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cli-147-2226
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@@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9029</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9031</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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@@ -172,15 +172,15 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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<span></span>
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<span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">count_R</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">count_IR</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">count_I</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
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<span><span class="fu">count_S</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">count_SI</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">count_S</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
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<span><span class="fu">count_I</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">count_IR</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">count_R</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">count_all</span><span class="op">(</span><span class="va">...</span>, only_all_tested <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span>
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<span></span>
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@@ -298,17 +298,21 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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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">count_S</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> Using count_S() is discouraged; use count_susceptible() instead to also</span>
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<span class="r-msg co"><span class="r-pr">#></span> consider "I" being susceptible. This note will be shown once for this</span>
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<span class="r-msg co"><span class="r-pr">#></span> session.</span>
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<span class="r-msg co"><span class="r-pr">#></span> consider "I" and "SDD" being susceptible. This note will be shown once for</span>
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<span class="r-msg co"><span class="r-pr">#></span> this session.</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 543</span>
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<span class="r-in"><span><span class="fu">count_SI</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> Note that count_SI() will also count dose-dependent susceptibility,</span>
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<span class="r-msg co"><span class="r-pr">#></span> 'SDD'. This note will be shown once for this session.</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 546</span>
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<span class="r-in"><span><span class="fu">count_I</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> Note that count_I() will also count dose-dependent susceptibility, 'SDD'.</span>
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<span class="r-msg co"><span class="r-pr">#></span> This note will be shown once for this session.</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 3</span>
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<span class="r-in"><span><span class="fu">count_IR</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> Using count_IR() is discouraged; use count_resistant() instead to not</span>
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<span class="r-msg co"><span class="r-pr">#></span> consider "I" being resistant. This note will be shown once for this</span>
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<span class="r-msg co"><span class="r-pr">#></span> session.</span>
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<span class="r-msg co"><span class="r-pr">#></span> consider "I" and "SDD" being resistant. This note will be shown once for</span>
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<span class="r-msg co"><span class="r-pr">#></span> this session.</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 807</span>
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<span class="r-in"><span><span class="fu">count_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] 804</span>
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@@ -373,21 +377,27 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
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<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 12 × 4</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 18 × 4</span></span>
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<span class="r-out co"><span class="r-pr">#></span> ward antibiotic interpretation value</span>
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<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;"><int></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical AMX SI 357</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Clinical AMX R 487</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical CIP SI 741</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical CIP R 128</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU AMX SI 158</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU AMX R 270</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU CIP SI 362</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU CIP R 85</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Outpatient AMX SI 31</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Outpatient AMX R 47</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Outpatient CIP SI 78</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Outpatient CIP R 15</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical AMX <span style="color: #BB0000;">NA</span> 0</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical CIP SI 741</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical CIP R 128</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical CIP <span style="color: #BB0000;">NA</span> 0</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU AMX SI 158</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU AMX R 270</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU AMX <span style="color: #BB0000;">NA</span> 0</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> ICU CIP SI 362</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> ICU CIP R 85</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> ICU CIP <span style="color: #BB0000;">NA</span> 0</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> Outpatient AMX SI 31</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">14</span> Outpatient AMX R 47</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">15</span> Outpatient AMX <span style="color: #BB0000;">NA</span> 0</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">16</span> Outpatient CIP SI 78</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">17</span> Outpatient CIP R 15</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">18</span> Outpatient CIP <span style="color: #BB0000;">NA</span> 0</span>
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<span class="r-in"><span><span class="co"># }</span></span></span>
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</code></pre></div>
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</div>
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