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2026-03-20 16:11:30 +00:00
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reference/interpretive_rules.html
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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
<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="">3.0.1.9035</small>
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@@ -228,11 +228,10 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># apply EUCAST rules: some results wil be changed</span></span></span>
<span class="r-in"><span><span class="va">b</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> class 'sir'. Transform them on beforehand, with e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - x %&gt;% as.sir(CXM:AMX)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - x %&gt;% mutate_if(is_sir_eligible, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - x %&gt;% mutate(across(where(is_sir_eligible), as.sir))</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()` (`?AMR::eucast_rules()`): not all columns with</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial results are of class <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: -</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">mutate_if</span><span style="color: #D7AF00;">(</span>is_sir_eligible, as.sir<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">across</span><span style="color: #BBBB00;">(</span><span style="font-weight: bold;">where</span><span style="color: #0000BB;">(</span>is_sir_eligible<span style="color: #0000BB;">)</span>, as.sir<span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">)</span></span>
<span class="r-in"><span></span></span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo VAN AMX COL CAZ CXM PEN FOX</span>
@@ -246,11 +245,10 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span><span class="co"># do not apply EUCAST rules, but rather get a data.frame</span></span></span>
<span class="r-in"><span><span class="co"># containing all details about the transformations:</span></span></span>
<span class="r-in"><span><span class="va">c</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()`: not all columns with antimicrobial results are of</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> class 'sir'. Transform them on beforehand, with e.g.:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - x %&gt;% as.sir(CXM:AMX)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - x %&gt;% mutate_if(is_sir_eligible, as.sir)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> - x %&gt;% mutate(across(where(is_sir_eligible), as.sir))</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in `eucast_rules()` (`?AMR::eucast_rules()`): not all columns with</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial results are of class <span style="color: #0000BB;">&lt;sir&gt;</span>. Transform them on beforehand, e.g.: -</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">as.sir</span><span style="color: #D7AF00;">(</span>CXM<span style="color: #D7AF00;">:</span>AMX<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span> <span style="font-weight: bold;">mutate_if</span><span style="color: #D7AF00;">(</span>is_sir_eligible, as.sir<span style="color: #D7AF00;">)</span> - x <span style="color: #D7AF00;">%&gt;%</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="font-weight: bold;">mutate</span><span style="color: #D7AF00;">(</span><span style="font-weight: bold;">across</span><span style="color: #BBBB00;">(</span><span style="font-weight: bold;">where</span><span style="color: #0000BB;">(</span>is_sir_eligible<span style="color: #0000BB;">)</span>, as.sir<span style="color: #BBBB00;">)</span><span style="color: #D7AF00;">)</span></span>
<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">c</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> row col mo_fullname old new rule rule_group</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1 AMX Staphylococcus aureus - S Breakpoints</span>
@@ -278,8 +276,8 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<span class="r-in"><span><span class="co"># Dosage guidelines:</span></span></span>
<span class="r-in"><span></span></span>
<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>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> Tables' v15.0 (2025). </span><span style="color: #BB0000;">This note will be shown once per session.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Tables' v15.0 (2025). <span style="color: #BB0000;">This note will be shown once per session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ab name standard_dosage high_dosage eucast_version</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&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;dbl&gt;</span></span>