pairedbinCUSUM: Paired binary CUSUM and its run-length computation

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

Paired binary CUSUM and its run-length computation

Description

CUSUM for paired binary data as described in Steiner et al. (1999).

Usage

pairedbinCUSUM(stsObj, control = list(range=NULL,theta0,theta1,
                                      h1,h2,h11,h22))
pairedbinCUSUM.runlength(p,w1,w2,h1,h2,h11,h22, sparse=FALSE)

Arguments

stsObj	Object of class sts containing the paired responses for each of the, say n, patients. The observed slot of stsObj is thus a n \times 2 matrix.
control	Control object as a list containing several parameters. range Vector of indices in the observed slot to monitor. theta0 In-control parameters of the paired binary CUSUM. theta1 Out-of-control parameters of the paired binary CUSUM. h1 Primary control limit (=threshold) of 1st CUSUM. h2 Primary control limit (=threshold) of 2nd CUSUM. h11 Secondary limit for 1st CUSUM. h22 Secondary limit for 2nd CUSUM.
p	Vector giving the probability of the four different possible states, i.e. c((death=0,near-miss=0),(death=1,near-miss=0), (death=0,near-miss=1),(death=1,near-miss=1)).
w1	The parameters w1 and w2 are the sample weights vectors for the two CUSUMs, see eqn. (2) in the paper. We have that w1 is equal to deaths
w2	As for w1
h1	decision barrier for 1st individual cusums
h2	decision barrier for 2nd cusums
h11	together with h22 this makes up the joing decision barriers
h22	together with h11 this makes up the joing decision barriers
sparse	Boolean indicating whether to use sparse matrix computations from the Matrix library (usually much faster!). Default: FALSE.

Details

For details about the method see the Steiner et al. (1999) reference listed below. Basically, two individual CUSUMs are run each based on a logistic regression model. The combined CUSUM not only signals if one of its two individual CUSUMs signals, but also if the two CUSUMs simultaneously cross the secondary limits.

Value

An sts object with observed, alarm, etc. slots trimmed to the control$range indices.

Author(s)

S. Steiner and M. Höhle

References

Steiner, S. H., Cook, R. J., and Farewell, V. T. (1999), Monitoring paired binary surgical outcomes using cumulative sum charts, Statistics in Medicine, 18, pp. 69–86.

See Also

categoricalCUSUM

Examples

#Set in-control and out-of-control parameters as in paper
theta0 <- c(-2.3,-4.5,2.5)
theta1 <- c(-1.7,-2.9,2.5)

#Small helper function to compute the paired-binary likelihood
#of the length two vector yz when the true parameters are theta
dPBin <- function(yz,theta) {
    exp(dbinom(yz[1],size=1,prob=plogis(theta[1]),log=TRUE) +
    dbinom(yz[2],size=1,prob=plogis(theta[2]+theta[3]*yz[1]),log=TRUE))
}

#Likelihood ratio for all four possible configurations
p <- c(dPBin(c(0,0), theta=theta0), dPBin(c(0,1), theta=theta0),
       dPBin(c(1,0), theta=theta0), dPBin(c(1,1), theta=theta0))
if (surveillance.options("allExamples"))
#Compute ARL using slow, non-sparse matrix operations
pairedbinCUSUM.runlength(p,w1=c(-1,37,-9,29),w2=c(-1,7),h1=70,h2=32,
                         h11=38,h22=17)

#Sparse computations can be considerably (!) faster
pairedbinCUSUM.runlength(p,w1=c(-1,37,-9,29),w2=c(-1,7),h1=70,h2=32,
                         h11=38,h22=17,sparse=TRUE)

#Use paired binary CUSUM on the De Leval et al. (1994) arterial switch
#operation data on 104 newborn babies
data("deleval")

#Switch between death and near misses
observed(deleval) <- observed(deleval)[,c(2,1)]

#Run paired-binary CUSUM without generating alarms.
pb.surv <- pairedbinCUSUM(deleval,control=list(theta0=theta0,
             theta1=theta1,h1=Inf,h2=Inf,h11=Inf,h22=Inf))

plot(pb.surv, xaxis.labelFormat=NULL, ylab="CUSUM Statistic")



######################################################################
#Scale the plots so they become comparable to the plots in Steiner et
#al. (1999). To this end a small helper function is defined.
######################################################################

######################################################################
#Log LR for conditional specification of the paired model
######################################################################
LLR.pairedbin <- function(yz,theta0, theta1) {
    #In control
    alphay0 <- theta0[1] ; alphaz0 <- theta0[2] ; beta0 <- theta0[3]
    #Out of control
    alphay1 <- theta1[1] ; alphaz1 <- theta1[2] ; beta1 <- theta1[3]
    #Likelihood ratios
    llry <- (alphay1-alphay0)*yz[1]+log(1+exp(alphay0))-log(1+exp(alphay1))
    llrz <- (alphaz1-alphaz0)*yz[2]+log(1+exp(alphaz0+beta0*yz[1]))-
                                    log(1+exp(alphaz1+beta1*yz[1]))
    return(c(llry=llry,llrz=llrz))
}


val <- expand.grid(0:1,0:1)
table <- t(apply(val,1, LLR.pairedbin, theta0=theta0, theta1=theta1))
w1 <- min(abs(table[,1]))
w2 <- min(abs(table[,2]))
S <- upperbound(pb.surv) / cbind(rep(w1,nrow(observed(pb.surv))),w2)

#Show results
opar <- par(mfcol=c(2,1))
plot(1:nrow(deleval),S[,1],type="l",main="Near Miss",xlab="Patient No.",
     ylab="CUSUM Statistic")
lines(c(0,1e99), c(32,32),lty=2,col=2)
lines(c(0,1e99), c(17,17),lty=2,col=3)

plot(1:nrow(deleval),S[,2],type="l",main="Death",xlab="Patient No.",
     ylab="CUSUM Statistic")
    lines(c(0,1e99), c(70,70),lty=2,col=2)
    lines(c(0,1e99), c(38,38),lty=2,col=3)
par(opar)

######################################################################
# Run the CUSUM with thresholds as in Steiner et al. (1999).
# After each alarm the CUSUM statistic is set to zero and
# monitoring continues from this point. Triangles indicate alarm
# in the respective CUSUM (nearmiss or death). If in both
# simultaneously then an alarm is caused by the secondary limits.
######################################################################
pb.surv2 <- pairedbinCUSUM(deleval,control=list(theta0=theta0,
             theta1=theta1,h1=70*w1,h2=32*w2,h11=38*w1,h22=17*w2))

plot(pb.surv2, xaxis.labelFormat=NULL)

surveillance documentation built on Oct. 2, 2024, 1:08 a.m.