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<img src="../logo.svg" class="logo" alt=""><h1>Determine Clinical or Epidemic Episodes</h1>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/get_episode.R" class="external-link"><code>R/get_episode.R</code></a></small>
<div class="d-none name"><code>get_episode.Rd</code></div>
</div>
<div class="ref-description section level2">
<p>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 <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. Both absolute and relative episode determination are supported.</p>
</div>
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">x</span>, episode_days <span class="op">=</span> <span class="cn">NULL</span>, case_free_days <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">x</span>, episode_days <span class="op">=</span> <span class="cn">NULL</span>, case_free_days <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
<dd><p>Vector of dates (class <code>Date</code> or <code>POSIXt</code>), will be sorted internally to determine episodes.</p></dd>
<dt id="arg-episode-days">episode_days<a class="anchor" aria-label="anchor" href="#arg-episode-days"></a></dt>
<dd><p>Episode length in days to specify the time period after which a new episode begins, can also be less than a day or <code>Inf</code>, see <em>Details</em>.</p></dd>
<dt id="arg-case-free-days">case_free_days<a class="anchor" aria-label="anchor" href="#arg-case-free-days"></a></dt>
<dd><p>(inter-epidemic) interval length in days after which a new episode will start, can also be less than a day or <code>Inf</code>, see <em>Details</em>.</p></dd>
<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
<dd><p>Ignored, only in place to allow future extensions.</p></dd>
</dl></div>
<div class="section level2">
<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
<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>
<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>
</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>Episodes can be determined in two ways: absolute and relative.</p><ol><li><p>Absolute</p>
<p>This method uses <code>episode_days</code> to define an episode length in days, after which a new episode will start. A common use case in AMR data analysis is microbial epidemiology: episodes of <em>S. aureus</em> bacteraemia in ICU patients for example. The episode length could then be 30 days, so that new <em>S. aureus</em> isolates after an ICU episode of 30 days will be considered a different (or new) episode.</p>
<p>Thus, this method counts <strong>since the start of the previous episode</strong>.</p></li>
<li><p>Relative</p>
<p>This method uses <code>case_free_days</code> to quantify the duration of case-free days (the inter-epidemic interval), after which a new episode will start. A common use case is infectious disease epidemiology: episodes of norovirus outbreaks in a hospital for example. The case-free period could then be 14 days, so that new norovirus cases after that time will be considered a different (or new) episode.</p>
<p>Thus, this methods counts <strong>since the last case in the previous episode</strong>.</p></li>
</ol><p>In a table:</p><table class="table table"><tr><td>Date</td><td>Using <code>episode_days = 7</code></td><td>Using <code>case_free_days = 7</code></td></tr><tr><td>2023-01-01</td><td>1</td><td>1</td></tr><tr><td>2023-01-02</td><td>1</td><td>1</td></tr><tr><td>2023-01-05</td><td>1</td><td>1</td></tr><tr><td>2023-01-08</td><td>2**</td><td>1</td></tr><tr><td>2023-02-21</td><td>3</td><td>2***</td></tr><tr><td>2023-02-22</td><td>3</td><td>2</td></tr><tr><td>2023-02-23</td><td>3</td><td>2</td></tr><tr><td>2023-02-24</td><td>3</td><td>2</td></tr><tr><td>2023-03-01</td><td>4</td><td>2</td></tr></table><p>** This marks the start of a new episode, because 8 January 2023 is more than 7 days since the start of the previous episode (1 January 2023). <br>
*** This marks the start of a new episode, because 21 January 2023 is more than 7 days since the last case in the previous episode (8 January 2023).</p>
<p>Either <code>episode_days</code> or <code>case_free_days</code> must be provided in the function.</p><div class="section">
<h3 id="difference-between-get-episode-and-is-new-episode-">Difference between <code>get_episode()</code> and <code>is_new_episode()</code><a class="anchor" aria-label="anchor" href="#difference-between-get-episode-and-is-new-episode-"></a></h3>
<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>
<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>
<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>
<div class="section">
<h3 id="other">Other<a class="anchor" aria-label="anchor" href="#other"></a></h3>
<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>
<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>
</div>
</div>
<div class="section level2">
<h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
<div class="dont-index"><p><code><a href="first_isolate.html">first_isolate()</a></code></p></div>
</div>
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># difference between absolute and relative determination of episodes:</span></span></span>
<span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>dates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></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></span>
<span class="r-in"><span> <span class="st">"2021-01-01"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-01-02"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-01-05"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-01-08"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-02-21"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-02-22"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-02-23"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-02-24"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-03-01"</span>,</span></span>
<span class="r-in"><span> <span class="st">"2021-03-01"</span></span></span>
<span class="r-in"><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">$</span><span class="va">absolute</span> <span class="op">&lt;-</span> <span class="fu">get_episode</span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">dates</span>, episode_days <span class="op">=</span> <span class="fl">7</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span><span class="op">$</span><span class="va">relative</span> <span class="op">&lt;-</span> <span class="fu">get_episode</span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">dates</span>, case_free_days <span class="op">=</span> <span class="fl">7</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">x</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> dates absolute relative</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 2021-01-01 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 2021-01-02 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 2021-01-05 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 2021-01-08 2 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 2021-02-21 3 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 2021-02-22 3 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 2021-02-23 3 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 2021-02-24 3 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 2021-03-01 4 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 2021-03-01 4 2</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># `example_isolates` is a data set available in the AMR package.</span></span></span>
<span class="r-in"><span><span class="co"># See ?example_isolates</span></span></span>
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</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>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 17 19 32 7 48 16 36 11 41 30 43 42 3 37 6 42 16 46 12 6 38 15 31 23 44</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] 35 42 21 10 21 18 22 9 29 40 8 22 14 31 47 18 26 28 18 25 20 11 49 8 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] 50 23 46 3 27 6 31 1 33 10 23 31 11 20 46 13 4 24 4 27 8 48 16 2 20</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [76] 35 31 19 33 34 16 14 33 17 46 24 15 17 7 9 39 14 50 5 12 2 45 35 8 28</span>
<span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [13] TRUE TRUE TRUE FALSE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [25] TRUE TRUE FALSE TRUE TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [37] FALSE TRUE FALSE TRUE FALSE TRUE TRUE FALSE TRUE TRUE FALSE TRUE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [49] FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] FALSE FALSE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [73] FALSE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [85] FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [97] TRUE 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">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> date patient age gender ward mo PEN OXA FLC AMX </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-23 F35553 51 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-07-23 F35553 51 M ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># FOS &lt;sir&gt;, LNZ &lt;sir&gt;, CIP &lt;sir&gt;, MFX &lt;sir&gt;, VAN &lt;sir&gt;, TEC &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, RIF &lt;sir&gt;</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">#&gt;</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">%&gt;%</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">%&gt;%</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">%&gt;%</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">%&gt;%</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">%&gt;%</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">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, condition [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient date condition new_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 011307 2011-09-20 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 011307 2011-09-20 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 021368 2016-03-25 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 060287 2007-03-11 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 078381 2014-07-17 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 097186 2015-10-28 B TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 0DBB93 2003-10-02 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 0DBF93 2015-12-03 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 114570 2003-04-22 A TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 141061 2014-10-22 C TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 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">%&gt;%</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">%&gt;%</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">%&gt;%</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">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: ward, patient [93]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward date patient new_index new_logical</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;date&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2011-09-20 011307 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2011-09-20 011307 1 FALSE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Outpatient 2016-03-25 021368 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2007-03-11 060287 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU 2014-07-17 078381 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2015-10-28 097186 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU 2003-10-02 0DBB93 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU 2015-12-03 0DBF93 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU 2003-04-22 114570 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2014-10-22 141061 1 TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 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">%&gt;%</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">%&gt;%</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">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> ward n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical 51 12 33 43</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU 31 11 26 30</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 11 8 11 11</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">&lt;-</span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</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">&lt;-</span> <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</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">%&gt;%</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">%&gt;%</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">#&gt;</span> [1] TRUE</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">%&gt;%</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">%&gt;%</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">%&gt;%</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">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups: patient, mo, ward [95]</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> patient mo ward flag_episode</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 690B42 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 550406 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> F86227 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 859863 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 987C84 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E19440 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI ICU TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> F42C5F <span style="color: #949494;">B_</span>MRGNL<span style="color: #949494;">_</span>MRGN Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> F54261 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 5D1690 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI Outpatient TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 874171 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>CONS Clinical TRUE </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
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