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Built site for AMR: 1.8.2.9118@c51fb24

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2023-02-11 21:38:01 +00:00
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commit 31fd5db33b
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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="">1.8.2.9115</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9118</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">
@ -851,13 +851,135 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_is_gram_positive()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For glycopeptides() using columns 'VAN' (vancomycin) and 'TEC'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (teicoplanin)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Group Drug CoNS E. fa…¹ S. au…² S. ep…³ S. ho…⁴ S. pn…⁵</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;chr&gt;</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;chr&gt;</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;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> <span style="color: #949494;">"</span>Glycopeptides<span style="color: #949494;">"</span> Teicoplanin (TE… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span>64.1%… <span style="color: #949494;">"</span> 6.8%… <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> <span style="color: #949494;">""</span> Vancomycin (VAN… <span style="color: #949494;">"</span> 0.… <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span> 0.0%… <span style="color: #949494;">"</span> 0.0%…</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with abbreviated variable names ¹​`E. faecalis`, ²​`S. aureus`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ³​`S. epidermidis`, ⁴​`S. hominis`, ⁵​`S. pneumoniae`</span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S" and "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S1".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ID: "S".</span>
<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in (function (..., na.last = TRUE, decreasing = FALSE, method = c("auto", "shell", "radix")) { z &lt;- list(...) decreasing &lt;- as.logical(decreasing) if (length(z) == 1L &amp;&amp; is.numeric(x &lt;- z[[1L]]) &amp;&amp; !is.object(x) &amp;&amp; length(x) &gt; 0) { if (.Internal(sorted_fpass(x, decreasing, na.last))) return(seq_along(x)) } method &lt;- match.arg(method) if (any(vapply(z, is.object, logical(1L)))) { z &lt;- lapply(z, function(x) if (is.object(x)) as.vector(xtfrm(x)) else x) return(do.call("order", c(z, list(na.last = na.last, decreasing = decreasing, method = method)))) } if (method == "auto") { useRadix &lt;- all(vapply(z, function(x) { (is.numeric(x) || is.factor(x) || is.logical(x)) &amp;&amp; is.integer(length(x)) }, logical(1L))) method &lt;- if (useRadix) "radix" else "shell" } if (method != "radix" &amp;&amp; !is.na(na.last)) { if (length(decreasing) &gt; 1L) stop("'decreasing' of length &gt; 1 is only for method = \"radix\"") return(.Internal(order(na.last, decreasing, ...))) } if (method == "radix") { decreasing &lt;- rep_len(as.logical(decreasing), length(z)) return(.Internal(radixsort(na.last, decreasing, FALSE, TRUE, ...))) } if (any(diff((l.z &lt;- lengths(z)) != 0L))) stop("argument lengths differ") na &lt;- vapply(z, is.na, rep.int(NA, l.z[1L])) ok &lt;- if (is.matrix(na)) rowSums(na) == 0L else !any(na) if (all(!ok)) return(integer()) z[[1L]][!ok] &lt;- NA ans &lt;- do.call("order", c(z, list(decreasing = decreasing))) ans[ok[ans]]})(NULL, NULL, NULL):</span> argument 1 is not a vector</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="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> some_column <span class="op">=</span> <span class="st">"some_value"</span>,</span></span>