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@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
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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="">3.0.1.9041</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9042</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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@@ -61,7 +61,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">interpretive_rules</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</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_interpretive_rules"</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>
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<span> <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, guideline <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_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, version_breakpoints <span class="op">=</span> <span class="fl">15</span>,</span>
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<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, version_breakpoints <span class="op">=</span> <span class="fl">16</span>,</span>
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<span> version_expected_phenotypes <span class="op">=</span> <span class="fl">1.2</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>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
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<span> custom_rules <span class="op">=</span> <span class="cn">NULL</span>, overwrite <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
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@@ -119,15 +119,15 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<dt id="arg-version-breakpoints">version_breakpoints<a class="anchor" aria-label="anchor" href="#arg-version-breakpoints"></a></dt>
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<dd><p>The version number to use for the EUCAST Clinical Breakpoints guideline. Can be "15.0", "14.0", "13.1", "12.0", "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 .val 16.0, .val 15.0, .val 14.0, .val 13.1, .val 12.0, .val 11.0, or .val 10.0.</p></dd>
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<dt id="arg-version-expected-phenotypes">version_expected_phenotypes<a class="anchor" aria-label="anchor" href="#arg-version-expected-phenotypes"></a></dt>
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<dd><p>The version number to use for the EUCAST Expected Phenotypes. Can be "1.2".</p></dd>
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<dd><p>The version number to use for the EUCAST Expected Phenotypes. Can be .val 1.2.</p></dd>
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<dt id="arg-version-expertrules">version_expertrules<a class="anchor" aria-label="anchor" href="#arg-version-expertrules"></a></dt>
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<dd><p>The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".</p></dd>
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<dd><p>The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be .val 3.3, .val 3.2, or .val 3.1.</p></dd>
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<dt id="arg-ampc-cephalosporin-resistance">ampc_cephalosporin_resistance<a class="anchor" aria-label="anchor" href="#arg-ampc-cephalosporin-resistance"></a></dt>
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@@ -155,7 +155,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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<dt id="arg-administration">administration<a class="anchor" aria-label="anchor" href="#arg-administration"></a></dt>
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<dd><p>Route of administration, either "", "im", "iv", "oral", or NA.</p></dd>
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<dd><p>Route of administration, either .val , .val im, .val iv, .val oral, or NA.</p></dd>
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</dl></div>
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<div class="section level2">
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@@ -164,7 +164,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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</div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p><strong>Note:</strong> This function does not translate MIC values to SIR values. Use <code><a href="as.sir.html">as.sir()</a></code> for that. <br><strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br></p>
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<p><strong>Note:</strong> This function does not translate MIC or disk values to SIR values. Use <code><a href="as.sir.html">as.sir()</a></code> for that. <br><strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br></p>
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<p>The file containing all EUCAST rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The <code>AMR</code> package contains the full microbial taxonomy updated until June 24th, 2024, see <a href="microorganisms.html">microorganisms</a>.</p><div class="section">
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<h3 id="custom-rules">Custom Rules<a class="anchor" aria-label="anchor" href="#custom-rules"></a></h3>
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@@ -252,22 +252,22 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
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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 Expected phenotypes</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 1 COL Staphylococcus aureus - R Expected phenotypes</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 2 CAZ Enterococcus faecalis - R Expected phenotypes</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 2 COL Enterococcus faecalis - R Expected phenotypes</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 1 CXM Staphylococcus aureus - I Breakpoints</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 1 CXM Staphylococcus aureus I S Breakpoints</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 1 CAZ Staphylococcus aureus - R Expected phenotypes</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 1 COL Staphylococcus aureus - R Expected phenotypes</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 2 CAZ Enterococcus faecalis - R Expected phenotypes</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: Expected resistant phenotype in gram-positive bacteria</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 Staphylococcus</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 Table 4: Expected resistant phenotype in gram-positive bacteria</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 Table 4: Expected resistant phenotype in gram-positive bacteria</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 Table 4: Expected resistant phenotype 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' v15.0, 2025</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 'EUCAST Clinical Breakpoint Tables' v15.0, 2025</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 'EUCAST Expected Resistant Phenotypes' v1.2, 2023</span>
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<span class="r-out co"><span class="r-pr">#></span> 1 'EUCAST Clinical Breakpoint Tables' v16.0, 2026</span>
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<span class="r-out co"><span class="r-pr">#></span> 2 'EUCAST Clinical Breakpoint Tables' v16.0, 2026</span>
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<span class="r-out co"><span class="r-pr">#></span> 3 'EUCAST Clinical Breakpoint Tables' v16.0, 2026</span>
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<span class="r-out co"><span class="r-pr">#></span> 4 'EUCAST Expected Resistant Phenotypes' v1.2, 2023</span>
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<span class="r-out co"><span class="r-pr">#></span> 5 'EUCAST Expected Resistant Phenotypes' v1.2, 2023</span>
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<span class="r-out co"><span class="r-pr">#></span> 6 'EUCAST Expected Resistant Phenotypes' v1.2, 2023</span>
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