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@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9028</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9030</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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@ -315,7 +315,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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<h2 id="interpretation-of-sir">Interpretation of SIR<a class="anchor" aria-label="anchor" href="#interpretation-of-sir"></a></h2>
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<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (<a href="https://www.eucast.org/newsiandr/" class="external-link">https://www.eucast.org/newsiandr/</a>):</p><ul><li><p><strong>S - Susceptible, standard dosing regimen</strong><br>
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<p>In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R as shown below (<a href="https://www.eucast.org/newsiandr" class="external-link">https://www.eucast.org/newsiandr</a>):</p><ul><li><p><strong>S - Susceptible, standard dosing regimen</strong><br>
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A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.</p></li>
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<li><p><strong>I - Susceptible, increased exposure</strong> <em><br>
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A microorganism is categorised as "Susceptible, Increased exposure</em>" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.</p></li>
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@ -334,63 +334,44 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># example_isolates is a data set available in the AMR package.</span></span></span>
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<span class="r-in"><span><span class="co"># run ?example_isolates for more info.</span></span></span>
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<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 × 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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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;"># ℹ 1,990 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …</span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># base R ------------------------------------------------------------</span></span></span>
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<span class="r-in"><span><span class="co"># determines %R</span></span></span>
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<span class="r-in"><span><span class="fu">resistance</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5955556</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> in resistance(): NULL value passed as symbol address</span>
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<span class="r-in"><span><span class="fu">sir_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5688204 0.6218738</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
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<span class="r-in"><span><span class="fu">sir_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span>,</span></span>
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<span class="r-in"><span> confidence_level <span class="op">=</span> <span class="fl">0.975</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5650148 0.6255670</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
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<span class="r-in"><span><span class="fu">sir_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span>,</span></span>
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<span class="r-in"><span> confidence_level <span class="op">=</span> <span class="fl">0.975</span>,</span></span>
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<span class="r-in"><span> collapse <span class="op">=</span> <span class="st">", "</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "0.565, 0.626"</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># determines %S+I:</span></span></span>
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<span class="r-in"><span><span class="fu">susceptibility</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.4044444</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> in susceptibility(): NULL value passed as symbol address</span>
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<span class="r-in"><span><span class="fu">sir_confidence_interval</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span>,</span></span>
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<span class="r-in"><span> ab_result <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"I"</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.3781262 0.4311796</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># be more specific</span></span></span>
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<span class="r-in"><span><span class="fu">proportion_S</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.4022222</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> in proportion_S(): NULL value passed as symbol address</span>
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<span class="r-in"><span><span class="fu">proportion_SI</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.4044444</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> in proportion_SI(): NULL value passed as symbol address</span>
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<span class="r-in"><span><span class="fu">proportion_I</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.002222222</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> in proportion_I(): NULL value passed as symbol address</span>
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<span class="r-in"><span><span class="fu">proportion_IR</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5977778</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> in proportion_IR(): NULL value passed as symbol address</span>
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<span class="r-in"><span><span class="fu">proportion_R</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 0.5955556</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> in proportion_R(): NULL value passed as symbol address</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------</span></span></span>
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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@ -402,12 +383,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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<span class="r-in"><span> n <span class="op">=</span> <span class="fu"><a href="count.html">n_sir</a></span><span class="op">(</span><span class="va">CIP</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="op">)</span> <span class="co"># n_sir works like n_distinct in dplyr, see ?n_sir</span></span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 3</span></span>
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<span class="r-out co"><span class="r-pr">#></span> ward r n</span>
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<span class="r-out co"><span class="r-pr">#></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;"><int></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 0.147 869</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 0.190 447</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 0.161 93</span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in summarise(., r = resistance(CIP), n = n_sir(CIP)):</span> <span style="color: #00BBBB;">ℹ</span> In argument: `r = resistance(CIP)`.</span>
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<span class="r-err co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In group 1: `ward = "Clinical"`.</span>
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<span class="r-err co"><span class="r-pr">#></span> <span style="font-weight: bold;">Caused by error:</span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> in resistance(): NULL value passed as symbol address</span>
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<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>
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<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>
|
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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@ -417,12 +396,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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<span class="r-in"><span> ci_max <span class="op">=</span> <span class="fu">sir_confidence_interval</span><span class="op">(</span><span class="va">CIP</span>, side <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span>,</span></span>
|
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<span class="r-in"><span> <span class="op">)</span></span></span>
|
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<span class="r-in"><span><span class="op">}</span></span></span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 4</span></span>
|
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<span class="r-out co"><span class="r-pr">#></span> ward cipro_R ci_min ci_max</span>
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<span class="r-out co"><span class="r-pr">#></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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 0.147 0.124 0.173</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 0.190 0.155 0.230</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 0.161 0.093<span style="text-decoration: underline;">2</span> 0.252</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in summarise(., cipro_R = resistance(CIP), ci_min = sir_confidence_interval(CIP, side = "min"), ci_max = sir_confidence_interval(CIP, side = "max"), ):</span> <span style="color: #00BBBB;">ℹ</span> In argument: `cipro_R = resistance(CIP)`.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In group 1: `ward = "Clinical"`.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="font-weight: bold;">Caused by error:</span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> in resistance(): NULL value passed as symbol address</span>
|
||||
<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="co"># scoped dplyr verbs with antibiotic selectors</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># (you could also use across() of course)</span></span></span>
|
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@ -433,22 +410,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-in"><span> <span class="va">resistance</span></span></span>
|
||||
<span class="r-in"><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> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>There was 1 warning in `summarise()`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In argument: `KAN = (function (..., minimum = 30, as_percent = FALSE,</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> only_all_tested = FALSE) ...`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In group 3: `ward = "Outpatient"`.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> Caused by warning:</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> Introducing NA: only 23 results available for KAN in group: ward =</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> "Outpatient" (minimum = 30).</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 7</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward GEN TOB AMK KAN IPM MEM</span>
|
||||
<span class="r-out co"><span class="r-pr">#></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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 0.229 0.315 0.626 1 0.049<span style="text-decoration: underline;">8</span> 0.045<span style="text-decoration: underline;">8</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 0.290 0.400 0.662 1 0.086<span style="text-decoration: underline;">2</span> 0.089<span style="text-decoration: underline;">4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 0.2 0.368 0.605 <span style="color: #BB0000;">NA</span> 0.054<span style="text-decoration: underline;">1</span> 0.054<span style="text-decoration: underline;">1</span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<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/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
@ -511,21 +473,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</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">sir_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</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: 12 × 7</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward antibiotic interpretation value ci_min ci_max isolates</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><ord></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical AMX SI 0.423 0.389 0.457 357</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical AMX R 0.577 0.543 0.611 487</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical CIP SI 0.853 0.827 0.876 741</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical CIP R 0.147 0.124 0.173 128</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU AMX SI 0.369 0.323 0.417 158</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU AMX R 0.631 0.583 0.677 270</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU CIP SI 0.810 0.770 0.845 362</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU CIP R 0.190 0.155 0.230 85</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Outpatient AMX SI 0.397 0.288 0.515 31</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Outpatient AMX R 0.603 0.485 0.712 47</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Outpatient CIP SI 0.839 0.748 0.907 78</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Outpatient CIP R 0.161 0.093<span style="text-decoration: underline;">2</span> 0.252 15</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in summarise(., R = resistance(CIP, as_percent = TRUE), SI = susceptibility(CIP, as_percent = TRUE), n1 = count_all(CIP), n2 = n_sir(CIP), total = n()):</span> <span style="color: #00BBBB;">ℹ</span> In argument: `R = resistance(CIP, as_percent = TRUE)`.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> In group 1: `ward = "Clinical"`.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="font-weight: bold;">Caused by error:</span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> in resistance(): NULL value passed as symbol address</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
Reference in New Issue
Block a user