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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.
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NCHS Mortality Surveillance System data are presented by the week the death occurred
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at the national, state, and HHS Region levels. Data on the percentage of deaths due
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to P&amp;I on a national level are released two weeks after the week of death to allow
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for collection of enough data to produce a stable percentage. States and HHS regions
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with less than 20
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reported by week during 2008-2012) will be marked as insufficient data. Collection
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of complete data is not expected at the time of initial report, and a reliable
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percentage of deaths due to P&amp;I is not anticipated at the U.S. Department of Health
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and Human Services region or state level within this two week period. The data for
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earlier weeks are continually revised and the proportion of deaths due to P&amp;I may
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increase or decrease as new and updated death certificate data are received by NCHS.
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The seasonal baseline of P&amp;I deaths is calculated using a periodic regression model
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that incorporates a robust regression procedure applied to data from the previous
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five years. An increase of 1.645 standard deviations above the seasonal baseline
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of P&amp;I deaths is considered the "epidemic threshold," i.e., the point at which
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the observed proportion of deaths attributed to pneumonia or influenza was
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significantly higher than would be expected at that time of the year in the
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absence of substantial influenza-related mortality. Baselines and thresholds are
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calculated at the national and regional level and by age group." />
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<div class="page-header">
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<h1>Pneumonia and Influenza Mortality Surveillance</h1>
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<div class="hidden name"><code>pi_mortality.Rd</code></div>
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</div>
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<div class="ref-description">
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<p>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
|
|
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 />
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<br />
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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
|
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for collection of enough data to produce a stable percentage. States and HHS regions
|
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with less than 20<!-- % of the expected total deaths (average number of total deaths -->
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reported by week during 2008-2012) will be marked as insufficient data. Collection
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of complete data is not expected at the time of initial report, and a reliable
|
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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
|
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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 />
|
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<br />
|
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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
|
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calculated at the national and regional level and by age group.</p>
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</div>
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<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>),
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<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>coverage_area</th>
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<td><p>coverage area for data (national, state or region)</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
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flu season 2014-2015). CDC has data for this API going back to 2009
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and up until the current, active flu season.
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Default value (<code>NULL</code>) means retrieve <strong>all</strong> years. NOTE: if you
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happen to specify a 2-digit season value (i.e. <code>57</code> == 2017-2018)
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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="note"><a class="anchor" href="#note"></a>Note</h2>
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<p>Queries for "state" and "region" are not necessarily as "instantaneous" as other API endpoints and can near or over 30s retrieval delays.</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/mortality.html'>Pneumonia and Influenza Mortality Surveillance Portal</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'>ndf</span> <span class='kw'><-</span> <span class='fu'>pi_mortality</span>()
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<span class='no'>sdf</span> <span class='kw'><-</span> <span class='fu'>pi_mortality</span>(<span class='st'>"state"</span>)
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<span class='no'>rdf</span> <span class='kw'><-</span> <span class='fu'>pi_mortality</span>(<span class='st'>"region"</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="#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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<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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