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64 lines
3.2 KiB
64 lines
3.2 KiB
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/pi-mortality.r
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\name{pi_mortality}
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\alias{pi_mortality}
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\title{Pneumonia and Influenza Mortality Surveillance}
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\usage{
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pi_mortality(coverage_area = c("national", "state", "region"), years = NULL)
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}
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\arguments{
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\item{coverage_area}{coverage area for data (national, state or region)}
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\item{years}{a vector of years to retrieve data for (i.e. \code{2014} 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}) means retrieve \strong{all} years. NOTE: if you
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happen to specify a 2-digit season value (i.e. \code{57} == 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.}
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}
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\description{
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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&I) deaths are identified based on ICD-10
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multiple cause of death codes.\cr
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\cr
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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&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
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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&I may
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increase or decrease as new and updated death certificate data are received by NCHS.\cr
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\cr
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The seasonal baseline of P&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&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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}
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\note{
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Queries for "state" and "region" are not necessarily as "instantaneous" as other API endpoints and can near or over 30s retrieval delays.
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For consistency with \code{\link{ilinet}} columns indicating the week now contain 'week' instead of the previously abbreviation 'wk'.
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}
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\examples{
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\dontrun{
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ndf <- pi_mortality()
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sdf <- pi_mortality("state")
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rdf <- pi_mortality("region")
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}
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}
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\references{
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\itemize{
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\item \href{https://gis.cdc.gov/grasp/fluview/mortality.html}{Pneumonia and Influenza Mortality Surveillance Portal}
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}
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}
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