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(v1.5.0.9010) MDRO vignette update, get_episode for < day

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dr. M.S. (Matthijs) Berends
2021-01-24 14:48:56 +01:00
parent 1a88caa119
commit 286eaa9699
52 changed files with 319 additions and 210 deletions
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docs/reference/get_episode.html
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@ -82,7 +82,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9008</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9010</span>
</span>
</div>
@ -255,11 +255,11 @@
</tr>
<tr>
<th>episode_days</th>
<td><p>length of the required episode in days, see <em>Details</em></p></td>
<td><p>length of the required episode length in days, can also be less than a day, see <em>Details</em></p></td>
</tr>
<tr>
<th>...</th>
<td><p>arguments passed on to <code><a href='https://rdrr.io/r/base/as.Date.html'>as.Date()</a></code></p></td>
<td><p>arguments passed on to <code><a href='https://rdrr.io/r/base/as.POSIXlt.html'>as.POSIXct()</a></code></p></td>
</tr>
</table>
@ -293,15 +293,20 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='first_isolate.html'>first_isolate()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><span class='co'># `example_isolates` is a dataset available in the AMR package.</span>
<pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>60</span><span class='op'>)</span>
<span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>60</span><span class='op'>)</span>
<span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</span><span class='va'>date</span>, episode_days <span class='op'>=</span> <span class='fl'>60</span><span class='op'>)</span> <span class='co'># indices</span>
<span class='fu'>is_new_episode</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>$</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 class='co'># filter on results from the third 60-day episode only, using base R</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/which.html'>which</a></span><span class='op'>(</span><span class='fu'>get_episode</span><span class='op'>(</span><span class='va'>example_isolates</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 class='co'># the functions also work for less than a day, e.g. to include one per hour:</span>
<span class='fu'>get_episode</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>Sys.time</a></span><span class='op'>(</span><span class='op'>)</span>,
<span class='fu'><a href='https://rdrr.io/r/base/Sys.time.html'>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 class='op'>)</span>,
episode_days <span class='op'>=</span> <span class='fl'>1</span><span class='op'>/</span><span class='fl'>24</span><span class='op'>)</span>
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># is_new_episode() can also be used in dplyr verbs to determine patient</span>