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@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9050</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9051</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -147,7 +147,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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<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>,</span>
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<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 class="st">"expert"</span><span class="op">)</span><span class="op">)</span>,</span>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> version_breakpoints <span class="op">=</span> <span class="fl">11</span>,</span>
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<span> version_breakpoints <span class="op">=</span> <span class="fl">12</span>,</span>
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<span> version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span>
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<span> ampc_cephalosporin_resistance <span class="op">=</span> <span class="cn">NA</span>,</span>
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<span> only_rsi_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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@ -155,7 +155,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span>
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<span></span>
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<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">11</span><span class="op">)</span></span></code></pre></div>
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<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">12</span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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@ -194,7 +194,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<dt>version_breakpoints</dt>
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<dd><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "11.0" or "10.0".</p></dd>
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<dd><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "12.0", "11.0" or "10.0".</p></dd>
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<dt>version_expertrules</dt>
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@ -311,7 +311,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">b</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo VAN AMX COL CAZ CXM PEN FOX</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 Staphylococcus aureus - S R R S S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 Staphylococcus aureus - S R S S S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 Enterococcus faecalis - - R R R S R</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 Escherichia coli R - - - - R S</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 Klebsiella pneumoniae R R - - - R S</span>
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@ -330,20 +330,20 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<span class="r-out co"><span class="r-pr">#></span> row col mo_fullname old new rule rule_group</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 1 AMX Staphylococcus aureus - S Breakpoints</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 1 CXM Staphylococcus aureus - S Breakpoints</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 1 CAZ Staphylococcus aureus - R Expert Rules</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 1 COL Staphylococcus aureus - R Expert Rules</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 2 CAZ Enterococcus faecalis - R Expert Rules</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 2 COL Enterococcus faecalis - R Expert Rules</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 1 CAZ Staphylococcus aureus R S Expert Rules</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 1 CAZ Staphylococcus aureus - R Expert Rules</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 1 COL Staphylococcus aureus - R Expert Rules</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 2 CAZ Enterococcus faecalis - R Expert Rules</span>
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<span class="r-out co"><span class="r-pr">#></span> rule_name</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 Staphylococcus</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 Staphylococcus</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 Table 4: Intrinsic resistance in gram-positive bacteria</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 Expert Rules on Staphylococcus</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 Table 4: Intrinsic resistance in gram-positive bacteria</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 Table 4: Intrinsic resistance in gram-positive bacteria</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 Table 4: Intrinsic resistance in gram-positive bacteria</span>
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<span class="r-out co"><span class="r-pr">#></span> rule_source</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 'EUCAST Clinical Breakpoint Tables' v11.0, 2021</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 'EUCAST Clinical Breakpoint Tables' v11.0, 2021</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 'EUCAST Clinical Breakpoint Tables' v12.0, 2022</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 'EUCAST Clinical Breakpoint Tables' v12.0, 2022</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021</span>
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@ -354,7 +354,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">eucast_dosage</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="st">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span>
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<span class="r-msg co"><span class="r-pr">#></span> Tables' v11.0 (2021). This note will be shown once per session.</span>
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<span class="r-msg co"><span class="r-pr">#></span> Tables' v12.0 (2022). This note will be shown once per session.</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 4</span></span>
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<span class="r-out co"><span class="r-pr">#></span> ab name standard_dosage high_dosage </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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