Surveillance for a count data time series using the Farrington method.

Description

The function takes range values of the surveillance time series disProgObj and for each time point uses a GLM to predict the number of counts according to the procedure by Farrington et al. (1996). This is then compared to the observed number of counts. If the observation is above a specific quantile of the prediction interval, then an alarm is raised.

Usage

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  algo.farrington(disProgObj, control=list(range=NULL, b=3, w=3,
  reweight=TRUE,verbose=FALSE,alpha=0.01,trend=TRUE,limit54=c(5,4),
  powertrans="2/3",
  fitFun=c("algo.farrington.fitGLM.fast","algo.farrington.fitGLM",
           "algo.farrington.fitGLM.populationOffset")))

Arguments

disProgObj

object of class disProgObj (including the observed and the state time series.)

control

Control object

range

Specifies the index of all timepoints which should be tested. If range is NULL the maximum number of possible weeks is used (i.e. as many weeks as possible while still having enough reference values).

b

how many years back in time to include when forming the base counts.

w

windows size, i.e. number of weeks to include before and after the current week

reweight

Boolean specifying whether to perform reweight step

trend

If true a trend is included and kept in case the conditions documented in Farrington et al. (1996) are met (see the results). If false then NO trend is fit.

verbose

Boolean indicating whether to show extra debugging information.

plot

Boolean specifying whether to show the final GLM model fit graphically (use History|Recording to see all pictures).

powertrans

Power transformation to apply to the data. Use either "2/3" for skewness correction (Default), "1/2" for variance stabilizing transformation or "none" for no transformation.

alpha

An approximate (two-sided) (1-α) prediction interval is calculated.

limit54

To avoid alarms in cases where the time series only has about 0-2 cases the algorithm uses the following heuristic criterion (see Section 3.8 of the Farrington paper) to protect against low counts: no alarm is sounded if fewer than cases=5 reports were received in the past period=4 weeks. limit54=c(cases,period) is a vector allowing the user to change these numbers. Note: As of version 0.9-7 the term "last" period of weeks includes the current week - otherwise no alarm is sounded for horrible large numbers if the four weeks before that are too low.

fitFun

String containing the name of the fit function to be used for fitting the GLM. The options are algo.farrington.fitGLM.fast (default) and algo.farrington.fitGLM or algo.farrington.fitGLM.populationOffset. See details of algo.farrington.fitGLM for more information.

Details

The following steps are performed according to the Farrington et al. (1996) paper.

  1. fit of the initial model and initial estimation of mean and overdispersion.

  2. calculation of the weights omega (correction for past outbreaks)

  3. refitting of the model

  4. revised estimation of overdispersion

  5. rescaled model

  6. omission of the trend, if it is not significant

  7. repetition of the whole procedure

  8. calculation of the threshold value

  9. computation of exceedance score

Value

An object of class SurvRes.

Author(s)

M. Höhle

Source

A statistical algorithm for the early detection of outbreaks of infectious disease, Farrington, C.P., Andrews, N.J, Beale A.D. and Catchpole, M.A. (1996), J. R. Statist. Soc. A, 159, 547-563.

See Also

algo.farrington.fitGLM,algo.farrington.threshold

Examples

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#Read Salmonella Agona data
data("salmonella.agona")

#Do surveillance for the last 100 weeks.
n <- length(salmonella.agona$observed)
#Set control parameters.
control <- list(b=4,w=3,range=(n-100):n,reweight=TRUE, verbose=FALSE,alpha=0.01)
res <- algo.farrington(salmonella.agona,control=control)
#Plot the result.
plot(res,disease="Salmonella Agona",method="Farrington")

## Not run: 
#Generate Poisson counts and convert into an "sts" object
set.seed(123)
x <- rpois(520,lambda=1)
sts <- sts(observed=x, state=x*0, freq=52)

#Compare timing of the two possible fitters for algo.farrington (here using S4)
system.time( sts1 <- farrington(sts, control=list(range=312:520,
                       fitFun="algo.farrington.fitGLM.fast")))
system.time( sts2 <- farrington(sts, control=list(range=312:520,
                       fitFun="algo.farrington.fitGLM")))

#Check if results are the same
stopifnot(upperbound(sts1) == upperbound(sts2))

## End(Not run)

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