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@ -9,7 +9,7 @@ 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="">2.1.1.9110</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9111</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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@ -220,13 +220,13 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<span class="r-in"><span><span class="va">b</span> <span class="op"><-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span><span class="op">)</span></span></span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in eucast_rules(): not all columns with antimicrobial results are of</span>
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<span class="r-wrn co"><span class="r-pr">#></span> class 'sir'. Transform them on beforehand, with e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> - a %>% as.sir(CXM:AMX)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> - a %>% as.sir(PEN:FOX)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> - a %>% mutate_if(is_sir_eligible, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> - a %>% mutate(across(where(is_sir_eligible), as.sir))</span>
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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 S S S S</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 Staphylococcus aureus - - R R 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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@ -238,27 +238,27 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<span class="r-in"><span><span class="va">c</span> <span class="op"><-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in eucast_rules(): not all columns with antimicrobial results are of</span>
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<span class="r-wrn co"><span class="r-pr">#></span> class 'sir'. Transform them on beforehand, with e.g.:</span>
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<span class="r-wrn co"><span class="r-pr">#></span> - a %>% as.sir(CXM:AMX)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> - a %>% as.sir(PEN:FOX)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> - a %>% mutate_if(is_sir_eligible, as.sir)</span>
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<span class="r-wrn co"><span class="r-pr">#></span> - a %>% mutate(across(where(is_sir_eligible), as.sir))</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">c</span><span class="op">)</span></span></span>
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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 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> 1 1 CXM Staphylococcus aureus - S Breakpoints</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 1 CAZ Staphylococcus aureus - R Expert Rules</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 1 COL Staphylococcus aureus - R Expert Rules</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 2 CAZ Enterococcus faecalis - R Expert Rules</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 2 COL Enterococcus faecalis - R Expert Rules</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 2 CXM 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 Expert Rules on Staphylococcus</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 Table 4: Intrinsic resistance in gram-positive bacteria</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> 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' 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> 2 '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> 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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