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reference/AMR-options.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9036</small>
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reference/AMR.html
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@ -24,7 +24,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
<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="">2.1.1.9035</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9036</small>
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reference/WHOCC.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
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reference/WHONET.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
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reference/ab_from_text.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9036</small>
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2
reference/ab_property.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
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2
reference/add_custom_antimicrobials.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
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2
reference/add_custom_microorganisms.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9036</small>
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22
reference/age.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9036</small>
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@ -222,16 +222,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.48361 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.24590 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.57650 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.28962 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.27596 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.38525 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.75683 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.34153 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.95082 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.80328 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 58 58.48634 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 44 44.24863 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 74 74.57923 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 77 77.29235 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 84 84.27869 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 36 36.38798 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 26 26.75956 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 46 46.34426 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 51 51.95355 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 37 37.80601 13</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

2
reference/age_groups.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9036</small>
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2
reference/antibiogram.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
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2
reference/antibiotic_class_selectors.html
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@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
<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="">2.1.1.9035</small>
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2
reference/antibiotics.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9036</small>
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2
reference/as.ab.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
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2
reference/as.av.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
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2
reference/as.disk.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
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4
reference/as.mic.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9036</small>
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@ -307,7 +307,7 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: AMX, EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: for AMX, EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> NOTE </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> pneumoniae - assuming body site 'Meningitis'.</span>

2
reference/as.mo.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9035</small>
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32
reference/as.sir.html
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@ -24,7 +24,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
<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="">2.1.1.9035</small>
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@ -607,19 +607,19 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 13 × 14</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_user mo_user ab mo input</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;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-05-30 <span style="color: #949494;">14:43:21</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-05-30 <span style="color: #949494;">14:43:21</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-05-30 <span style="color: #949494;">14:43:21</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-05-30 <span style="color: #949494;">14:43:21</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-05-30 <span style="color: #949494;">14:43:16</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-05-30 <span style="color: #949494;">14:43:16</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-05-30 <span style="color: #949494;">14:43:16</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-05-30 <span style="color: #949494;">14:43:16</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-05-30 <span style="color: #949494;">14:43:16</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-05-30 <span style="color: #949494;">14:43:16</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-05-30 <span style="color: #949494;">14:43:16</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-05-30 <span style="color: #949494;">14:43:16</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-05-30 <span style="color: #949494;">14:43:16</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2024-05-31 <span style="color: #949494;">08:01:26</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2024-05-31 <span style="color: #949494;">08:01:26</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2024-05-31 <span style="color: #949494;">08:01:26</span> 1 CIP Escherich… CIP B_[ORD]_ENTRBCTR 0.256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2024-05-31 <span style="color: #949494;">08:01:26</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2024-05-31 <span style="color: #949494;">08:01:21</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 0.01 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2024-05-31 <span style="color: #949494;">08:01:21</span> 2 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2024-05-31 <span style="color: #949494;">08:01:21</span> 3 AMX B_STRPT_P… AMX B_STRPT_PNMN 4 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2024-05-31 <span style="color: #949494;">08:01:21</span> 4 AMX B_STRPT_P… AMX B_STRPT_PNMN 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2024-05-31 <span style="color: #949494;">08:01:21</span> 1 AMX B_STRPT_P… AMX B_STRPT_PNMN 2 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2024-05-31 <span style="color: #949494;">08:01:21</span> 1 TOB Escherich… TOB B_[ORD]_ENTRBCTR 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> 2024-05-31 <span style="color: #949494;">08:01:21</span> 1 GEN Escherich… GEN B_[ORD]_ENTRBCTR 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> 2024-05-31 <span style="color: #949494;">08:01:20</span> 1 AMP Escherich… AMP B_[ORD]_ENTRBCTR 20 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> 2024-05-31 <span style="color: #949494;">08:01:20</span> 1 ampicillin Strep pneu AMP B_STRPT_PNMN 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 7 more variables: outcome &lt;sir&gt;, method &lt;chr&gt;, breakpoint_S_R &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># guideline &lt;chr&gt;, host &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;</span></span>
<span class="r-in"><span></span></span>
@ -828,7 +828,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column NIT, EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column for NIT, EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> infection.</span>
@ -837,7 +837,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> microorganisms might not have breakpoints for each antimicrobial drug in</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> EUCAST 2023.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column NIT, EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Interpreting MIC values: column for NIT, EUCAST 2023...</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> OK </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Run sir_interpretation_history() afterwards to retrieve a logbook with</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> all the details of the breakpoint interpretations. Note that some</span>

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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -10,7 +10,7 @@
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@ -16,7 +16,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
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@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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70
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@ -171,7 +171,7 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>...</dt>
<dd><p>rules in <a href="https://rdrr.io/r/base/tilde.html" class="external-link">formula</a> notation, see <em>Examples</em></p></dd>
<dd><p>rules in <a href="https://rdrr.io/r/base/tilde.html" class="external-link">formula</a> notation, see below for instructions, and in <em>Examples</em></p></dd>
</dl></div>
<div class="section level2">
@ -235,37 +235,45 @@
</div>
<div class="section">
<h3 id="usage-of-antibiotic-group-names">Usage of antibiotic group names<a class="anchor" aria-label="anchor" href="#usage-of-antibiotic-group-names"></a></h3>
<h3 id="usage-of-multiple-antibiotics-and-antibiotic-group-names">Usage of multiple antibiotics and antibiotic group names<a class="anchor" aria-label="anchor" href="#usage-of-multiple-antibiotics-and-antibiotic-group-names"></a></h3>
<p>It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part <em>after</em> the tilde. In above examples, the antibiotic group <code>aminopenicillins</code> is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the drugs that will be matched when running the rule.</p><ul><li><p>"aminoglycosides"<br>(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
<li><p>"aminopenicillins"<br>(amoxicillin and ampicillin)</p></li>
<li><p>"antifungals"<br>(amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
<li><p>"antimycobacterials"<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
<li><p>"betalactams"<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, and ticarcillin/clavulanic acid)</p></li>
<li><p>"carbapenems"<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)</p></li>
<li><p>"cephalosporins"<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>"cephalosporins_1st"<br>(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine)</p></li>
<li><p>"cephalosporins_2nd"<br>(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef)</p></li>
<li><p>"cephalosporins_3rd"<br>(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)</p></li>
<li><p>"cephalosporins_4th"<br>(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)</p></li>
<li><p>"cephalosporins_5th"<br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam)</p></li>
<li><p>"cephalosporins_except_caz"<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>"fluoroquinolones"<br>(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>"glycopeptides"<br>(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod)</p></li>
<li><p>"glycopeptides_except_lipo"<br>(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, and vancomycin-macromethod)</p></li>
<li><p>"lincosamides"<br>(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin, and tylvalosin)</p></li>
<li><p>"lipoglycopeptides"<br>(dalbavancin, oritavancin, and telavancin)</p></li>
<li><p>"macrolides"<br>(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin)</p></li>
<li><p>"oxazolidinones"<br>(cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone)</p></li>
<li><p>"penicillins"<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin, and ticarcillin/clavulanic acid)</p></li>
<li><p>"polymyxins"<br>(colistin, polymyxin B, and polymyxin B/polysorbate 80)</p></li>
<li><p>"quinolones"<br>(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>"streptogramins"<br>(pristinamycin and quinupristin/dalfopristin)</p></li>
<li><p>"tetracyclines"<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tigecycline)</p></li>
<li><p>"tetracyclines_except_tgc"<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, and tetracycline)</p></li>
<li><p>"trimethoprims"<br>(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole)</p></li>
<li><p>"ureidopenicillins"<br>(azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam)</p></li>
<p>You can define antibiotic groups instead of single antibiotics for the rule consequence, which is the part <em>after</em> the tilde (~). In the examples above, the antibiotic group <code>aminopenicillins</code> includes both ampicillin and amoxicillin.</p>
<p>Rules can also be applied to multiple antibiotics and antibiotic groups simultaneously. Use the <code><a href="https://rdrr.io/r/base/c.html" class="external-link">c()</a></code> function to combine multiple antibiotics. For instance, the following example sets all aminopenicillins and ureidopenicillins to "R" if column TZP (piperacillin/tazobactam) is "R":</p>
<p></p><div class="sourceCode r"><pre><code><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <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="va">aminopenicillins</span>, <span class="va">ureidopenicillins</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span>
<span><span class="va">x</span></span>
<span><span class="co">#&gt; A set of custom EUCAST rules:</span></span>
<span><span class="co">#&gt; </span></span>
<span><span class="co">#&gt; 1. If TZP is "R" then set to "R":</span></span>
<span><span class="co">#&gt; amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)</span></span></code></pre><p></p></div>
<p>These 28 antibiotic groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
<li><p>aminopenicillins<br>(amoxicillin and ampicillin)</p></li>
<li><p>antifungals<br>(amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
<li><p>betalactams<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, and ticarcillin/clavulanic acid)</p></li>
<li><p>carbapenems<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)</p></li>
<li><p>cephalosporins<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>cephalosporins_1st<br>(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, and cephradine)</p></li>
<li><p>cephalosporins_2nd<br>(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil, and loracarbef)</p></li>
<li><p>cephalosporins_3rd<br>(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, and latamoxef)</p></li>
<li><p>cephalosporins_4th<br>(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome, and cefquinome)</p></li>
<li><p>cephalosporins_5th<br>(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam)</p></li>
<li><p>cephalosporins_except_caz<br>(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, and loracarbef)</p></li>
<li><p>fluoroquinolones<br>(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>glycopeptides<br>(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, and vancomycin-macromethod)</p></li>
<li><p>glycopeptides_except_lipo<br>(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, and vancomycin-macromethod)</p></li>
<li><p>lincosamides<br>(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin, and tylvalosin)</p></li>
<li><p>lipoglycopeptides<br>(dalbavancin, oritavancin, and telavancin)</p></li>
<li><p>macrolides<br>(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, and tylvalosin)</p></li>
<li><p>oxazolidinones<br>(cadazolid, cycloserine, linezolid, tedizolid, and thiacetazone)</p></li>
<li><p>penicillins<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin, and ticarcillin/clavulanic acid)</p></li>
<li><p>polymyxins<br>(colistin, polymyxin B, and polymyxin B/polysorbate 80)</p></li>
<li><p>quinolones<br>(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin)</p></li>
<li><p>streptogramins<br>(pristinamycin and quinupristin/dalfopristin)</p></li>
<li><p>tetracyclines<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, and tigecycline)</p></li>
<li><p>tetracyclines_except_tgc<br>(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, and tetracycline)</p></li>
<li><p>trimethoprims<br>(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, and trimethoprim/sulfamethoxazole)</p></li>
<li><p>ureidopenicillins<br>(azlocillin, mezlocillin, piperacillin, and piperacillin/tazobactam)</p></li>
</ul></div>
</div>

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@ -10,7 +10,7 @@
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reference/key_antimicrobials.html
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@ -10,7 +10,7 @@
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reference/kurtosis.html
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@ -10,7 +10,7 @@
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reference/like.html
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@ -10,7 +10,7 @@
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reference/mdro.html
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@ -10,7 +10,7 @@
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reference/mean_amr_distance.html
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@ -10,7 +10,7 @@
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reference/microorganisms.codes.html
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@ -10,7 +10,7 @@
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reference/microorganisms.groups.html
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@ -10,7 +10,7 @@
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reference/microorganisms.html
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@ -10,7 +10,7 @@
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reference/mo_matching_score.html
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@ -10,7 +10,7 @@
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reference/mo_property.html
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@ -10,7 +10,7 @@
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reference/mo_source.html
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@ -12,7 +12,7 @@ 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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@ -10,7 +10,7 @@
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reference/plot.html
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@ -12,7 +12,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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reference/proportion.html
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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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reference/random.html
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@ -10,7 +10,7 @@
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reference/resistance_predict.html
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@ -10,7 +10,7 @@
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reference/skewness.html
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@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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reference/translate.html
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