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This package was submitted to CRAN on 2019-01-24. |
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Once it is accepted, delete this file and tag the release (commit 2b6698f1c2). |
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<title>Contributor Code of Conduct • cdcfluview</title> |
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<a class="navbar-link" href="index.html">cdcfluview</a> |
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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 class="page-header"> |
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<h1>Contributor Code of Conduct</h1> |
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</div> |
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<div id="contributor-code-of-conduct" class="section level1"> |
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<p>As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.</p> |
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<p>We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.</p> |
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<p>Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.</p> |
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<p>Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed from the project team.</p> |
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<p>Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.</p> |
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<p>This Code of Conduct is adapted from the Contributor Covenant (<a href="http:contributor-covenant.org" class="uri">http:contributor-covenant.org</a>), version 1.0.0, available at <a href="http://contributor-covenant.org/version/1/0/0/" class="uri">http://contributor-covenant.org/version/1/0/0/</a></p> |
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<footer> |
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<div class="copyright"> |
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<p>Developed by Bob Rudis.</p> |
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</div> |
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<div class="pkgdown"> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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<!-- Generated by pkgdown: do not edit by hand --> |
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<!DOCTYPE html> |
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<html lang="en"> |
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<head> |
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<meta name="viewport" content="width=device-width, initial-scale=1.0"> |
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<title>License • cdcfluview</title> |
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<!-- jquery --> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> |
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</button> |
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<a class="navbar-link" href="index.html">cdcfluview</a> |
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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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<h1>License</h1> |
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</div> |
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<pre>YEAR: 2015-2018 |
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COPYRIGHT HOLDER: Bob Rudis |
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</pre> |
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<footer> |
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<p>Developed by Bob Rudis.</p> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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<meta name="viewport" content="width=device-width, initial-scale=1.0"> |
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<title>Authors • cdcfluview</title> |
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<!-- jquery --> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> |
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<span class="icon-bar"></span> |
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</button> |
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<a class="navbar-link" href="index.html">cdcfluview</a> |
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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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<p><strong>Bob Rudis</strong>. Author, maintainer. <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> |
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</p> |
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<li> |
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<p><strong>Craig McGowan</strong>. Contributor. <a href='https://orcid.org/0000-0002-6298-0185' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a> |
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</p> |
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</li> |
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<li> |
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<p><strong>JJ Chen</strong>. Contributor. <a href='https://orcid.org/0000-0001-8482-8398' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a> |
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</p> |
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</li> |
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<li> |
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<p><strong>Sebastian Meyer</strong>. Contributor. <a href='https://orcid.org/0000-0002-1791-9449' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a> |
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</p> |
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</li> |
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<li> |
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<p><strong>James Turtle</strong>. Contributor. <a href='https://orcid.org/0000-0003-0735-7769' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a> |
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and Prevention ('CDC') 'FluView' Portal • cdcfluview</title> |
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<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous"> |
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and Prevention ('CDC') 'FluView' Portal"> |
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<meta property="og:description" content="The 'U.S.' Centers for Disease Control and Prevention (CDC) maintain |
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a portal <http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for |
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accessing state, regional and national influenza statistics as well as |
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mortality surveillance data. The web interface makes it difficult and |
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time-consuming to select and retrieve influenza data. Tools are provided |
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to access the data provided by the portal's underlying 'API'."> |
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<a class="navbar-link" href="index.html">cdcfluview</a> |
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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 class="page-header"><h1 class="hasAnchor"> |
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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> |
||||
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<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> |
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<div id="mask-cdcfluview" class="section level1"> |
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<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 & 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 <chr> "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "20… |
||||
|
## $ age_label <fct> 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 <fct> A (Subtyping not Performed), A (Subtyping not Performed), A (Subtyping not Performed), A (S… |
||||
|
## $ count <int> 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 <int> 2806, 2807, 2808, 2809, 2810, 2811, 2812, 2813, 2814, 2815, 2816, 2817, 2818, 2819, 2820, 2… |
||||
|
## $ seasonid <int> 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55,… |
||||
|
## $ publishyearweekid <int> 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2976, 2… |
||||
|
## $ sea_description <chr> "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "… |
||||
|
## $ sea_startweek <int> 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2806, 2… |
||||
|
## $ sea_endweek <int> 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2857, 2… |
||||
|
## $ vir_description <chr> "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "A-Unk", "… |
||||
|
## $ vir_startmmwrid <int> 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1397, 1… |
||||
|
## $ vir_endmmwrid <int> 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3131, 3… |
||||
|
## $ wk_start <date> 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 <date> 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 <int> 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 <chr> "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Alabama", "Al… |
||||
|
## $ url <chr> "http://adph.org/influenza/", "http://adph.org/influenza/", "http://adph.org/influenza/", "… |
||||
|
## $ website <chr> "Influenza Surveillance", "Influenza Surveillance", "Influenza Surveillance", "Influenza Su… |
||||
|
## $ activity_estimate <chr> "No Activity", "No Activity", "No Activity", "Local Activity", "Sporadic", "Sporadic", "Spo… |
||||
|
## $ weekend <date> 2003-10-04, 2003-10-11, 2003-10-18, 2003-10-25, 2003-11-01, 2003-11-08, 2003-11-15, 2003-1… |
||||
|
## $ season <chr> "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "2003-04", "20… |
||||
|
## $ weeknumber <chr> "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 <-<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 <chr> "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "FluSurv-NET", "… |
||||
|
## $ region <chr> "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network", "… |
||||
|
## $ year <int> 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2009, 2… |
||||
|
## $ season <int> 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 <date> 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 <date> 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 <int> 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 <dbl> 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 <dbl> 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 <int> 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 <fct> 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 <chr> "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "2009-10", "20… |
||||
|
## $ sea_description <chr> "Season 2009-10", "Season 2009-10", "Season 2009-10", "Season 2009-10", "Season 2009-10", "… |
||||
|
## $ mmwrid <int> 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 <chr> "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", … |
||||
|
## $ region <chr> "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network", "… |
||||
|
## $ year <int> 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2016, 2016, 2… |
||||
|
## $ season <int> 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 <date> 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 <date> 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 <int> 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 <dbl> 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 <dbl> 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 <int> 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 <fct> 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 <chr> "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "20… |
||||
|
## $ sea_description <chr> "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "… |
||||
|
## $ mmwrid <int> 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 <chr> "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", "EIP", … |
||||
|
## $ region <chr> "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colorado", "Colora… |
||||
|
## $ year <int> 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2016, 2016, 2… |
||||
|
## $ season <int> 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 <date> 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 <date> 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 <int> 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 <dbl> 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 <dbl> 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 <int> 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 <fct> 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 <chr> "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "20… |
||||
|
## $ sea_description <chr> "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "… |
||||
|
## $ mmwrid <int> 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 <chr> "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IH… |
||||
|
## $ region <chr> "Entire Network", "Entire Network", "Entire Network", "Entire Network", "Entire Network", "… |
||||
|
## $ year <int> 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2015, 2016, 2016, 2… |
||||
|
## $ season <int> 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 <date> 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 <date> 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 <int> 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 <dbl> 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 <dbl> 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 <int> 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 <fct> 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 <chr> "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "2015-16", "20… |
||||
|
## $ sea_description <chr> "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "Season 2015-16", "… |
||||
|
## $ mmwrid <int> 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 <chr> "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IHSP", "IH… |
||||
|
## $ region <chr> "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklahoma", "Oklaho… |
||||
|
## $ year <int> 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2011, 2011, 2… |
||||
|
## $ season <int> 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 <date> 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 <date> 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 <int> 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 <dbl> 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 <dbl> 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 <int> 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 <fct> 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 <chr> "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "2010-11", "20… |
||||
|
## $ sea_description <chr> "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "Season 2010-11", "… |
||||
|
## $ mmwrid <int> 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 <-<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>) -><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 <chr> "National", "National", "National", "National", "National", "National", "National", "Nationa… |
||||
|
## $ region <chr> "National", "National", "National", "National", "National", "National", "National", "Nationa… |
||||
|
## $ year <int> 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1998, 19… |
||||
|
## $ week <int> 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 <dbl> 1.101480, 1.200070, 1.378760, 1.199200, 1.656180, 1.413260, 1.986800, 2.447490, 1.739010, 1.… |
||||
|
## $ unweighted_ili <dbl> 1.216860, 1.280640, 1.239060, 1.144730, 1.261120, 1.282750, 1.445790, 1.647960, 1.675170, 1.… |
||||
|
## $ age_0_4 <dbl> 179, 199, 228, 188, 217, 178, 294, 288, 268, 299, 346, 348, 510, 579, 639, 690, 856, 824, 88… |
||||
|
## $ age_25_49 <dbl> 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 <dbl> 157, 151, 153, 193, 162, 148, 240, 293, 206, 282, 268, 235, 404, 584, 759, 654, 679, 817, 76… |
||||
|
## $ age_5_24 <dbl> 205, 242, 266, 236, 280, 281, 328, 456, 343, 415, 388, 362, 492, 576, 810, 1121, 1440, 1600,… |
||||
|
## $ age_50_64 <dbl> 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 <dbl> 29, 23, 34, 36, 41, 48, 70, 63, 69, 102, 81, 59, 113, 207, 207, 148, 151, 196, 233, 146, 119… |
||||
|
## $ ilitotal <dbl> 570, 615, 681, 653, 700, 655, 932, 1100, 886, 1098, 1083, 1004, 1519, 1946, 2415, 2613, 3126… |
||||
|
## $ num_of_providers <dbl> 192, 191, 219, 213, 213, 195, 248, 256, 252, 253, 242, 190, 251, 250, 254, 255, 245, 245, 23… |
||||
|
## $ total_patients <dbl> 46842, 48023, 54961, 57044, 55506, 51062, 64463, 66749, 52890, 67887, 61314, 47719, 48429, 5… |
||||
|
## $ week_start <date> 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 |
||||
|
## <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
||||
|
## 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 <dbl>, num_of_providers <dbl>, total_patients <dbl>, |
||||
|
## # week_start <date></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 <chr> "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "HHS Regions", "H… |
||||
|
## $ region <fct> Region 1, Region 2, Region 3, Region 4, Region 5, Region 6, Region 7, Region 8, Region 9, Re… |
||||
|
## $ year <int> 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 19… |
||||
|
## $ week <int> 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 <dbl> 0.498535, 0.374963, 1.354280, 0.400338, 1.229260, 1.018980, 0.871791, 0.516017, 1.807610, 4.… |
||||
|
## $ unweighted_ili <dbl> 0.623848, 0.384615, 1.341720, 0.450010, 0.901266, 0.747384, 1.152860, 0.422654, 2.258780, 4.… |
||||
|
## $ age_0_4 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 7053, 780, 2385, 10222, 9875, 669, 2342, 1183, 10758, 1575, 6987, 872, 2740, 11310, 9618, 68… |
||||
|
## $ week_start <date> 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 |
||||
|
## <chr> <fct> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
||||
|
## 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 <dbl>, num_of_providers <dbl>, total_patients <dbl>, |
||||
|
## # week_start <date></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 <chr> "Census Regions", "Census Regions", "Census Regions", "Census Regions", "Census Regions", "C… |
||||
|
## $ region <chr> "New England", "Mid-Atlantic", "East North Central", "West North Central", "South Atlantic",… |
||||
|
## $ year <int> 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 1997, 19… |
||||
|
## $ week <int> 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 <dbl> 0.4985350, 0.8441440, 0.7924860, 1.7640500, 0.5026620, 0.0542283, 1.0189800, 2.2587800, 2.04… |
||||
|
## $ unweighted_ili <dbl> 0.6238480, 1.3213800, 0.8187380, 1.2793900, 0.7233800, 0.0688705, 0.7473840, 2.2763300, 3.23… |
||||
|
## $ age_0_4 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 7053, 2119, 9649, 2892, 6912, 4356, 669, 10719, 2473, 6987, 2384, 9427, 2823, 7591, 4947, 68… |
||||
|
## $ week_start <date> 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 |
||||
|
## <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
||||
|
## 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 <dbl>, num_of_providers <dbl>, total_patients <dbl>, |
||||
|
## # week_start <date></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 <chr> "States", "States", "States", "States", "States", "States", "States", "States", "States", "S… |
||||
|
## $ region <chr> "Alabama", "Alaska", "Arizona", "Arkansas", "California", "Colorado", "Connecticut", "Delawa… |
||||
|
## $ year <int> 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 2010, 20… |
||||
|
## $ week <int> 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 <dbl> 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 <dbl> 2.1347700, 0.8751460, 0.6747210, 0.6960560, 1.9541200, 0.6606840, 0.0783085, 0.1001250, 2.80… |
||||
|
## $ age_0_4 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> 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 <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, … |
||||
|
## $ ilitotal <dbl> 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 <dbl> 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 <dbl> 11664, 1714, 25492, 2586, 32342, 20282, 3831, 3995, 2599, NA, 40314, 1943, 4579, 39390, 1252… |
||||
|
## $ week_start <date> 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 |
||||
|
## <chr> <chr> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
||||
|
## 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 <dbl>, num_of_providers <dbl>, total_patients <dbl>, |
||||
|
## # week_start <date></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 |
||||
|
## * <chr> <chr> <chr> <dbl> <chr> <date> <chr> <dbl> |
||||
|
## 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 & 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 <-<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">%>%</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">%>%</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 <-<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 |
||||
|
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
||||
|
## 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 <chr>, geo_description <chr>, age_label <chr>, |
||||
|
## # wk_start <date>, wk_end <date>, year_wk_num <int>, mmwrid <chr>, coverage_area <chr>, region_name <chr>, |
||||
|
## # callout <chr></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">%>%</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">%>%</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&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&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 <-<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 |
||||
|
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
||||
|
## 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 <chr>, geo_description <chr>, age_label <chr>, |
||||
|
## # wk_start <date>, wk_end <date>, year_wk_num <int>, mmwrid <chr>, coverage_area <chr>, region_name <chr>, |
||||
|
## # callout <chr></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 <-<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 |
||||
|
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> |
||||
|
## 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 <chr>, geo_description <chr>, age_label <chr>, |
||||
|
## # wk_start <date>, wk_end <date>, year_wk_num <int>, mmwrid <chr>, coverage_area <chr>, region_name <chr>, |
||||
|
## # callout <chr></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 |
||||
|
## * <chr> <chr> <chr> <chr> <chr> |
||||
|
## 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 & 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 <-<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">%>%</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 |
||||
|
## <chr> <chr> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <date> |
||||
|
## 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 |
||||
|
## <chr> <chr> <int> <int> <int> <int> <int> <dbl> <dbl> <dbl> <date> |
||||
|
## 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 |
||||
|
## <chr> <chr> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <date> |
||||
|
## 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 |
||||
|
## <chr> <chr> <int> <int> <int> <int> <int> <dbl> <dbl> <dbl> <date> |
||||
|
## 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 |
||||
|
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> |
||||
|
## 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 <NA> <NA> <NA> <NA> <NA> <NA> <NA> <NA> |
||||
|
## # … with 44 more rows, and 1 more variable: wk_date <date> |
||||
|
## |
||||
|
## $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 |
||||
|
## <chr> <chr> <int> <int> <chr> <chr> <chr> <chr> <chr> <chr> <date> |
||||
|
## 1 States Alabama 2016 40 406 4 1 1.23 0.99 0.25 2016-10-02 |
||||
|
## 2 States Alaska 2016 40 <NA> <NA> <NA> <NA> <NA> <NA> 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 <NA> <NA> <NA> <NA> <NA> <NA> 2016-10-02 |
||||
|
## 10 States Florida 2016 40 <NA> <NA> <NA> <NA> <NA> <NA> 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> |
||||
|
</div> |
||||
|
</div> |
||||
|
</div> |
||||
|
|
||||
|
|
||||
|
<footer><div class="copyright"> |
||||
|
<p>Developed by Bob Rudis.</p> |
||||
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</div> |
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<div class="pkgdown"> |
||||
|
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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</footer> |
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</body> |
||||
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</html> |
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After Width: | Height: | Size: 164 KiB |
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After Width: | Height: | Size: 810 B |
@ -0,0 +1,189 @@ |
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<!DOCTYPE html> |
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<html lang="en"> |
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<head> |
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<meta name="viewport" content="width=device-width, initial-scale=1.0"> |
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<title>Changelog • cdcfluview</title> |
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<!-- jquery --> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> |
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||||
|
<!-- Font Awesome icons --> |
||||
|
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" /> |
||||
|
|
||||
|
<!-- clipboard.js --> |
||||
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> |
||||
|
|
||||
|
<!-- sticky kit --> |
||||
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> |
||||
|
|
||||
|
<!-- pkgdown --> |
||||
|
<link href="../pkgdown.css" rel="stylesheet"> |
||||
|
<script src="../pkgdown.js"></script> |
||||
|
|
||||
|
|
||||
|
|
||||
|
<meta property="og:title" content="Changelog" /> |
||||
|
|
||||
|
|
||||
|
|
||||
|
<!-- mathjax --> |
||||
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> |
||||
|
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> |
||||
|
|
||||
|
<!--[if lt IE 9]> |
||||
|
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> |
||||
|
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> |
||||
|
<![endif]--> |
||||
|
|
||||
|
|
||||
|
</head> |
||||
|
|
||||
|
<body> |
||||
|
<div class="container template-news"> |
||||
|
<header> |
||||
|
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> |
||||
|
<div class="container"> |
||||
|
<div class="navbar-header"> |
||||
|
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> |
||||
|
<span class="sr-only">Toggle navigation</span> |
||||
|
<span class="icon-bar"></span> |
||||
|
<span class="icon-bar"></span> |
||||
|
<span class="icon-bar"></span> |
||||
|
</button> |
||||
|
<span class="navbar-brand"> |
||||
|
<a class="navbar-link" href="../index.html">cdcfluview</a> |
||||
|
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.0</span> |
||||
|
</span> |
||||
|
</div> |
||||
|
|
||||
|
<div id="navbar" class="navbar-collapse collapse"> |
||||
|
<ul class="nav navbar-nav"> |
||||
|
<li> |
||||
|
<a href="../index.html"> |
||||
|
<span class="fa fa-home fa-lg"></span> |
||||
|
|
||||
|
</a> |
||||
|
</li> |
||||
|
<li> |
||||
|
<a href="../reference/index.html">Reference</a> |
||||
|
</li> |
||||
|
<li> |
||||
|
<a href="../news/index.html">Changelog</a> |
||||
|
</li> |
||||
|
</ul> |
||||
|
|
||||
|
<ul class="nav navbar-nav navbar-right"> |
||||
|
|
||||
|
</ul> |
||||
|
|
||||
|
</div><!--/.nav-collapse --> |
||||
|
</div><!--/.container --> |
||||
|
</div><!--/.navbar --> |
||||
|
|
||||
|
|
||||
|
</header> |
||||
|
|
||||
|
<div class="row"> |
||||
|
<div class="col-md-9 contents"> |
||||
|
<div class="page-header"> |
||||
|
<h1>Changelog <small></small></h1> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<div id="cdcfluview-0-9-0" class="section level1"> |
||||
|
<h1 class="page-header"> |
||||
|
<a href="#cdcfluview-0-9-0" class="anchor"></a>cdcfluview 0.9.0<small> 2019-01-24 </small> |
||||
|
</h1> |
||||
|
<ul> |
||||
|
<li>fix bug in epiweek computation in ilinet() thanks to a bug report by <a href='https://github.com/jturtle'>@jturtle</a> (#19)</li> |
||||
|
<li>included cloc metrics and refreshed README</li> |
||||
|
<li> |
||||
|
</li> |
||||
|
</ul> |
||||
|
</div> |
||||
|
<div id="cdcfluview-0-7-0" class="section level1"> |
||||
|
<h1 class="page-header"> |
||||
|
<a href="#cdcfluview-0-7-0" class="anchor"></a>cdcfluview 0.7.0<small> 2017-11-14 </small> |
||||
|
</h1> |
||||
|
<ul> |
||||
|
<li>The CDC changed most of their API endpoints to support a new HTML interface and re-jiggered the back-end API. Craig McGowan updated the old cdcfluview API function to account for the changes. However, the new API endpoints provided additional data features and it seemed to make sense to revamp the package to fit more in line with the way the APIs were structured. Legacy cdcfluview functions have been deprecated and will display deprecation messages when run. The new cdcfluview package API changes a few things about how you work with the data but the README and examples show how to work with it.</li> |
||||
|
</ul> |
||||
|
</div> |
||||
|
<div id="cdcfluview-0-5-2" class="section level1"> |
||||
|
<h1 class="page-header"> |
||||
|
<a href="#cdcfluview-0-5-2" class="anchor"></a>cdcfluview 0.5.2<small> Unreleased </small> |
||||
|
</h1> |
||||
|
<ul> |
||||
|
<li>Modified behavior of <code><a href="../reference/get_flu_data.html">get_flu_data()</a></code> to actually grab current flu season year if a single year was specified and it is the current year and the return is a 0 length data frame (fixes #7)</li> |
||||
|
<li>Added code coverage tests for all API functions.</li> |
||||
|
</ul> |
||||
|
</div> |
||||
|
<div id="cdcfluview-0-5-1" class="section level1"> |
||||
|
<h1 class="page-header"> |
||||
|
<a href="#cdcfluview-0-5-1" class="anchor"></a>cdcfluview 0.5.1<small> 2016-12-07 </small> |
||||
|
</h1> |
||||
|
<ul> |
||||
|
<li>Replaced <code>http</code> URLs with <code>https</code> as <code>http</code> ones no longer work (fixes #6)</li> |
||||
|
<li>Fixed State data download (CDC changed the hidden API)</li> |
||||
|
</ul> |
||||
|
</div> |
||||
|
<div id="cdcfluview-0-5-0" class="section level1"> |
||||
|
<h1 class="page-header"> |
||||
|
<a href="#cdcfluview-0-5-0" class="anchor"></a>cdcfluview 0.5.0<small> Unreleased </small> |
||||
|
</h1> |
||||
|
<ul> |
||||
|
<li>Fixed issue with WHO data format change</li> |
||||
|
<li>Added Mortality Surveillance Data retrieval function</li> |
||||
|
<li>Switched to readr::read_csv() and since it handles column names better this will break your scripts until you use the new column names.</li> |
||||
|
</ul> |
||||
|
</div> |
||||
|
<div id="cdcfluview-0-4-0" class="section level1"> |
||||
|
<h1 class="page-header"> |
||||
|
<a href="#cdcfluview-0-4-0" class="anchor"></a>cdcfluview 0.4.0<small> 2015-08-09 </small> |
||||
|
</h1> |
||||
|
<ul> |
||||
|
<li>First CRAN release</li> |
||||
|
</ul> |
||||
|
</div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
||||
|
<div id="tocnav"> |
||||
|
<h2>Contents</h2> |
||||
|
<ul class="nav nav-pills nav-stacked"> |
||||
|
<li><a href="#cdcfluview-0-9-0">0.9.0</a></li> |
||||
|
<li><a href="#cdcfluview-0-7-0">0.7.0</a></li> |
||||
|
<li><a href="#cdcfluview-0-5-2">0.5.2</a></li> |
||||
|
<li><a href="#cdcfluview-0-5-1">0.5.1</a></li> |
||||
|
<li><a href="#cdcfluview-0-5-0">0.5.0</a></li> |
||||
|
<li><a href="#cdcfluview-0-4-0">0.4.0</a></li> |
||||
|
</ul> |
||||
|
</div> |
||||
|
</div> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<footer> |
||||
|
<div class="copyright"> |
||||
|
<p>Developed by Bob Rudis.</p> |
||||
|
</div> |
||||
|
|
||||
|
<div class="pkgdown"> |
||||
|
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
||||
|
</div> |
||||
|
</footer> |
||||
|
</div> |
||||
|
|
||||
|
|
||||
|
|
||||
|
</body> |
||||
|
</html> |
||||
|
|
||||
@ -0,0 +1,236 @@ |
|||||
|
/* Sticky footer */ |
||||
|
|
||||
|
/** |
||||
|
* Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/ |
||||
|
* Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css |
||||
|
* |
||||
|
* .Site -> body > .container |
||||
|
* .Site-content -> body > .container .row |
||||
|
* .footer -> footer |
||||
|
* |
||||
|
* Key idea seems to be to ensure that .container and __all its parents__ |
||||
|
* have height set to 100% |
||||
|
* |
||||
|
*/ |
||||
|
|
||||
|
html, body { |
||||
|
height: 100%; |
||||
|
} |
||||
|
|
||||
|
body > .container { |
||||
|
display: flex; |
||||
|
height: 100%; |
||||
|
flex-direction: column; |
||||
|
|
||||
|
padding-top: 60px; |
||||
|
} |
||||
|
|
||||
|
body > .container .row { |
||||
|
flex: 1 0 auto; |
||||
|
} |
||||
|
|
||||
|
footer { |
||||
|
margin-top: 45px; |
||||
|
padding: 35px 0 36px; |
||||
|
border-top: 1px solid #e5e5e5; |
||||
|
color: #666; |
||||
|
display: flex; |
||||
|
flex-shrink: 0; |
||||
|
} |
||||
|
footer p { |
||||
|
margin-bottom: 0; |
||||
|
} |
||||
|
footer div { |
||||
|
flex: 1; |
||||
|
} |
||||
|
footer .pkgdown { |
||||
|
text-align: right; |
||||
|
} |
||||
|
footer p { |
||||
|
margin-bottom: 0; |
||||
|
} |
||||
|
|
||||
|
img.icon { |
||||
|
float: right; |
||||
|
} |
||||
|
|
||||
|
img { |
||||
|
max-width: 100%; |
||||
|
} |
||||
|
|
||||
|
/* Fix bug in bootstrap (only seen in firefox) */ |
||||
|
summary { |
||||
|
display: list-item; |
||||
|
} |
||||
|
|
||||
|
/* Typographic tweaking ---------------------------------*/ |
||||
|
|
||||
|
.contents h1.page-header { |
||||
|
margin-top: calc(-60px + 1em); |
||||
|
} |
||||
|
|
||||
|
/* Section anchors ---------------------------------*/ |
||||
|
|
||||
|
a.anchor { |
||||
|
margin-left: -30px; |
||||
|
display:inline-block; |
||||
|
width: 30px; |
||||
|
height: 30px; |
||||
|
visibility: hidden; |
||||
|
|
||||
|
background-image: url(./link.svg); |
||||
|
background-repeat: no-repeat; |
||||
|
background-size: 20px 20px; |
||||
|
background-position: center center; |
||||
|
} |
||||
|
|
||||
|
.hasAnchor:hover a.anchor { |
||||
|
visibility: visible; |
||||
|
} |
||||
|
|
||||
|
@media (max-width: 767px) { |
||||
|
.hasAnchor:hover a.anchor { |
||||
|
visibility: hidden; |
||||
|
} |
||||
|
} |
||||
|
|
||||
|
|
||||
|
/* Fixes for fixed navbar --------------------------*/ |
||||
|
|
||||
|
.contents h1, .contents h2, .contents h3, .contents h4 { |
||||
|
padding-top: 60px; |
||||
|
margin-top: -40px; |
||||
|
} |
||||
|
|
||||
|
/* Static header placement on mobile devices */ |
||||
|
@media (max-width: 767px) { |
||||
|
.navbar-fixed-top { |
||||
|
position: absolute; |
||||
|
} |
||||
|
.navbar { |
||||
|
padding: 0; |
||||
|
} |
||||
|
} |
||||
|
|
||||
|
|
||||
|
/* Sidebar --------------------------*/ |
||||
|
|
||||
|
#sidebar { |
||||
|
margin-top: 30px; |
||||
|
} |
||||
|
#sidebar h2 { |
||||
|
font-size: 1.5em; |
||||
|
margin-top: 1em; |
||||
|
} |
||||
|
|
||||
|
#sidebar h2:first-child { |
||||
|
margin-top: 0; |
||||
|
} |
||||
|
|
||||
|
#sidebar .list-unstyled li { |
||||
|
margin-bottom: 0.5em; |
||||
|
} |
||||
|
|
||||
|
.orcid { |
||||
|
height: 16px; |
||||
|
vertical-align: middle; |
||||
|
} |
||||
|
|
||||
|
/* Reference index & topics ----------------------------------------------- */ |
||||
|
|
||||
|
.ref-index th {font-weight: normal;} |
||||
|
|
||||
|
.ref-index td {vertical-align: top;} |
||||
|
.ref-index .icon {width: 40px;} |
||||
|
.ref-index .alias {width: 40%;} |
||||
|
.ref-index-icons .alias {width: calc(40% - 40px);} |
||||
|
.ref-index .title {width: 60%;} |
||||
|
|
||||
|
.ref-arguments th {text-align: right; padding-right: 10px;} |
||||
|
.ref-arguments th, .ref-arguments td {vertical-align: top;} |
||||
|
.ref-arguments .name {width: 20%;} |
||||
|
.ref-arguments .desc {width: 80%;} |
||||
|
|
||||
|
/* Nice scrolling for wide elements --------------------------------------- */ |
||||
|
|
||||
|
table { |
||||
|
display: block; |
||||
|
overflow: auto; |
||||
|
} |
||||
|
|
||||
|
/* Syntax highlighting ---------------------------------------------------- */ |
||||
|
|
||||
|
pre { |
||||
|
word-wrap: normal; |
||||
|
word-break: normal; |
||||
|
border: 1px solid #eee; |
||||
|
} |
||||
|
|
||||
|
pre, code { |
||||
|
background-color: #f8f8f8; |
||||
|
color: #333; |
||||
|
} |
||||
|
|
||||
|
pre code { |
||||
|
overflow: auto; |
||||
|
word-wrap: normal; |
||||
|
white-space: pre; |
||||
|
} |
||||
|
|
||||
|
pre .img { |
||||
|
margin: 5px 0; |
||||
|
} |
||||
|
|
||||
|
pre .img img { |
||||
|
background-color: #fff; |
||||
|
display: block; |
||||
|
height: auto; |
||||
|
} |
||||
|
|
||||
|
code a, pre a { |
||||
|
color: #375f84; |
||||
|
} |
||||
|
|
||||
|
a.sourceLine:hover { |
||||
|
text-decoration: none; |
||||
|
} |
||||
|
|
||||
|
.fl {color: #1514b5;} |
||||
|
.fu {color: #000000;} /* function */ |
||||
|
.ch,.st {color: #036a07;} /* string */ |
||||
|
.kw {color: #264D66;} /* keyword */ |
||||
|
.co {color: #888888;} /* comment */ |
||||
|
|
||||
|
.message { color: black; font-weight: bolder;} |
||||
|
.error { color: orange; font-weight: bolder;} |
||||
|
.warning { color: #6A0366; font-weight: bolder;} |
||||
|
|
||||
|
/* Clipboard --------------------------*/ |
||||
|
|
||||
|
.hasCopyButton { |
||||
|
position: relative; |
||||
|
} |
||||
|
|
||||
|
.btn-copy-ex { |
||||
|
position: absolute; |
||||
|
right: 0; |
||||
|
top: 0; |
||||
|
visibility: hidden; |
||||
|
} |
||||
|
|
||||
|
.hasCopyButton:hover button.btn-copy-ex { |
||||
|
visibility: visible; |
||||
|
} |
||||
|
|
||||
|
/* mark.js ----------------------------*/ |
||||
|
|
||||
|
mark { |
||||
|
background-color: rgba(255, 255, 51, 0.5); |
||||
|
border-bottom: 2px solid rgba(255, 153, 51, 0.3); |
||||
|
padding: 1px; |
||||
|
} |
||||
|
|
||||
|
/* vertical spacing after htmlwidgets */ |
||||
|
.html-widget { |
||||
|
margin-bottom: 10px; |
||||
|
} |
||||
@ -0,0 +1,110 @@ |
|||||
|
/* http://gregfranko.com/blog/jquery-best-practices/ */ |
||||
|
(function($) { |
||||
|
$(function() { |
||||
|
|
||||
|
$("#sidebar") |
||||
|
.stick_in_parent({offset_top: 40}) |
||||
|
.on('sticky_kit:bottom', function(e) { |
||||
|
$(this).parent().css('position', 'static'); |
||||
|
}) |
||||
|
.on('sticky_kit:unbottom', function(e) { |
||||
|
$(this).parent().css('position', 'relative'); |
||||
|
}); |
||||
|
|
||||
|
$('body').scrollspy({ |
||||
|
target: '#sidebar', |
||||
|
offset: 60 |
||||
|
}); |
||||
|
|
||||
|
$('[data-toggle="tooltip"]').tooltip(); |
||||
|
|
||||
|
var cur_path = paths(location.pathname); |
||||
|
var links = $("#navbar ul li a"); |
||||
|
var max_length = -1; |
||||
|
var pos = -1; |
||||
|
for (var i = 0; i < links.length; i++) { |
||||
|
if (links[i].getAttribute("href") === "#") |
||||
|
continue; |
||||
|
var nav_path = paths(links[i].pathname); |
||||
|
|
||||
|
var length = prefix_length(nav_path, cur_path); |
||||
|
if (length > max_length) { |
||||
|
max_length = length; |
||||
|
pos = i; |
||||
|
} |
||||
|
} |
||||
|
|
||||
|
// Add class to parent <li>, and enclosing <li> if in dropdown
|
||||
|
if (pos >= 0) { |
||||
|
var menu_anchor = $(links[pos]); |
||||
|
menu_anchor.parent().addClass("active"); |
||||
|
menu_anchor.closest("li.dropdown").addClass("active"); |
||||
|
} |
||||
|
}); |
||||
|
|
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return(pieces); |
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} |
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function prefix_length(needle, haystack) { |
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if (needle.length > haystack.length) |
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// Special case for length-0 haystack, since for loop won't run
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||||
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return(needle.length === 0 ? 1 : 0); |
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for (var i = 0; i < haystack.length; i++) { |
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if (needle[i] != haystack[i]) |
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return(i); |
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} |
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return(haystack.length); |
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} |
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/* Clipboard --------------------------*/ |
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function changeTooltipMessage(element, msg) { |
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var tooltipOriginalTitle=element.getAttribute('data-original-title'); |
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element.setAttribute('data-original-title', msg); |
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$(element).tooltip('show'); |
||||
|
element.setAttribute('data-original-title', tooltipOriginalTitle); |
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|
} |
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|
if(ClipboardJS.isSupported()) { |
||||
|
$(document).ready(function() { |
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|
var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>"; |
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|
$(".examples, div.sourceCode").addClass("hasCopyButton"); |
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||||
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// Insert copy buttons:
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$(copyButton).prependTo(".hasCopyButton"); |
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// Initialize tooltips:
|
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$('.btn-copy-ex').tooltip({container: 'body'}); |
||||
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|
||||
|
// Initialize clipboard:
|
||||
|
var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { |
||||
|
text: function(trigger) { |
||||
|
return trigger.parentNode.textContent; |
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} |
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}); |
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||||
|
clipboardBtnCopies.on('success', function(e) { |
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changeTooltipMessage(e.trigger, 'Copied!'); |
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e.clearSelection(); |
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}); |
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clipboardBtnCopies.on('error', function() { |
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|
changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); |
||||
|
}); |
||||
|
}); |
||||
|
} |
||||
|
})(window.jQuery || window.$) |
||||
@ -0,0 +1,5 @@ |
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pandoc: 2.3.1 |
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pkgdown: 1.2.0 |
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pkgdown_sha: ~ |
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articles: [] |
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@ -0,0 +1,170 @@ |
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<!-- Generated by pkgdown: do not edit by hand --> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> |
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<meta property="og:title" content="Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories — age_group_distribution" /> |
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<meta property="og:description" content="Retrieves the age group distribution of influenza positive tests that are reported by |
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public health laboratories by influenza virus type and subtype/lineage. Laboratory data |
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from multiple seasons and different age groups is provided." /> |
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<div class="row"> |
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<div class="col-md-9 contents"> |
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<div class="page-header"> |
||||
|
<h1>Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>age_group_distribution.Rd</code></div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="ref-description"> |
||||
|
|
||||
|
<p>Retrieves the age group distribution of influenza positive tests that are reported by |
||||
|
public health laboratories by influenza virus type and subtype/lineage. Laboratory data |
||||
|
from multiple seasons and different age groups is provided.</p> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<pre class="usage"><span class='fu'>age_group_distribution</span>(<span class='kw'>years</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
||||
|
<table class="ref-arguments"> |
||||
|
<colgroup><col class="name" /><col class="desc" /></colgroup> |
||||
|
<tr> |
||||
|
<th>years</th> |
||||
|
<td><p>a vector of years to retrieve data for (i.e. <code>2014</code> for CDC |
||||
|
flu season 2014-2015). CDC has data for this API going back to 1997. |
||||
|
Default value (<code>NULL</code>) means retrieve <strong>all</strong> years. NOTE: if you |
||||
|
happen to specify a 2-digit season value (i.e. <code>57</code> == 2017-2018) |
||||
|
the function is smart enough to retrieve by season ID vs convert that |
||||
|
to a year.</p></td> |
||||
|
</tr> |
||||
|
</table> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> |
||||
|
|
||||
|
<ul> |
||||
|
<li><p><a href='https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html'>CDC FluView Portal</a></p></li> |
||||
|
<li><p><a href='https://gis.cdc.gov/grasp/fluview/flu_by_age_virus.html'>AGD IPT Portal</a></p></li> |
||||
|
</ul> |
||||
|
|
||||
|
|
||||
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
||||
|
<pre class="examples"><div class='input'><span class='no'>agd</span> <span class='kw'><-</span> <span class='fu'>age_group_distribution</span>(<span class='kw'>years</span><span class='kw'>=</span><span class='fl'>2015</span>)</div></pre> |
||||
|
</div> |
||||
|
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
||||
|
<h2>Contents</h2> |
||||
|
<ul class="nav nav-pills nav-stacked"> |
||||
|
<li><a href="#arguments">Arguments</a></li> |
||||
|
|
||||
|
<li><a href="#references">References</a></li> |
||||
|
|
||||
|
<li><a href="#examples">Examples</a></li> |
||||
|
</ul> |
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</div> |
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<footer> |
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<div class="copyright"> |
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<p>Developed by Bob Rudis.</p> |
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</div> |
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<div class="pkgdown"> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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</html> |
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|
||||
@ -0,0 +1,180 @@ |
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<!-- Generated by pkgdown: do not edit by hand --> |
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|
<!DOCTYPE html> |
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<html lang="en"> |
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<head> |
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<meta charset="utf-8"> |
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<meta http-equiv="X-UA-Compatible" content="IE=edge"> |
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<meta name="viewport" content="width=device-width, initial-scale=1.0"> |
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|
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<title>Retrieve CDC U.S. Basemaps — cdc_basemap • cdcfluview</title> |
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<!-- jquery --> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> |
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> |
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<!-- Font Awesome icons --> |
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<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" /> |
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<!-- clipboard.js --> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> |
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<!-- sticky kit --> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> |
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<meta property="og:title" content="Retrieve CDC U.S. Basemaps — cdc_basemap" /> |
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|
<meta property="og:description" content="The CDC FluView application uses a composite basemaps of coverage areas |
||||
|
within the United States that elides and scales Alaska, Hawaii, |
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|
Puerto Rico &amp; the Virgin Islands and some further provide elided and scaled |
||||
|
breakouts for New York City and the District of Columbia. |
||||
|
|
||||
|
This function retrieves the given shapefile, projects to EPSG:5069 and |
||||
|
returns it as an sf (simple features) object." /> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> |
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</div><!--/.container --> |
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</header> |
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<div class="row"> |
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|
<div class="col-md-9 contents"> |
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|
<div class="page-header"> |
||||
|
<h1>Retrieve CDC U.S. Basemaps</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>cdc_basemap.Rd</code></div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="ref-description"> |
||||
|
|
||||
|
<p>The CDC FluView application uses a composite basemaps of coverage areas |
||||
|
within the United States that elides and scales Alaska, Hawaii, |
||||
|
Puerto Rico & the Virgin Islands and some further provide elided and scaled |
||||
|
breakouts for New York City and the District of Columbia.<br /> |
||||
|
<br /> |
||||
|
This function retrieves the given shapefile, projects to EPSG:5069 and |
||||
|
returns it as an <code>sf</code> (simple features) object.</p> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<pre class="usage"><span class='fu'>cdc_basemap</span>(<span class='kw'>basemap</span> <span class='kw'>=</span> <span class='fu'><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'>"states"</span>, <span class='st'>"spread"</span>, |
||||
|
<span class='st'>"surv"</span>))</pre> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
||||
|
<table class="ref-arguments"> |
||||
|
<colgroup><col class="name" /><col class="desc" /></colgroup> |
||||
|
<tr> |
||||
|
<th>basemap</th> |
||||
|
<td><p>select the CDC basemap. One of:</p><ul> |
||||
|
<li><p>"<code>national</code>": outline of the U.S. + AK, HI, PR + VI</p></li> |
||||
|
<li><p>"<code>hhs</code>": outline of the U.S. + HHS Region Outlines + AK, HI, PR + VI</p></li> |
||||
|
<li><p>"<code>census</code>": outline of the U.S. + Census Region Outlines + AK, HI, PR + VI</p></li> |
||||
|
<li><p>"<code>states</code>": outline of the U.S. + State Outlines + AK, HI, PR + VI</p></li> |
||||
|
<li><p>"<code>spread</code>": outline of the U.S. + State Outlines + AK, HI, PR + VI & Guam</p></li> |
||||
|
<li><p>"<code>surv</code>": outline of the U.S. + State Outlines + AK, HI, PR + VI</p></li> |
||||
|
</ul></td> |
||||
|
</tr> |
||||
|
</table> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> |
||||
|
|
||||
|
<p>These are just the basemaps. You need to pair it with the data you wish to visualize.</p> |
||||
|
|
||||
|
|
||||
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
||||
|
<pre class="examples"><span class='co'># NOT RUN {</span> |
||||
|
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='fu'>cdc_basemap</span>(<span class='st'>"national"</span>)) |
||||
|
<span class='co'># }</span></pre> |
||||
|
</div> |
||||
|
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
||||
|
<h2>Contents</h2> |
||||
|
<ul class="nav nav-pills nav-stacked"> |
||||
|
<li><a href="#arguments">Arguments</a></li> |
||||
|
|
||||
|
<li><a href="#note">Note</a></li> |
||||
|
|
||||
|
<li><a href="#examples">Examples</a></li> |
||||
|
</ul> |
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</div> |
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<footer> |
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<div class="copyright"> |
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<p>Developed by Bob Rudis.</p> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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@ -0,0 +1,149 @@ |
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<div class="col-md-9 contents"> |
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<div class="page-header"> |
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<h1>Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention ('CDC') 'FluView' Portal</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>cdcfluview.Rd</code></div> |
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</div> |
||||
|
|
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<div class="ref-description"> |
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|
||||
|
<p>The U.S. Centers for Disease Control (CDC) maintains a portal |
||||
|
<a href='http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html'>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> |
||||
|
|
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|
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</div> |
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<h2>Contents</h2> |
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<ul class="nav nav-pills nav-stacked"> |
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</ul> |
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|
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<h2>Author</h2> |
||||
|
<p>Bob Rudis (bob@rud.is)</p> |
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</div> |
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</div> |
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<p>Developed by Bob Rudis.</p> |
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@ -0,0 +1,168 @@ |
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<!-- Generated by pkgdown: do not edit by hand --> |
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<meta name="viewport" content="width=device-width, initial-scale=1.0"> |
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<title>Census Region Table — census_regions • cdcfluview</title> |
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<meta property="og:description" content="This dataset contains the states belonging to the (presently) 4 |
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|
U.S. Census regions in "long" format. It consists of a data.frame |
||||
|
with the following columns: |
||||
|
|
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region: the official Census region name (e.g. "East") |
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state: state belonging to the region |
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|
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</a> |
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<li> |
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<a href="../reference/index.html">Reference</a> |
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</li> |
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<li> |
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|
<a href="../news/index.html">Changelog</a> |
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</div><!--/.container --> |
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|
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</header> |
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|
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|
<div class="row"> |
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|
<div class="col-md-9 contents"> |
||||
|
<div class="page-header"> |
||||
|
<h1>Census Region Table</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>census_regions.Rd</code></div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="ref-description"> |
||||
|
|
||||
|
<p>This dataset contains the states belonging to the (presently) 4 |
||||
|
U.S. Census regions in "long" format. It consists of a <code>data.frame</code> |
||||
|
with the following columns:</p> |
||||
|
<ul> |
||||
|
<li><p><code>region</code>: the official Census region name (e.g. "<code>East</code>")</p></li> |
||||
|
<li><p><code>state</code>: state belonging to the region</p></li> |
||||
|
</ul> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<pre class="usage"><span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/data'>data</a></span>(<span class='no'>census_regions</span>)</pre> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> |
||||
|
|
||||
|
<p>A data frame with 51 rows and 2 variables</p> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> |
||||
|
|
||||
|
<p>Last updated 2015-08-09.</p> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> |
||||
|
|
||||
|
<p><a href='https://www.cdc.gov/std/stats12/images/CensusMap.png'>https://www.cdc.gov/std/stats12/images/CensusMap.png</a></p> |
||||
|
|
||||
|
|
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|
</div> |
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|
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
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|
<h2>Contents</h2> |
||||
|
<ul class="nav nav-pills nav-stacked"> |
||||
|
|
||||
|
<li><a href="#format">Format</a></li> |
||||
|
|
||||
|
<li><a href="#note">Note</a></li> |
||||
|
|
||||
|
<li><a href="#references">References</a></li> |
||||
|
</ul> |
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</div> |
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<footer> |
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|
<p>Developed by Bob Rudis.</p> |
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</div> |
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<div class="pkgdown"> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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</html> |
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@ -0,0 +1,160 @@ |
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<!-- Generated by pkgdown: do not edit by hand --> |
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<html lang="en"> |
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<meta http-equiv="X-UA-Compatible" content="IE=edge"> |
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<h1>State and Territorial Epidemiologists Reports of Geographic Spread of Influenza</h1> |
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|
||||
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<div class="hidden name"><code>geographic_spread.Rd</code></div> |
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</div> |
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|
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<div class="ref-description"> |
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|
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<p>State and Territorial Epidemiologists Reports of Geographic Spread of Influenza</p> |
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|
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</div> |
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|
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<pre class="usage"><span class='fu'>geographic_spread</span>(<span class='kw'>years</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> |
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|
||||
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
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<table class="ref-arguments"> |
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<colgroup><col class="name" /><col class="desc" /></colgroup> |
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<tr> |
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|
<th>years</th> |
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|
<td><p>a vector of years to retrieve data for (i.e. <code>2014</code> for CDC |
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|
flu season 2014-2015). CDC has data for this API going back to 2003 |
||||
|
and up until the current, active flu season. |
||||
|
Default value (<code>NULL</code>) means retrieve <strong>all</strong> years. NOTE: if you |
||||
|
happen to specify a 2-digit season value (i.e. <code>57</code> == 2017-2018) |
||||
|
the function is smart enough to retrieve by season ID vs convert that |
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|
to a year.</p></td> |
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</tr> |
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</table> |
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
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<pre class="examples"><span class='co'># NOT RUN {</span> |
||||
|
<span class='no'>gs</span> <span class='kw'><-</span> <span class='fu'>geographic_spread</span>() |
||||
|
<span class='co'># }</span></pre> |
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|
</div> |
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
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|
<h2>Contents</h2> |
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<ul class="nav nav-pills nav-stacked"> |
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|
<li><a href="#arguments">Arguments</a></li> |
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|
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<li><a href="#examples">Examples</a></li> |
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</div> |
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<div class="copyright"> |
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<p>Developed by Bob Rudis.</p> |
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</div> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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@ -0,0 +1,203 @@ |
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CDC FluView |
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and provides flu reporting data as either a single data frame or a list of |
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<div class="col-md-9 contents"> |
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<div class="page-header"> |
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|
<h1>Retrieves state, regional or national influenza statistics from the CDC (deprecated)</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>get_flu_data.Rd</code></div> |
||||
|
</div> |
||||
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|
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|
<div class="ref-description"> |
||||
|
|
||||
|
<p>Uses the data source from the |
||||
|
<a href='https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html'>CDC FluView</a> |
||||
|
and provides flu reporting data as either a single data frame or a list of |
||||
|
data frames (depending on whether either <code>WHO NREVSS</code> or <code>ILINet</code> |
||||
|
(or both) is chosen.</p> |
||||
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|
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</div> |
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||||
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<pre class="usage"><span class='fu'>get_flu_data</span>(<span class='kw'>region</span> <span class='kw'>=</span> <span class='st'>"hhs"</span>, <span class='kw'>sub_region</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>10</span>, |
||||
|
<span class='kw'>data_source</span> <span class='kw'>=</span> <span class='st'>"ilinet"</span>, <span class='kw'>years</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/numeric'>as.numeric</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Sys.time'>Sys.Date</a></span>(), |
||||
|
<span class='st'>"%Y"</span>)))</pre> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
||||
|
<table class="ref-arguments"> |
||||
|
<colgroup><col class="name" /><col class="desc" /></colgroup> |
||||
|
<tr> |
||||
|
<th>region</th> |
||||
|
<td><p>one of "<code>hhs</code>", "<code>census</code>", "<code>national</code>", |
||||
|
"<code>state</code>"</p></td> |
||||
|
</tr> |
||||
|
<tr> |
||||
|
<th>sub_region</th> |
||||
|
<td><p>depends on the <code>region_type</code>.<br /> |
||||
|
For "<code>national</code>", the <code>sub_region</code> should be <code>NA</code>.<br /> |
||||
|
For "<code>hhs</code>", should be a vector between <code>1:10</code>.<br /> |
||||
|
For "<code>census</code>", should be a vector between <code>1:9</code>.<br /> |
||||
|
For "<code>state</code>", should be a vector of state/territory names |
||||
|
or "<code>all</code>".</p></td> |
||||
|
</tr> |
||||
|
<tr> |
||||
|
<th>data_source</th> |
||||
|
<td><p>either of "<code>who</code>" (for WHO NREVSS) or "<code>ilinet</code>" |
||||
|
or "<code>all</code>" (for both)</p></td> |
||||
|
</tr> |
||||
|
<tr> |
||||
|
<th>years</th> |
||||
|
<td><p>a vector of years to retrieve data for (i.e. <code>2014</code> for CDC |
||||
|
flu season 2014-2015). Default value is the current year and all |
||||
|
<code>years</code> values should be > <code>1997</code></p></td> |
||||
|
</tr> |
||||
|
</table> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> |
||||
|
|
||||
|
<p>If only a single <code>data_source</code> is specified, then a single |
||||
|
<code>data.frame</code> is returned, otherwise a named list with each |
||||
|
<code>data.frame</code> is returned.</p> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> |
||||
|
|
||||
|
<p>A lookup table between HHS regions and their member states/territories |
||||
|
is provided in <code><a href='hhs_regions.html'>hhs_regions</a></code>.</p> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> |
||||
|
|
||||
|
<p>There is often a noticeable delay when making the API request to the CDC. |
||||
|
This is not due to a large download size, but the time it takes for their |
||||
|
servers to crunch the data. Wrap the function call in <code><a href='https://www.rdocumentation.org/packages/httr/topics/with_config'>httr::with_verbose</a></code> |
||||
|
if you would like to see what's going on.</p> |
||||
|
|
||||
|
|
||||
|
</div> |
||||
|
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
||||
|
<h2>Contents</h2> |
||||
|
<ul class="nav nav-pills nav-stacked"> |
||||
|
<li><a href="#arguments">Arguments</a></li> |
||||
|
|
||||
|
<li><a href="#value">Value</a></li> |
||||
|
|
||||
|
<li><a href="#details">Details</a></li> |
||||
|
|
||||
|
<li><a href="#note">Note</a></li> |
||||
|
</ul> |
||||
|
|
||||
|
</div> |
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|
</div> |
||||
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|
||||
|
<footer> |
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<div class="copyright"> |
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|
<p>Developed by Bob Rudis.</p> |
||||
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</div> |
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|
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|
<div class="pkgdown"> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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</html> |
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|
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@ -0,0 +1,190 @@ |
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|
<!-- Generated by pkgdown: do not edit by hand --> |
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and provides influenza hospitalization reporting data as a data frame." /> |
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<h1>Retrieves influenza hospitalization statistics from the CDC (deprecated)</h1> |
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|
||||
|
<div class="hidden name"><code>get_hosp_data.Rd</code></div> |
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</div> |
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<div class="ref-description"> |
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<p>Uses the data source from the |
||||
|
<a href='https://gis.cdc.gov/GRASP/Fluview/FluHospRates.html'>CDC FluView</a> |
||||
|
and provides influenza hospitalization reporting data as a data frame.</p> |
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|
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</div> |
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<pre class="usage"><span class='fu'>get_hosp_data</span>(<span class='kw'>area</span> <span class='kw'>=</span> <span class='st'>"flusurvnet"</span>, <span class='kw'>age_group</span> <span class='kw'>=</span> <span class='st'>"overall"</span>, |
||||
|
<span class='kw'>years</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/numeric'>as.numeric</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Sys.time'>Sys.Date</a></span>(), <span class='st'>"%Y"</span>)) - <span class='fl'>1</span>)</pre> |
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
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<table class="ref-arguments"> |
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<colgroup><col class="name" /><col class="desc" /></colgroup> |
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<tr> |
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<th>area</th> |
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<td><p>one of "<code>flusurvnet</code>", "<code>eip</code>", "<code>ihsp</code>", or two |
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|
digit state abbreviation for an individual site. Exceptions are |
||||
|
New York - Albany ("<code>nya</code>") and New York - Rochester |
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|
("<code>nyr</code>")</p></td> |
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|
</tr> |
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<tr> |
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<th>age_group</th> |
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<td><p>a vector of age groups to pull data for. Possible values are: |
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"<code>overall</code>", "<code>0-4y</code>", "<code>5-17y</code>, "<code>18-49y</code>, |
||||
|
"<code>50-64y</code>, "<code>65+y</code>".</p></td> |
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|
</tr> |
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<tr> |
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<th>years</th> |
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|
<td><p>a vector of years to retrieve data for (i.e. <code>2014</code> for CDC |
||||
|
flu season 2014-2015). Default value is the current year and all |
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|
<code>years</code> values should be >= <code>2009</code></p></td> |
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</tr> |
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</table> |
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|
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> |
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|
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<p>A single <code>data.frame</code>.</p> |
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|
||||
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<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> |
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|
||||
|
<p>There is often a noticeable delay when making the API request to the CDC. |
||||
|
This is not due to a large download size, but the time it takes for their |
||||
|
servers to crunch the data. Wrap the function call in <code><a href='https://www.rdocumentation.org/packages/httr/topics/with_config'>httr::with_verbose</a></code> |
||||
|
if you would like to see what's going on.</p> |
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|
||||
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|
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
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<pre class="examples"><span class='co'># NOT RUN {</span> |
||||
|
<span class='co'># All of FluSurv-NET, 50-64 years old, 2010/11-2014/15 flu seasons</span> |
||||
|
<span class='no'>hosp</span> <span class='kw'><-</span> <span class='fu'>get_hosp_data</span>(<span class='st'>"flusurvnet"</span>, <span class='st'>"50-64y"</span>, <span class='kw'>years</span><span class='kw'>=</span><span class='fl'>2010</span>:<span class='fl'>2014</span>) |
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|
<span class='co'># }</span></pre> |
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</div> |
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
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<h2>Contents</h2> |
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<ul class="nav nav-pills nav-stacked"> |
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<li><a href="#arguments">Arguments</a></li> |
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<li><a href="#value">Value</a></li> |
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<li><a href="#note">Note</a></li> |
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|
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<li><a href="#examples">Examples</a></li> |
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<p>Developed by Bob Rudis.</p> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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<title>Retrieves state/territory-level influenza statistics from the CDC (deprecated) — get_state_data • cdcfluview</title> |
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<meta property="og:description" content="Uses the data source from the CDC' State-levelFluView |
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https://gis.cdc.gov/grasp/fluview/main.html and provides state flu |
||||
|
reporting data as a single data frame. |
||||
|
|
||||
|
This function provides similar data to get_weekly_flu_report but |
||||
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provides more metadata about the reporting sources and has access to more |
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historical infomation." /> |
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<div class="page-header"> |
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<h1>Retrieves state/territory-level influenza statistics from the CDC (deprecated)</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>get_state_data.Rd</code></div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="ref-description"> |
||||
|
|
||||
|
<p>Uses the data source from the CDC' State-levelFluView |
||||
|
<a href='https://gis.cdc.gov/grasp/fluview/main.html'>https://gis.cdc.gov/grasp/fluview/main.html</a> and provides state flu |
||||
|
reporting data as a single data frame.<br /> |
||||
|
<br /> |
||||
|
This function provides similar data to <code><a href='get_weekly_flu_report.html'>get_weekly_flu_report</a></code> but |
||||
|
provides more metadata about the reporting sources and has access to more |
||||
|
historical infomation.</p> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<pre class="usage"><span class='fu'>get_state_data</span>(<span class='kw'>years</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/numeric'>as.numeric</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Sys.time'>Sys.Date</a></span>(), <span class='st'>"%Y"</span>)))</pre> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
||||
|
<table class="ref-arguments"> |
||||
|
<colgroup><col class="name" /><col class="desc" /></colgroup> |
||||
|
<tr> |
||||
|
<th>years</th> |
||||
|
<td><p>a vector of years to retrieve data for (i.e. <code>2014</code> for CDC |
||||
|
flu season 2014-2015). Default value is the current year and all |
||||
|
<code>years</code> values should be >= <code>2008</code></p></td> |
||||
|
</tr> |
||||
|
</table> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> |
||||
|
|
||||
|
<p>A <code>data.frame</code> of state-level data for the specified seasons |
||||
|
(also classed as <code>cdcstatedata</code>)</p> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> |
||||
|
|
||||
|
<p>There is often a noticeable delay when making the API request to the CDC. This |
||||
|
is not due to a large download size, but the time it takes for their |
||||
|
servers to crunch the data. Wrap the function call in <code><a href='https://www.rdocumentation.org/packages/httr/topics/with_config'>httr::with_verbose</a></code> |
||||
|
if you would like to see what's going on.</p> |
||||
|
|
||||
|
|
||||
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
||||
|
<pre class="examples"><div class='input'><span class='no'>state_data</span> <span class='kw'><-</span> <span class='fu'>get_state_data</span>(<span class='fl'>2014</span>)</div><div class='output co'>#> <span class='message'>This function has been deprecated and will be removed in future releases.</span> |
||||
|
#> <span class='message'>Use ili_weekly_activity_indicators() instead.</span></div><span class='co'># NOT RUN {</span> |
||||
|
<span class='no'>gsd</span> <span class='kw'><-</span> <span class='fu'>get_state_data</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>2013</span>, <span class='fl'>2014</span>)) |
||||
|
<span class='no'>gsd</span> <span class='kw'><-</span> <span class='fu'>get_state_data</span>(<span class='fl'>2010</span>:<span class='fl'>2014</span>) |
||||
|
<span class='co'># }</span></pre> |
||||
|
</div> |
||||
|
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
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<h2>Contents</h2> |
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<ul class="nav nav-pills nav-stacked"> |
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|
<li><a href="#arguments">Arguments</a></li> |
||||
|
|
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|
<li><a href="#value">Value</a></li> |
||||
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|
||||
|
<li><a href="#note">Note</a></li> |
||||
|
|
||||
|
<li><a href="#examples">Examples</a></li> |
||||
|
</ul> |
||||
|
|
||||
|
</div> |
||||
|
</div> |
||||
|
|
||||
|
<footer> |
||||
|
<div class="copyright"> |
||||
|
<p>Developed by Bob Rudis.</p> |
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</div> |
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<div class="pkgdown"> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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</html> |
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@ -0,0 +1,172 @@ |
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<title>Retrieves (high-level) weekly (XML) influenza surveillance report from the CDC — get_weekly_flu_report • cdcfluview</title> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> |
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<meta property="og:description" content="The CDC publishes a weekly |
||||
|
influenza report detailing high-level flu activity per-state. They also |
||||
|
publish a data file (see References) of historical report readings. |
||||
|
This function reads that XML file and produces a long data_frame |
||||
|
with the historical surveillance readings. |
||||
|
|
||||
|
This function provides similar data to get_state_data but without |
||||
|
the reporting source metadata and a limit on the historical flu information." /> |
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<div class="row"> |
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|
<div class="col-md-9 contents"> |
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|
<div class="page-header"> |
||||
|
<h1>Retrieves (high-level) weekly (XML) influenza surveillance report from the CDC</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>get_weekly_flu_report.Rd</code></div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="ref-description"> |
||||
|
|
||||
|
<p>The CDC publishes a <a href='https://www.cdc.gov/flu/weekly/usmap.htm'>weekly |
||||
|
influenza report</a> detailing high-level flu activity per-state. They also |
||||
|
publish a data file (see <code>References</code>) of historical report readings. |
||||
|
This function reads that XML file and produces a long <code>data_frame</code> |
||||
|
with the historical surveillance readings.<br /> |
||||
|
<br /> |
||||
|
This function provides similar data to <code><a href='get_state_data.html'>get_state_data</a></code> but without |
||||
|
the reporting source metadata and a limit on the historical flu information.</p> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<pre class="usage"><span class='fu'>get_weekly_flu_report</span>()</pre> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> |
||||
|
|
||||
|
<p><code>tbl_df</code> (also classed with <code>cdcweeklyreport</code>) with six |
||||
|
columns: <code>year</code>, <code>week_number</code>, <code>state</code>, <code>color</code>, |
||||
|
<code>label</code>, <code>subtitle</code></p> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> |
||||
|
|
||||
|
<p><a href='https://www.cdc.gov/flu/weekly/flureport.xml'>https://www.cdc.gov/flu/weekly/flureport.xml</a></p> |
||||
|
|
||||
|
|
||||
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
||||
|
<pre class="examples"><span class='co'># NOT RUN {</span> |
||||
|
<span class='no'>wfr</span> <span class='kw'><-</span> <span class='fu'>get_weekly_flu_report</span>() |
||||
|
<span class='co'># }</span></pre> |
||||
|
</div> |
||||
|
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
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|
<h2>Contents</h2> |
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|
<ul class="nav nav-pills nav-stacked"> |
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|
|
||||
|
<li><a href="#value">Value</a></li> |
||||
|
|
||||
|
<li><a href="#references">References</a></li> |
||||
|
|
||||
|
<li><a href="#examples">Examples</a></li> |
||||
|
</ul> |
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|
|
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</div> |
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|
</div> |
||||
|
|
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|
<footer> |
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|
<div class="copyright"> |
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|
<p>Developed by Bob Rudis.</p> |
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</div> |
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|
|
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|
<div class="pkgdown"> |
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|
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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</footer> |
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</html> |
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|
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@ -0,0 +1,174 @@ |
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|
<!-- Generated by pkgdown: do not edit by hand --> |
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|
<!DOCTYPE html> |
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|
<html lang="en"> |
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|
<head> |
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|
<meta charset="utf-8"> |
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|
<meta http-equiv="X-UA-Compatible" content="IE=edge"> |
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|
<meta name="viewport" content="width=device-width, initial-scale=1.0"> |
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|
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<title>HHS Region Table — hhs_regions • cdcfluview</title> |
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<!-- jquery --> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> |
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<meta property="og:title" content="HHS Region Table — hhs_regions" /> |
||||
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|
||||
|
<meta property="og:description" content="This dataset contains the names, numbers, regional offices for-, |
||||
|
and states/territories belonging to the (presently) 10 HHS U.S. |
||||
|
regions in "long" format. It consists of a data.frame |
||||
|
with the following columns: |
||||
|
|
||||
|
region: the official HHS region name (e.g. "Region 1") |
||||
|
region_number: the associated region number |
||||
|
regional_office: the HHS regional office for the entire region |
||||
|
state_or_territory: state or territory belonging to the region |
||||
|
" /> |
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<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> |
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<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> |
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<![endif]--> |
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</head> |
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<body> |
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<div class="container template-reference-topic"> |
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<header> |
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<div class="navbar navbar-default navbar-fixed-top" role="navigation"> |
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<div class="container"> |
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<div class="navbar-header"> |
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<span class="sr-only">Toggle navigation</span> |
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<a class="navbar-link" href="../index.html">cdcfluview</a> |
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<div id="navbar" class="navbar-collapse collapse"> |
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<li> |
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<span class="fa fa-home fa-lg"></span> |
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|
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</a> |
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</li> |
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<a href="../reference/index.html">Reference</a> |
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<a href="../news/index.html">Changelog</a> |
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</div><!--/.container --> |
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|
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</header> |
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|
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|
<div class="row"> |
||||
|
<div class="col-md-9 contents"> |
||||
|
<div class="page-header"> |
||||
|
<h1>HHS Region Table</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>hhs_regions.Rd</code></div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="ref-description"> |
||||
|
|
||||
|
<p>This dataset contains the names, numbers, regional offices for-, |
||||
|
and states/territories belonging to the (presently) 10 HHS U.S. |
||||
|
regions in "long" format. It consists of a <code>data.frame</code> |
||||
|
with the following columns:</p> |
||||
|
<ul> |
||||
|
<li><p><code>region</code>: the official HHS region name (e.g. "<code>Region 1</code>")</p></li> |
||||
|
<li><p><code>region_number</code>: the associated region number</p></li> |
||||
|
<li><p><code>regional_office</code>: the HHS regional office for the entire region</p></li> |
||||
|
<li><p><code>state_or_territory</code>: state or territory belonging to the region</p></li> |
||||
|
</ul> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<pre class="usage"><span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/data'>data</a></span>(<span class='no'>hhs_regions</span>)</pre> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> |
||||
|
|
||||
|
<p>A data frame with 59 rows and 4 variables</p> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> |
||||
|
|
||||
|
<p>Last updated 2015-08-09.</p> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> |
||||
|
|
||||
|
<p><a href='https://www.hhs.gov/about/agencies/iea/regional-offices/index.html'>https://www.hhs.gov/about/agencies/iea/regional-offices/index.html</a></p> |
||||
|
|
||||
|
|
||||
|
</div> |
||||
|
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
||||
|
<h2>Contents</h2> |
||||
|
<ul class="nav nav-pills nav-stacked"> |
||||
|
|
||||
|
<li><a href="#format">Format</a></li> |
||||
|
|
||||
|
<li><a href="#note">Note</a></li> |
||||
|
|
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<h1>Laboratory-Confirmed Influenza Hospitalizations</h1> |
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<div class="hidden name"><code>hospitalizations.Rd</code></div> |
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</div> |
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<p>Laboratory-Confirmed Influenza Hospitalizations</p> |
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</div> |
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<pre class="usage"><span class='fu'>hospitalizations</span>(<span class='kw'>surveillance_area</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"flusurv"</span>, <span class='st'>"eip"</span>, <span class='st'>"ihsp"</span>), |
||||
|
<span class='kw'>region</span> <span class='kw'>=</span> <span class='st'>"all"</span>, <span class='kw'>years</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> |
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|
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
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<table class="ref-arguments"> |
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<colgroup><col class="name" /><col class="desc" /></colgroup> |
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<tr> |
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<th>surveillance_area</th> |
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<td><p>one of "<code>flusurv</code>", "<code>eip</code>", or "<code>ihsp</code>"</p></td> |
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</tr> |
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<tr> |
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<th>region</th> |
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<td><p>Using "<code>all</code>" mimics selecting "Entire Network" from the |
||||
|
CDC FluView application drop down. Individual regions for each |
||||
|
surveillance area can also be selected. Use <code><a href='surveillance_areas.html'>surveillance_areas()</a></code> to |
||||
|
see a list of valid sub-regions for each surveillance area.</p></td> |
||||
|
</tr> |
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|
<tr> |
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|
<th>years</th> |
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|
<td><p>a vector of years to retrieve data for (i.e. <code>2014</code> for CDC |
||||
|
flu season 2014-2015). CDC has data for this API going back to 2009 |
||||
|
and up until the <em>previous</em> flu season. |
||||
|
Default value (<code>NULL</code>) means retrieve <strong>all</strong> years. NOTE: if you |
||||
|
happen to specify a 2-digit season value (i.e. <code>56</code> == 2016-2017) |
||||
|
the function is smart enough to retrieve by season ID vs convert that |
||||
|
to a year.</p></td> |
||||
|
</tr> |
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|
</table> |
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|
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<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> |
||||
|
|
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|
<ul> |
||||
|
<li><p><a href='https://gis.cdc.gov/GRASP/Fluview/FluHospRates.html'>Hospital Portal</a></p></li> |
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|
</ul> |
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|
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|
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
||||
|
<pre class="examples"><div class='input'><span class='no'>hosp_fs</span> <span class='kw'><-</span> <span class='fu'>hospitalizations</span>(<span class='st'>"flusurv"</span>, <span class='kw'>years</span><span class='kw'>=</span><span class='fl'>2015</span>)</div><span class='co'># NOT RUN {</span> |
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|
<span class='no'>hosp_eip</span> <span class='kw'><-</span> <span class='fu'>hospitalizations</span>(<span class='st'>"eip"</span>) |
||||
|
<span class='no'>hosp_ihsp</span> <span class='kw'><-</span> <span class='fu'>hospitalizations</span>(<span class='st'>"ihsp"</span>) |
||||
|
<span class='co'># }</span></pre> |
||||
|
</div> |
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
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<h2>Contents</h2> |
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<ul class="nav nav-pills nav-stacked"> |
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|
<li><a href="#arguments">Arguments</a></li> |
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|
|
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<li><a href="#references">References</a></li> |
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|
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<li><a href="#examples">Examples</a></li> |
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@ -0,0 +1,186 @@ |
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<h1>Retrieve weekly state-level ILI indicators per-state for a given season</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>ili_weekly_activity_indicators.Rd</code></div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="ref-description"> |
||||
|
|
||||
|
<p>Retrieve weekly state-level ILI indicators per-state for a given season</p> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<pre class="usage"><span class='fu'>ili_weekly_activity_indicators</span>(<span class='kw'>years</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
||||
|
<table class="ref-arguments"> |
||||
|
<colgroup><col class="name" /><col class="desc" /></colgroup> |
||||
|
<tr> |
||||
|
<th>years</th> |
||||
|
<td><p>a vector of years to retrieve data for (i.e. <code>2014</code> for CDC |
||||
|
flu season 2014-2015). CDC has data for this API going back to 2008 |
||||
|
and up until the current, active flu season. |
||||
|
Default value (<code>NULL</code>) means retrieve <strong>all</strong> years. NOTE: if you |
||||
|
happen to specify a 2-digit season value (i.e. <code>57</code> == 2017-2018) |
||||
|
the function is smart enough to retrieve by season ID vs convert that |
||||
|
to a year.</p></td> |
||||
|
</tr> |
||||
|
</table> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> |
||||
|
|
||||
|
<p>These statistics use the proportion of outpatient visits to healthcare providers |
||||
|
for influenza-like illness to measure the ILI activity level within a state. They do |
||||
|
not, however, measure the extent of geographic spread of flu within a state. Therefore, |
||||
|
outbreaks occurring in a single city could cause the state to display high activity levels.<br /> |
||||
|
<br /> |
||||
|
Data collected in ILINet may disproportionately represent certain populations within |
||||
|
a state, and therefore may not accurately depict the full picture of influenza activity |
||||
|
for the whole state.<br /> |
||||
|
<br /> |
||||
|
All summary statistics are based on either data collected in ILINet, or reports from |
||||
|
state and territorial epidemiologists. Differences in the summary data presented by |
||||
|
CDC and state health departments likely represent differing levels of data completeness |
||||
|
with data presented by the state likely being the more complete.</p> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> |
||||
|
|
||||
|
<ul> |
||||
|
<li><p><a href='https://gis.cdc.gov/grasp/fluview/main.html'>ILI Activity Indicator Map Portal</a></p></li> |
||||
|
</ul> |
||||
|
|
||||
|
|
||||
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
||||
|
<pre class="examples"><span class='co'># NOT RUN {</span> |
||||
|
<span class='no'>iwai</span> <span class='kw'><-</span> <span class='fu'>ili_weekly_activity_indicators</span>(<span class='fl'>2016</span>) |
||||
|
<span class='co'># }</span></pre> |
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<h2>Contents</h2> |
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<ul class="nav nav-pills nav-stacked"> |
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<li><a href="#arguments">Arguments</a></li> |
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<li><a href="#note">Note</a></li> |
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<li><a href="#references">References</a></li> |
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<li><a href="#examples">Examples</a></li> |
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<p>Developed by Bob Rudis.</p> |
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ILINet (Influenza-like Illness Surveillance Network) and WHO/NREVSS |
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<h1>Retrieve ILINet Surveillance Data</h1> |
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|
||||
|
<div class="hidden name"><code>ilinet.Rd</code></div> |
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</div> |
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|
||||
|
<div class="ref-description"> |
||||
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|
||||
|
<p>The CDC FluView Portal provides in-season and past seasons' national, regional, |
||||
|
and state-level outpatient illness and viral surveillance data from both |
||||
|
ILINet (Influenza-like Illness Surveillance Network) and WHO/NREVSS |
||||
|
(National Respiratory and Enteric Virus Surveillance System).</p> |
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</div> |
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<pre class="usage"><span class='fu'>ilinet</span>(<span class='kw'>region</span> <span class='kw'>=</span> <span class='fu'><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='kw'>years</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> |
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
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<table class="ref-arguments"> |
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<colgroup><col class="name" /><col class="desc" /></colgroup> |
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<tr> |
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<th>region</th> |
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|
<td><p>one of "<code>national</code>", "<code>hhs</code>", "<code>census</code>", or "<code>state</code>"</p></td> |
||||
|
</tr> |
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|
<tr> |
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|
<th>years</th> |
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|
<td><p>a vector of years to retrieve data for (i.e. <code>2014</code> for CDC |
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|
flu season 2014-2015). CDC has data for this API going back to 1997. |
||||
|
Default value (<code>NULL</code>) means retrieve <strong>all</strong> years. NOTE: if you |
||||
|
happen to specify a 2-digit season value (i.e. <code>57</code> == 2017-2018) |
||||
|
the function is smart enough to retrieve by season ID vs convert that |
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|
to a year.</p></td> |
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|
</tr> |
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|
</table> |
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|
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|
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> |
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|
|
||||
|
<p>This function retrieves current and historical ILINet surveillance data for |
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|
the identified region.</p> |
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|
|
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|
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> |
||||
|
|
||||
|
<ul> |
||||
|
<li><p><a href='https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html'>CDC FluView Portal</a></p></li> |
||||
|
<li><p><a href='https://wwwn.cdc.gov/ilinet/'>ILINet Portal</a> (Login required)</p></li> |
||||
|
<li><p><a href='https://www.cdc.gov/surveillance/nrevss/index.html'>WHO/NREVSS</a></p></li> |
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|
</ul> |
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|
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|
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
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|
<pre class="examples"><div class='input'><span class='no'>national_ili</span> <span class='kw'><-</span> <span class='fu'>ilinet</span>(<span class='st'>"national"</span>, <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>2017</span>)</div><span class='co'># NOT RUN {</span> |
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|
<span class='no'>hhs_ili</span> <span class='kw'><-</span> <span class='fu'>ilinet</span>(<span class='st'>"hhs"</span>) |
||||
|
<span class='no'>census_ili</span> <span class='kw'><-</span> <span class='fu'>ilinet</span>(<span class='st'>"census"</span>) |
||||
|
<span class='no'>state_ili</span> <span class='kw'><-</span> <span class='fu'>ilinet</span>(<span class='st'>"state"</span>) |
||||
|
|
||||
|
<span class='no'>all_ili</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/warning'>suppressWarnings</a></span>( |
||||
|
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/message'>suppressMessages</a></span>(<span class='kw pkg'>purrr</span><span class='kw ns'>::</span><span class='fu'><a href='https://purrr.tidyverse.org/reference/map.html'>map_df</a></span>(<span class='fu'><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='no'>ilinet</span>))) |
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|
<span class='co'># }</span></pre> |
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</div> |
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
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<h2>Contents</h2> |
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<ul class="nav nav-pills nav-stacked"> |
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<li><a href="#arguments">Arguments</a></li> |
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|
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<li><a href="#details">Details</a></li> |
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|
||||
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<li><a href="#references">References</a></li> |
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|
||||
|
<li><a href="#examples">Examples</a></li> |
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</div> |
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<p>Developed by Bob Rudis.</p> |
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@ -0,0 +1,269 @@ |
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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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<a href="../reference/index.html">Reference</a> |
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<div class="contents col-md-9"> |
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<div class="page-header"> |
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<h1>Reference</h1> |
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</div> |
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|
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|
<table class="ref-index"> |
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|
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|
<colgroup> |
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|
|
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<col class="alias" /> |
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<col class="title" /> |
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</colgroup> |
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|
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|
<tbody> |
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|
<tr> |
||||
|
<th colspan="2"> |
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|
<h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2> |
||||
|
<p class="section-desc"></p> |
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|
</th> |
||||
|
</tr> |
||||
|
<tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="age_group_distribution.html">age_group_distribution()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Age Group Distribution of Influenza Positive Tests Reported by Public Health Laboratories</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="cdc_basemap.html">cdc_basemap()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Retrieve CDC U.S. Basemaps</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="cdcfluview.html">cdcfluview</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention ('CDC') 'FluView' Portal</p></td> |
||||
|
</tr><tr> |
||||
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|
||||
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<td> |
||||
|
<p><code><a href="census_regions.html">census_regions</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Census Region Table</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="geographic_spread.html">geographic_spread()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>State and Territorial Epidemiologists Reports of Geographic Spread of Influenza</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="get_flu_data.html">get_flu_data()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Retrieves state, regional or national influenza statistics from the CDC (deprecated)</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="get_hosp_data.html">get_hosp_data()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Retrieves influenza hospitalization statistics from the CDC (deprecated)</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="get_state_data.html">get_state_data()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Retrieves state/territory-level influenza statistics from the CDC (deprecated)</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="get_weekly_flu_report.html">get_weekly_flu_report()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Retrieves (high-level) weekly (XML) influenza surveillance report from the CDC</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="hhs_regions.html">hhs_regions</a></code> </p> |
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</td> |
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|
<td><p>HHS Region Table</p></td> |
||||
|
</tr><tr> |
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|
|
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|
<td> |
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|
<p><code><a href="hospitalizations.html">hospitalizations()</a></code> </p> |
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|
</td> |
||||
|
<td><p>Laboratory-Confirmed Influenza Hospitalizations</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="ili_weekly_activity_indicators.html">ili_weekly_activity_indicators()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Retrieve weekly state-level ILI indicators per-state for a given season</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="ilinet.html">ilinet()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Retrieve ILINet Surveillance Data</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="mmwr_week.html">mmwr_week()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Convert a Date to an MMWR day+week+year</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="mmwr_week_to_date.html">mmwr_week_to_date()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Convert an MMWR year+week or year+week+day to a Date object</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="mmwr_weekday.html">mmwr_weekday()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Convert a Date to an MMWR weekday</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="mmwrid_map.html">mmwrid_map</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>MMWR ID to Calendar Mappings</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="pi_mortality.html">pi_mortality()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Pneumonia and Influenza Mortality Surveillance</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="state_data_providers.html">state_data_providers()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Retrieve metadata about U.S. State CDC Provider Data</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="surveillance_areas.html">surveillance_areas()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Retrieve a list of valid sub-regions for each surveillance area.</p></td> |
||||
|
</tr><tr> |
||||
|
|
||||
|
<td> |
||||
|
<p><code><a href="who_nrevss.html">who_nrevss()</a></code> </p> |
||||
|
</td> |
||||
|
<td><p>Retrieve WHO/NREVSS Surveillance Data</p></td> |
||||
|
</tr> |
||||
|
</tbody> |
||||
|
</table> |
||||
|
</div> |
||||
|
|
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
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|
<h2>Contents</h2> |
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<ul class="nav nav-pills nav-stacked"> |
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<li><a href="#section-all-functions">All functions</a></li> |
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</div> |
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<footer> |
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<div class="copyright"> |
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|
<p>Developed by Bob Rudis.</p> |
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|
</div> |
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<div class="pkgdown"> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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|
</body> |
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|
</html> |
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|
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@ -0,0 +1,160 @@ |
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<title>Convert a Date to an MMWR day+week+year — mmwr_week • cdcfluview</title> |
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<meta property="og:description" content="This is a reformat and re-export of a function in the MMWRweek package. |
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It provides a snake case version of its counterpart, produces a tibble" /> |
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<h1>Convert a Date to an MMWR day+week+year</h1> |
||||
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|
||||
|
<div class="hidden name"><code>mmwr_week.Rd</code></div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="ref-description"> |
||||
|
|
||||
|
<p>This is a reformat and re-export of a function in the <code>MMWRweek</code> package. |
||||
|
It provides a snake case version of its counterpart, produces a <code>tibble</code></p> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<pre class="usage"><span class='fu'>mmwr_week</span>(<span class='no'>x</span>)</pre> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
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|
<table class="ref-arguments"> |
||||
|
<colgroup><col class="name" /><col class="desc" /></colgroup> |
||||
|
<tr> |
||||
|
<th>x</th> |
||||
|
<td><p>a vector of <code>Date</code> objects or a character vector in <code>YYYY-mm-dd</code> format.</p></td> |
||||
|
</tr> |
||||
|
</table> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> |
||||
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|
||||
|
<p>data frame (tibble)</p> |
||||
|
|
||||
|
|
||||
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
||||
|
<pre class="examples"><div class='input'><span class='no'>mwk</span> <span class='kw'><-</span> <span class='fu'>mmwr_week</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Sys.time'>Sys.Date</a></span>())</div></pre> |
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</div> |
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<h2>Contents</h2> |
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<ul class="nav nav-pills nav-stacked"> |
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<li><a href="#arguments">Arguments</a></li> |
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<li><a href="#value">Value</a></li> |
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<li><a href="#examples">Examples</a></li> |
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@ -0,0 +1,165 @@ |
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<title>Convert an MMWR year+week or year+week+day to a Date object — mmwr_week_to_date • cdcfluview</title> |
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<li> |
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<a href="../index.html"> |
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<span class="fa fa-home fa-lg"></span> |
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</a> |
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<li> |
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<a href="../reference/index.html">Reference</a> |
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</li> |
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<a href="../news/index.html">Changelog</a> |
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</li> |
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</ul> |
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<ul class="nav navbar-nav navbar-right"> |
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<div class="row"> |
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<div class="col-md-9 contents"> |
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<div class="page-header"> |
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<h1>Convert an MMWR year+week or year+week+day to a Date object</h1> |
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|
||||
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<div class="hidden name"><code>mmwr_week_to_date.Rd</code></div> |
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</div> |
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|
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<div class="ref-description"> |
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|
||||
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<p>This is a reformat and re-export of a function in the <code>MMWRweek</code> package. |
||||
|
It provides a snake case version of its counterpart and produces a vector |
||||
|
of <code>Date</code> objects that corresponds to the input MMWR year+week or year+week+day |
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vectors. This also adds some parameter checking and cleanup to avoid exceptions.</p> |
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|
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</div> |
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|
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<pre class="usage"><span class='fu'>mmwr_week_to_date</span>(<span class='no'>year</span>, <span class='no'>week</span>, <span class='kw'>day</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> |
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
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<table class="ref-arguments"> |
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<colgroup><col class="name" /><col class="desc" /></colgroup> |
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<tr> |
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|
<th>year, week, day</th> |
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|
<td><p>Year, week and month vectors. All must be the same length |
||||
|
unless <code>day</code> is <code>NULL</code>.</p></td> |
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|
</tr> |
||||
|
</table> |
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|
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> |
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|
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<p>vector of <code>Date</code> objects</p> |
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|
||||
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|
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
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<pre class="examples"><div class='input'><span class='no'>mwd</span> <span class='kw'><-</span> <span class='fu'>mmwr_week_to_date</span>(<span class='fl'>2016</span>,<span class='fl'>10</span>,<span class='fl'>3</span>)</div></pre> |
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</div> |
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
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<h2>Contents</h2> |
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<ul class="nav nav-pills nav-stacked"> |
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<li><a href="#arguments">Arguments</a></li> |
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|
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<li><a href="#value">Value</a></li> |
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|
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<li><a href="#examples">Examples</a></li> |
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</div> |
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<footer> |
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<div class="copyright"> |
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<p>Developed by Bob Rudis.</p> |
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</div> |
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<div class="pkgdown"> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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</html> |
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@ -0,0 +1,174 @@ |
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<meta property="og:description" content="This is a reformat and re-export of a function in the MMWRweek package. |
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It provides a snake case version of its counterpart, produces a factor of |
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weekday names (Sunday-Saturday)." /> |
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<div class="row"> |
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<div class="col-md-9 contents"> |
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<div class="page-header"> |
||||
|
<h1>Convert a Date to an MMWR weekday</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>mmwr_weekday.Rd</code></div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="ref-description"> |
||||
|
|
||||
|
<p>This is a reformat and re-export of a function in the <code>MMWRweek</code> package. |
||||
|
It provides a snake case version of its counterpart, produces a <code>factor</code> of |
||||
|
weekday names (Sunday-Saturday).</p> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<pre class="usage"><span class='fu'>mmwr_weekday</span>(<span class='no'>x</span>, <span class='kw'>abbr</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
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<table class="ref-arguments"> |
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|
<colgroup><col class="name" /><col class="desc" /></colgroup> |
||||
|
<tr> |
||||
|
<th>x</th> |
||||
|
<td><p>a vector of <code>Date</code> objects or a character vector in <code>YYYY-mm-dd</code> format.</p></td> |
||||
|
</tr> |
||||
|
<tr> |
||||
|
<th>abbr</th> |
||||
|
<td><p>(logical) if <code>TRUE</code>, return abbreviated weekday names, otherwise full |
||||
|
weekday names (see Note).</p></td> |
||||
|
</tr> |
||||
|
</table> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> |
||||
|
|
||||
|
<p>ordered factor</p> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> |
||||
|
|
||||
|
<p>Weekday names are explicitly mapped to "Sunday-Saturday" or "Sun-Sat" and |
||||
|
do not change with your locale.</p> |
||||
|
|
||||
|
|
||||
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
||||
|
<pre class="examples"><div class='input'><span class='no'>mwday</span> <span class='kw'><-</span> <span class='fu'>mmwr_weekday</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Sys.time'>Sys.Date</a></span>())</div></pre> |
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</div> |
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
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<h2>Contents</h2> |
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<ul class="nav nav-pills nav-stacked"> |
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|
<li><a href="#arguments">Arguments</a></li> |
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|
|
||||
|
<li><a href="#value">Value</a></li> |
||||
|
|
||||
|
<li><a href="#note">Note</a></li> |
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|
|
||||
|
<li><a href="#examples">Examples</a></li> |
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</div> |
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<p>Developed by Bob Rudis.</p> |
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<div class="pkgdown"> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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</html> |
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@ -0,0 +1,161 @@ |
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<!-- Generated by pkgdown: do not edit by hand --> |
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<!DOCTYPE html> |
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<html lang="en"> |
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<head> |
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<meta charset="utf-8"> |
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<meta http-equiv="X-UA-Compatible" content="IE=edge"> |
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<title>MMWR ID to Calendar Mappings — mmwrid_map • cdcfluview</title> |
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<meta property="og:description" content="The CDC uses a unique "Morbidity and Mortality Weekly Report" identifier |
||||
|
for each week that starts at 1 (Ref: &lt; https://www.cdc.gov/mmwr/preview/mmwrhtml/su6004a9.htm&gt;). |
||||
|
This data frame consists of 4 columns: |
||||
|
wk_start: Start date (Sunday) for the week (Date) |
||||
|
wk_end: End date (Saturday) for the week (Date) |
||||
|
year_wk_num: The week of the calendar year |
||||
|
mmwrid: The unique MMWR identifier |
||||
|
These can be "left-joined" to data provided from the CDC to perform MMWR identifier |
||||
|
to date mappings. |
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|
<h1>MMWR ID to Calendar Mappings</h1> |
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|
||||
|
<div class="hidden name"><code>mmwrid_map.Rd</code></div> |
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|
</div> |
||||
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|
||||
|
<div class="ref-description"> |
||||
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|
||||
|
<p>The CDC uses a unique "Morbidity and Mortality Weekly Report" identifier |
||||
|
for each week that starts at 1 (Ref: < https://www.cdc.gov/mmwr/preview/mmwrhtml/su6004a9.htm>). |
||||
|
This data frame consists of 4 columns:</p><ul> |
||||
|
<li><p><code>wk_start</code>: Start date (Sunday) for the week (<code>Date</code>)</p></li> |
||||
|
<li><p><code>wk_end</code>: End date (Saturday) for the week (<code>Date</code>)</p></li> |
||||
|
<li><p><code>year_wk_num</code>: The week of the calendar year</p></li> |
||||
|
<li><p><code>mmwrid</code>: The unique MMWR identifier |
||||
|
These can be "left-joined" to data provided from the CDC to perform MMWR identifier |
||||
|
to date mappings.</p></li> |
||||
|
</ul> |
||||
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||||
|
</div> |
||||
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|
||||
|
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> |
||||
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|
||||
|
<p>A data frame with 4,592 rows and 4 columns</p> |
||||
|
|
||||
|
|
||||
|
</div> |
||||
|
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
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<h2>Contents</h2> |
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<ul class="nav nav-pills nav-stacked"> |
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|
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<li><a href="#format">Format</a></li> |
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<div class="copyright"> |
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<p>Developed by Bob Rudis.</p> |
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<div class="pkgdown"> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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</html> |
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<meta property="og:title" content="Pneumonia and Influenza Mortality Surveillance — pi_mortality" /> |
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<meta property="og:description" content="The National Center for Health Statistics (NCHS) collects and disseminates the Nation's |
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official vital statistics. NCHS collects death certificate data from state vital |
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statistics offices for virtually all deaths occurring in the United States. Pneumonia |
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and influenza (P&amp;I) deaths are identified based on ICD-10 |
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multiple cause of death codes. |
||||
|
|
||||
|
NCHS Mortality Surveillance System data are presented by the week the death occurred |
||||
|
at the national, state, and HHS Region levels. Data on the percentage of deaths due |
||||
|
to P&amp;I on a national level are released two weeks after the week of death to allow |
||||
|
for collection of enough data to produce a stable percentage. States and HHS regions |
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|
with less than 20 |
||||
|
reported by week during 2008-2012) will be marked as insufficient data. Collection |
||||
|
of complete data is not expected at the time of initial report, and a reliable |
||||
|
percentage of deaths due to P&amp;I is not anticipated at the U.S. Department of Health |
||||
|
and Human Services region or state level within this two week period. The data for |
||||
|
earlier weeks are continually revised and the proportion of deaths due to P&amp;I may |
||||
|
increase or decrease as new and updated death certificate data are received by NCHS. |
||||
|
|
||||
|
The seasonal baseline of P&amp;I deaths is calculated using a periodic regression model |
||||
|
that incorporates a robust regression procedure applied to data from the previous |
||||
|
five years. An increase of 1.645 standard deviations above the seasonal baseline |
||||
|
of P&amp;I deaths is considered the "epidemic threshold," i.e., the point at which |
||||
|
the observed proportion of deaths attributed to pneumonia or influenza was |
||||
|
significantly higher than would be expected at that time of the year in the |
||||
|
absence of substantial influenza-related mortality. Baselines and thresholds are |
||||
|
calculated at the national and regional level and by age group." /> |
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<a href="../reference/index.html">Reference</a> |
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<div class="row"> |
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<div class="col-md-9 contents"> |
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<div class="page-header"> |
||||
|
<h1>Pneumonia and Influenza Mortality Surveillance</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>pi_mortality.Rd</code></div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="ref-description"> |
||||
|
|
||||
|
<p>The National Center for Health Statistics (NCHS) collects and disseminates the Nation's |
||||
|
official vital statistics. NCHS collects death certificate data from state vital |
||||
|
statistics offices for virtually all deaths occurring in the United States. Pneumonia |
||||
|
and influenza (P&I) deaths are identified based on ICD-10 |
||||
|
multiple cause of death codes.<br /> |
||||
|
<br /> |
||||
|
NCHS Mortality Surveillance System data are presented by the week the death occurred |
||||
|
at the national, state, and HHS Region levels. Data on the percentage of deaths due |
||||
|
to P&I on a national level are released two weeks after the week of death to allow |
||||
|
for collection of enough data to produce a stable percentage. States and HHS regions |
||||
|
with less than 20<!-- % of the expected total deaths (average number of total deaths --> |
||||
|
reported by week during 2008-2012) will be marked as insufficient data. Collection |
||||
|
of complete data is not expected at the time of initial report, and a reliable |
||||
|
percentage of deaths due to P&I is not anticipated at the U.S. Department of Health |
||||
|
and Human Services region or state level within this two week period. The data for |
||||
|
earlier weeks are continually revised and the proportion of deaths due to P&I may |
||||
|
increase or decrease as new and updated death certificate data are received by NCHS.<br /> |
||||
|
<br /> |
||||
|
The seasonal baseline of P&I deaths is calculated using a periodic regression model |
||||
|
that incorporates a robust regression procedure applied to data from the previous |
||||
|
five years. An increase of 1.645 standard deviations above the seasonal baseline |
||||
|
of P&I deaths is considered the "epidemic threshold," i.e., the point at which |
||||
|
the observed proportion of deaths attributed to pneumonia or influenza was |
||||
|
significantly higher than would be expected at that time of the year in the |
||||
|
absence of substantial influenza-related mortality. Baselines and thresholds are |
||||
|
calculated at the national and regional level and by age group.</p> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<pre class="usage"><span class='fu'>pi_mortality</span>(<span class='kw'>coverage_area</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"national"</span>, <span class='st'>"state"</span>, <span class='st'>"region"</span>), |
||||
|
<span class='kw'>years</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
||||
|
<table class="ref-arguments"> |
||||
|
<colgroup><col class="name" /><col class="desc" /></colgroup> |
||||
|
<tr> |
||||
|
<th>coverage_area</th> |
||||
|
<td><p>coverage area for data (national, state or region)</p></td> |
||||
|
</tr> |
||||
|
<tr> |
||||
|
<th>years</th> |
||||
|
<td><p>a vector of years to retrieve data for (i.e. <code>2014</code> for CDC |
||||
|
flu season 2014-2015). CDC has data for this API going back to 2009 |
||||
|
and up until the current, active flu season. |
||||
|
Default value (<code>NULL</code>) means retrieve <strong>all</strong> years. NOTE: if you |
||||
|
happen to specify a 2-digit season value (i.e. <code>57</code> == 2017-2018) |
||||
|
the function is smart enough to retrieve by season ID vs convert that |
||||
|
to a year.</p></td> |
||||
|
</tr> |
||||
|
</table> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> |
||||
|
|
||||
|
<p>Queries for "state" and "region" are not necessarily as "instantaneous" as other API endpoints and can near or over 30s retrieval delays.</p> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> |
||||
|
|
||||
|
<ul> |
||||
|
<li><p><a href='https://gis.cdc.gov/grasp/fluview/mortality.html'>Pneumonia and Influenza Mortality Surveillance Portal</a></p></li> |
||||
|
</ul> |
||||
|
|
||||
|
|
||||
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
||||
|
<pre class="examples"><span class='co'># NOT RUN {</span> |
||||
|
<span class='no'>ndf</span> <span class='kw'><-</span> <span class='fu'>pi_mortality</span>() |
||||
|
<span class='no'>sdf</span> <span class='kw'><-</span> <span class='fu'>pi_mortality</span>(<span class='st'>"state"</span>) |
||||
|
<span class='no'>rdf</span> <span class='kw'><-</span> <span class='fu'>pi_mortality</span>(<span class='st'>"region"</span>) |
||||
|
<span class='co'># }</span></pre> |
||||
|
</div> |
||||
|
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
||||
|
<h2>Contents</h2> |
||||
|
<ul class="nav nav-pills nav-stacked"> |
||||
|
<li><a href="#arguments">Arguments</a></li> |
||||
|
|
||||
|
<li><a href="#note">Note</a></li> |
||||
|
|
||||
|
<li><a href="#references">References</a></li> |
||||
|
|
||||
|
<li><a href="#examples">Examples</a></li> |
||||
|
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</div> |
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<div class="copyright"> |
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<p>Developed by Bob Rudis.</p> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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@ -0,0 +1,142 @@ |
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<meta name="viewport" content="width=device-width, initial-scale=1.0"> |
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<title>Retrieve metadata about U.S. State CDC Provider Data — state_data_providers • cdcfluview</title> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> |
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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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</span> |
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|
</div> |
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|
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|
<div id="navbar" class="navbar-collapse collapse"> |
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|
<ul class="nav navbar-nav"> |
||||
|
<li> |
||||
|
<a href="../index.html"> |
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|
<span class="fa fa-home fa-lg"></span> |
||||
|
|
||||
|
</a> |
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</li> |
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<li> |
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<a href="../reference/index.html">Reference</a> |
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<a href="../news/index.html">Changelog</a> |
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</li> |
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</ul> |
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|
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<ul class="nav navbar-nav navbar-right"> |
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</header> |
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|
<div class="row"> |
||||
|
<div class="col-md-9 contents"> |
||||
|
<div class="page-header"> |
||||
|
<h1>Retrieve metadata about U.S. State CDC Provider Data</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>state_data_providers.Rd</code></div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="ref-description"> |
||||
|
|
||||
|
<p>Retrieve metadata about U.S. State CDC Provider Data</p> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<pre class="usage"><span class='fu'>state_data_providers</span>()</pre> |
||||
|
|
||||
|
|
||||
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
||||
|
<pre class="examples"><div class='input'><span class='no'>sdp</span> <span class='kw'><-</span> <span class='fu'>state_data_providers</span>()</div></pre> |
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|
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<h2>Contents</h2> |
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<li><a href="#examples">Examples</a></li> |
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@ -0,0 +1,142 @@ |
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||||
|
<h1>Retrieve a list of valid sub-regions for each surveillance area.</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>surveillance_areas.Rd</code></div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="ref-description"> |
||||
|
|
||||
|
<p>Retrieve a list of valid sub-regions for each surveillance area.</p> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<pre class="usage"><span class='fu'>surveillance_areas</span>()</pre> |
||||
|
|
||||
|
|
||||
|
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
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|
<pre class="examples"><div class='input'><span class='no'>sa</span> <span class='kw'><-</span> <span class='fu'>surveillance_areas</span>()</div></pre> |
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</html> |
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|
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@ -0,0 +1,212 @@ |
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<!-- Generated by pkgdown: do not edit by hand --> |
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<!DOCTYPE html> |
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<html lang="en"> |
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<meta http-equiv="X-UA-Compatible" content="IE=edge"> |
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<meta name="viewport" content="width=device-width, initial-scale=1.0"> |
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||||
|
<meta property="og:description" content="The CDC FluView Portal provides in-season and past seasons' national, regional, |
||||
|
and state-level outpatient illness and viral surveillance data from both |
||||
|
ILINet (Influenza-like Illness Surveillance Network) and WHO/NREVSS |
||||
|
(National Respiratory and Enteric Virus Surveillance System)." /> |
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|
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|
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|
<div class="row"> |
||||
|
<div class="col-md-9 contents"> |
||||
|
<div class="page-header"> |
||||
|
<h1>Retrieve WHO/NREVSS Surveillance Data</h1> |
||||
|
|
||||
|
<div class="hidden name"><code>who_nrevss.Rd</code></div> |
||||
|
</div> |
||||
|
|
||||
|
<div class="ref-description"> |
||||
|
|
||||
|
<p>The CDC FluView Portal provides in-season and past seasons' national, regional, |
||||
|
and state-level outpatient illness and viral surveillance data from both |
||||
|
ILINet (Influenza-like Illness Surveillance Network) and WHO/NREVSS |
||||
|
(National Respiratory and Enteric Virus Surveillance System).</p> |
||||
|
|
||||
|
</div> |
||||
|
|
||||
|
<pre class="usage"><span class='fu'>who_nrevss</span>(<span class='kw'>region</span> <span class='kw'>=</span> <span class='fu'><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='kw'>years</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> |
||||
|
<table class="ref-arguments"> |
||||
|
<colgroup><col class="name" /><col class="desc" /></colgroup> |
||||
|
<tr> |
||||
|
<th>region</th> |
||||
|
<td><p>one of "<code>national</code>", "<code>hhs</code>", "<code>census</code>", or "<code>state</code>"</p></td> |
||||
|
</tr> |
||||
|
<tr> |
||||
|
<th>years</th> |
||||
|
<td><p>a vector of years to retrieve data for (i.e. <code>2014</code> for CDC |
||||
|
flu season 2014-2015). CDC has data for this API going back to 1997. |
||||
|
Default value (<code>NULL</code>) means retrieve <strong>all</strong> years. NOTE: if you |
||||
|
happen to specify a 2-digit season value (i.e. <code>57</code> == 2017-2018) |
||||
|
the function is smart enough to retrieve by season ID vs convert that |
||||
|
to a year.</p></td> |
||||
|
</tr> |
||||
|
</table> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> |
||||
|
|
||||
|
<p>list of data frames identified by</p><ul> |
||||
|
<li><p><code>combined_prior_to_2015_16</code></p></li> |
||||
|
<li><p><code>public_health_labs</code></p></li> |
||||
|
<li><p><code>clinical_labs</code></p></li> |
||||
|
</ul> |
||||
|
|
||||
|
|
||||
|
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> |
||||
|
|
||||
|
<p>This function retrieves current and historical WHO/NREVSS surveillance data for |
||||
|
the identified region.</p> |
||||
|
|
||||
|
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> |
||||
|
|
||||
|
<p>HHS, Census and State data retrieval is not as "instantaneous" as their ILINet |
||||
|
counterparts.<br /><br /> |
||||
|
Also, beginning for the 2015-16 season, reports from public health and clinical |
||||
|
laboratories are presented separately in the weekly influenza update. This is |
||||
|
the reason why a list of data frames is returned.<br /><br /> |
||||
|
<strong>ALSO</strong> The new CDC API seems to be missing some public health lab data fields.</p> |
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<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> |
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<ul> |
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<li><p><a href='https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html'>CDC FluView Portal</a></p></li> |
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<li><p><a href='https://wwwn.cdc.gov/ilinet/'>ILINet Portal</a> (Login required)</p></li> |
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<li><p><a href='https://www.cdc.gov/surveillance/nrevss/index.html'>WHO/NREVSS</a></p></li> |
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</ul> |
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> |
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<pre class="examples"><span class='co'># NOT RUN {</span> |
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<span class='no'>national_who</span> <span class='kw'><-</span> <span class='fu'>who_nrevss</span>(<span class='st'>"national"</span>) |
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<span class='no'>hhs_who</span> <span class='kw'><-</span> <span class='fu'>who_nrevss</span>(<span class='st'>"hhs"</span>) |
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<span class='no'>census_who</span> <span class='kw'><-</span> <span class='fu'>who_nrevss</span>(<span class='st'>"census"</span>) |
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<span class='no'>state_who</span> <span class='kw'><-</span> <span class='fu'>who_nrevss</span>(<span class='st'>"state"</span>) |
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<span class='co'># }</span></pre> |
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</div> |
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |
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<h2>Contents</h2> |
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<ul class="nav nav-pills nav-stacked"> |
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<li><a href="#arguments">Arguments</a></li> |
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<li><a href="#value">Value</a></li> |
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<li><a href="#details">Details</a></li> |
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<li><a href="#note">Note</a></li> |
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<li><a href="#references">References</a></li> |
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<li><a href="#examples">Examples</a></li> |
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</ul> |
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</div> |
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</div> |
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<footer> |
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<div class="copyright"> |
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<p>Developed by Bob Rudis.</p> |
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</div> |
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<div class="pkgdown"> |
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<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.2.0.</p> |
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</div> |
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</footer> |
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</div> |
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</body> |
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</html> |
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