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@ -1,6 +1,6 @@
|
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content='These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group (according to the antibiotics data set), without the need to define the columns or antibiotic abbreviations.
|
||||
In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up by cephalosporins().'><title>Antibiotic Selectors — antibiotic_class_selectors • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.7/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Antibiotic Selectors — antibiotic_class_selectors"><meta property="og:description" content='These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group (according to the antibiotics data set), without the need to define the columns or antibiotic abbreviations.
|
||||
In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up by cephalosporins().'><title>Antibiotic Selectors — antibiotic_class_selectors • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.8/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Antibiotic Selectors — antibiotic_class_selectors"><meta property="og:description" content='These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group (according to the antibiotics data set), without the need to define the columns or antibiotic abbreviations.
|
||||
In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up by cephalosporins().'><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
|
||||
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
|
||||
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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@ -627,10 +627,10 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
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<span class="r-out co"><span class="r-pr">#></span> kefzol</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><sir></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> I </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> S </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> I </span>
|
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<span class="r-in"><span></span></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"># get AMR for all aminoglycosides e.g., per ward:</span></span></span>
|
||||
@ -929,7 +929,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
||||
<span class="r-in"><span><span class="co"># base R, but add `with = FALSE` if using a single AB selector.</span></span></span>
|
||||
<span class="r-in"><span></span></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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">dt</span> <span class="op"><-</span> <span class="fu"><a href="https://Rdatatable.gitlab.io/data.table/reference/as.data.table.html" class="external-link">as.data.table</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">dt</span> <span class="op"><-</span> <span class="fu"><a href="https://rdatatable.gitlab.io/data.table/reference/as.data.table.html" class="external-link">as.data.table</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># this does not work, it returns column *names*</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">dt</span><span class="op">[</span>, <span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
@ -952,18 +952,19 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
||||
<span class="r-in"><span> <span class="va">dt</span><span class="op">[</span>, <span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, with <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">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> IPM MEM</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1996: <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1997: S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1998: S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1999: S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2000: S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> IPM MEM</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1996: <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1997: S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1998: S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1999: S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2000: S S</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># for multiple selections or AB selectors, `with = FALSE` is not needed:</span></span></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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
@ -971,90 +972,109 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo GEN TOB AMK KAN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: B_ESCHR_COLI <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: B_ESCHR_COLI <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: B_STPHY_EPDR <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: B_STPHY_EPDR <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: B_STPHY_EPDR <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1996: B_STRPT_PNMN R R R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1997: B_ESCHR_COLI S S S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1998: B_STPHY_CONS S <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1999: B_ESCHR_COLI S S <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2000: B_KLBSL_PNMN S S <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo GEN TOB AMK KAN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <mo> <sir> <sir> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: B_ESCHR_COLI <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: B_ESCHR_COLI <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: B_STPHY_EPDR <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: B_STPHY_EPDR <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: B_STPHY_EPDR <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1996: B_STRPT_PNMN R R R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1997: B_ESCHR_COLI S S S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1998: B_STPHY_CONS S <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1999: B_ESCHR_COLI S S <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2000: B_KLBSL_PNMN S S <NA> <NA></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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">dt</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</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">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> IPM MEM GEN TOB AMK KAN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: <NA> <NA> <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: <NA> <NA> <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: <NA> <NA> <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: <NA> <NA> <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: <NA> <NA> <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1996: <NA> <NA> R R R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1997: S S S S S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1998: S S S <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1999: S S S S <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2000: S S S S <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> IPM MEM GEN TOB AMK KAN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <sir> <sir> <sir> <sir> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: <NA> <NA> <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: <NA> <NA> <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: <NA> <NA> <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: <NA> <NA> <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: <NA> <NA> <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1996: <NA> <NA> R R R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1997: S S S S S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1998: S S S <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1999: S S S S <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2000: S S S S <NA> <NA></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># row filters are also supported:</span></span></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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">dt</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"S"</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">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: 2002-02-05 067927 45 F ICU B_SERRT_MRCS R <NA> <NA> R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 905: 2005-04-12 D71461 70 M ICU B_ESCHR_COLI R <NA> <NA> S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 906: 2009-11-12 650870 69 F Outpatient B_ESCHR_COLI R <NA> <NA> S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 907: 2012-06-14 8CBCF2 41 F Clinical B_STPHY_CONS R S S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 908: 2012-10-11 175532 78 M Clinical B_ESCHR_COLI R <NA> <NA> R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 909: 2013-11-23 A97263 77 M Clinical B_KLBSL_PNMN R <NA> <NA> R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMC AMP TZP CZO FEP CXM FOX CTX CAZ CRO GEN TOB AMK KAN TMP</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: I <NA> <NA> <NA> <NA> S <NA> S <NA> S <NA> S <NA> <NA> S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: I <NA> <NA> <NA> <NA> S <NA> S <NA> S <NA> S <NA> <NA> S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: I <NA> <NA> <NA> <NA> S <NA> S S S <NA> <NA> <NA> <NA> S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: I <NA> <NA> <NA> <NA> S <NA> S S S <NA> <NA> <NA> <NA> S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: R R <NA> R <NA> R R <NA> <NA> <NA> <NA> <NA> <NA> <NA> S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 905: S S S <NA> S S S S S S S S S <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 906: S S S S S S S S S S S S S <NA> S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 907: S <NA> <NA> S S S S S R S S <NA> <NA> <NA> S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 908: S R S <NA> S R R S S S S S <NA> <NA> R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 909: S R S <NA> S S S S S S S S <NA> <NA> S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> SXT NIT FOS LNZ CIP MFX VAN TEC TCY TGC DOX ERY CLI AZM IPM MEM</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: S <NA> <NA> R <NA> <NA> R R <NA> <NA> <NA> R R R S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: S <NA> <NA> R <NA> <NA> R R <NA> <NA> <NA> R R R S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: S R <NA> R S <NA> R R R R R R R R S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: S R <NA> R S <NA> R R R R R R R R S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: S R <NA> R S <NA> R R R R R R R R S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <Date> <char> <num> <char> <char> <mo> <sir> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: 2002-01-22 F35553 50 M ICU B_PROTS_MRBL R <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: 2002-02-05 067927 45 F ICU B_SERRT_MRCS R <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 905: S S <NA> R S <NA> R R <NA> <NA> <NA> R R R S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 906: S S <NA> R S <NA> R R <NA> <NA> <NA> R R R S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 907: S <NA> <NA> <NA> S <NA> S <NA> <NA> <NA> <NA> S S S S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 908: R R <NA> R R R R R <NA> <NA> <NA> R R R S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 909: S S <NA> R S <NA> R R <NA> <NA> <NA> R R R S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> MTR CHL COL MUP RIF</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: <NA> <NA> <NA> <NA> R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: <NA> <NA> <NA> <NA> R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: <NA> <NA> R <NA> R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: <NA> <NA> R <NA> R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: <NA> <NA> R <NA> R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 905: <NA> <NA> <NA> <NA> R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 906: <NA> <NA> <NA> <NA> R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 907: <NA> <NA> R <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 908: <NA> <NA> S <NA> R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 909: <NA> <NA> S <NA> R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 905: 2005-04-12 D71461 70 M ICU B_ESCHR_COLI R <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 906: 2009-11-12 650870 69 F Outpatient B_ESCHR_COLI R <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 907: 2012-06-14 8CBCF2 41 F Clinical B_STPHY_CONS R S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 908: 2012-10-11 175532 78 M Clinical B_ESCHR_COLI R <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 909: 2013-11-23 A97263 77 M Clinical B_KLBSL_PNMN R <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> AMX AMC AMP TZP CZO FEP CXM FOX CTX CAZ CRO GEN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: <NA> I <NA> <NA> <NA> <NA> S <NA> S <NA> S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: <NA> I <NA> <NA> <NA> <NA> S <NA> S <NA> S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: <NA> I <NA> <NA> <NA> <NA> S <NA> S S S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: <NA> I <NA> <NA> <NA> <NA> S <NA> S S S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: R R R <NA> R <NA> R R <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 905: S S S S <NA> S S S S S S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 906: S S S S S S S S S S S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 907: <NA> S <NA> <NA> S S S S S R S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 908: R S R S <NA> S R R S S S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 909: R S R S <NA> S S S S S S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TOB AMK KAN TMP SXT NIT FOS LNZ CIP MFX VAN TEC</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: S <NA> <NA> S S <NA> <NA> R <NA> <NA> R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: S <NA> <NA> S S <NA> <NA> R <NA> <NA> R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: <NA> <NA> <NA> S S R <NA> R S <NA> R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: <NA> <NA> <NA> S S R <NA> R S <NA> R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: <NA> <NA> <NA> S S R <NA> R S <NA> R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 905: S S <NA> <NA> S S <NA> R S <NA> R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 906: S S <NA> S S S <NA> R S <NA> R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 907: <NA> <NA> <NA> S S <NA> <NA> <NA> S <NA> S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 908: S <NA> <NA> R R R <NA> R R R R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 909: S <NA> <NA> S S S <NA> R S <NA> R R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> TCY TGC DOX ERY CLI AZM IPM MEM MTR CHL COL MUP</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: <NA> <NA> <NA> R R R S <NA> <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: <NA> <NA> <NA> R R R S <NA> <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: R R R R R R S <NA> <NA> <NA> R <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: R R R R R R S <NA> <NA> <NA> R <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: R R R R R R S <NA> <NA> <NA> R <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 905: <NA> <NA> <NA> R R R S S <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 906: <NA> <NA> <NA> R R R S S <NA> <NA> <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 907: <NA> <NA> <NA> S S S S S <NA> <NA> R <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 908: <NA> <NA> <NA> R R R S S <NA> <NA> S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 909: <NA> <NA> <NA> R R R S S <NA> <NA> S <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> RIF</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 905: R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 906: R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 907: <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 908: R</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 909: R</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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">dt</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"S"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span>, with <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>
|
||||
@ -1063,18 +1083,19 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (piperacillin/tazobactam)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> PEN OXA FLC AMX AMC AMP TZP</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: R <NA> <NA> <NA> I <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: R <NA> <NA> <NA> I <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: R <NA> <NA> <NA> I <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: R <NA> <NA> <NA> I <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: R <NA> <NA> R R R <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 905: R <NA> <NA> S S S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 906: R <NA> <NA> S S S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 907: R S S <NA> S <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 908: R <NA> <NA> R S R S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 909: R <NA> <NA> R S R S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> PEN OXA FLC AMX AMC AMP TZP</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <sir> <sir> <sir> <sir> <sir> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: R <NA> <NA> <NA> I <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 2: R <NA> <NA> <NA> I <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 3: R <NA> <NA> <NA> I <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 4: R <NA> <NA> <NA> I <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 5: R <NA> <NA> R R R <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> --- </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 905: R <NA> <NA> S S S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 906: R <NA> <NA> S S S S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 907: R S S <NA> S <NA> <NA></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 908: R <NA> <NA> R S R S</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 909: R <NA> <NA> R S R S</span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
Reference in New Issue
Block a user