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<title>Retrieve Flu Season Data from the United States Centers for Disease Control
and Prevention ('CDC') 'FluView' Portal • cdcfluview</title>
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a portal &lt;http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html&gt; for
accessing state, regional and national influenza statistics as well as
mortality surveillance data. The web interface makes it difficult and
time-consuming to select and retrieve influenza data. Tools are provided
to access the data provided by the portal's underlying 'API'.">
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.0</span>
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<div id="i-m-p-o-r-t-a-n-t" class="section level1">
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<a href="#i-m-p-o-r-t-a-n-t" class="anchor"></a>I M P O R T A N T</h1></div>
<p>The CDC migrated to a new non-Flash portal and back-end APIs changed. This is a complete reimagining of the package and — as such — all your code is going to break…eventually. Older functions have been deprecated with warnings and will be removed at some point.</p>
<p>All folks providing feedback, code or suggestions will be added to the DESCRIPTION file. Please include how you would prefer to be cited in any issues you file.</p>
<p>If there’s a particular data set from <a href="https://www.cdc.gov/flu/weekly/fluviewinteractive.htm" class="uri">https://www.cdc.gov/flu/weekly/fluviewinteractive.htm</a> that you want and that isn’t in the package, please file it as an issue and be as specific as you can (screen shot if possible).</p>
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<div id="mask-cdcfluview" class="section level1">
<h1 class="hasAnchor">
<a href="#mask-cdcfluview" class="anchor"></a>:mask: cdcfluview</h1>
<p>Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention (‘CDC’) ‘FluView’ Portal</p>
<div id="description" class="section level2">
<h2 class="hasAnchor">
<a href="#description" class="anchor"></a>Description</h2>
<p>The U.S. Centers for Disease Control (CDC) maintains a portal <a href="http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html" class="uri">http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html</a> for accessing state, regional and national influenza statistics as well as Mortality Surveillance Data. The Flash interface makes it difficult and time-consuming to select and retrieve influenza data. This package provides functions to access the data provided by the portal’s underlying API.</p>
</div>
<div id="whats-inside-the-tin" class="section level2">
<h2 class="hasAnchor">
<a href="#whats-inside-the-tin" class="anchor"></a>What’s Inside The Tin</h2>
<p>The following functions are implemented:</p>
<ul>
<li>
<code>age_group_distribution</code>: Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories</li>
<li>
<code>cdc_basemap</code>: Retrieve CDC U.S. Basemaps</li>
<li>
<code>geographic_spread</code>: State and Territorial Epidemiologists Reports of Geographic Spread of Influenza</li>
<li>
<code>get_weekly_flu_report</code>: Retrieves (high-level) weekly (XML) influenza surveillance report from the CDC</li>
<li>
<code>hospitalizations</code>: Laboratory-Confirmed Influenza Hospitalizations</li>
<li>
<code>ilinet</code>: Retrieve ILINet Surveillance Data</li>
<li>
<code>ili_weekly_activity_indicators</code>: Retrieve weekly state-level ILI indicators per-state for a given season</li>
<li>
<code>pi_mortality</code>: Pneumonia and Influenza Mortality Surveillance</li>
<li>
<code>state_data_providers</code>: Retrieve metadata about U.S. State CDC Provider Data</li>
<li>
<code>surveillance_areas</code>: Retrieve a list of valid sub-regions for each surveillance area.</li>
<li>
<code>who_nrevss</code>: Retrieve WHO/NREVSS Surveillance Data</li>
</ul>
<p>MMWR ID Utilities:</p>
<ul>
<li>
<code>mmwrid_map</code>: MMWR ID to Calendar Mappings</li>
<li>
<code>mmwr_week</code>: Convert a Date to an MMWR day+week+year</li>
<li>
<code>mmwr_weekday</code>: Convert a Date to an MMWR weekday</li>
<li>
<code>mmwr_week_to_date</code>: Convert an MMWR year+week or year+week+day to a Date object</li>
</ul>
<p>Deprecated functions:</p>
<ul>
<li>
<code>get_flu_data</code>: Retrieves state, regional or national influenza statistics from the CDC (deprecated)</li>
<li>
<code>get_hosp_data</code>: Retrieves influenza hospitalization statistics from the CDC (deprecated)</li>
<li>
<code>get_state_data</code>: Retrieves state/territory-level influenza statistics from the CDC (deprecated)</li>
</ul>
<p>The following data sets are included:</p>
<ul>
<li>
<code>hhs_regions</code>: HHS Region Table (a data frame with 59 rows and 4 variables)</li>
<li>
<code>census_regions</code>: Census Region Table (a data frame with 51 rows and 2 variables)</li>
<li>
<code>mmwrid_map</code>: MMWR ID to Calendar Mappings (it is exported &amp; available, no need to use <code><a href="https://www.rdocumentation.org/packages/utils/topics/data">data()</a></code>)</li>
</ul>
</div>
<div id="note" class="section level2">
<h2 class="hasAnchor">
<a href="#note" class="anchor"></a>NOTE</h2>
<p>All development happens in branches now with only critical fixes being back-ported to the master branch when necessary.</p>
</div>
<div id="installation" class="section level2">
<h2 class="hasAnchor">
<a href="#installation" class="anchor"></a>Installation</h2>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="co"># CRAN</span></a>
<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"cdcfluview"</span>)</a>
<a class="sourceLine" id="cb1-3" data-line-number="3"><span class="co"># master branch</span></a>
<a class="sourceLine" id="cb1-4" data-line-number="4">devtools<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/devtools/topics/reexports">install_git</a></span>(<span class="st">"https://sr.ht/~hrbrmstr/cdcfluview"</span>)</a>
<a class="sourceLine" id="cb1-5" data-line-number="5">devtools<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/devtools/topics/reexports">install_git</a></span>(<span class="st">"https://gitlab.com/hrbrmstr/cdcfluview"</span>)</a>
<a class="sourceLine" id="cb1-6" data-line-number="6">devtools<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/devtools/topics/reexports">install_github</a></span>(<span class="st">"hrbrmstr/cdcfluview"</span>)</a></code></pre></div>
</div>
<div id="usage" class="section level2">
<h2 class="hasAnchor">
<a href="#usage" class="anchor"></a>Usage</h2>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(cdcfluview)</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(hrbrthemes)</a>
<a class="sourceLine" id="cb2-3" data-line-number="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(tidyverse)</a>
<a class="sourceLine" id="cb2-4" data-line-number="4"></a>
<a class="sourceLine" id="cb2-5" data-line-number="5"><span class="co"># current verison</span></a>
<a class="sourceLine" id="cb2-6" data-line-number="6"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/packageDescription">packageVersion</a></span>(<span class="st">"cdcfluview"</span>)</a></code></pre></div>
<pre><code>## [1] '0.9.0'</code></pre>
<div id="age-group-distribution-of-influenza-positive-tests-reported-by-public-health-laboratories" class="section level3">
<h3 class="hasAnchor">
<a href="#age-group-distribution-of-influenza-positive-tests-reported-by-public-health-laboratories" class="anchor"></a>Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories</h3>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw">glimpse</span>(<span class="kw"><a href="reference/age_group_distribution.html">age_group_distribution</a></span>(<span class="dt">years=</span><span class="dv">2015</span>))</a></code></pre></div>
<pre><code>## Observations: 1,872
## Variables: 16
## $ sea_label &lt;chr&gt; "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "20…
## $ age_label &lt;fct&gt; 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4…
## $ vir_label &lt;fct&gt; A (Subtyping not Performed), A (Subtyping not Performed), A (Subtyping not Performed), A (S…
## $ count &lt;int&gt; 0, 1, 0, 1, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 2, 2, 3, 2, 2, 3, 3, 3, 0, 0, 2, 0, 1, 1, 0, 0…
## $ mmwrid &lt;int&gt; 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820, 2…
## $ seasonid &lt;int&gt; 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55,…
## $ publishyearweekid &lt;int&gt; 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2…
## $ sea_description &lt;chr&gt; "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "…
## $ sea_startweek &lt;int&gt; 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2…
## $ sea_endweek &lt;int&gt; 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2…
## $ vir_description &lt;chr&gt; "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "…
## $ vir_startmmwrid &lt;int&gt; 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1…
## $ vir_endmmwrid &lt;int&gt; 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3…
## $ wk_start &lt;date&gt; 2015-10-04, 2015-10-11, 2015-10-18, 2015-10-25, 2015-11-01, 2015-11-08, 2015-11-15, 2015-1…
## $ wk_end &lt;date&gt; 2015-10-10, 2015-10-17, 2015-10-24, 2015-10-31, 2015-11-07, 2015-11-14, 2015-11-21, 2015-1…
## $ year_wk_num &lt;int&gt; 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, …</code></pre>
</div>
<div id="retrieve-cdc-u-s--coverage-map" class="section level3">
<h3 class="hasAnchor">
<a href="#retrieve-cdc-u-s--coverage-map" class="anchor"></a>Retrieve CDC U.S. Coverage Map</h3>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(<span class="kw"><a href="reference/cdc_basemap.html">cdc_basemap</a></span>(<span class="st">"national"</span>))</a></code></pre></div>
<p><img src="index_files/figure-html/cdc-basemaps-1.png" width="700"></p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(<span class="kw"><a href="reference/cdc_basemap.html">cdc_basemap</a></span>(<span class="st">"hhs"</span>))</a></code></pre></div>
<p><img src="index_files/figure-html/cdc-basemaps-2.png" width="700"></p>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(<span class="kw"><a href="reference/cdc_basemap.html">cdc_basemap</a></span>(<span class="st">"census"</span>))</a></code></pre></div>
<p><img src="index_files/figure-html/cdc-basemaps-3.png" width="700"></p>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(<span class="kw"><a href="reference/cdc_basemap.html">cdc_basemap</a></span>(<span class="st">"states"</span>))</a></code></pre></div>
<p><img src="index_files/figure-html/cdc-basemaps-4.png" width="700"></p>
<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(<span class="kw"><a href="reference/cdc_basemap.html">cdc_basemap</a></span>(<span class="st">"spread"</span>))</a></code></pre></div>
<p><img src="index_files/figure-html/cdc-basemaps-5.png" width="700"></p>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(<span class="kw"><a href="reference/cdc_basemap.html">cdc_basemap</a></span>(<span class="st">"surv"</span>))</a></code></pre></div>
<p><img src="index_files/figure-html/cdc-basemaps-6.png" width="700"></p>
</div>
<div id="state-and-territorial-epidemiologists-reports-of-geographic-spread-of-influenza" class="section level3">
<h3 class="hasAnchor">
<a href="#state-and-territorial-epidemiologists-reports-of-geographic-spread-of-influenza" class="anchor"></a>State and Territorial Epidemiologists Reports of Geographic Spread of Influenza</h3>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw">glimpse</span>(<span class="kw"><a href="reference/geographic_spread.html">geographic_spread</a></span>())</a></code></pre></div>
<pre><code>## Observations: 28,151
## Variables: 7
## $ statename &lt;chr&gt; "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Al…
## $ url &lt;chr&gt; "http://adph.org/influenza/", "http://adph.org/influenza/", "http://adph.org/influenza/", "…
## $ website &lt;chr&gt; "Influenza Surveillance", "Influenza Surveillance", "Influenza Surveillance", "Influenza Su…
## $ activity_estimate &lt;chr&gt; "No Activity", "No Activity", "No Activity", "Local Activity", "Sporadic", "Sporadic", "Spo…
## $ weekend &lt;date&gt; 2003-10-04, 2003-10-11, 2003-10-18, 2003-10-25, 2003-11-01, 2003-11-08, 2003-11-15, 2003-1…
## $ season &lt;chr&gt; "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "20…
## $ weeknumber &lt;chr&gt; "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", "51", "52", "53", "1", "2…</code></pre>
</div>
<div id="laboratory-confirmed-influenza-hospitalizations" class="section level3">
<h3 class="hasAnchor">
<a href="#laboratory-confirmed-influenza-hospitalizations" class="anchor"></a>Laboratory-Confirmed Influenza Hospitalizations</h3>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1"><span class="kw"><a href="reference/surveillance_areas.html">surveillance_areas</a></span>()</a></code></pre></div>
<pre><code>## surveillance_area region
## 1 flusurv Entire Network
## 2 eip California
## 3 eip Colorado
## 4 eip Connecticut
## 5 eip Entire Network
## 6 eip Georgia
## 7 eip Maryland
## 8 eip Minnesota
## 9 eip New Mexico
## 10 eip New York - Albany
## 11 eip New York - Rochester
## 12 eip Oregon
## 13 eip Tennessee
## 14 ihsp Entire Network
## 15 ihsp Idaho
## 16 ihsp Iowa
## 17 ihsp Michigan
## 18 ihsp Ohio
## 19 ihsp Oklahoma
## 20 ihsp Rhode Island
## 21 ihsp South Dakota
## 22 ihsp Utah</code></pre>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1"><span class="kw">glimpse</span>(fs_nat &lt;-<span class="st"> </span><span class="kw"><a href="reference/hospitalizations.html">hospitalizations</a></span>(<span class="st">"flusurv"</span>))</a></code></pre></div>
<pre><code>## Observations: 1,746
## Variables: 14
## $ surveillance_area &lt;chr&gt; "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "…
## $ region &lt;chr&gt; "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network", "…
## $ year &lt;int&gt; 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2…
## $ season &lt;int&gt; 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49,…
## $ wk_start &lt;date&gt; 2009-08-30, 2009-09-06, 2009-09-13, 2009-09-20, 2009-09-27, 2009-10-04, 2009-10-11, 2009-1…
## $ wk_end &lt;date&gt; 2009-09-05, 2009-09-12, 2009-09-19, 2009-09-26, 2009-10-03, 2009-10-10, 2009-10-17, 2009-1…
## $ year_wk_num &lt;int&gt; 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 1, 2, 3, 4, 5, 6, 7…
## $ rate &lt;dbl&gt; 0.5, 2.5, 4.6, 6.7, 10.9, 18.1, 28.3, 39.1, 47.3, 53.3, 57.5, 60.1, 61.6, 62.9, 64.1, 65.1,…
## $ weeklyrate &lt;dbl&gt; 0.5, 2.0, 2.0, 2.1, 4.3, 7.2, 10.2, 10.8, 8.2, 6.0, 4.2, 2.6, 1.5, 1.3, 1.3, 1.0, 1.2, 1.1,…
## $ age &lt;int&gt; 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1…
## $ age_label &lt;fct&gt; 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4…
## $ sea_label &lt;chr&gt; "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "20…
## $ sea_description &lt;chr&gt; "Season 2009-10", "Season 2009-10", "Season 2009-10", "Season 2009-10", "Season 2009-10", "…
## $ mmwrid &lt;int&gt; 2488, 2489, 2490, 2491, 2492, 2493, 2494, 2495, 2496, 2497, 2498, 2499, 2500, 2501, 2502, 2…</code></pre>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1"><span class="kw">ggplot</span>(fs_nat, <span class="kw">aes</span>(wk_end, rate)) <span class="op">+</span><span class="st"> </span></a>
<a class="sourceLine" id="cb18-2" data-line-number="2"><span class="st"> </span><span class="kw">geom_line</span>(<span class="kw">aes</span>(<span class="dt">color=</span>age_label, <span class="dt">group=</span>age_label)) <span class="op">+</span></a>
<a class="sourceLine" id="cb18-3" data-line-number="3"><span class="st"> </span><span class="kw">facet_wrap</span>(<span class="op">~</span>sea_description, <span class="dt">scales=</span><span class="st">"free_x"</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb18-4" data-line-number="4"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/hrbrthemes/topics/scale_ipsum">scale_color_ipsum</a></span>(<span class="dt">name=</span><span class="ot">NULL</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb18-5" data-line-number="5"><span class="st"> </span><span class="kw">labs</span>(<span class="dt">x=</span><span class="ot">NULL</span>, <span class="dt">y=</span><span class="st">"Rates per 100,000 population"</span>,</a>
<a class="sourceLine" id="cb18-6" data-line-number="6"> <span class="dt">title=</span><span class="st">"FluSurv-NET :: Entire Network :: All Seasons :: Cumulative Rate"</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb18-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/hrbrthemes/topics/theme_ipsum_rc">theme_ipsum_rc</a></span>()</a></code></pre></div>
<p><img src="index_files/figure-html/surveillance-areas-1.png" width="960"></p>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1"><span class="kw">glimpse</span>(<span class="kw"><a href="reference/hospitalizations.html">hospitalizations</a></span>(<span class="st">"eip"</span>, <span class="dt">years=</span><span class="dv">2015</span>))</a></code></pre></div>
<pre><code>## Observations: 180
## Variables: 14
## $ surveillance_area &lt;chr&gt; "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", …
## $ region &lt;chr&gt; "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network", "…
## $ year &lt;int&gt; 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2016, 2016, 2…
## $ season &lt;int&gt; 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55,…
## $ wk_start &lt;date&gt; 2015-10-04, 2015-10-11, 2015-10-18, 2015-10-25, 2015-11-01, 2015-11-08, 2015-11-15, 2015-1…
## $ wk_end &lt;date&gt; 2015-10-10, 2015-10-17, 2015-10-24, 2015-10-31, 2015-11-07, 2015-11-14, 2015-11-21, 2015-1…
## $ year_wk_num &lt;int&gt; 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, …
## $ rate &lt;dbl&gt; 0.1, 0.3, 0.4, 0.5, 0.8, 0.8, 1.1, 1.4, 1.6, 1.7, 1.8, 2.1, 2.4, 2.9, 3.2, 3.5, 4.1, 5.3, 6…
## $ weeklyrate &lt;dbl&gt; 0.1, 0.3, 0.1, 0.1, 0.3, 0.0, 0.3, 0.3, 0.2, 0.1, 0.1, 0.3, 0.3, 0.5, 0.3, 0.3, 0.6, 1.2, 1…
## $ age &lt;int&gt; 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2…
## $ age_label &lt;fct&gt; 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4…
## $ sea_label &lt;chr&gt; "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "20…
## $ sea_description &lt;chr&gt; "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "…
## $ mmwrid &lt;int&gt; 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820, 2…</code></pre>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw">glimpse</span>(<span class="kw"><a href="reference/hospitalizations.html">hospitalizations</a></span>(<span class="st">"eip"</span>, <span class="st">"Colorado"</span>, <span class="dt">years=</span><span class="dv">2015</span>))</a></code></pre></div>
<pre><code>## Observations: 180
## Variables: 14
## $ surveillance_area &lt;chr&gt; "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", …
## $ region &lt;chr&gt; "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colora…
## $ year &lt;int&gt; 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2016, 2016, 2…
## $ season &lt;int&gt; 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55,…
## $ wk_start &lt;date&gt; 2015-10-04, 2015-10-11, 2015-10-18, 2015-10-25, 2015-11-01, 2015-11-08, 2015-11-15, 2015-1…
## $ wk_end &lt;date&gt; 2015-10-10, 2015-10-17, 2015-10-24, 2015-10-31, 2015-11-07, 2015-11-14, 2015-11-21, 2015-1…
## $ year_wk_num &lt;int&gt; 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, …
## $ rate &lt;dbl&gt; 0.0, 0.0, 0.6, 0.6, 0.6, 0.6, 1.2, 1.7, 1.7, 1.7, 1.7, 1.7, 2.9, 3.5, 3.5, 3.5, 4.1, 6.4, 8…
## $ weeklyrate &lt;dbl&gt; 0.0, 0.0, 0.6, 0.0, 0.0, 0.0, 0.6, 0.6, 0.0, 0.0, 0.0, 0.0, 1.2, 0.6, 0.0, 0.0, 0.6, 2.3, 2…
## $ age &lt;int&gt; 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2…
## $ age_label &lt;fct&gt; 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4…
## $ sea_label &lt;chr&gt; "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "20…
## $ sea_description &lt;chr&gt; "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "…
## $ mmwrid &lt;int&gt; 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820, 2…</code></pre>
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="1"><span class="kw">glimpse</span>(<span class="kw"><a href="reference/hospitalizations.html">hospitalizations</a></span>(<span class="st">"ihsp"</span>, <span class="dt">years=</span><span class="dv">2015</span>))</a></code></pre></div>
<pre><code>## Observations: 180
## Variables: 14
## $ surveillance_area &lt;chr&gt; "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IH…
## $ region &lt;chr&gt; "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network", "…
## $ year &lt;int&gt; 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2016, 2016, 2…
## $ season &lt;int&gt; 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55,…
## $ wk_start &lt;date&gt; 2015-10-04, 2015-10-11, 2015-10-18, 2015-10-25, 2015-11-01, 2015-11-08, 2015-11-15, 2015-1…
## $ wk_end &lt;date&gt; 2015-10-10, 2015-10-17, 2015-10-24, 2015-10-31, 2015-11-07, 2015-11-14, 2015-11-21, 2015-1…
## $ year_wk_num &lt;int&gt; 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, …
## $ rate &lt;dbl&gt; 0.0, 0.0, 0.4, 0.4, 0.4, 1.1, 1.1, 1.1, 1.1, 1.5, 1.8, 2.2, 2.2, 2.6, 2.6, 2.6, 2.9, 4.0, 5…
## $ weeklyrate &lt;dbl&gt; 0.0, 0.0, 0.4, 0.0, 0.0, 0.7, 0.0, 0.0, 0.0, 0.4, 0.4, 0.4, 0.0, 0.4, 0.0, 0.0, 0.4, 1.1, 1…
## $ age &lt;int&gt; 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2…
## $ age_label &lt;fct&gt; 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4…
## $ sea_label &lt;chr&gt; "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "20…
## $ sea_description &lt;chr&gt; "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "…
## $ mmwrid &lt;int&gt; 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820, 2…</code></pre>
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1"><span class="kw">glimpse</span>(<span class="kw"><a href="reference/hospitalizations.html">hospitalizations</a></span>(<span class="st">"ihsp"</span>, <span class="st">"Oklahoma"</span>, <span class="dt">years=</span><span class="dv">2015</span>))</a></code></pre></div>
<pre><code>## Observations: 180
## Variables: 14
## $ surveillance_area &lt;chr&gt; "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IH…
## $ region &lt;chr&gt; "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklaho…
## $ year &lt;int&gt; 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 2011, 2…
## $ season &lt;int&gt; 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50,…
## $ wk_start &lt;date&gt; 2010-10-03, 2010-10-10, 2010-10-17, 2010-10-24, 2010-10-31, 2010-11-07, 2010-11-14, 2010-1…
## $ wk_end &lt;date&gt; 2010-10-09, 2010-10-16, 2010-10-23, 2010-10-30, 2010-11-06, 2010-11-13, 2010-11-20, 2010-1…
## $ year_wk_num &lt;int&gt; 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, …
## $ rate &lt;dbl&gt; 0.0, 0.0, 1.2, 1.2, 1.2, 1.2, 1.2, 1.2, 1.2, 2.4, 2.4, 6.1, 14.6, 17.0, 32.8, 49.9, 76.6, 9…
## $ weeklyrate &lt;dbl&gt; 0.0, 0.0, 1.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.2, 0.0, 3.6, 8.5, 2.4, 15.8, 17.0, 26.8, 21.…
## $ age &lt;int&gt; 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2…
## $ age_label &lt;fct&gt; 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4 yr, 0-4…
## $ sea_label &lt;chr&gt; "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "20…
## $ sea_description &lt;chr&gt; "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "…
## $ mmwrid &lt;int&gt; 2545, 2546, 2547, 2548, 2549, 2550, 2551, 2552, 2553, 2554, 2555, 2556, 2557, 2558, 2559, 2…</code></pre>
</div>
<div id="retrieve-ilinet-surveillance-data" class="section level3">
<h3 class="hasAnchor">
<a href="#retrieve-ilinet-surveillance-data" class="anchor"></a>Retrieve ILINet Surveillance Data</h3>
<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1"><span class="kw">walk</span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"national"</span>, <span class="st">"hhs"</span>, <span class="st">"census"</span>, <span class="st">"state"</span>), <span class="op">~</span>{</a>
<a class="sourceLine" id="cb27-2" data-line-number="2"> </a>
<a class="sourceLine" id="cb27-3" data-line-number="3"> ili_df &lt;-<span class="st"> </span><span class="kw"><a href="reference/ilinet.html">ilinet</a></span>(<span class="dt">region =</span> .x)</a>
<a class="sourceLine" id="cb27-4" data-line-number="4"> </a>
<a class="sourceLine" id="cb27-5" data-line-number="5"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(<span class="kw">glimpse</span>(ili_df))</a>
<a class="sourceLine" id="cb27-6" data-line-number="6"> </a>
<a class="sourceLine" id="cb27-7" data-line-number="7"> <span class="kw">ggplot</span>(ili_df, <span class="kw">aes</span>(week_start, unweighted_ili, <span class="dt">group=</span>region, <span class="dt">color=</span>region)) <span class="op">+</span></a>
<a class="sourceLine" id="cb27-8" data-line-number="8"><span class="st"> </span><span class="kw">geom_line</span>() <span class="op">+</span></a>
<a class="sourceLine" id="cb27-9" data-line-number="9"><span class="st"> </span>viridis<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/viridis/topics/scale_viridis">scale_color_viridis</a></span>(<span class="dt">discrete=</span><span class="ot">TRUE</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb27-10" data-line-number="10"><span class="st"> </span><span class="kw">labs</span>(<span class="dt">x=</span><span class="ot">NULL</span>, <span class="dt">y=</span><span class="st">"Unweighted ILI"</span>, <span class="dt">title=</span>ili_df<span class="op">$</span>region_type[<span class="dv">1</span>]) <span class="op">+</span></a>
<a class="sourceLine" id="cb27-11" data-line-number="11"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/hrbrthemes/topics/theme_ipsum_rc">theme_ipsum_rc</a></span>(<span class="dt">grid=</span><span class="st">"XY"</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb27-12" data-line-number="12"><span class="st"> </span><span class="kw">theme</span>(<span class="dt">legend.position =</span> <span class="st">"none"</span>) -&gt;<span class="st"> </span>gg</a>
<a class="sourceLine" id="cb27-13" data-line-number="13"> </a>
<a class="sourceLine" id="cb27-14" data-line-number="14"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(gg)</a>
<a class="sourceLine" id="cb27-15" data-line-number="15"> </a>
<a class="sourceLine" id="cb27-16" data-line-number="16">})</a></code></pre></div>
<pre><code>## Observations: 1,111
## Variables: 16
## $ region_type &lt;chr&gt; "National", "National", "National", "National", "National", "National", "National", "Nationa…
## $ region &lt;chr&gt; "National", "National", "National", "National", "National", "National", "National", "Nationa…
## $ year &lt;int&gt; 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1998, 19…
## $ week &lt;int&gt; 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 1…
## $ weighted_ili &lt;dbl&gt; 1.101480, 1.200070, 1.378760, 1.199200, 1.656180, 1.413260, 1.986800, 2.447490, 1.739010, 1.…
## $ unweighted_ili &lt;dbl&gt; 1.216860, 1.280640, 1.239060, 1.144730, 1.261120, 1.282750, 1.445790, 1.647960, 1.675170, 1.…
## $ age_0_4 &lt;dbl&gt; 179, 199, 228, 188, 217, 178, 294, 288, 268, 299, 346, 348, 510, 579, 639, 690, 856, 824, 88…
## $ age_25_49 &lt;dbl&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ age_25_64 &lt;dbl&gt; 157, 151, 153, 193, 162, 148, 240, 293, 206, 282, 268, 235, 404, 584, 759, 654, 679, 817, 76…
## $ age_5_24 &lt;dbl&gt; 205, 242, 266, 236, 280, 281, 328, 456, 343, 415, 388, 362, 492, 576, 810, 1121, 1440, 1600,…
## $ age_50_64 &lt;dbl&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ age_65 &lt;dbl&gt; 29, 23, 34, 36, 41, 48, 70, 63, 69, 102, 81, 59, 113, 207, 207, 148, 151, 196, 233, 146, 119…
## $ ilitotal &lt;dbl&gt; 570, 615, 681, 653, 700, 655, 932, 1100, 886, 1098, 1083, 1004, 1519, 1946, 2415, 2613, 3126…
## $ num_of_providers &lt;dbl&gt; 192, 191, 219, 213, 213, 195, 248, 256, 252, 253, 242, 190, 251, 250, 254, 255, 245, 245, 23…
## $ total_patients &lt;dbl&gt; 46842, 48023, 54961, 57044, 55506, 51062, 64463, 66749, 52890, 67887, 61314, 47719, 48429, 5…
## $ week_start &lt;date&gt; 1997-09-28, 1997-10-05, 1997-10-12, 1997-10-19, 1997-10-26, 1997-11-02, 1997-11-09, 1997-11…
## # A tibble: 1,111 x 16
## region_type region year week weighted_ili unweighted_ili age_0_4 age_25_49 age_25_64 age_5_24 age_50_64 age_65
## &lt;chr&gt; &lt;chr&gt; &lt;int&gt; &lt;int&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;
## 1 National Natio… 1997 40 1.10 1.22 179 NA 157 205 NA 29
## 2 National Natio… 1997 41 1.20 1.28 199 NA 151 242 NA 23
## 3 National Natio… 1997 42 1.38 1.24 228 NA 153 266 NA 34
## 4 National Natio… 1997 43 1.20 1.14 188 NA 193 236 NA 36
## 5 National Natio… 1997 44 1.66 1.26 217 NA 162 280 NA 41
## 6 National Natio… 1997 45 1.41 1.28 178 NA 148 281 NA 48
## 7 National Natio… 1997 46 1.99 1.45 294 NA 240 328 NA 70
## 8 National Natio… 1997 47 2.45 1.65 288 NA 293 456 NA 63
## 9 National Natio… 1997 48 1.74 1.68 268 NA 206 343 NA 69
## 10 National Natio… 1997 49 1.94 1.62 299 NA 282 415 NA 102
## # … with 1,101 more rows, and 4 more variables: ilitotal &lt;dbl&gt;, num_of_providers &lt;dbl&gt;, total_patients &lt;dbl&gt;,
## # week_start &lt;date&gt;</code></pre>
<p><img src="index_files/figure-html/ili-df-1.png" width="700"></p>
<pre><code>## Observations: 11,110
## Variables: 16
## $ region_type &lt;chr&gt; "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "H…
## $ region &lt;fct&gt; Region 1, Region 2, Region 3, Region 4, Region 5, Region 6, Region 7, Region 8, Region 9, Re…
## $ year &lt;int&gt; 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 19…
## $ week &lt;int&gt; 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 42, 42, 42, …
## $ weighted_ili &lt;dbl&gt; 0.498535, 0.374963, 1.354280, 0.400338, 1.229260, 1.018980, 0.871791, 0.516017, 1.807610, 4.…
## $ unweighted_ili &lt;dbl&gt; 0.623848, 0.384615, 1.341720, 0.450010, 0.901266, 0.747384, 1.152860, 0.422654, 2.258780, 4.…
## $ age_0_4 &lt;dbl&gt; 15, 0, 6, 12, 31, 2, 0, 2, 80, 31, 14, 0, 4, 21, 36, 2, 0, 0, 103, 19, 35, 0, 3, 19, 66, 2, …
## $ age_25_49 &lt;dbl&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ age_25_64 &lt;dbl&gt; 7, 3, 7, 23, 24, 1, 4, 0, 76, 12, 14, 2, 19, 7, 23, 2, 0, 1, 76, 7, 15, 0, 17, 15, 29, 2, 3,…
## $ age_5_24 &lt;dbl&gt; 22, 0, 15, 11, 30, 2, 18, 3, 74, 30, 29, 0, 16, 14, 41, 2, 13, 8, 84, 35, 35, 0, 24, 18, 75,…
## $ age_50_64 &lt;dbl&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ age_65 &lt;dbl&gt; 0, 0, 4, 0, 4, 0, 5, 0, 13, 3, 0, 0, 3, 2, 4, 0, 2, 0, 11, 1, 0, 1, 2, 2, 16, 0, 2, 0, 9, 2,…
## $ ilitotal &lt;dbl&gt; 44, 3, 32, 46, 89, 5, 27, 5, 243, 76, 57, 2, 42, 44, 104, 6, 15, 9, 274, 62, 85, 1, 46, 54, …
## $ num_of_providers &lt;dbl&gt; 32, 7, 16, 29, 49, 4, 14, 5, 23, 13, 29, 7, 17, 31, 48, 4, 14, 6, 23, 12, 40, 7, 15, 33, 64,…
## $ total_patients &lt;dbl&gt; 7053, 780, 2385, 10222, 9875, 669, 2342, 1183, 10758, 1575, 6987, 872, 2740, 11310, 9618, 68…
## $ week_start &lt;date&gt; 1997-09-28, 1997-09-28, 1997-09-28, 1997-09-28, 1997-09-28, 1997-09-28, 1997-09-28, 1997-09…
## # A tibble: 11,110 x 16
## region_type region year week weighted_ili unweighted_ili age_0_4 age_25_49 age_25_64 age_5_24 age_50_64 age_65
## &lt;chr&gt; &lt;fct&gt; &lt;int&gt; &lt;int&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;
## 1 HHS Regions Regio… 1997 40 0.499 0.624 15 NA 7 22 NA 0
## 2 HHS Regions Regio… 1997 40 0.375 0.385 0 NA 3 0 NA 0
## 3 HHS Regions Regio… 1997 40 1.35 1.34 6 NA 7 15 NA 4
## 4 HHS Regions Regio… 1997 40 0.400 0.450 12 NA 23 11 NA 0
## 5 HHS Regions Regio… 1997 40 1.23 0.901 31 NA 24 30 NA 4
## 6 HHS Regions Regio… 1997 40 1.02 0.747 2 NA 1 2 NA 0
## 7 HHS Regions Regio… 1997 40 0.872 1.15 0 NA 4 18 NA 5
## 8 HHS Regions Regio… 1997 40 0.516 0.423 2 NA 0 3 NA 0
## 9 HHS Regions Regio… 1997 40 1.81 2.26 80 NA 76 74 NA 13
## 10 HHS Regions Regio… 1997 40 4.74 4.83 31 NA 12 30 NA 3
## # … with 11,100 more rows, and 4 more variables: ilitotal &lt;dbl&gt;, num_of_providers &lt;dbl&gt;, total_patients &lt;dbl&gt;,
## # week_start &lt;date&gt;</code></pre>
<p><img src="index_files/figure-html/ili-df-2.png" width="700"></p>
<pre><code>## Observations: 9,999
## Variables: 16
## $ region_type &lt;chr&gt; "Census Regions", "Census Regions", "Census Regions", "Census Regions", "Census Regions", "C…
## $ region &lt;chr&gt; "New England", "Mid-Atlantic", "East North Central", "West North Central", "South Atlantic",…
## $ year &lt;int&gt; 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 19…
## $ week &lt;int&gt; 40, 40, 40, 40, 40, 40, 40, 40, 40, 41, 41, 41, 41, 41, 41, 41, 41, 41, 42, 42, 42, 42, 42, …
## $ weighted_ili &lt;dbl&gt; 0.4985350, 0.8441440, 0.7924860, 1.7640500, 0.5026620, 0.0542283, 1.0189800, 2.2587800, 2.04…
## $ unweighted_ili &lt;dbl&gt; 0.6238480, 1.3213800, 0.8187380, 1.2793900, 0.7233800, 0.0688705, 0.7473840, 2.2763300, 3.23…
## $ age_0_4 &lt;dbl&gt; 15, 4, 28, 3, 14, 0, 2, 87, 26, 14, 4, 36, 0, 21, 0, 2, 93, 29, 35, 3, 65, 1, 19, 0, 2, 84, …
## $ age_25_49 &lt;dbl&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ age_25_64 &lt;dbl&gt; 7, 8, 20, 8, 22, 3, 1, 71, 17, 14, 13, 23, 1, 14, 1, 2, 72, 11, 15, 11, 27, 5, 21, 0, 2, 55,…
## $ age_5_24 &lt;dbl&gt; 22, 12, 28, 20, 14, 0, 2, 71, 36, 29, 8, 39, 18, 22, 0, 2, 80, 44, 35, 16, 74, 9, 24, 2, 2, …
## $ age_50_64 &lt;dbl&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ age_65 &lt;dbl&gt; 0, 4, 3, 6, 0, 0, 0, 15, 1, 0, 2, 2, 4, 3, 0, 0, 10, 2, 0, 3, 12, 6, 2, 0, 0, 9, 2, 0, 1, 14…
## $ ilitotal &lt;dbl&gt; 44, 28, 79, 37, 50, 3, 5, 244, 80, 57, 27, 100, 23, 60, 1, 6, 255, 86, 85, 33, 178, 21, 66, …
## $ num_of_providers &lt;dbl&gt; 32, 13, 47, 17, 30, 9, 4, 16, 24, 29, 13, 46, 17, 32, 10, 4, 17, 23, 40, 12, 62, 16, 33, 10,…
## $ total_patients &lt;dbl&gt; 7053, 2119, 9649, 2892, 6912, 4356, 669, 10719, 2473, 6987, 2384, 9427, 2823, 7591, 4947, 68…
## $ week_start &lt;date&gt; 1997-09-28, 1997-09-28, 1997-09-28, 1997-09-28, 1997-09-28, 1997-09-28, 1997-09-28, 1997-09…
## # A tibble: 9,999 x 16
## region_type region year week weighted_ili unweighted_ili age_0_4 age_25_49 age_25_64 age_5_24 age_50_64 age_65
## &lt;chr&gt; &lt;chr&gt; &lt;int&gt; &lt;int&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;
## 1 Census Reg… New E… 1997 40 0.499 0.624 15 NA 7 22 NA 0
## 2 Census Reg… Mid-A… 1997 40 0.844 1.32 4 NA 8 12 NA 4
## 3 Census Reg… East … 1997 40 0.792 0.819 28 NA 20 28 NA 3
## 4 Census Reg… West … 1997 40 1.76 1.28 3 NA 8 20 NA 6
## 5 Census Reg… South… 1997 40 0.503 0.723 14 NA 22 14 NA 0
## 6 Census Reg… East … 1997 40 0.0542 0.0689 0 NA 3 0 NA 0
## 7 Census Reg… West … 1997 40 1.02 0.747 2 NA 1 2 NA 0
## 8 Census Reg… Mount… 1997 40 2.26 2.28 87 NA 71 71 NA 15
## 9 Census Reg… Pacif… 1997 40 2.05 3.23 26 NA 17 36 NA 1
## 10 Census Reg… New E… 1997 41 0.643 0.816 14 NA 14 29 NA 0
## # … with 9,989 more rows, and 4 more variables: ilitotal &lt;dbl&gt;, num_of_providers &lt;dbl&gt;, total_patients &lt;dbl&gt;,
## # week_start &lt;date&gt;</code></pre>
<p><img src="index_files/figure-html/ili-df-3.png" width="700"></p>
<pre><code>## Observations: 23,120
## Variables: 16
## $ region_type &lt;chr&gt; "States", "States", "States", "States", "States", "States", "States", "States", "States", "S…
## $ region &lt;chr&gt; "Alabama", "Alaska", "Arizona", "Arkansas", "California", "Colorado", "Connecticut", "Delawa…
## $ year &lt;int&gt; 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 20…
## $ week &lt;int&gt; 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, …
## $ weighted_ili &lt;dbl&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ unweighted_ili &lt;dbl&gt; 2.1347700, 0.8751460, 0.6747210, 0.6960560, 1.9541200, 0.6606840, 0.0783085, 0.1001250, 2.80…
## $ age_0_4 &lt;dbl&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ age_25_49 &lt;dbl&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ age_25_64 &lt;dbl&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ age_5_24 &lt;dbl&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ age_50_64 &lt;dbl&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ age_65 &lt;dbl&gt; NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, …
## $ ilitotal &lt;dbl&gt; 249, 15, 172, 18, 632, 134, 3, 4, 73, NA, 647, 20, 19, 505, 65, 10, 39, 19, 391, 22, 117, 16…
## $ num_of_providers &lt;dbl&gt; 35, 7, 49, 15, 112, 14, 12, 13, 4, NA, 62, 18, 12, 74, 44, 6, 40, 14, 41, 30, 17, 56, 47, 17…
## $ total_patients &lt;dbl&gt; 11664, 1714, 25492, 2586, 32342, 20282, 3831, 3995, 2599, NA, 40314, 1943, 4579, 39390, 1252…
## $ week_start &lt;date&gt; 2010-10-03, 2010-10-03, 2010-10-03, 2010-10-03, 2010-10-03, 2010-10-03, 2010-10-03, 2010-10…
## # A tibble: 23,120 x 16
## region_type region year week weighted_ili unweighted_ili age_0_4 age_25_49 age_25_64 age_5_24 age_50_64 age_65
## &lt;chr&gt; &lt;chr&gt; &lt;int&gt; &lt;int&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;
## 1 States Alaba… 2010 40 NA 2.13 NA NA NA NA NA NA
## 2 States Alaska 2010 40 NA 0.875 NA NA NA NA NA NA
## 3 States Arizo… 2010 40 NA 0.675 NA NA NA NA NA NA
## 4 States Arkan… 2010 40 NA 0.696 NA NA NA NA NA NA
## 5 States Calif… 2010 40 NA 1.95 NA NA NA NA NA NA
## 6 States Color… 2010 40 NA 0.661 NA NA NA NA NA NA
## 7 States Conne… 2010 40 NA 0.0783 NA NA NA NA NA NA
## 8 States Delaw… 2010 40 NA 0.100 NA NA NA NA NA NA
## 9 States Distr… 2010 40 NA 2.81 NA NA NA NA NA NA
## 10 States Flori… 2010 40 NA NA NA NA NA NA NA NA
## # … with 23,110 more rows, and 4 more variables: ilitotal &lt;dbl&gt;, num_of_providers &lt;dbl&gt;, total_patients &lt;dbl&gt;,
## # week_start &lt;date&gt;</code></pre>
<p><img src="index_files/figure-html/ili-df-4.png" width="700"></p>
</div>
<div id="retrieve-weekly-state-level-ili-indicators-per-state-for-a-given-season" class="section level3">
<h3 class="hasAnchor">
<a href="#retrieve-weekly-state-level-ili-indicators-per-state-for-a-given-season" class="anchor"></a>Retrieve weekly state-level ILI indicators per-state for a given season</h3>
<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" data-line-number="1"><span class="kw"><a href="reference/ili_weekly_activity_indicators.html">ili_weekly_activity_indicators</a></span>(<span class="dv">2017</span>)</a></code></pre></div>
<pre><code>## # A tibble: 2,805 x 8
## statename url website activity_level activity_level_l… weekend season weeknumber
## * &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; &lt;date&gt; &lt;chr&gt; &lt;dbl&gt;
## 1 Alabama http://adph.org/influenza/ Influenza Sur… 2 Minimal 2017-10-07 2017-… 40
## 2 Alaska "http://dhss.alaska.gov/dp… Influenza Sur… 1 Minimal 2017-10-07 2017-… 40
## 3 Arizona http://www.azdhs.gov/phs/o… Influenza &amp; R… 2 Minimal 2017-10-07 2017-… 40
## 4 Arkansas http://www.healthy.arkansa… Communicable … 1 Minimal 2017-10-07 2017-… 40
## 5 California https://www.cdph.ca.gov/Pr… Influenza (Fl… 2 Minimal 2017-10-07 2017-… 40
## 6 Colorado https://www.colorado.gov/p… Influenza Sur… 1 Minimal 2017-10-07 2017-… 40
## 7 Connecticut http://www.portal.ct.gov/D… Flu Statistics 1 Minimal 2017-10-07 2017-… 40
## 8 Delaware http://dhss.delaware.gov/d… Weekly Influe… 1 Minimal 2017-10-07 2017-… 40
## 9 District of… http://doh.dc.gov/page/inf… Influenza Inf… 2 Minimal 2017-10-07 2017-… 40
## 10 Florida "http://www.floridahealth.… Weekly Influe… 1 Minimal 2017-10-07 2017-… 40
## # … with 2,795 more rows</code></pre>
<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" data-line-number="1">xdf &lt;-<span class="st"> </span><span class="kw">map_df</span>(<span class="dv">2008</span><span class="op">:</span><span class="dv">2017</span>, ili_weekly_activity_indicators)</a>
<a class="sourceLine" id="cb34-2" data-line-number="2"></a>
<a class="sourceLine" id="cb34-3" data-line-number="3"><span class="kw">count</span>(xdf, weekend, activity_level_label) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb34-4" data-line-number="4"><span class="st"> </span><span class="kw">complete</span>(weekend, activity_level_label) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb34-5" data-line-number="5"><span class="st"> </span><span class="kw">ggplot</span>(<span class="kw">aes</span>(weekend, activity_level_label, <span class="dt">fill=</span>n)) <span class="op">+</span><span class="st"> </span></a>
<a class="sourceLine" id="cb34-6" data-line-number="6"><span class="st"> </span><span class="kw">geom_tile</span>(<span class="dt">color=</span><span class="st">"#c2c2c2"</span>, <span class="dt">size=</span><span class="fl">0.1</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb34-7" data-line-number="7"><span class="st"> </span><span class="kw">scale_x_date</span>(<span class="dt">expand=</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>,<span class="dv">0</span>)) <span class="op">+</span></a>
<a class="sourceLine" id="cb34-8" data-line-number="8"><span class="st"> </span>viridis<span class="op">::</span><span class="kw"><a href="https://www.rdocumentation.org/packages/viridis/topics/scale_viridis">scale_fill_viridis</a></span>(<span class="dt">name=</span><span class="st">"# States"</span>, <span class="dt">na.value=</span><span class="st">"White"</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb34-9" data-line-number="9"><span class="st"> </span><span class="kw">labs</span>(<span class="dt">x=</span><span class="ot">NULL</span>, <span class="dt">y=</span><span class="ot">NULL</span>, <span class="dt">title=</span><span class="st">"Weekly ILI Indicators (all states)"</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb34-10" data-line-number="10"><span class="st"> </span><span class="kw">coord_fixed</span>(<span class="dv">100</span><span class="op">/</span><span class="dv">1</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb34-11" data-line-number="11"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/hrbrthemes/topics/theme_ipsum_rc">theme_ipsum_rc</a></span>(<span class="dt">grid=</span><span class="st">""</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb34-12" data-line-number="12"><span class="st"> </span><span class="kw">theme</span>(<span class="dt">legend.position=</span><span class="st">"bottom"</span>)</a></code></pre></div>
<p><img src="index_files/figure-html/ili-weekly-activity-1.png" width="960"></p>
</div>
<div id="pneumonia-and-influenza-mortality-surveillance" class="section level3">
<h3 class="hasAnchor">
<a href="#pneumonia-and-influenza-mortality-surveillance" class="anchor"></a>Pneumonia and Influenza Mortality Surveillance</h3>
<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" data-line-number="1">(nat_pi &lt;-<span class="st"> </span><span class="kw"><a href="reference/pi_mortality.html">pi_mortality</a></span>(<span class="st">"national"</span>))</a></code></pre></div>
<pre><code>## # A tibble: 483 x 19
## seasonid baseline threshold percent_pni percent_complete number_influenza number_pneumonia all_deaths total_pni
## &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;
## 1 58 0.055 0.0580 0.0560 1 10 2880 51416 2890
## 2 58 0.0560 0.059 0.055 1 12 2765 50411 2777
## 3 58 0.0560 0.06 0.0560 1 18 2802 50742 2820
## 4 58 0.057 0.061 0.057 1 22 2895 51425 2917
## 5 58 0.0580 0.062 0.0560 1 23 2819 51136 2842
## 6 58 0.059 0.063 0.0560 1 28 2819 50945 2847
## 7 58 0.06 0.064 0.0580 1 25 2953 51618 2978
## 8 58 0.061 0.065 0.057 1 31 2905 51109 2936
## 9 58 0.062 0.066 0.059 1 34 2923 49720 2957
## 10 58 0.064 0.067 0.06 1 48 2857 48381 2905
## # … with 473 more rows, and 10 more variables: weeknumber &lt;chr&gt;, geo_description &lt;chr&gt;, age_label &lt;chr&gt;,
## # wk_start &lt;date&gt;, wk_end &lt;date&gt;, year_wk_num &lt;int&gt;, mmwrid &lt;chr&gt;, coverage_area &lt;chr&gt;, region_name &lt;chr&gt;,
## # callout &lt;chr&gt;</code></pre>
<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" data-line-number="1"><span class="kw">select</span>(nat_pi, wk_end, percent_pni, baseline, threshold) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb37-2" data-line-number="2"><span class="st"> </span><span class="kw">gather</span>(measure, value, <span class="op">-</span>wk_end) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb37-3" data-line-number="3"><span class="st"> </span><span class="kw">ggplot</span>(<span class="kw">aes</span>(wk_end, value)) <span class="op">+</span><span class="st"> </span></a>
<a class="sourceLine" id="cb37-4" data-line-number="4"><span class="st"> </span><span class="kw">geom_line</span>(<span class="kw">aes</span>(<span class="dt">group=</span>measure, <span class="dt">color=</span>measure)) <span class="op">+</span><span class="st"> </span></a>
<a class="sourceLine" id="cb37-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/hrbrthemes/topics/scale_x_percent">scale_y_percent</a></span>() <span class="op">+</span></a>
<a class="sourceLine" id="cb37-6" data-line-number="6"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/hrbrthemes/topics/scale_ipsum">scale_color_ipsum</a></span>(<span class="dt">name =</span> <span class="ot">NULL</span>, <span class="dt">labels=</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"Baseline"</span>, <span class="st">"Percent P&amp;I"</span>, <span class="st">"Threshold"</span>)) <span class="op">+</span></a>
<a class="sourceLine" id="cb37-7" data-line-number="7"><span class="st"> </span><span class="kw">labs</span>(<span class="dt">x=</span><span class="ot">NULL</span>, <span class="dt">y=</span><span class="st">"% of all deaths due to P&amp;I"</span>,</a>
<a class="sourceLine" id="cb37-8" data-line-number="8"> <span class="dt">title=</span><span class="st">"Percentage of all deaths due to pneumonia and influenza, National Summary"</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb37-9" data-line-number="9"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/hrbrthemes/topics/theme_ipsum_rc">theme_ipsum_rc</a></span>(<span class="dt">grid=</span><span class="st">"XY"</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb37-10" data-line-number="10"><span class="st"> </span><span class="kw">theme</span>(<span class="dt">legend.position=</span><span class="st">"bottom"</span>)</a></code></pre></div>
<p><img src="index_files/figure-html/nat-pi-mortality-1.png" width="700"></p>
<div class="sourceCode" id="cb38"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb38-1" data-line-number="1">(st_pi &lt;-<span class="st"> </span><span class="kw"><a href="reference/pi_mortality.html">pi_mortality</a></span>(<span class="st">"state"</span>, <span class="dt">years=</span><span class="dv">2015</span>))</a></code></pre></div>
<pre><code>## # A tibble: 2,704 x 19
## seasonid baseline threshold percent_pni percent_complete number_influenza number_pneumonia all_deaths total_pni
## &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;
## 1 55 NA NA 0.047 1 0 46 979 46
## 2 55 NA NA 0.038 0.963 0 34 889 34
## 3 55 NA NA 0.053 1 0 52 978 52
## 4 55 NA NA 0.07 1 0 68 968 68
## 5 55 NA NA 0.053 0.981 0 48 906 48
## 6 55 NA NA 0.0580 1 0 56 968 56
## 7 55 NA NA 0.051 1 0 53 1041 53
## 8 55 NA NA 0.062 1 1 63 1031 64
## 9 55 NA NA 0.0560 1 0 55 976 55
## 10 55 NA NA 0.054 1 0 56 1045 56
## # … with 2,694 more rows, and 10 more variables: weeknumber &lt;chr&gt;, geo_description &lt;chr&gt;, age_label &lt;chr&gt;,
## # wk_start &lt;date&gt;, wk_end &lt;date&gt;, year_wk_num &lt;int&gt;, mmwrid &lt;chr&gt;, coverage_area &lt;chr&gt;, region_name &lt;chr&gt;,
## # callout &lt;chr&gt;</code></pre>
<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" data-line-number="1">(reg_pi &lt;-<span class="st"> </span><span class="kw"><a href="reference/pi_mortality.html">pi_mortality</a></span>(<span class="st">"region"</span>, <span class="dt">years=</span><span class="dv">2015</span>))</a></code></pre></div>
<pre><code>## # A tibble: 520 x 19
## seasonid baseline threshold percent_pni percent_complete number_influenza number_pneumonia all_deaths total_pni
## &lt;chr&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;
## 1 55 0.065 0.072 0.07 1 0 178 2525 178
## 2 55 0.065 0.073 0.064 1 0 160 2512 160
## 3 55 0.066 0.074 0.0580 1 1 141 2457 142
## 4 55 0.067 0.075 0.07 1 0 171 2426 171
## 5 55 0.068 0.076 0.065 1 2 166 2565 168
## 6 55 0.069 0.077 0.067 1 1 162 2415 163
## 7 55 0.071 0.078 0.079 1 0 198 2491 198
## 8 55 0.072 0.08 0.072 1 1 176 2469 177
## 9 55 0.073 0.081 0.067 1 3 154 2353 157
## 10 55 0.075 0.0820 0.062 1 0 151 2441 151
## # … with 510 more rows, and 10 more variables: weeknumber &lt;chr&gt;, geo_description &lt;chr&gt;, age_label &lt;chr&gt;,
## # wk_start &lt;date&gt;, wk_end &lt;date&gt;, year_wk_num &lt;int&gt;, mmwrid &lt;chr&gt;, coverage_area &lt;chr&gt;, region_name &lt;chr&gt;,
## # callout &lt;chr&gt;</code></pre>
</div>
<div id="retrieve-metadata-about-u-s--state-cdc-provider-data" class="section level3">
<h3 class="hasAnchor">
<a href="#retrieve-metadata-about-u-s--state-cdc-provider-data" class="anchor"></a>Retrieve metadata about U.S. State CDC Provider Data</h3>
<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" data-line-number="1"><span class="kw"><a href="reference/state_data_providers.html">state_data_providers</a></span>()</a></code></pre></div>
<pre><code>## # A tibble: 59 x 5
## statename statehealthdeptname url statewebsitename statefluphonenum
## * &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt;
## 1 Alabama Alabama Department of Publi… http://adph.org/influenza/ Influenza Surveillance 334-206-5300
## 2 Alaska State of Alaska Health and … "http://dhss.alaska.gov/dph/Epi/… Influenza Surveillance… 907-269-8000
## 3 Arizona Arizona Department of Healt… http://www.azdhs.gov/phs/oids/ep… Influenza &amp; RSV Survei… 602-542-1025
## 4 Arkansas Arkansas Department of Heal… http://www.healthy.arkansas.gov/… Communicable Disease a… 501-661-2000
## 5 California California Department of Pu… https://www.cdph.ca.gov/Programs… Influenza (Flu) 916-558-1784
## 6 Colorado Colorado Department of Publ… https://www.colorado.gov/pacific… Influenza Surveillance 303-692-2000
## 7 Connecticut Connecticut Department of P… http://www.portal.ct.gov/DPH/Inf… Flu Statistics 860-509-8000
## 8 Delaware Delaware Health and Social … http://dhss.delaware.gov/dhss/dp… Weekly Influenza Surve… 302-744-4700
## 9 District of … District of Columbia Depart… http://doh.dc.gov/page/influenza… Influenza Information 202-442-5955
## 10 Florida Florida Department of Health "http://www.floridahealth.gov/di… Weekly Influenza Surve… 850-245-4300
## # … with 49 more rows</code></pre>
</div>
<div id="retrieve-whonrevss-surveillance-data" class="section level3">
<h3 class="hasAnchor">
<a href="#retrieve-whonrevss-surveillance-data" class="anchor"></a>Retrieve WHO/NREVSS Surveillance Data</h3>
<div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" data-line-number="1"><span class="kw">glimpse</span>(xdat &lt;-<span class="st"> </span><span class="kw"><a href="reference/who_nrevss.html">who_nrevss</a></span>(<span class="st">"national"</span>))</a></code></pre></div>
<pre><code>## List of 3
## $ combined_prior_to_2015_16:Classes 'tbl_df', 'tbl' and 'data.frame': 940 obs. of 14 variables:
## ..$ region_type : chr [1:940] "National" "National" "National" "National" ...
## ..$ region : chr [1:940] "National" "National" "National" "National" ...
## ..$ year : int [1:940] 1997 1997 1997 1997 1997 1997 1997 1997 1997 1997 ...
## ..$ week : int [1:940] 40 41 42 43 44 45 46 47 48 49 ...
## ..$ total_specimens : int [1:940] 1291 1513 1552 1669 1897 2106 2204 2533 2242 2607 ...
## ..$ percent_positive : num [1:940] 0 0.727 1.095 0.419 0.527 ...
## ..$ a_2009_h1n1 : int [1:940] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ a_h1 : int [1:940] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ a_h3 : int [1:940] 0 0 3 0 9 0 3 5 14 11 ...
## ..$ a_subtyping_not_performed: int [1:940] 0 11 13 7 1 6 4 17 22 28 ...
## ..$ a_unable_to_subtype : int [1:940] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ b : int [1:940] 0 0 1 0 0 0 1 1 1 1 ...
## ..$ h3n2v : int [1:940] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ wk_date : Date[1:940], format: "1997-09-28" "1997-10-05" "1997-10-12" "1997-10-19" ...
## $ public_health_labs :Classes 'tbl_df', 'tbl' and 'data.frame': 171 obs. of 13 variables:
## ..$ region_type : chr [1:171] "National" "National" "National" "National" ...
## ..$ region : chr [1:171] "National" "National" "National" "National" ...
## ..$ year : int [1:171] 2015 2015 2015 2015 2015 2015 2015 2015 2015 2015 ...
## ..$ week : int [1:171] 40 41 42 43 44 45 46 47 48 49 ...
## ..$ total_specimens : int [1:171] 1139 1152 1198 1244 1465 1393 1458 1157 1550 1518 ...
## ..$ a_2009_h1n1 : int [1:171] 4 5 10 9 4 11 17 17 27 38 ...
## ..$ a_h3 : int [1:171] 65 41 50 31 23 34 42 24 36 37 ...
## ..$ a_subtyping_not_performed: int [1:171] 2 2 1 4 4 1 1 0 3 3 ...
## ..$ b : int [1:171] 10 7 8 9 9 10 4 4 9 11 ...
## ..$ bvic : int [1:171] 0 3 3 1 1 4 0 3 3 2 ...
## ..$ byam : int [1:171] 1 0 2 4 4 2 4 9 12 11 ...
## ..$ h3n2v : int [1:171] 0 0 0 0 0 0 0 0 0 0 ...
## ..$ wk_date : Date[1:171], format: "2015-10-04" "2015-10-11" "2015-10-18" "2015-10-25" ...
## $ clinical_labs :Classes 'tbl_df', 'tbl' and 'data.frame': 171 obs. of 11 variables:
## ..$ region_type : chr [1:171] "National" "National" "National" "National" ...
## ..$ region : chr [1:171] "National" "National" "National" "National" ...
## ..$ year : int [1:171] 2015 2015 2015 2015 2015 2015 2015 2015 2015 2015 ...
## ..$ week : int [1:171] 40 41 42 43 44 45 46 47 48 49 ...
## ..$ total_specimens : int [1:171] 12029 13111 13441 13537 14687 15048 15250 15234 16201 16673 ...
## ..$ total_a : int [1:171] 84 116 97 98 97 122 84 119 145 140 ...
## ..$ total_b : int [1:171] 43 54 52 52 68 86 98 92 81 106 ...
## ..$ percent_positive: num [1:171] 1.06 1.3 1.11 1.11 1.12 ...
## ..$ percent_a : num [1:171] 0.698 0.885 0.722 0.724 0.66 ...
## ..$ percent_b : num [1:171] 0.357 0.412 0.387 0.384 0.463 ...
## ..$ wk_date : Date[1:171], format: "2015-10-04" "2015-10-11" "2015-10-18" "2015-10-25" ...</code></pre>
<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" data-line-number="1"><span class="kw">mutate</span>(xdat<span class="op">$</span>combined_prior_to_<span class="dv">2015</span>_<span class="dv">16</span>, </a>
<a class="sourceLine" id="cb46-2" data-line-number="2"> <span class="dt">percent_positive =</span> percent_positive <span class="op">/</span><span class="st"> </span><span class="dv">100</span>) <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb46-3" data-line-number="3"><span class="st"> </span><span class="kw">ggplot</span>(<span class="kw">aes</span>(wk_date, percent_positive)) <span class="op">+</span></a>
<a class="sourceLine" id="cb46-4" data-line-number="4"><span class="st"> </span><span class="kw">geom_line</span>() <span class="op">+</span></a>
<a class="sourceLine" id="cb46-5" data-line-number="5"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/hrbrthemes/topics/scale_x_percent">scale_y_percent</a></span>(<span class="dt">name=</span><span class="st">"% Positive"</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb46-6" data-line-number="6"><span class="st"> </span><span class="kw">labs</span>(<span class="dt">x=</span><span class="ot">NULL</span>, <span class="dt">title=</span><span class="st">"WHO/NREVSS Surveillance Data (National)"</span>) <span class="op">+</span></a>
<a class="sourceLine" id="cb46-7" data-line-number="7"><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/hrbrthemes/topics/theme_ipsum_rc">theme_ipsum_rc</a></span>(<span class="dt">grid=</span><span class="st">"XY"</span>)</a></code></pre></div>
<p><img src="index_files/figure-html/who-vrevss-1.png" width="700"></p>
<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" data-line-number="1"><span class="kw"><a href="reference/who_nrevss.html">who_nrevss</a></span>(<span class="st">"hhs"</span>, <span class="dt">years=</span><span class="dv">2016</span>)</a></code></pre></div>
<pre><code>## $public_health_labs
## # A tibble: 520 x 13
## region_type region year week total_specimens a_2009_h1n1 a_h3 a_subtyping_not… b bvic byam h3n2v wk_date
## &lt;chr&gt; &lt;chr&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;date&gt;
## 1 HHS Regions Region… 2016 40 31 0 6 0 0 0 0 0 2016-10-02
## 2 HHS Regions Region… 2016 40 31 0 6 0 0 2 0 0 2016-10-02
## 3 HHS Regions Region… 2016 40 112 2 2 0 0 0 0 0 2016-10-02
## 4 HHS Regions Region… 2016 40 112 1 11 0 1 2 0 0 2016-10-02
## 5 HHS Regions Region… 2016 40 204 0 7 0 0 0 1 0 2016-10-02
## 6 HHS Regions Region… 2016 40 39 1 1 0 0 0 0 0 2016-10-02
## 7 HHS Regions Region… 2016 40 24 0 2 0 0 1 0 0 2016-10-02
## 8 HHS Regions Region… 2016 40 46 2 8 0 0 0 0 0 2016-10-02
## 9 HHS Regions Region… 2016 40 186 3 27 0 0 0 3 0 2016-10-02
## 10 HHS Regions Region… 2016 40 113 0 17 0 0 0 0 0 2016-10-02
## # … with 510 more rows
##
## $clinical_labs
## # A tibble: 520 x 11
## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b wk_date
## &lt;chr&gt; &lt;chr&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;date&gt;
## 1 HHS Regions Region 1 2016 40 654 5 1 0.917 0.765 0.153 2016-10-02
## 2 HHS Regions Region 2 2016 40 1307 10 3 0.995 0.765 0.230 2016-10-02
## 3 HHS Regions Region 3 2016 40 941 1 4 0.531 0.106 0.425 2016-10-02
## 4 HHS Regions Region 4 2016 40 2960 46 63 3.68 1.55 2.13 2016-10-02
## 5 HHS Regions Region 5 2016 40 2386 8 5 0.545 0.335 0.210 2016-10-02
## 6 HHS Regions Region 6 2016 40 1914 22 13 1.83 1.15 0.679 2016-10-02
## 7 HHS Regions Region 7 2016 40 723 0 0 0 0 0 2016-10-02
## 8 HHS Regions Region 8 2016 40 913 8 0 0.876 0.876 0 2016-10-02
## 9 HHS Regions Region 9 2016 40 992 6 1 0.706 0.605 0.101 2016-10-02
## 10 HHS Regions Region 10 2016 40 590 14 0 2.37 2.37 0 2016-10-02
## # … with 510 more rows</code></pre>
<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" data-line-number="1"><span class="kw"><a href="reference/who_nrevss.html">who_nrevss</a></span>(<span class="st">"census"</span>, <span class="dt">years=</span><span class="dv">2016</span>)</a></code></pre></div>
<pre><code>## $public_health_labs
## # A tibble: 468 x 13
## region_type region year week total_specimens a_2009_h1n1 a_h3 a_subtyping_not… b bvic byam h3n2v wk_date
## &lt;chr&gt; &lt;chr&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;date&gt;
## 1 Census Regi… New E… 2016 40 31 0 6 0 0 0 0 0 2016-10-02
## 2 Census Regi… Mid-A… 2016 40 50 0 8 0 0 2 0 0 2016-10-02
## 3 Census Regi… East … 2016 40 139 0 4 0 0 0 1 0 2016-10-02
## 4 Census Regi… West … 2016 40 103 0 6 0 0 1 0 0 2016-10-02
## 5 Census Regi… South… 2016 40 181 3 11 0 1 2 0 0 2016-10-02
## 6 Census Regi… East … 2016 40 24 0 0 0 0 0 0 0 2016-10-02
## 7 Census Regi… West … 2016 40 27 0 1 0 0 0 0 0 2016-10-02
## 8 Census Regi… Mount… 2016 40 54 3 10 0 0 0 1 0 2016-10-02
## 9 Census Regi… Pacif… 2016 40 289 3 41 0 0 0 2 0 2016-10-02
## 10 Census Regi… New E… 2016 41 14 0 2 0 0 0 0 0 2016-10-09
## # … with 458 more rows
##
## $clinical_labs
## # A tibble: 468 x 11
## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b wk_date
## &lt;chr&gt; &lt;chr&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;int&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;date&gt;
## 1 Census Regio… New England 2016 40 654 5 1 0.917 0.765 0.153 2016-10-02
## 2 Census Regio… Mid-Atlant… 2016 40 1579 10 4 0.887 0.633 0.253 2016-10-02
## 3 Census Regio… East North… 2016 40 2176 6 5 0.506 0.276 0.230 2016-10-02
## 4 Census Regio… West North… 2016 40 1104 3 0 0.272 0.272 0 2016-10-02
## 5 Census Regio… South Atla… 2016 40 2785 43 62 3.77 1.54 2.23 2016-10-02
## 6 Census Regio… East South… 2016 40 844 4 4 0.948 0.474 0.474 2016-10-02
## 7 Census Regio… West South… 2016 40 1738 21 13 1.96 1.21 0.748 2016-10-02
## 8 Census Regio… Mountain 2016 40 1067 8 0 0.750 0.750 0 2016-10-02
## 9 Census Regio… Pacific 2016 40 1433 20 1 1.47 1.40 0.0698 2016-10-02
## 10 Census Regio… New England 2016 41 810 5 1 0.741 0.617 0.123 2016-10-09
## # … with 458 more rows</code></pre>
<div class="sourceCode" id="cb51"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb51-1" data-line-number="1"><span class="kw"><a href="reference/who_nrevss.html">who_nrevss</a></span>(<span class="st">"state"</span>, <span class="dt">years=</span><span class="dv">2016</span>)</a></code></pre></div>
<pre><code>## $public_health_labs
## # A tibble: 54 x 12
## region_type region season_descript… total_specimens a_2009_h1n1 a_h3 a_subtyping_not… b bvic byam h3n2v
## &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt;
## 1 States Alaba… Season 2016-17 570 3 227 1 2 15 14 0
## 2 States Alaska Season 2016-17 5222 14 905 3 252 2 11 0
## 3 States Arizo… Season 2016-17 2975 63 1630 0 5 227 578 0
## 4 States Arkan… Season 2016-17 121 0 51 0 0 4 0 0
## 5 States Calif… Season 2016-17 14074 184 4696 120 116 28 152 0
## 6 States Color… Season 2016-17 714 3 267 2 4 31 219 0
## 7 States Conne… Season 2016-17 1348 19 968 0 0 62 263 0
## 8 States Delaw… Season 2016-17 3090 5 659 4 11 27 127 1
## 9 States Distr… Season 2016-17 73 1 34 0 3 0 4 0
## 10 States Flori… Season 2016-17 &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;
## # … with 44 more rows, and 1 more variable: wk_date &lt;date&gt;
##
## $clinical_labs
## # A tibble: 2,808 x 11
## region_type region year week total_specimens total_a total_b percent_positive percent_a percent_b wk_date
## &lt;chr&gt; &lt;chr&gt; &lt;int&gt; &lt;int&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;chr&gt; &lt;date&gt;
## 1 States Alabama 2016 40 406 4 1 1.23 0.99 0.25 2016-10-02
## 2 States Alaska 2016 40 &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; 2016-10-02
## 3 States Arizona 2016 40 133 0 0 0 0 0 2016-10-02
## 4 States Arkansas 2016 40 47 0 0 0 0 0 2016-10-02
## 5 States California 2016 40 668 2 0 0.3 0.3 0 2016-10-02
## 6 States Colorado 2016 40 260 0 0 0 0 0 2016-10-02
## 7 States Connecticut 2016 40 199 3 0 1.51 1.51 0 2016-10-02
## 8 States Delaware 2016 40 40 0 0 0 0 0 2016-10-02
## 9 States District of … 2016 40 &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; 2016-10-02
## 10 States Florida 2016 40 &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; 2016-10-02
## # … with 2,798 more rows</code></pre>
</div>
</div>
<div id="cdcfluview-metrics" class="section level2">
<h2 class="hasAnchor">
<a href="#cdcfluview-metrics" class="anchor"></a>cdcfluview Metrics</h2>
<table class="table table">
<thead><tr class="header">
<th align="left">Lang</th>
<th align="right"># Files</th>
<th align="right">(%)</th>
<th align="right">LoC</th>
<th align="right">(%)</th>
<th align="right">Blank lines</th>
<th align="right">(%)</th>
<th align="right"># Lines</th>
<th align="right">(%)</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">R</td>
<td align="right">21</td>
<td align="right">0.91</td>
<td align="right">841</td>
<td align="right">0.88</td>
<td align="right">303</td>
<td align="right">0.80</td>
<td align="right">509</td>
<td align="right">0.85</td>
</tr>
<tr class="even">
<td align="left">Rmd</td>
<td align="right">1</td>
<td align="right">0.04</td>
<td align="right">80</td>
<td align="right">0.08</td>
<td align="right">67</td>
<td align="right">0.18</td>
<td align="right">87</td>
<td align="right">0.15</td>
</tr>
<tr class="odd">
<td align="left">make</td>
<td align="right">1</td>
<td align="right">0.04</td>
<td align="right">32</td>
<td align="right">0.03</td>
<td align="right">11</td>
<td align="right">0.03</td>
<td align="right">1</td>
<td align="right">0.00</td>
</tr>
</tbody>
</table>
</div>
<div id="code-of-conduct" class="section level2">
<h2 class="hasAnchor">
<a href="#code-of-conduct" class="anchor"></a>Code of Conduct</h2>
<p>Please note that this project is released with a <a href="CONDUCT.html">Contributor Code of Conduct</a>. By participating in this project you agree to abide by its terms.</p>
</div>
</div>
</div>
<div class="col-md-3" id="sidebar">
<div class="links">
<h2>Links</h2>
<ul class="list-unstyled">
<li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=cdcfluview">https://​cloud.r-project.org/​package=cdcfluview</a>
</li>
<li>Report a bug at <br><a href="https://gitlab.com/hrbrmstr/cdcfluview/issues">https://​gitlab.com/​hrbrmstr/​cdcfluview/​issues</a>
</li>
</ul>
</div>
<div class="license">
<h2>License</h2>
<ul class="list-unstyled">
<li>
<a href="https://opensource.org/licenses/mit-license.php">MIT</a> + file <a href="LICENSE-text.html">LICENSE</a>
</li>
</ul>
</div>
<div class="developers">
<h2>Developers</h2>
<ul class="list-unstyled">
<li>Bob Rudis <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-5670-2640" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li><a href="authors.html">All authors...</a></li>
</ul>
</div>
<div class="dev-status">
<h2>Dev status</h2>
<ul class="list-unstyled">
<li><a href="https://cran.r-project.org/package=cdcfluview"><img src="http://www.r-pkg.org/badges/version/cdcfluview" alt="CRAN_Status_Badge"></a></li>
<li><a href="https://travis-ci.org/hrbrmstr/cdcfluview"><img src="https://travis-ci.org/hrbrmstr/cdcfluview.svg?branch=master" alt="Travis-CI Build Status"></a></li>
<li><a href="https://codecov.io/github/hrbrmstr/cdcfluview?branch=master"><img src="https://img.shields.io/codecov/c/github/hrbrmstr/cdcfluview/master.svg" alt="Coverage Status"></a></li>
</ul>
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<footer><div class="copyright">
<p>Developed by Bob Rudis.</p>
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