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getting-started.html
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<!DOCTYPE html>
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<img src="" class="logo" alt=""><h1>Getting Started with healthyR</h1>
<h3 data-toc-skip class="subtitle">A Quick Introduction</h3>
<h4 data-toc-skip class="author">Steven P.
Sanderson II, MPH</h4>
<h4 data-toc-skip class="date">2023-04-18</h4>
<small class="dont-index">Source: <a href="https://github.com/spsanderson/healthyR/blob/HEAD/vignettes/getting-started.Rmd" class="external-link"><code>vignettes/getting-started.Rmd</code></a></small>
<div class="d-none name"><code>getting-started.Rmd</code></div>
</div>
<blockquote>
<p>healthyR: A toolkit for hospital data</p>
</blockquote>
<div class="section level2">
<h2 id="libaray-load">Libaray Load<a class="anchor" aria-label="anchor" href="#libaray-load"></a>
</h2>
<p>First things first, lets load in the library:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="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/spsanderson/healthyR" class="external-link">healthyR</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="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/spsanderson/healthyR.data" class="external-link">healthyR.data</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="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/business-science/timetk" class="external-link">timetk</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://purrr.tidyverse.org/" class="external-link">purrr</a></span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="generate-sample-data">Generate Sample Data<a class="anchor" aria-label="anchor" href="#generate-sample-data"></a>
</h2>
<p>First we are going to take a look at some time series plotting
functions. These are fairly straight forward and therefore should seem
intuitive. We are going to generate some random numbers to simulate
different daily average length of stay data. We will set a seed for
reproducibility.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># Get Length of Stay Data</span></span>
<span><span class="va">data_tbl</span> <span class="op"><-</span> <span class="va">healthyR_data</span></span>
<span></span>
<span><span class="va">df_tbl</span> <span class="op"><-</span> <span class="va">data_tbl</span> <span class="op"><a href="../reference/pipe.html">%>%</a></span></span>
<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="va">ip_op_flag</span> <span class="op">==</span> <span class="st">"I"</span><span class="op">)</span> <span class="op"><a href="../reference/pipe.html">%>%</a></span></span>
<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">visit_end_date_time</span>, <span class="va">length_of_stay</span><span class="op">)</span> <span class="op"><a href="../reference/pipe.html">%>%</a></span></span>
<span> <span class="fu"><a href="https://rdrr.io/pkg/timetk/man/summarise_by_time.html" class="external-link">summarise_by_time</a></span><span class="op">(</span></span>
<span> .date_var <span class="op">=</span> <span class="va">visit_end_date_time</span></span>
<span> , .by <span class="op">=</span> <span class="st">"day"</span></span>
<span> , visits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="va">length_of_stay</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span> <span class="op">)</span> <span class="op"><a href="../reference/pipe.html">%>%</a></span></span>
<span> <span class="fu"><a href="https://rdrr.io/pkg/timetk/man/filter_by_time.html" class="external-link">filter_by_time</a></span><span class="op">(</span></span>
<span> .date_var <span class="op">=</span> <span class="va">visit_end_date_time</span></span>
<span> , .start_date <span class="op">=</span> <span class="st">"2012"</span></span>
<span> , .end_date <span class="op">=</span> <span class="st">"2019"</span></span>
<span> <span class="op">)</span> <span class="op"><a href="../reference/pipe.html">%>%</a></span></span>
<span> <span class="fu"><a href="https://rlang.r-lib.org/reference/set_names.html" class="external-link">set_names</a></span><span class="op">(</span><span class="st">"Date"</span>,<span class="st">"Values"</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="plot-the-time-series">Plot the Time Series<a class="anchor" aria-label="anchor" href="#plot-the-time-series"></a>
</h2>
<p>Now that we have our data lets see how easy it is to generate an ALOS
chart:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/ts_alos_plt.html">ts_alos_plt</a></span><span class="op">(</span></span>
<span> .data <span class="op">=</span> <span class="va">df_tbl</span></span>
<span> , .date_col <span class="op">=</span> <span class="va">Date</span></span>
<span> , .value_col <span class="op">=</span> <span class="va">Values</span></span>
<span> , .by <span class="op">=</span> <span class="st">"month"</span></span>
<span> , .interactive <span class="op">=</span> <span class="cn">FALSE</span></span>
<span><span class="op">)</span></span></code></pre></div>
<p><img src="getting-started_files/figure-html/alos_plot-1.png" width="95%" style="display: block; margin: auto;"></p>
<p>And with the <code>.interactive</code> option set to
<strong>TRUE</strong>:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/ts_alos_plt.html">ts_alos_plt</a></span><span class="op">(</span></span>
<span> .data <span class="op">=</span> <span class="va">df_tbl</span></span>
<span> , .date_col <span class="op">=</span> <span class="va">Date</span></span>
<span> , .value_col <span class="op">=</span> <span class="va">Values</span></span>
<span> , .by <span class="op">=</span> <span class="st">"month"</span></span>
<span> , .interactive <span class="op">=</span> <span class="cn">TRUE</span></span>
<span><span class="op">)</span></span></code></pre></div>
<div class="plotly html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-c94df8b1b1a47b28be1f" style="width:95%;height:450px;"></div>
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(y) ","x"],"51647d031164":["function (y) ","x"]},"highlight":{"on":"plotly_click","persistent":false,"dynamic":false,"selectize":false,"opacityDim":0.2,"selected":{"opacity":1},"debounce":0},"shinyEvents":["plotly_hover","plotly_click","plotly_selected","plotly_relayout","plotly_brushed","plotly_brushing","plotly_clickannotation","plotly_doubleclick","plotly_deselect","plotly_afterplot","plotly_sunburstclick"],"base_url":"https://plot.ly"},"evals":[],"jsHooks":[]}</script><p>As we can see, this function has the ability to return either a
static plot or and interactive plot. Under the hood it is using the
<code><a href="https://rdrr.io/pkg/timetk/man/plot_time_series.html" class="external-link">timetk::plot_time_series</a></code> function. You can find out more on
the the timetk function <a href="https://business-science.github.io/timetk/reference/plot_time_series.html" class="external-link">here.</a></p>
<p>That is the end of this first and very quick tutorial on the
<code>ts_alos_plt</code> function.</p>
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