code>BDP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01EA02&amp;showdescription=no" class="external-link">J01EA02</a>), carbenicillin (<code>CRB</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA03&amp;showdescription=no" class="external-link">J01CA03</a>), carindacillin (<code>CRN</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA05&amp;showdescription=no" class="external-link">J01CA05</a>), carumonam (<code>CAR</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF02&amp;showdescription=no" class="external-link">J01DF02</a>), cefacetrile (<code>CAC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB10&amp;showdescription=no" class="external-link">J01DB10</a>), cefaclor (<code>CEC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DC04&amp;showdescription=no" class="external-link">J01DC04</a>), cefadroxil (<code>CFR</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB05&amp;showdescription=no" class="external-link">J01DB05</a>), cefalexin (<code>LEX</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB01&amp;showdescription=no" class="external-link">J01DB01</a>), cefaloridine (<code>RID</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB02&amp;showdescription=no" class="external-link">J01DB02</a>), cefalotin (<code>CEP</code>, <a href="https://atcddd.fhi.no/atc_ddd_Line truncated
<p>To let the function automatically detect antimicrobial column names, do not provide any named arguments. It will then use <code><a href="guess_ab_col.html">guess_ab_col()</a></code> to find them.</p>
<p>To manually specify a column, provide its name (case-insensitive) as an argument, e.g. <code>AMX = "amoxicillin"</code>. To skip a specific antimicrobial, set it to <code>NULL</code>, e.g. <code>TIC = NULL</code> to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.</p>
</div>
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<h2 id="download-our-reference-data">Download Our Reference Data<a class="anchor" aria-label="anchor" href="#download-our-reference-data"></a></h2>
reference/example_isolates.html
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@@ -7,7 +7,7 @@
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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="">2.1.1.9275</small>
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@@ -9,7 +9,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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+1 -1
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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/get_episode.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/ggplot_pca.html
+1 -1
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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="">2.1.1.9275</small>
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reference/ggplot_sir.html
+1 -1
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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="">2.1.1.9275</small>
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reference/guess_ab_col.html
+2 -2
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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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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@@ -76,7 +76,7 @@
<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>).</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antimicrobial columns must be included that were transformed to class <a href="as.sir.html">sir</a> on beforehand. Defaults to <code>FALSE</code> if no columns of <code>x</code> have a class <a href="as.sir.html">sir</a>.</p></dd>
</dl></div>
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+1 -1
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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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+1 -1
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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/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="">2.1.1.9275</small>
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reference/key_antimicrobials.html
+4 -4
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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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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@@ -62,9 +62,9 @@
<span> <span class="st">"ceftazidime"</span>, <span class="st">"meropenem"</span><span class="op">)</span>, gram_positive <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"vancomycin"</span>, <span class="st">"teicoplanin"</span>,</span>
<span> <span class="st">"tetracycline"</span>, <span class="st">"erythromycin"</span>, <span class="st">"oxacillin"</span>, <span class="st">"rifampin"</span><span class="op">)</span>,</span>
<span> antifungal <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"anidulafungin"</span>, <span class="st">"caspofungin"</span>, <span class="st">"fluconazole"</span>, <span class="st">"miconazole"</span>,</span>
<span> <span class="st">"nystatin"</span>, <span class="st">"voriconazole"</span><span class="op">)</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span> <span class="st">"nystatin"</span>, <span class="st">"voriconazole"</span><span class="op">)</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">all_antimicrobials</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">all_antimicrobials</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">y</span>, <span class="va">z</span>, type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"points"</span>, <span class="st">"keyantimicrobials"</span><span class="op">)</span>,</span>
<span> ignore_I <span class="op">=</span> <span class="cn">TRUE</span>, points_threshold <span class="op">=</span> <span class="fl">2</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
@@ -99,7 +99,7 @@
<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only columns must be included that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>).</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antimicrobial columns must be included that were transformed to class <a href="as.sir.html">sir</a> on beforehand. Defaults to <code>FALSE</code> if no columns of <code>x</code> have a class <a href="as.sir.html">sir</a>.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</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">
reference/like.html
+1 -1
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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</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">
reference/mdro.html
+11 -11
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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</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">
@@ -58,19 +58,20 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mdro</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, guideline <span class="op">=</span> <span class="st">"CMI2012"</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, esbl <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> carbapenemase <span class="op">=</span> <span class="cn">NA</span>, mecA <span class="op">=</span> <span class="cn">NA</span>, mecC <span class="op">=</span> <span class="cn">NA</span>, vanA <span class="op">=</span> <span class="cn">NA</span>, vanB <span class="op">=</span> <span class="cn">NA</span>,</span>
<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, pct_required_classes <span class="op">=</span> <span class="fl">0.5</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">custom_mdro_guideline</span><span class="op">(</span><span class="va">...</span>, as_factor <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">brmo</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">brmo</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mrgn</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mrgn</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mdr_tb</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mdr_tb</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mdr_cmi2012</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">mdr_cmi2012</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span> <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">eucast_exceptional_phenotypes</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span><span class="fu">eucast_exceptional_phenotypes</span><span class="op">(</span>x <span class="op">=</span> <span class="cn">NULL</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
@@ -135,7 +136,7 @@
<dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antimicrobial columns must be detected that were transformed to class <code>sir</code> (see <code><a href="as.sir.html">as.sir()</a></code>) on beforehand (default is <code>FALSE</code>).</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether only antimicrobial columns must be included that were transformed to class <a href="as.sir.html">sir</a> on beforehand. Defaults to <code>FALSE</code> if no columns of <code>x</code> have a class <a href="as.sir.html">sir</a>.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
@@ -228,9 +229,8 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
<h2 id="antimicrobials">Antimicrobials<a class="anchor" aria-label="anchor" href="#antimicrobials"></a></h2>
<p>To define antimicrobials column names, leave as it is to determine it automatically with <code><a href="guess_ab_col.html">guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antimicrobials are eligible for the functions <code><a href="eucast_rules.html">eucast_rules()</a></code> and <code>mdro()</code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href="https://atcddd.fhi.no/atc/structure_and_principles/" class="external-link">ATC code</a>)', sorted alphabetically:</p>
<p>Amikacin (<code>AMK</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01GB06&amp;showdescription=no" class="external-link">J01GB06</a>), amoxicillin (<code>AMX</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&amp;showdescription=no" class="external-link">J01CA04</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&amp;showdescription=no" class="external-link">J01CR02</a>), amoxicillin/sulbactam (<code>AXS</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&amp;showdescription=no" class="external-link">J01CR02</a>), ampicillin (<code>AMP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA01&amp;showdescription=no" class="external-link">J01CA01</a>), ampicillin/sulbactam (<code>SAM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CR01&amp;showdescription=no" class="external-link">J01CR01</a>), apramycin (<code>APR</code>, <a href="https://atcddd.fhi.no/atcvet/atcvet_index/?code=QA07AA92&amp;showdescription=no" class="external-link">QA07AA92</a>), arbekacin (<code>ARB</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01GB12&amp;showdescription=no" class="external-link">J01GB12</a>), aspoxicillin (<code>APX</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA19&amp;showdescription=no" class="external-link">J01CA19</a>), azidocillin (<code>AZD</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE04&amp;showdescription=no" class="external-link">J01CE04</a>), azithromycin (<code>AZM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01FA10&amp;showdescription=no" class="external-link">J01FA10</a>), azlocillin (<code>AZL</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA09&amp;showdescription=no" class="external-link">J01CA09</a>), aztreonam (<code>ATM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF01&amp;showdescription=no" class="external-link">J01DF01</a>), aztreonam/avibactam (<code>AZA</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&amp;showdescription=no" class="external-link">J01DF51</a>), aztreonam/nacubactam (<code>ANC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&amp;showdescription=no" class="external-link">J01DF51</a>), bacampicillin (<code>BAM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA06&amp;showdescription=no" class="external-link">J01CA06</a>), bekanamycin (<code>BEK</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01GB13&amp;showdescription=no" class="external-link">J01GB13</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE08&amp;showdescription=no" class="external-link">J01CE08</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE10&amp;showdescription=no" class="external-link">J01CE10</a>), benzylpenicillin (<code>PEN</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CE01&amp;showdescription=no" class="external-link">J01CE01</a>), besifloxacin (<code>BES</code>, <a href="https://atcddd.fhi.no/atcvet/atcvet_index/?code=QS01AE08&amp;showdescription=no" class="external-link">QS01AE08</a>), biapenem (<code>BIA</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&amp;showdescription=no" class="external-link">J01DH05</a>), bleomycin (<code>BLM</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=L01DC01&amp;showdescription=no" class="external-link">L01DC01</a>), brodimoprim (<code>BDP</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01EA02&amp;showdescription=no" class="external-link">J01EA02</a>), carbenicillin (<code>CRB</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA03&amp;showdescription=no" class="external-link">J01CA03</a>), carindacillin (<code>CRN</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01CA05&amp;showdescription=no" class="external-link">J01CA05</a>), carumonam (<code>CAR</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DF02&amp;showdescription=no" class="external-link">J01DF02</a>), cefacetrile (<code>CAC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB10&amp;showdescription=no" class="external-link">J01DB10</a>), cefaclor (<code>CEC</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DC04&amp;showdescription=no" class="external-link">J01DC04</a>), cefadroxil (<code>CFR</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB05&amp;showdescription=no" class="external-link">J01DB05</a>), cefalexin (<code>LEX</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB01&amp;showdescription=no" class="external-link">J01DB01</a>), cefaloridine (<code>RID</code>, <a href="https://atcddd.fhi.no/atc_ddd_index//?code=J01DB02&amp;showdescription=no" class="external-link">J01DB02</a>), cefalotin (<code>CEP</code>, <a href="https://atcddd.fhi.no/atc_ddd_Line truncated
<p>To let the function automatically detect antimicrobial column names, do not provide any named arguments. It will then use <code><a href="guess_ab_col.html">guess_ab_col()</a></code> to find them.</p>
<p>To manually specify a column, provide its name (case-insensitive) as an argument, e.g. <code>AMX = "amoxicillin"</code>. To skip a specific antimicrobial, set it to <code>NULL</code>, e.g. <code>TIC = NULL</code> to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.</p>
</div>
<div class="section level2">
<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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reference/microorganisms.codes.html
+1 -1
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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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reference/microorganisms.groups.html
+1 -1
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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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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reference/microorganisms.html
+1 -1
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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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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reference/mo_matching_score.html
+1 -1
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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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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reference/mo_property.html
+1 -1
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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="">2.1.1.9275</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9276</small>
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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
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reference/pca.html
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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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