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2025-01-31 15:09:26 +00:00
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@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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@ -180,22 +180,22 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># be more specific</span></span></span>
<span class="r-in"><span><span class="fu">count_S</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Using count_S() is discouraged; use count_susceptible() instead to also</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> consider "I" and "SDD" being susceptible. This note will be shown once for</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> this session.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Using </span><span style="color: #0000BB; background-color: #EEEEEE;">count_S()</span><span style="color: #0000BB;"> is discouraged; use </span><span style="color: #0000BB; background-color: #EEEEEE;">count_susceptible()</span><span style="color: #0000BB;"> instead to also</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">consider "I" and "SDD" being susceptible. This note will be shown once for</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">this session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 543</span>
<span class="r-in"><span><span class="fu">count_SI</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note that count_SI() will also count dose-dependent susceptibility,</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> 'SDD'. This note will be shown once for this session.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Note that </span><span style="color: #0000BB; background-color: #EEEEEE;">count_SI()</span><span style="color: #0000BB;"> will also count dose-dependent susceptibility,</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">'SDD'. This note will be shown once for this session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span>
<span class="r-in"><span><span class="fu">count_I</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Note that count_I() will also count dose-dependent susceptibility, 'SDD'.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> This note will be shown once for this session.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Note that </span><span style="color: #0000BB; background-color: #EEEEEE;">count_I()</span><span style="color: #0000BB;"> will also count dose-dependent susceptibility, 'SDD'.</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">This note will be shown once for this session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3</span>
<span class="r-in"><span><span class="fu">count_IR</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Using count_IR() is discouraged; use count_resistant() instead to not</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> consider "I" and "SDD" being resistant. This note will be shown once for</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> this session.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Using </span><span style="color: #0000BB; background-color: #EEEEEE;">count_IR()</span><span style="color: #0000BB;"> is discouraged; use </span><span style="color: #0000BB; background-color: #EEEEEE;">count_resistant()</span><span style="color: #0000BB;"> instead to not</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">consider "I" and "SDD" being resistant. This note will be shown once for</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">this session.</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 807</span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 804</span>
@ -258,8 +258,8 @@ 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">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu">count_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-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 12 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward antibiotic interpretation value</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ord&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>