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@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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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="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -180,7 +180,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<dt id="arg-substitute-missing-r-breakpoint">substitute_missing_r_breakpoint<a class="anchor" aria-label="anchor" href="#arg-substitute-missing-r-breakpoint"></a></dt>
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<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that a missing clinical breakpoints for R (resistant) must be substituted with R - the default is <code>FALSE</code>. Some (especially CLSI) breakpoints only have a breakpoint for S, meaning the outcome can only be <code>"S"</code> or <code>NA</code>. Setting this to <code>TRUE</code> will convert the <code>NA</code>s to <code>"R"</code> only if the R breakpoint is missing. Can also be set with the package option <code><a href="AMR-options.html">AMR_substitute_missing_r_breakpoint</a></code>.</p></dd>
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<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that a missing clinical breakpoints for R (resistant) must be substituted with R - the default is <code>FALSE</code>. Some (especially CLSI) breakpoints only have a breakpoint for S, meaning that the outcome can only be <code>"S"</code> or <code>NA</code>. Setting this to <code>TRUE</code> will convert the <code>NA</code>s in these cases to <code>"R"</code>. Can also be set with the package option <code><a href="AMR-options.html">AMR_substitute_missing_r_breakpoint</a></code>.</p></dd>
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<dt id="arg-include-screening">include_screening<a class="anchor" aria-label="anchor" href="#arg-include-screening"></a></dt>
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@ -212,7 +212,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<dt id="arg-parallel">parallel<a class="anchor" aria-label="anchor" href="#arg-parallel"></a></dt>
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<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. This requires no additional packages, as the used <code>parallel</code> package is part of base <span style="R">R</span>. On Windows and on <span style="R">R</span> < 4.0.0 <code><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">parallel::parLapply()</a></code> will be used, in all other cases the most efficient <code><a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply()</a></code> will be used.</p></dd>
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<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. This requires no additional packages, as the used <code>parallel</code> package is part of base <span style="R">R</span>. On Windows and on <span style="R">R</span> < 4.0.0 <code><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">parallel::parLapply()</a></code> will be used, in all other cases the more efficient <code><a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply()</a></code> will be used.</p></dd>
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<dt id="arg-max-cores">max_cores<a class="anchor" aria-label="anchor" href="#arg-max-cores"></a></dt>
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@ -353,7 +353,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …</span></span>
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<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span> <span class="co"># see all SIR results at a glance</span></span></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/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span><span class="op">)</span> <span class="co"># see all SIR results at a glance</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> date patient age gender </span>
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<span class="r-out co"><span class="r-pr">#></span> Min. :2002-01-02 Length:2000 Min. : 0.00 Length:2000 </span>
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<span class="r-out co"><span class="r-pr">#></span> 1st Qu.:2005-07-31 Class :character 1st Qu.:63.00 Class :character </span>
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@ -375,94 +376,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
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<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.2% (n=3) </span>
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<span class="r-out co"><span class="r-pr">#></span> %R :31.2% (n=114) %R :29.5% (n=278) %R :59.6% (n=804) </span>
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<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> AMC AMP TZP </span>
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<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
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<span class="r-out co"><span class="r-pr">#></span> %S :71.4% (n=1342) %S :40.2% (n=543) %S :86.1% (n=862) </span>
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<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> %I : 4.8% (n=91) %I : 0.2% (n=3) %I : 1.3% (n=13) </span>
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<span class="r-out co"><span class="r-pr">#></span> %R :23.7% (n=446) %R :59.6% (n=804) %R :12.6% (n=126) </span>
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<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> CZO FEP CXM </span>
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<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
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<span class="r-out co"><span class="r-pr">#></span> %S :54.9% (n=245) %S :85.6% (n=620) %S :72.5% (n=1297) </span>
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<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> %I : 0.4% (n=2) %I : 0.1% (n=1) %I : 1.2% (n=22) </span>
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<span class="r-out co"><span class="r-pr">#></span> %R :44.6% (n=199) %R :14.2% (n=103) %R :26.3% (n=470) </span>
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<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> FOX CTX CAZ </span>
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<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
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<span class="r-out co"><span class="r-pr">#></span> %S :71.6% (n=586) %S :84.4% (n=796) %S :33.5% (n=607) </span>
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<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> %I : 1.0% (n=8) %I : 0.1% (n=1) %I : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> %R :27.4% (n=224) %R :15.5% (n=146) %R :66.5% (n=1204) </span>
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<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> CRO GEN TOB </span>
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<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
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<span class="r-out co"><span class="r-pr">#></span> %S :84.4% (n=796) %S :74.0% (n=1372) %S :65.1% (n=879) </span>
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<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> %I : 0.1% (n=1) %I : 1.5% (n=27) %I : 0.5% (n=7) </span>
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<span class="r-out co"><span class="r-pr">#></span> %R :15.5% (n=146) %R :24.6% (n=456) %R :34.4% (n=465) </span>
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<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> AMK KAN TMP </span>
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<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
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<span class="r-out co"><span class="r-pr">#></span> %S :36.3% (n=251) %S : 0.0% (n=0) %S :61.2% (n=918) </span>
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<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.7% (n=10) </span>
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<span class="r-out co"><span class="r-pr">#></span> %R :63.7% (n=441) %R :100.0% (n=471) %R :38.1% (n=571) </span>
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<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> SXT NIT FOS </span>
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<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
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<span class="r-out co"><span class="r-pr">#></span> %S :79.1% (n=1392) %S :76.0% (n=565) %S :57.8% (n=203) </span>
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<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> %I : 0.3% (n=6) %I : 6.9% (n=51) %I : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> %R :20.5% (n=361) %R :17.1% (n=127) %R :42.2% (n=148) </span>
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<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> LNZ CIP MFX </span>
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<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
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<span class="r-out co"><span class="r-pr">#></span> %S :30.7% (n=314) %S :78.9% (n=1112) %S :64.5% (n=136) </span>
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<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 4.9% (n=69) %I : 1.9% (n=4) </span>
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<span class="r-out co"><span class="r-pr">#></span> %R :69.3% (n=709) %R :16.2% (n=228) %R :33.6% (n=71) </span>
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<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> VAN TEC TCY </span>
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<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
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<span class="r-out co"><span class="r-pr">#></span> %S :61.7% (n=1149) %S :24.3% (n=237) %S :68.3% (n=820) </span>
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<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 1.9% (n=23) </span>
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<span class="r-out co"><span class="r-pr">#></span> %R :38.3% (n=712) %R :75.7% (n=739) %R :29.8% (n=357) </span>
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<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> TGC DOX ERY </span>
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<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
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<span class="r-out co"><span class="r-pr">#></span> %S :87.3% (n=697) %S :71.7% (n=814) %S :42.3% (n=801) </span>
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<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.6% (n=7) %I : 0.5% (n=9) </span>
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<span class="r-out co"><span class="r-pr">#></span> %R :12.7% (n=101) %R :27.7% (n=315) %R :57.2% (n=1084) </span>
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<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> CLI AZM IPM </span>
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<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
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<span class="r-out co"><span class="r-pr">#></span> %S :38.6% (n=586) %S :42.3% (n=801) %S :92.7% (n=824) </span>
|
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<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> %I : 0.3% (n=4) %I : 0.5% (n=9) %I : 1.1% (n=10) </span>
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<span class="r-out co"><span class="r-pr">#></span> %R :61.2% (n=930) %R :57.2% (n=1084) %R : 6.2% (n=55) </span>
|
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<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
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<span class="r-out co"><span class="r-pr">#></span> MEM MTR CHL </span>
|
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<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
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<span class="r-out co"><span class="r-pr">#></span> %S :94.1% (n=780) %S :85.3% (n=29) %S :78.6% (n=121) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 0.0% (n=0) %I : 0.0% (n=0) </span>
|
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<span class="r-out co"><span class="r-pr">#></span> %R : 5.9% (n=49) %R :14.7% (n=5) %R :21.4% (n=33) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> COL MUP RIF </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:sir Class:sir Class:sir </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %S :18.8% (n=309) %S :93.0% (n=251) %S :30.2% (n=303) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %I : 0.0% (n=0) %I : 1.1% (n=3) %I : 0.2% (n=2) </span>
|
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<span class="r-out co"><span class="r-pr">#></span> %R :81.2% (n=1331) %R : 5.9% (n=16) %R :69.6% (n=698) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span>
|
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<span class="r-in"><span></span></span>
|
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<span class="r-in"><span><span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
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<span class="r-in"><span></span></span>
|
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<span class="r-in"><span><span class="co"># example data sets, with combined MIC values and disk zones</span></span></span>
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<span class="r-in"><span><span class="co"># create some example data sets, with combined MIC values and disk zones</span></span></span>
|
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<span class="r-in"><span><span class="va">df_wide</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
|
||||
<span class="r-in"><span> amoxicillin <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">8</span><span class="op">)</span>,</span></span>
|
||||
@ -478,6 +393,11 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-in"><span> disks <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></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="fl">6</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">18</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> guideline <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">"EUCAST 2021"</span>, <span class="st">"EUCAST 2022"</span>, <span class="st">"EUCAST 2023"</span>, <span class="st">"EUCAST 2024"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># and clean previous SIR interpretation logs</span></span></span>
|
||||
<span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu">sir_interpretation_history</span><span class="op">(</span>clean <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># For INTERPRETING disk diffusion and MIC values -----------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># most basic application:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span><span class="op">)</span></span></span>
|
||||
@ -486,23 +406,13 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 14 × 18</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></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 style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-04-30 <span style="color: #949494;">15:38:32</span> 1 DISK ampicillin Strep pn… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK AMP Escheric… human 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK GEN Escheric… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK TOB Escheric… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 1 MIC AMX B_STRPT_… human 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 1 MIC AMX B_STRPT_… human 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 2 MIC AMX B_STRPT_… human 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 3 MIC AMX B_STRPT_… human 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 4 MIC AMX B_STRPT_… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> 2025-04-30 <span style="color: #949494;">15:38:40</span> 1 MIC amoxicillin Escheric… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> 2025-04-30 <span style="color: #949494;">15:38:40</span> 1 MIC cipro Escheric… human 0.256 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> 2025-04-30 <span style="color: #949494;">15:38:41</span> 1 DISK tobra Escheric… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">14</span> 2025-04-30 <span style="color: #949494;">15:38:41</span> 1 DISK genta Escheric… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></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 style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2025-05-01 <span style="color: #949494;">09:53:45</span> 1 MIC amoxicillin Escherich… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2025-05-01 <span style="color: #949494;">09:53:45</span> 1 MIC cipro Escherich… human 0.256 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2025-05-01 <span style="color: #949494;">09:53:45</span> 1 DISK tobra Escherich… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2025-05-01 <span style="color: #949494;">09:53:45</span> 1 DISK genta Escherich… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
|
||||
@ -675,34 +585,6 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co">## Using base R ------------------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism amoxicillin cipro tobra genta ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># return a 'logbook' about the results:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">sir_interpretation_history</span><span class="op">(</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 114 × 18</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> datetime index method ab_given mo_given host_given input_given</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></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 style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2025-04-30 <span style="color: #949494;">15:38:32</span> 1 DISK ampicillin Strep pneu human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK AMP Escherich… human 20 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK GEN Escherich… human 18 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2025-04-30 <span style="color: #949494;">15:38:33</span> 1 DISK TOB Escherich… human 16 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 1 MIC AMX B_STRPT_P… human 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 1 MIC AMX B_STRPT_P… human 0.01 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 2 MIC AMX B_STRPT_P… human 2 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 3 MIC AMX B_STRPT_P… human 4 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2025-04-30 <span style="color: #949494;">15:38:34</span> 4 MIC AMX B_STRPT_P… human 8 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 104 more rows</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># breakpoint_S_R <chr>, site <chr></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># using parallel computing, which is available in base R</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism amoxicillin cipro tobra genta ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># for single values</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span></span></span>
|
||||
@ -741,6 +623,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-in"><span><span class="co"># as common in R, you can use as.integer() to return factor indices:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer</a></span><span class="op">(</span><span class="fu">as.sir</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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2 3 4 5 NA</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># but for computational use, as.double() will return 1 for S, 2 for I/SDD, and 3 for R:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/double.html" class="external-link">as.double</a></span><span class="op">(</span><span class="fu">as.sir</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">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2 2 3 NA NA</span>
|
||||
@ -757,7 +640,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
|
||||
<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is_sir_eligible</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># since dplyr 1.0.0, this can also be:</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># since dplyr 1.0.0, this can also be the more impractical:</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># example_isolates %>%</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># mutate(across(where(is_sir_eligible), as.sir))</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
|
||||
Reference in New Issue
Block a user