algo.farrington: Surveillance for a count data time series using the...

In jimhester/surveillance: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic Phenomena

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

  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 perfomed 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

#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 random data and convert into sts object
set.seed(123)
x <- matrix(rpois(1000,lambda=1),ncol=1)
sts <- new("sts", observed=x, epoch=1:nrow(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=c(500:1000),
                       fitFun="algo.farrington.fitGLM.fast")))
system.time( sts2 <- farrington(sts, control=list(range=c(500:1000),
                       fitFun="algo.farrington.fitGLM")))

#Check if results are the same
sum(upperbound(sts1) - upperbound(sts2))

## End(Not run)

jimhester/surveillance documentation built on May 19, 2019, 10:33 a.m.