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reference/custom_eucast_rules.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9135</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9136</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">
@ -180,11 +180,11 @@
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> A set of custom EUCAST rules:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1. If AMC is "R" and genus is "Klebsiella" then set to R :</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> amoxicillin (AMX), ampicillin (AMP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #080808;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2. If AMC is "I" and genus is "Klebsiella" then set to I :</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> amoxicillin (AMX), ampicillin (AMP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FFD787;"> I </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #080808;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FFD787;"> I </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># run the custom rule set (verbose = TRUE will return a logbook instead of the data set):</span></span></span>
<span class="r-in"><span><span class="fu"><a href="eucast_rules.html">eucast_rules</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
@ -213,17 +213,17 @@
<span class="r-in"><span><span class="va">x2</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> A set of custom EUCAST rules:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1. If AMC is "R" and genus is "Klebsiella" then set to R :</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> amoxicillin (AMX), ampicillin (AMP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #080808;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2. If AMC is "I" and genus is "Klebsiella" then set to I :</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> amoxicillin (AMX), ampicillin (AMP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">AMC</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FFD787;"> I </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">genus</span><span style="color: #080808;"> is </span><span style="color: #0000BB;">"Klebsiella"</span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FFD787;"> I </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">amoxicillin</span> (AMX), <span style="color: #0000BB;">ampicillin</span> (AMP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3. If TZP is "R" then set to R :</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM),</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM),</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN),</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), tebipenem (TBP)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">TZP</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="font-weight: bold;"> then </span>set to <span style="color: #080808; background-color: #FF5F5F;"> R </span>:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">biapenem</span> (BIA), <span style="color: #0000BB;">doripenem</span> (DOR), <span style="color: #0000BB;">ertapenem</span> (ETP), <span style="color: #0000BB;">imipenem</span> (IPM),</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">imipenem/EDTA</span> (IPE), <span style="color: #0000BB;">imipenem/relebactam</span> (IMR), <span style="color: #0000BB;">meropenem</span> (MEM),</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">meropenem/nacubactam</span> (MNC), <span style="color: #0000BB;">meropenem/vaborbactam</span> (MEV), <span style="color: #0000BB;">panipenem</span> (PAN),</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">razupenem</span> (RZM), <span style="color: #0000BB;">ritipenem</span> (RIT), <span style="color: #0000BB;">ritipenem acoxil</span> (RIA), <span style="color: #0000BB;">tebipenem</span> (TBP)</span>
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