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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, based on the argument episode_days. 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, and is thus equal to !duplicated(get_episode(...))."><title>Determine (Clinical) 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) 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, based on the argument episode_days. 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, and is thus equal to !duplicated(get_episode(...))."><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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<img src="../logo.svg" class="logo" alt=""><h1>Determine (Clinical) 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 class="ref-description section level2">
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<p>These functions determine which items in a vector can be considered (the start of) a new episode, based on the argument <code>episode_days</code>. This can be used to determine clinical episodes for any epidemiological analysis. The <code>get_episode()</code> function returns the index number of the episode per group, while 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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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">x</span>, <span class="va">episode_days</span>, <span class="va">...</span><span class="op">)</span></span>
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<span></span>
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<span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">x</span>, <span class="va">episode_days</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>x</dt>
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<dd><p>vector of dates (class <code>Date</code> or <code>POSIXt</code>), will be sorted internally to determine episodes</p></dd>
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<dt>episode_days</dt>
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<dd><p>required episode length in days, can also be less than a day or <code>Inf</code>, see <em>Details</em></p></dd>
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<dt>...</dt>
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<dd><p>ignored, only in place to allow future extensions</p></dd>
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</dl></div>
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<div class="section level2">
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<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
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<ul><li><p><code>get_episode()</code>: an <a href="https://rdrr.io/r/base/integer.html" class="external-link">integer</a> vector</p></li>
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<li><p><code>is_new_episode()</code>: a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> vector</p></li>
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</ul></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>The functions <code>get_episode()</code> and <code>is_new_episode()</code> differ in this way when setting <code>episode_days</code> to 365:</p><table class="table table"><tr><td>person_id</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><p>Dates are first sorted from old to new. The oldest date will mark the start of the first episode. After this date, the next date will be marked that is at least <code>episode_days</code> days later than the start of the first episode. From that second marked date on, the next date will be marked that is at least <code>episode_days</code> days later than the start of the second episode which will be the start of the third episode, and so on. Before the vector is being returned, the original order will be restored.</p>
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<p>The <code><a href="first_isolate.html">first_isolate()</a></code> function is a wrapper around the <code>is_new_episode()</code> function, but is more efficient for data sets containing microorganism codes or names and allows for different isolate selection methods.</p>
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<p>The <code>dplyr</code> package is not required for these functions to work, but these episode functions do support <a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">variable grouping</a> and work conveniently inside <code>dplyr</code> verbs such as <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>.</p>
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</div>
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<div class="section level2">
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<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
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<div class="dont-index"><p><code><a href="first_isolate.html">first_isolate()</a></code></p></div>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># `example_isolates` is a data set available in the AMR package.</span></span></span>
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<span class="r-in"><span><span class="co"># See ?example_isolates</span></span></span>
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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">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 41 12 5 11 39 27 43 35 7 21 18 14 45 44 26 41 9 36 34 1 14 14 31 4 38</span>
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<span class="r-out co"><span class="r-pr">#></span> [26] 5 28 40 15 27 26 34 16 46 10 33 18 9 7 8 41 3 3 22 36 42 13 12 22 15</span>
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<span class="r-out co"><span class="r-pr">#></span> [51] 11 19 21 39 20 2 9 25 3 13 37 12 29 11 2 23 31 6 28 47 29 5 32 24 25</span>
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<span class="r-out co"><span class="r-pr">#></span> [76] 3 43 30 24 36 2 1 14 18 40 6 19 9 20 11 19 15 31 12 3 17 32 24 45 38</span>
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<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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>
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<span class="r-out co"><span class="r-pr">#></span> [13] TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [25] TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE TRUE TRUE TRUE TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [37] FALSE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [49] FALSE FALSE FALSE TRUE FALSE FALSE TRUE TRUE FALSE TRUE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [61] TRUE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE TRUE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [73] TRUE TRUE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
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<span class="r-out co"><span class="r-pr">#></span> [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE</span>
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<span class="r-out co"><span class="r-pr">#></span> [97] FALSE FALSE FALSE FALSE</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 on results from the third 60-day episode only, using base R</span></span></span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 5 × 46</span></span>
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<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
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<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>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> 2003-05-26 065187 76 F ICU B_STPHY_AURS R NA S R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> 2003-04-30 6BC362 62 M ICU B_STPHY_EPDR R NA R R </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> 2003-06-01 CBC201 87 F Clinical B_STPHY_CONS S NA S NA </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> 2003-04-22 114570 74 M ICU B_STPHY_CONS R NA R R </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> 2003-04-08 114570 74 M ICU B_STRPT_PYGN S NA S S </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>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>,</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MUP <sir>, RIF <sir></span></span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># the functions also work for less than a day, e.g. to include one per hour:</span></span></span>
|
||
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/Sys.time.html" class="external-link">Sys.time</a></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/Sys.time.html" class="external-link">Sys.time</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fl">60</span> <span class="op">*</span> <span class="fl">60</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> episode_days <span class="op">=</span> <span class="fl">1</span> <span class="op">/</span> <span class="fl">24</span></span></span>
|
||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] 1 2</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># \donttest{</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"># is_new_episode() can also be used in dplyr verbs to determine patient</span></span></span>
|
||
<span class="r-in"><span> <span class="co"># episodes based on any (combination of) grouping variables:</span></span></span>
|
||
<span class="r-in"><span> <span class="va">df</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/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>condition <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></span>
|
||
<span class="r-in"><span> x <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">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> size <span class="op">=</span> <span class="fl">100</span>,</span></span>
|
||
<span class="r-in"><span> replace <span class="op">=</span> <span class="cn">TRUE</span></span></span>
|
||
<span class="r-in"><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/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</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/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>new_episode <span class="op">=</span> <span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, <span class="fl">365</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="va">patient</span>, <span class="va">date</span>, <span class="va">condition</span>, <span class="va">new_episode</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/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</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 × 4</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Groups: patient, condition [97]</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> patient date condition new_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;"><date></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> 065133 2011-12-19 B TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 065187 2003-05-26 B TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 080086 2007-10-26 C TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 114570 2003-04-08 A TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 114570 2003-04-22 B TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 126334 2009-11-26 A TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 146120 2011-09-23 A TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 15D386 2004-09-06 A TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 161740 2005-06-21 A TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 16F0F7 2010-01-17 C 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>
|
||
<span class="r-in"><span> <span class="va">df</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/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span>, <span class="va">patient</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/transmute.html" class="external-link">transmute</a></span><span class="op">(</span><span class="va">date</span>,</span></span>
|
||
<span class="r-in"><span> <span class="va">patient</span>,</span></span>
|
||
<span class="r-in"><span> new_index <span class="op">=</span> <span class="fu">get_episode</span><span class="op">(</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> new_logical <span class="op">=</span> <span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><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/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 [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> Clinical 2011-12-19 065133 1 TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU 2003-05-26 065187 1 TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Clinical 2007-10-26 080086 1 TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> ICU 2003-04-08 114570 1 FALSE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU 2003-04-22 114570 1 TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Outpatient 2009-11-26 126334 1 TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical 2011-09-23 146120 1 TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> ICU 2004-09-06 15D386 1 TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Clinical 2005-06-21 161740 1 TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical 2010-01-17 16F0F7 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>
|
||
<span class="r-in"><span> <span class="va">df</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/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> n_patients <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/n_distinct.html" class="external-link">n_distinct</a></span><span class="op">(</span><span class="va">patient</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> n_episodes_365 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">365</span><span class="op">)</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> n_episodes_60 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">is_new_episode</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="op">)</span>,</span></span>
|
||
<span class="r-in"><span> n_episodes_30 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">30</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="op">}</span></span></span>
|
||
<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 60 13 33 45</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> ICU 27 9 21 24</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Outpatient 8 6 7 7</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>
|
||
<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="va">x</span> <span class="op"><-</span> <span class="va">df</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="first_isolate.html">filter_first_isolate</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> include_unknown <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
|
||
<span class="r-in"><span> method <span class="op">=</span> <span class="st">"episode-based"</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="va">y</span> <span class="op"><-</span> <span class="va">df</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/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">mo</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/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, <span class="fl">365</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/group_by.html" class="external-link">ungroup</a></span><span class="op">(</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/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</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> [1] FALSE</span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="co"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span>
|
||
<span class="r-in"><span><span class="co"># since you can now group on anything that seems relevant:</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="va">df</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/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">mo</span>, <span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>flag_episode <span class="op">=</span> <span class="fu">is_new_episode</span><span class="op">(</span><span class="va">date</span>, <span class="fl">365</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"><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 [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> E52521 B_KLBSL_AERG Clinical TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 6D6319 B_STPHY_CONS Outpatient TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 984417 B_STPHY_AURS ICU TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 161740 B_STPHY_CONS Clinical TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 904640 B_PROTS_MRBL Clinical TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 387C40 B_KLBSL_PNMN Clinical TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 59F400 B_STRPT_PNMN ICU TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> A97263 B_ESCHR_COLI Clinical TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 619705 B_KLBSL_PNMN ICU TRUE </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 314039 UNKNOWN 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>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||
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|
||
|
||
|
||
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|
||
<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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|
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|
||
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
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