pi_mortality: Pneumonia and Influenza Mortality Surveillance

In cdcfluview: Retrieve Flu Season Data from the United States Centers for Disease Control and Prevention ('CDC') 'FluView' Portal

Description

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.

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.

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.

Usage

pi_mortality(coverage_area = c("national", "state", "region"), years = NULL)

Arguments

coverage_area	coverage area for data (national, state or region)
years	a vector of years to retrieve data for (i.e. 2014 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 (NULL) means retrieve all years. NOTE: if you happen to specify a 2-digit season value (i.e. 57 == 2017-2018) the function is smart enough to retrieve by season ID vs convert that to a year.

Note

Queries for "state" and "region" are not necessarily as "instantaneous" as other API endpoints and can near or over 30s retrieval delays.

For consistency with ilinet columns indicating the week now contain 'week' instead of the previously abbreviation 'wk'.

References

• Pneumonia and Influenza Mortality Surveillance Portal

Examples

## Not run: 
ndf <- pi_mortality()
sdf <- pi_mortality("state")
rdf <- pi_mortality("region")

## End(Not run)

cdcfluview documentation built on May 22, 2021, 5:07 p.m.