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@ -10,7 +10,7 @@
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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="">1.8.1.9030</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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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@ -305,7 +305,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
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<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <a href="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
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<p>All data sets in this <code>AMR</code> package (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
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</div>
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<div class="section level2">
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
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@ -315,172 +315,167 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">example_isolates</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 49</span></span>
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<span class="r-out co"><span class="r-pr">#></span> date hospit…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 B TRUE FALSE FALSE 79 F 858515 B_STPHY_EPDR</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
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<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi></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 R/SI results at a glance</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> date hospital_id ward_icu ward_clinical </span>
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<span class="r-out co"><span class="r-pr">#></span> Min. :2002-01-02 A:321 Mode :logical Mode :logical </span>
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<span class="r-out co"><span class="r-pr">#></span> 1st Qu.:2005-07-31 B:663 FALSE:1354 FALSE:536 </span>
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<span class="r-out co"><span class="r-pr">#></span> Median :2009-07-31 C:254 TRUE :646 TRUE :1464 </span>
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<span class="r-out co"><span class="r-pr">#></span> Mean :2009-11-20 D:762 </span>
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<span class="r-out co"><span class="r-pr">#></span> 3rd Qu.:2014-05-30 </span>
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<span class="r-out co"><span class="r-pr">#></span> Max. :2017-12-28 </span>
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<span class="r-out co"><span class="r-pr">#></span> ward_outpatient age gender patient_id </span>
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<span class="r-out co"><span class="r-pr">#></span> Mode :logical Min. : 0.00 Length:2000 Length:2000 </span>
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<span class="r-out co"><span class="r-pr">#></span> FALSE:1880 1st Qu.:63.00 Class :character Class :character </span>
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<span class="r-out co"><span class="r-pr">#></span> TRUE :120 Median :74.00 Mode :character Mode :character </span>
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<span class="r-out co"><span class="r-pr">#></span> Mean :70.69 </span>
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<span class="r-out co"><span class="r-pr">#></span> 3rd Qu.:82.00 </span>
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<span class="r-out co"><span class="r-pr">#></span> Max. :97.00 </span>
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<span class="r-out co"><span class="r-pr">#></span> mo PEN OXA </span>
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<span class="r-out co"><span class="r-pr">#></span> Class :mo Class:rsi Class:rsi </span>
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<span class="r-out co"><span class="r-pr">#></span> <NA> :0 %R :73.7% (n=1201) %R :31.2% (n=114) </span>
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<span class="r-out co"><span class="r-pr">#></span> Unique:90 %SI :26.3% (n=428) %SI :68.8% (n=251) </span>
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<span class="r-out co"><span class="r-pr">#></span> #1 :B_ESCHR_COLI - %S :25.6% (n=417) - %S :68.8% (n=251) </span>
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<span class="r-out co"><span class="r-pr">#></span> #2 :B_STPHY_CONS - %I : 0.7% (n=11) - %I : 0.0% (n=0) </span>
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<span class="r-out co"><span class="r-pr">#></span> #3 :B_STPHY_AURS </span>
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<span class="r-out co"><span class="r-pr">#></span> FLC AMX AMC </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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<span class="r-out co"><span class="r-pr">#></span> Median :2009-07-31 Mode :character Median :74.00 Mode :character </span>
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<span class="r-out co"><span class="r-pr">#></span> Mean :2009-11-20 Mean :70.69 </span>
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<span class="r-out co"><span class="r-pr">#></span> 3rd Qu.:2014-05-30 3rd Qu.:82.00 </span>
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<span class="r-out co"><span class="r-pr">#></span> Max. :2017-12-28 Max. :97.00 </span>
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<span class="r-out co"><span class="r-pr">#></span> ward mo PEN </span>
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<span class="r-out co"><span class="r-pr">#></span> Length:2000 Class :mo Class:rsi </span>
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<span class="r-out co"><span class="r-pr">#></span> Class :character <NA> :0 %R :73.7% (n=1201) </span>
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<span class="r-out co"><span class="r-pr">#></span> Mode :character Unique:90 %SI :26.3% (n=428) </span>
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<span class="r-out co"><span class="r-pr">#></span> #1 :B_ESCHR_COLI - %S :25.6% (n=417) </span>
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<span class="r-out co"><span class="r-pr">#></span> #2 :B_STPHY_CONS - %I : 0.7% (n=11) </span>
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<span class="r-out co"><span class="r-pr">#></span> #3 :B_STPHY_AURS </span>
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<span class="r-out co"><span class="r-pr">#></span> OXA FLC AMX </span>
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<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </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> %SI :68.8% (n=251) %SI :70.5% (n=665) %SI :40.4% (n=546) </span>
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<span class="r-out co"><span class="r-pr">#></span> - %S :68.8% (n=251) - %S :70.5% (n=665) - %S :40.2% (n=543) </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 : 0.2% (n=3) </span>
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<span class="r-out co"><span class="r-pr">#></span> </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:rsi Class:rsi Class:rsi </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> %SI :76.3% (n=1433) %SI :40.4% (n=546) %SI :87.4% (n=875) </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> - %I : 4.8% (n=91) - %I : 0.2% (n=3) - %I : 1.3% (n=13) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CZO FEP CXM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :29.5% (n=278) %R :59.6% (n=804) %R :23.7% (n=446) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :70.5% (n=665) %SI :40.4% (n=546) %SI :76.3% (n=1433) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :70.5% (n=665) - %S :40.2% (n=543) - %S :71.4% (n=1342) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.2% (n=3) - %I : 4.8% (n=91) </span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :55.4% (n=247) %SI :85.8% (n=621) %SI :73.7% (n=1319) </span>
|
||||
<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>
|
||||
<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> </span>
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||||
<span class="r-out co"><span class="r-pr">#></span> AMP TZP CZO </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :59.6% (n=804) %R :12.6% (n=126) %R :44.6% (n=199) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :40.4% (n=546) %SI :87.4% (n=875) %SI :55.4% (n=247) </span>
|
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<span class="r-out co"><span class="r-pr">#></span> - %S :40.2% (n=543) - %S :86.1% (n=862) - %S :54.9% (n=245) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.2% (n=3) - %I : 1.3% (n=13) - %I : 0.4% (n=2) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> FEP CXM FOX </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:rsi Class:rsi Class:rsi </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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :72.6% (n=594) %SI :84.5% (n=797) %SI :33.5% (n=607) </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>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CRO GEN TOB </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :14.2% (n=103) %R :26.3% (n=470) %R :27.4% (n=224) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :85.8% (n=621) %SI :73.7% (n=1319) %SI :72.6% (n=594) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :85.6% (n=620) - %S :72.5% (n=1297) - %S :71.6% (n=586) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.1% (n=1) - %I : 1.2% (n=22) - %I : 1.0% (n=8) </span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :84.5% (n=797) %SI :75.4% (n=1399) %SI :65.6% (n=886) </span>
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CTX CAZ CRO </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMK KAN TMP </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :15.5% (n=146) %R :66.5% (n=1204) %R :15.5% (n=146) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :84.5% (n=797) %SI :33.5% (n=607) %SI :84.5% (n=797) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :84.4% (n=796) - %S :33.5% (n=607) - %S :84.4% (n=796) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.1% (n=1) - %I : 0.0% (n=0) - %I : 0.1% (n=1) </span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :36.3% (n=251) %SI : 0.0% (n=0) %SI :61.9% (n=928) </span>
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> GEN TOB AMK </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> SXT NIT FOS </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :24.6% (n=456) %R :34.4% (n=465) %R :63.7% (n=441) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :75.4% (n=1399) %SI :65.6% (n=886) %SI :36.3% (n=251) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :74.0% (n=1372) - %S :65.1% (n=879) - %S :36.3% (n=251) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 1.5% (n=27) - %I : 0.5% (n=7) - %I : 0.0% (n=0) </span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :79.5% (n=1398) %SI :82.9% (n=616) %SI :57.8% (n=203) </span>
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> KAN TMP SXT </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :100.0% (n=471) %R :38.1% (n=571) %R :20.5% (n=361) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI : 0.0% (n=0) %SI :61.9% (n=928) %SI :79.5% (n=1398) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S : 0.0% (n=0) - %S :61.2% (n=918) - %S :79.1% (n=1392) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 0.7% (n=10) - %I : 0.3% (n=6) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> NIT FOS LNZ </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :17.1% (n=127) %R :42.2% (n=148) %R :69.3% (n=709) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :82.9% (n=616) %SI :57.8% (n=203) %SI :30.7% (n=314) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :76.0% (n=565) - %S :57.8% (n=203) - %S :30.7% (n=314) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 6.9% (n=51) - %I : 0.0% (n=0) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CIP MFX VAN </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :16.2% (n=228) %R :33.6% (n=71) %R :38.3% (n=712) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :83.8% (n=1181) %SI :66.4% (n=140) %SI :61.7% (n=1149) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :78.9% (n=1112) - %S :64.5% (n=136) - %S :61.7% (n=1149) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 4.9% (n=69) - %I : 1.9% (n=4) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TEC TCY TGC </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :75.7% (n=739) %R :29.8% (n=357) %R :12.7% (n=101) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :24.3% (n=237) %SI :70.3% (n=843) %SI :87.3% (n=697) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :24.3% (n=237) - %S :68.3% (n=820) - %S :87.3% (n=697) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.0% (n=0) - %I : 1.9% (n=23) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> DOX ERY CLI </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> LNZ CIP MFX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :27.7% (n=315) %R :57.2% (n=1084) %R :61.2% (n=930) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :72.3% (n=821) %SI :42.8% (n=810) %SI :38.8% (n=590) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :71.7% (n=814) - %S :42.3% (n=801) - %S :38.6% (n=586) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.6% (n=7) - %I : 0.5% (n=9) - %I : 0.3% (n=4) </span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :30.7% (n=314) %SI :83.8% (n=1181) %SI :66.4% (n=140) </span>
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AZM IPM MEM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> VAN TEC TCY </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :57.2% (n=1084) %R : 6.2% (n=55) %R : 5.9% (n=49) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :42.8% (n=810) %SI :93.8% (n=834) %SI :94.1% (n=780) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :42.3% (n=801) - %S :92.7% (n=824) - %S :94.1% (n=780) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 0.5% (n=9) - %I : 1.1% (n=10) - %I : 0.0% (n=0) </span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :61.7% (n=1149) %SI :24.3% (n=237) %SI :70.3% (n=843) </span>
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TGC DOX ERY </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :87.3% (n=697) %SI :72.3% (n=821) %SI :42.8% (n=810) </span>
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> CLI AZM IPM </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :38.8% (n=590) %SI :42.8% (n=810) %SI :93.8% (n=834) </span>
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MEM MTR CHL </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<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> %SI :94.1% (n=780) %SI :85.3% (n=29) %SI :78.6% (n=121) </span>
|
||||
<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> - %I : 0.0% (n=0) - %I : 0.0% (n=0) - %I : 0.0% (n=0) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </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:rsi Class:rsi Class:rsi </span>
|
||||
<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> %SI :18.8% (n=309) %SI :94.1% (n=254) %SI :30.4% (n=305) </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> - %I : 0.0% (n=0) - %I : 1.1% (n=3) - %I : 0.2% (n=2) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MTR CHL COL </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R :14.7% (n=5) %R :21.4% (n=33) %R :81.2% (n=1331) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :85.3% (n=29) %SI :78.6% (n=121) %SI :18.8% (n=309) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :85.3% (n=29) - %S :78.6% (n=121) - %S :18.8% (n=309) </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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MUP RIF </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class:rsi Class:rsi </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %R : 5.9% (n=16) %R :69.6% (n=698) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> %SI :94.1% (n=254) %SI :30.4% (n=305) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %S :93.0% (n=251) - %S :30.2% (n=303) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> - %I : 1.1% (n=3) - %I : 0.2% (n=2) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></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></span>
|
||||
<span class="r-in"><span><span class="co"># a whole data set, even with combined MIC values and disk zones</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</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>microorganism <span class="op">=</span> <span class="st">"Escherichia coli"</span>,</span></span>
|
||||
<span class="r-in"><span> AMP <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>
|
||||
<span class="r-in"><span> CIP <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">0.256</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> GEN <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> TOB <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">16</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> ERY <span class="op">=</span> <span class="st">"R"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</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> AMP <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>
|
||||
<span class="r-in"><span> CIP <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">0.256</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> GEN <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> TOB <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">16</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> ERY <span class="op">=</span> <span class="st">"R"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'microorganism' as input for `col_mo`.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'AMP' (AMP, ampicillin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'AMP' (ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'CIP' (ciprofloxacin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'CIP' (CIP, ciprofloxacin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'GEN' (gentamicin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'GEN' (GEN, gentamicin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'TOB' (TOB, tobramycin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of column 'TOB' (tobramycin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (NIT, nitrofurantoin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
@ -491,22 +486,26 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S <NA> 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.rsi</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S. pneumoniae"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMP"</span>,</span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="as.mic.html">as.mic</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"S. pneumoniae"</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"AMP"</span>,</span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "S. pneumoniae" (assuming</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Streptococcus pneumoniae). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class <rsi></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span>x <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"Strep pneu"</span>, <span class="co"># `mo` will be coerced with as.mo()</span></span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span></span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">as.rsi</span><span class="op">(</span></span></span>
|
||||
<span class="r-in"><span> x <span class="op">=</span> <span class="fu"><a href="as.disk.html">as.disk</a></span><span class="op">(</span><span class="fl">18</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> mo <span class="op">=</span> <span class="st">"Strep pneu"</span>, <span class="co"># `mo` will be coerced with as.mo()</span></span></span>
|
||||
<span class="r-in"><span> ab <span class="op">=</span> <span class="st">"ampicillin"</span>, <span class="co"># and `ab` with as.ab()</span></span></span>
|
||||
<span class="r-in"><span> guideline <span class="op">=</span> <span class="st">"EUCAST"</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'ampicillin' according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
@ -521,122 +520,126 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span>, <span class="va">as.rsi</span><span class="op">)</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="va">df</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_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="va">.</span><span class="op">$</span><span class="va">microorganism</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"># to include information about urinary tract infections (UTI)</span></span></span>
|
||||
<span class="r-in"><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>mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <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">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> from_the_bladder <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="cn">TRUE</span>, <span class="cn">FALSE</span><span class="op">)</span><span class="op">)</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://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> mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <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">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> from_the_bladder <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="cn">TRUE</span>, <span class="cn">FALSE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</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">as.rsi</span><span class="op">(</span>uti <span class="op">=</span> <span class="st">"from_the_bladder"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><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>mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <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">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> specimen <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">"urine"</span>, <span class="st">"blood"</span><span class="op">)</span><span class="op">)</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></span>
|
||||
<span class="r-in"><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> mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
|
||||
<span class="r-in"><span> NIT <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">"<= 2"</span>, <span class="fl">32</span><span class="op">)</span>,</span></span>
|
||||
<span class="r-in"><span> specimen <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">"urine"</span>, <span class="st">"blood"</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</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">as.rsi</span><span class="op">(</span><span class="op">)</span> <span class="co"># automatically determines urine isolates</span></span></span>
|
||||
<span class="r-in"><span> </span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="va">df</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_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">NIT</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</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_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">NIT</span><span class="op">)</span>, <span class="va">as.rsi</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (NIT, nitrofurantoin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (nitrofurantoin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (NIT, nitrofurantoin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (nitrofurantoin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (NIT, nitrofurantoin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (nitrofurantoin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of nitrofurantoin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) based on</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> column 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 'microorganism' according to EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (gentamicin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of gentamicin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> WARNING.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (tobramycin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in `as.rsi()`: interpretation of tobramycin is only available for</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> argument `uti` to set which isolates are from urine. See ?as.rsi.</span>
|
||||
@ -644,8 +647,8 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `col_mo`.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (NIT, nitrofurantoin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Assuming value "urine" in column 'specimen' reflects a urinary tract</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> infection.</span>
|
||||
@ -653,26 +656,26 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `col_mo`.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (NIT, nitrofurantoin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> coli). Run `mo_uncertainties()` to review this.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (AMP, ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (CIP, ciprofloxacin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (gentamicin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'GEN' (GEN, gentamicin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (TOB, tobramycin) according</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> to EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (NIT, nitrofurantoin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting disk diffusion zones of 'TOB' (tobramycin) according to</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> EUCAST 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> => Interpreting MIC values of 'NIT' (nitrofurantoin) according to EUCAST</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> 2022...</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> OK.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> microorganism AMP CIP GEN TOB NIT ERY</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1 Escherichia coli S I S S S R</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
@ -689,7 +692,7 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span><span class="va">rsi_data</span> <span class="op"><-</span> <span class="fu">as.rsi</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="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="fl">474</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"I"</span>, <span class="fl">36</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="st">"R"</span>, <span class="fl">370</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">is.rsi</span><span class="op">(</span><span class="va">rsi_data</span><span class="op">)</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE</span>
|
||||
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">rsi_data</span><span class="op">)</span> <span class="co"># for percentages</span></span></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">rsi_data</span><span class="op">)</span> <span class="co"># for percentages</span></span></span>
|
||||
<span class="r-plt img"><img src="as.rsi-1.png" alt="" width="700" height="433"></span>
|
||||
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot</a></span><span class="op">(</span><span class="va">rsi_data</span><span class="op">)</span> <span class="co"># for frequencies</span></span></span>
|
||||
<span class="r-plt img"><img src="as.rsi-2.png" alt="" width="700" height="433"></span>
|
||||
@ -698,38 +701,38 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
|
||||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<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_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">PEN</span><span class="op">:</span><span class="va">RIF</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># same: </span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># same:</span></span></span>
|
||||
<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">as.rsi</span><span class="op">(</span><span class="va">PEN</span><span class="op">:</span><span class="va">RIF</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"># fastest way to transform all columns with already valid AMR results to class `rsi`:</span></span></span>
|
||||
<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.rsi.eligible</span>, <span class="va">as.rsi</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></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"># example_isolates %>%</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># mutate(across(where(is.rsi.eligible), as.rsi))</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 49</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date hospit…¹ ward_…² ward_…³ ward_…⁴ age gender patie…⁵ mo </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><fct></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 D FALSE TRUE FALSE 65 F A77334 B_ESCHR_COLI</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 D FALSE TRUE FALSE 78 M 462729 B_STPHY_AURS</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 B TRUE FALSE FALSE 45 F 067927 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 B TRUE FALSE FALSE 79 F 858515 B_STPHY_EPDR</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, 40 more variables: PEN <rsi>, OXA <rsi>, FLC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AMX <rsi>, AMC <rsi>, AMP <rsi>, TZP <rsi>, CZO <rsi>, FEP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <rsi>, FOX <rsi>, CTX <rsi>, CAZ <rsi>, CRO <rsi>, GEN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <rsi>, AMK <rsi>, KAN <rsi>, TMP <rsi>, SXT <rsi>, NIT <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <rsi>, LNZ <rsi>, CIP <rsi>, MFX <rsi>, VAN <rsi>, TEC <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <rsi>, TGC <rsi>, DOX <rsi>, ERY <rsi>, CLI <rsi>, AZM <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <rsi>, MEM <rsi>, MTR <rsi>, CHL <rsi>, COL <rsi>, MUP <rsi>, …</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></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;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
Reference in New Issue
Block a user