flubase {flubase}R Documentation

Baseline free of influenza epidemic effects

Description

This function estimates the mortality (or other indicator) baseline free of influenza epidemics for one or more than one time series (age groups, gender, regions, etc) using one of four methods made available in the package, implemented respectively in baseRM, baseSA, baseIt_RM and baseIt_SA.

Usage

flubase(dat, groups, per, pe = 0, method, indicator = "mortality", g_label)

Arguments

dat a data.frame with all the variables needed: dados$group indicating the group where each time series belongs, dados$year indicating the civil year, dados$todeath is the time unit index that can be week or month, dados$nod are the number of deaths observed at that time and dados$epi is an indicator variable of the epidemic period (dados$epi=1 if the week or month belongs to the epidemic period and dados$epi=0 otherwise).
groups number of groups considered, e.g. number of age groups, regions, etc.
per per=52 for weekly data or per=12 for monthly data
pe pe = 0 if the user provides the epidemic periods in dados$epi and pe = 1 otherwise, in case which the function uses a fixed period from week 48 to week 17 or from month 12 to month 4.
method the method used to estimate the baseline, method=c("nrm","nsa","irm","isa"). method=nrm: non iterative multiple regression, method=nsa: non iterative seasonal ARIMA, method=irm: iterative cmultiple regression and method=isa: iterative seasonal ARIMA
indicator a text string indicating the name of the indicator. By default indicator="mortality"
g_label a vector string of length the number of groups, containing the labels for the groups, e.g. g_label=c("male","female") or g_label=c("0-14 yrs","15-44 yrs","45-64 yrs","65+ yrs")

Details

In order to use the methods irm and isa the time series must initiate in the week 27 or month 7 and end at week 26 or month 6 of the next year.

Value

The function will return a list flubase, with the original data set plus

flubase$beta0 containing the mortality (or other indicator) baseline of without the effect of influenza epidemics
flubase$beta_up containg the upper 95 CI for the baseline
flubase$da a dummy variable indicating the periods with excess deaths
flubase$ex the excess deaths


This function delivers the following outputs: a text file with the original data set plus four new variables, the baseline (base0), the upper 95 confidence limit (dados$base_up), the periods whith excess deaths (dados$da) and the excess deaths, estimated for each week or month (dados$ex); a time series graph for each group (age group, gender, etc) where the blue line represents the observed mortality, the black line the estimated baseline, the red line the upper 95 confidence limit of the baseline, the gray rectangles the epidemic periods and the yellow rectangles the periods with excess deaths.

Author(s)

Nunes B, Natario I and Carvalho L.

References

Nunes B, Natario I, Carvalho L. Time series methods for obtaining excess mortality. Submitted to Statistical Methods in Medical Research (2009).

Serfling RE Methods for Current Statistical Analysis of Excess Mortality Pneumonia-Influenza Deaths Public Heath Reports 1963; 78 6:494 506.

K. Choi and S.B. Thacker An evaluation of influenza mortality surveillance 1962-1979. American Journal of Epidemiology 1981; 113 3: 215 216.

Lui K-J and Kendal A.P. Impact of influenza epidemics on mortality in the united states from October 1972 to May 1985. American Journal of Public Health 1987; 77(6):712 716.

L. Simonsen, M.J. Clarke, D. Williamson, D.F. Stroup, N.H. Arden and L.B. Schonberger The impact of influenza vaccination on seasonal mortality in the US elderly population. American Journal of Public Health 1997; 87(12):1994 1950.

See Also

baseIt_RM, baseSA, baseIt_SA, baseRM


[Package flubase version 1.0 Index]