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@@ -9,7 +9,7 @@ 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="">3.0.1.9035</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9036</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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@@ -174,16 +174,18 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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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="fu">count_resistant</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 class="co"># counts "R"</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ `count_resistant()` assumes the EUCAST guideline and thus considers the</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> 'I' category susceptible. Set the `guideline` argument or the</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> `count_resistant()` (`?AMR::count_resistant()`) assumes the EUCAST guideline</span>
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<span class="r-msg co"><span class="r-pr">#></span> and thus considers the 'I' category susceptible. Set the `guideline` argument</span>
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<span class="r-msg co"><span class="r-pr">#></span> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span>
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<span class="r-msg co"><span class="r-pr">#></span> (`?AMR::AMR-options`).</span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 804</span>
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<span class="r-in"><span><span class="fu">count_susceptible</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 class="co"># counts "S" and "I"</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ `count_susceptible()` assumes the EUCAST guideline and thus considers the</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> 'I' category susceptible. Set the `guideline` argument or the</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> `count_susceptible()` (`?AMR::count_susceptible()`) assumes the EUCAST</span>
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<span class="r-msg co"><span class="r-pr">#></span> guideline and thus considers the 'I' category susceptible. Set the</span>
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<span class="r-msg co"><span class="r-pr">#></span> `guideline` argument or the `AMR_guideline` option to either "CLSI" or</span>
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<span class="r-msg co"><span class="r-pr">#></span> "EUCAST", see AMR-options (`?AMR::AMR-options`).</span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per 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_all</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S", "I" and "R"</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 1350</span>
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@@ -213,10 +215,11 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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<span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</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] 546</span>
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<span class="r-in"><span><span class="fu"><a href="proportion.html">susceptibility</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="op">*</span> <span class="fu">n_sir</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</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> <span style="color: #0000BB;">ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> 'I' category susceptible. Set the `guideline` argument or the</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> `AMR_guideline` option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ This message will be shown once per session.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> `susceptibility()` (`?AMR::susceptibility()`) assumes the EUCAST guideline</span>
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<span class="r-msg co"><span class="r-pr">#></span> and thus considers the 'I' category susceptible. Set the `guideline` argument</span>
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<span class="r-msg co"><span class="r-pr">#></span> or the `AMR_guideline` option to either "CLSI" or "EUCAST", see AMR-options</span>
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<span class="r-msg co"><span class="r-pr">#></span> (`?AMR::AMR-options`).</span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per 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></span>
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<span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------</span></span></span>
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@@ -262,8 +265,8 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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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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<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>
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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> <span style="color: #0000BB;">ℹ For `aminoglycosides()` 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>
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<span class="r-msg co"><span class="r-pr">#></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>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns '<span style="font-weight: bold;">GEN</span>' (gentamicin), '<span style="font-weight: bold;">TOB</span>' (tobramycin),</span>
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<span class="r-msg co"><span class="r-pr">#></span> '<span style="font-weight: bold;">AMK</span>' (amikacin), and '<span style="font-weight: bold;">KAN</span>' (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> ward antibiotic interpretation value</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;"><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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