AnnualFlu

Influenza mortality

Mortality due to influenza in the US: an annualized regression approach using multiple-cause mortality data.

Am. J. Epidemiol. 163:181, Jonathan Dushoff, Joshua B. Plotkin, Cecile Viboud, David J. D. Earn, Lone Simonsen

Data files

US mortality data

Age groups 0-4, 5-14, 15-54, 55-64, 65-74, 75-84, 85+, total

All deaths all.txt.
Multiple-cause influenza deaths multflu.txt.
Multiple-cause P&I deaths multpi.txt.
Multiple-cause R&C deaths multrc.txt.
Underlying-cause influenza deaths undflu.txt.
Underlying-cause P&I deaths undpi.txt.
Underlying-cause R&C deaths undrc.txt.
All US mortality files

New York metro mortality data

Age groups 0-4, 5-14, 15-54, 55-64, 65-74, 75-84, 85+, total

All deaths nyall.txt.
Multiple-cause influenza deaths nymultflu.txt.
Multiple-cause P&I deaths nymultpi.txt.
Multiple-cause R&C deaths nymultrc.txt.
Underlying-cause influenza deaths nyundflu.txt.
Underlying-cause P&I deaths nyundpi.txt.
Underlying-cause R&C deaths nyundrc.txt.
All NY mortality files

IL and IN mortality data

Age groups 0-4, 5-14, 15-54, 55-64, 65-74, 75-84, 85+, total

All deaths iiall.txt.
Multiple-cause influenza deaths iimultflu.txt.
Multiple-cause P&I deaths iimultpi.txt.
Multiple-cause R&C deaths iimultrc.txt.
Underlying-cause influenza deaths iiundflu.txt.
Underlying-cause P&I deaths iiundpi.txt.
Underlying-cause R&C deaths iiundrc.txt.
All IL and IN mortality files

R scripts

Import death data deaths.R deathframe.R

Normalization functions exc.R

Time series figure fit.R

Regression functions regress.R

Main regression, with CI conf.R

Different summer, winter choices: season.R main.R swin.R short.R ssum.R broad.R base.R

Removing surveillance trend trendmain.R

Serfling estimates serfdeaths.R serfling.R

Weather regressions wreg.R wmain.R

All R scripts

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When these files are used, appropriate citation should be made to the paper cited above, and to this web address (http://mac-theobio.github.io/AnnualFlu/).