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Built site for AMR: 1.8.2.9111@aa48c6b

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2023-02-08 16:01:47 +00:00
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reference/antibiotic_class_selectors.html
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@ -10,7 +10,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9103</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -42,6 +42,11 @@
Conduct AMR Analysis
</a>
<a class="dropdown-item" href="../reference/antibiogram.html">
<span class="fa fa-file-prescription"></span>
Generate Antibiogram (Trad./Syndromic/WISCA)
</a>
<a class="dropdown-item" href="../articles/resistance_predict.html">
<span class="fa fa-dice"></span>
@ -232,7 +237,7 @@
<dt>col_mo</dt>
<dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>version_expertrules</dt>
@ -596,7 +601,11 @@
<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-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 23 results available for KAN in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `summarise()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(aminoglycosides(), resistance)`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 3: `ward = "Outpatient"`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</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">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward GEN TOB AMK KAN</span>
@ -648,110 +657,14 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> (benzylpenicillin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'TEC'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (teicoplanin), 'ERY' (erythromycin), 'CLI' (clindamycin), 'AZM'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (azithromycin) and 'RIF' (rifampicin)</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: ward = "Clinical"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: ward = "ICU"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: ward = "Outpatient"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: ward = "Clinical"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: ward = "ICU"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: ward = "Outpatient"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for AMX in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for AMC in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for AMP in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 24 results available for TZP in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 23 results available for CZO in group: ward = "ICU"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 10 results available for CZO in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 20 results available for FEP in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for CXM in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 22 results available for FOX in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for CTX in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for CAZ in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for CRO in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for GEN in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for TOB in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 15 results available for AMK in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: ward = "Clinical"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: ward = "ICU"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: ward = "Outpatient"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 22 results available for TMP in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for SXT in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for NIT in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for FOS in group: ward = "ICU"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for FOS in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for CIP in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 15 results available for MFX in group: ward = "ICU"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 4 results available for MFX in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 5 results available for TCY in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Clinical" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for TCY in group: ward = "ICU"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for TCY in group: ward = "Outpatient"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 13 results available for TGC in group: ward = "ICU"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for TGC in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for DOX in group: ward = "Clinical"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for DOX in group: ward = "ICU"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for DOX in group: ward = "Outpatient"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 24 results available for IPM in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for MEM in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for MTR in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Clinical" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: ward = "ICU"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: ward = "Outpatient"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: ward = "Clinical"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: ward = "ICU"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: ward = "Outpatient"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 9 results available for COL in group: ward =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: ward = "Clinical"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: ward = "ICU"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: ward = "Outpatient"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 52 warnings in `summarise()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(not_intrinsic_resistant(), resistance)`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 1: `ward = "Clinical"`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: no results available for OXA in group: ward = "Clinical"</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 51 remaining warnings.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 33</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward OXA FLC AMX AMC AMP TZP CZO FEP CXM FOX</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
@ -769,15 +682,14 @@
<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"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">ab_selector</span><span class="op">(</span><span class="va">name</span> <span class="op"><a href="like.html">%like%</a></span> <span class="st">"trim"</span><span class="op">)</span>, <span class="va">susceptibility</span><span class="op">)</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> Including isolates from ICU.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For ab_selector(name %like% "trim") using columns 'TMP' (trimethoprim)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> and 'SXT' (trimethoprim/sulfamethoxazole)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward TMP SXT</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 0.627 0.808</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 0.549 0.778</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 0.667 0.821</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 0.633 0.793</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 0.578 0.792</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 0.705 0.835</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"># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</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">%&gt;%</a></span></span></span>