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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="">3.0.1.9034</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9035</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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@@ -174,15 +174,15 @@ 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 </span><span style="color: #0000BB; background-color: #444444;">`count_resistant()`</span><span style="color: #0000BB;"> 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 </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span><span style="color: #0000BB;"> option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</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;">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-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 </span><span style="color: #0000BB; background-color: #444444;">`count_susceptible()`</span><span style="color: #0000BB;"> 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 </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span><span style="color: #0000BB;"> option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</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;">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-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">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S", "I" and "R"</span></span></span>
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@@ -213,9 +213,9 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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<span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</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 </span><span style="color: #0000BB; background-color: #444444;">`susceptibility()`</span><span style="color: #0000BB;"> 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 </span><span style="color: #0000BB; background-color: #444444;">`guideline`</span><span style="color: #0000BB;"> argument or the</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> </span><span style="color: #0000BB; background-color: #444444;">`AMR_guideline`</span><span style="color: #0000BB;"> option to either "CLSI" or "EUCAST", see </span><span style="color: #0000BB; background-color: #444444;">`?AMR-options`</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;">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-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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@@ -262,7 +262,7 @@ 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 </span><span style="color: #0000BB; background-color: #444444;">`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>
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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-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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