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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, 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", "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-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.5/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, 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", "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=Line truncated
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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-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.5/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.
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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]>
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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="">1.8.2.9148</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9150</small>
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@@ -143,7 +145,8 @@
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</div>
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<div class="ref-description section level2">
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<p>These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, 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", "CZO" and "J01DB04" will all be picked up by <code>cephalosporins()</code>.</p>
|
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<p>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 <a href="antibiotics.html">antibiotics</a> data set), without the need to define the columns or antibiotic abbreviations.</p>
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<p>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 <code>cephalosporins()</code>.</p>
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</div>
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<div class="section level2">
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</div>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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<p>These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the <a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">Tidyverse selection helpers</a> such as <code><a href="https://tidyselect.r-lib.org/reference/everything.html" class="external-link">everything()</a></code>, but also work in base <span style="R">R</span> and not only in <code>dplyr</code> verbs. Nonetheless, they are very convenient to use with <code>dplyr</code> functions such as <code><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, see <em>Examples</em>.</p>
|
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<p>These functions can be used in data set calls for selecting columns and filtering rows. They work with base <span style="R">R</span>, the Tidyverse, and <code>data.table</code>. They are heavily inspired by the <a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">Tidyverse selection helpers</a> such as <code><a href="https://tidyselect.r-lib.org/reference/everything.html" class="external-link">everything()</a></code>, but are not limited to <code>dplyr</code> verbs. Nonetheless, they are very convenient to use with <code>dplyr</code> functions such as <code><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, see <em>Examples</em>.</p>
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<p>All columns in the data in which these functions are called will be searched for known antibiotic names, abbreviations, brand names, and codes (ATC, EARS-Net, WHO, etc.) according to the <a href="antibiotics.html">antibiotics</a> data set. This means that a selector such as <code>aminoglycosides()</code> will pick up column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc.</p>
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<p>The <code>ab_class()</code> function can be used to filter/select on a manually defined antibiotic class. It searches for results in the <a href="antibiotics.html">antibiotics</a> data set within the columns <code>group</code>, <code>atc_group1</code> and <code>atc_group2</code>.</p>
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<p>The <code>ab_selector()</code> function can be used to internally filter the <a href="antibiotics.html">antibiotics</a> data set on any results, see <em>Examples</em>. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.</p>
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@@ -324,6 +327,10 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <sir>, COL <sir>, MUP <sir>, RIF <sir></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># Examples sections below are split into 'base R', 'dplyr', and 'data.table':</span></span></span>
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<span class="r-in"><span></span></span>
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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></span>
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<span class="r-in"><span><span class="co"># select columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span></span>
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@@ -511,7 +518,7 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># COL <sir>, MUP <sir>, RIF <sir></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># filter + select in one go: get penicillins in carbapenems-resistant strains</span></span></span>
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<span class="r-in"><span><span class="co"># filter + select in one go: get penicillins in carbapenem-resistant strains</span></span></span>
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<span class="r-in"><span><span class="va">example_isolates</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">"R"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA'</span>
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@@ -567,9 +574,9 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA S NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># ab_selector() applies a filter in the `antibiotics` data set and is thus very</span></span></span>
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<span class="r-in"><span><span class="co"># flexible. For instance, to select antibiotic columns with an oral DDD of at</span></span></span>
|
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<span class="r-in"><span><span class="co"># least 1 gram:</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># ab_selector() applies a filter in the `antibiotics` data set and is thus</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># very flexible. For instance, to select antibiotic columns with an oral DDD</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># of at least 1 gram:</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">ab_selector</span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">></span> <span class="fl">1</span> <span class="op">&</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</span><span class="op">)</span><span class="op">]</span></span></span>
|
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<span class="r-msg co"><span class="r-pr">#></span> ℹ For ab_selector(oral_ddd > 1 & oral_units == "g") using columns 'OXA'</span>
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<span class="r-msg co"><span class="r-pr">#></span> (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC'</span>
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@@ -591,8 +598,23 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA S NA NA NA NA NA NA S S NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
|
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------------</span></span></span>
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------------</span></span></span>
|
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<span class="r-in"><span></span></span>
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<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://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a></span><span class="op">(</span>kefzol <span class="op">=</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">5</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu">cephalosporins</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 cephalosporins() using column 'kefzol' (cefazolin)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 5 × 1</span></span>
|
||||
<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> I </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> R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> I </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> S </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://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>
|
||||
<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">%>%</a></span></span></span>
|
||||
@@ -883,6 +905,156 @@
|
||||
<span class="r-msg co"><span class="r-pr">#></span> prevent this note.</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> [1] TRUE</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># data.table --------------------------------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># data.table is supported as well, just use it in the same way as with</span></span></span>
|
||||
<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></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</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 class="co"># incorrect, returns column *names*</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</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>, with <span class="op">=</span> <span class="cn">FALSE</span><span class="op">]</span> <span class="co"># so `with = FALSE` is required</span></span></span>
|
||||
<span class="r-in"><span> <span class="op">)</span></span></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="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></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="st">"mo"</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-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></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-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="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</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 class="op">)</span></span></span>
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</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 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> Loading required package: data.table</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> Attaching package: ‘data.table’</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> The following objects are masked from ‘package:dplyr’:</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> between, first, last</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> The following objects are masked from ‘package:AMR’:</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> %like%, like</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> [1] "IPM" "MEM"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> attr(,"class")</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "ab_selector" "character" </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-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-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-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> --- </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-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 penicillins() using columns 'PEN' (benzylpenicillin), 'OXA'</span>
|
||||
<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-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
Reference in new issue
Block a user