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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 determine which items in a vector can be considered (the start of) a new episode. This can be used to determine clinical episodes for any epidemiological analysis. The get_episode() function returns the index number of the episode per group, while the is_new_episode() function returns TRUE for every new get_episode() index. Both absolute and relative episode determination are supported."><title>Determine (Clinical or Epidemic) Episodes — get_episode • 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="Determine (Clinical or Epidemic) Episodes — get_episode"><meta property="og:description" content="These functions determine which items in a vector can be considered (the start of) a new episode. This can be used to determine clinical episodes for any epidemiological analysis. The get_episode() function returns the index number of the episode per group, while the is_new_episode() function returns TRUE for every new get_episode() index. Both absolute and relative episode determination are supported."><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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<!-- 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 determine which items in a vector can be considered (the start of) a new episode. This can be used to determine clinical episodes for any epidemiological analysis. The get_episode() function returns the index number of the episode per group, while the is_new_episode() function returns TRUE for every new get_episode() index. Both absolute and relative episode determination are supported."><title>Determine Clinical or Epidemic Episodes — get_episode • 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="Determine Clinical or Epidemic Episodes — get_episode"><meta property="og:description" content="These functions determine which items in a vector can be considered (the start of) a new episode. This can be used to determine clinical episodes for any epidemiological analysis. The get_episode() function returns the index number of the episode per group, while the is_new_episode() function returns TRUE for every new get_episode() index. Both absolute and relative episode determination are supported."><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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@ -10,7 +10,7 @@
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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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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -137,7 +137,7 @@
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</nav><div class="container template-reference-topic">
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<div class="row">
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Determine (Clinical or Epidemic) Episodes</h1>
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<img src="../logo.svg" class="logo" alt=""><h1>Determine Clinical or Epidemic Episodes</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/get_episode.R" class="external-link"><code>R/get_episode.R</code></a></small>
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<div class="d-none name"><code>get_episode.Rd</code></div>
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</div>
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@ -193,7 +193,7 @@
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<p>The <code>get_episode()</code> function returns the index number of the episode, so all cases/patients/isolates in the first episode will have the number 1, all cases/patients/isolates in the second episode will have the number 2, etc.</p>
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<p>The <code>is_new_episode()</code> function returns <code>TRUE</code> for every new <code>get_episode()</code> index, and is thus equal to <code>!duplicated(get_episode(...))</code>.</p>
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<p>The <code>is_new_episode()</code> function on the other hand, returns <code>TRUE</code> for every new <code>get_episode()</code> index.</p>
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<p>To specify, when setting <code>episode_days = 365</code> (using method 1 as explained above), this is how the two functions differ:</p><table class="table table"><tr><td>patient</td><td>date</td><td><code>get_episode()</code></td><td><code>is_new_episode()</code></td></tr><tr><td>A</td><td>2019-01-01</td><td>1</td><td>TRUE</td></tr><tr><td>A</td><td>2019-03-01</td><td>1</td><td>FALSE</td></tr><tr><td>A</td><td>2021-01-01</td><td>2</td><td>TRUE</td></tr><tr><td>B</td><td>2008-01-01</td><td>1</td><td>TRUE</td></tr><tr><td>B</td><td>2008-01-01</td><td>1</td><td>FALSE</td></tr><tr><td>C</td><td>2020-01-01</td><td>1</td><td>TRUE</td></tr></table></div>
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<div class="section">
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@ -246,29 +246,28 @@
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<span class="r-in"><span><span class="va">df</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</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="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 8 36 16 50 29 40 17 1 46 26 52 49 35 37 3 37 52 40 21 51 38 22 29 5 21</span>
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<span class="r-out co"><span class="r-pr">#></span> [26] 37 31 17 49 13 20 44 35 29 9 49 8 11 30 6 8 5 41 27 44 12 39 12 21 3</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [51] 33 44 25 14 8 49 30 7 50 11 34 10 47 21 6 15 3 39 19 7 2 51 5 38 28</span>
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<span class="r-out co"><span class="r-pr">#></span> [76] 32 29 22 43 33 49 45 4 31 30 18 44 48 9 47 29 44 2 42 23 42 7 24 19 7</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 41 9 6 37 14 5 39 36 47 13 45 19 26 35 24 42 46 29 1 38 31 27 20 23 11</span>
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<span class="r-out co"><span class="r-pr">#></span> [26] 23 46 3 6 33 44 22 32 21 20 18 7 1 22 21 17 38 28 30 33 40 12 8 32 12</span>
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<span class="r-out co"><span class="r-pr">#></span> [51] 47 34 43 24 48 46 9 47 4 47 34 47 26 30 25 44 1 1 10 10 33 20 15 20 45</span>
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<span class="r-out co"><span class="r-pr">#></span> [76] 46 14 47 6 30 38 5 31 40 21 4 22 9 4 40 7 2 12 3 43 16 24 15 32 7</span>
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<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] FALSE FALSE TRUE FALSE FALSE TRUE TRUE TRUE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] FALSE TRUE TRUE TRUE FALSE FALSE TRUE TRUE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] TRUE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] FALSE FALSE TRUE TRUE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE TRUE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [13] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [25] TRUE FALSE FALSE TRUE FALSE TRUE TRUE TRUE TRUE TRUE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [37] TRUE FALSE FALSE FALSE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [61] FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [73] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE FALSE FALSE</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
|
||||
<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 46</span></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> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></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> 2002-12-14 144280 76 F Clinical B_STPHY_AURS R NA S R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-11-16 762305 87 F Clinical B_PROTS_MRBL R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2002-11-16 762305 87 F Clinical B_BCTRD_FRGL R NA NA R </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2003-01-06 894506 83 M ICU B_CRYNB S NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2002-11-18 956065 89 F Clinical B_ESCHR_COLI R NA NA NA </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>,</span></span>
|
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@ -306,16 +305,16 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, condition [98]</span></span>
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<span class="r-out co"><span class="r-pr">#></span> patient date condition new_episode</span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 074321 2015-09-20 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 088256 2003-01-25 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 097186 2015-10-28 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 0D7D34 2011-03-19 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 0E2483 2008-07-22 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 105248 2005-06-16 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 107DD1 2012-09-03 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 114570 2003-04-08 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 136315 2004-02-02 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 144280 2002-12-14 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 04C169 2012-07-18 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 051150 2007-01-02 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 05C73F 2006-01-12 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 092034 2016-08-07 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 0C0688 2014-09-05 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 0D7D34 2011-03-17 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 0D7D34 2011-03-16 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 0DBB93 2003-10-02 C TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 114570 2003-04-22 A TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 146120 2011-09-23 B TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 90 more rows</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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
@ -329,19 +328,19 @@
|
||||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [94]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: ward, patient [95]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward date patient new_index new_logical</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> ICU 2015-09-20 074321 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU 2003-01-25 088256 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2015-10-28 097186 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ICU 2011-03-19 0D7D34 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2008-07-22 0E2483 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical 2005-06-16 105248 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2012-09-03 107DD1 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2003-04-08 114570 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2004-02-02 136315 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2002-12-14 144280 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical 2012-07-18 04C169 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU 2007-01-02 051150 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2006-01-12 05C73F 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical 2016-08-07 092034 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Clinical 2014-09-05 0C0688 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> ICU 2011-03-16 0D7D34 1 FALSE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> ICU 2011-03-17 0D7D34 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2003-10-02 0DBB93 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU 2003-04-22 114570 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2011-09-23 146120 1 TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 90 more rows</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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
@ -357,9 +356,9 @@
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><int></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 64 14 44 54</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 29 10 22 24</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 1 1 1 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Clinical 62 13 35 48</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 27 9 22 23</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 6 4 6 6</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
|
||||
@ -388,19 +387,19 @@
|
||||
<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"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [98]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> E32B78 B_GEMLL_HMLY ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 672020 B_STPHY_EPDR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 578848 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 844790 B_STPHY_LGDN ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 409788 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 789292 B_STRPT_SLVR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 94BB11 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 495616 B_STPHY_EPDR Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 329C35 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> D19627 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, mo, ward [99]</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> patient mo ward flag_episode</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 310665 B_STPHY_CPTS Outpatient TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> B95551 B_STPHY_CONS Outpatient TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> F35553 B_ENTRC ICU TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 919B60 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 911753 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> CBC201 B_STPHY_CONS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> DC47C6 B_PSDMN_AERG Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 287666 B_ESCHR_COLI Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 594103 B_MCRCCC_LUTS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B12221 B_STPHY_AURS Clinical TRUE </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 90 more rows</span></span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
|
||||
Reference in New Issue
Block a user