Chapter 8 Code for Advanced Bayesian Methods for Medical Test Accuracy

BUGS CODE 8.1

model;

{

th1~dbeta(m1,m0)

ph0~dbeta(s0,r0)

ph1~dbeta(s1,r1)

th0<-1-th1

tpf<- ph1*th1/(ph1*th1+ph0*th0)

fpf<- (1-ph1)*th1/(1-ph1*th1-ph0*th0)

}

# hepatic scintigraphy example

# the following values assume a uniform prior

list(m0= 222,m1=430,s0=28,r0=55,r1=33,s1=322)

BUGS CODE 8.2

model;

{

g00~dgamma(m00,2)

g01~dgamma(m01,2)

g10~dgamma(m10,2)

g11~dgamma(m11,2)

h<-g00+g01+g10+g11

th00<-g00/h

th01<-g01/h

th10<-g10/h

th11<-g11/h

phi00~dbeta(s00,r00)

phi01~dbeta(s01,r01)

phi10~dbeta(s10,r10)

phi11~dbeta(s11,r11)

s1.<-s11+s10

r1.<-r11+r10

s.1<-s01+s11

r.1<- r01+r11

r0.<- r00+r01

s0.<-s00+s01

s.0<-s00+s10

r.0<-r00+r10

# for test 1=1 pd=1

ph1.~dbeta(s1.,r1.)

# for test 1=1 d=0

ph.1~dbeta(s.1,r.1)

# for test 1 = 0 d=1

ph0.~dbeta(s0.,r0.)

# for test 2=1 d=1

ph.0~dbeta(s.0,r.0)

th1.<-th11+th10

th.1<-th01+th11

th0.<-th01+th00

th.0<-th00+th10

# accuracy for test 1

tpf1<-ph1.*th1./pd1

fpf1<-(1-ph1.)*th1./(1-pd1)

pd1<-ph1.*th1.+ph0.*th0.

# accuracy for test 2

tpf2<-ph.1*th.1/pd2

fpf2<-(1-ph.1)*th.1/(1-pd2)

pd2<-ph.1*th.1+ph.0*th.0

}

# metastasis study

list(s00=8,r00=141,s01=65,r01=89,s10=20,r10=29,s11=210,r11=11,

m00=750,m01=257,m10=60,m11=234)

# alzheimers study

list(s00=5,r00=150,s01=85,r01=95,s10=25,r10=25,s11=191,r11=10,

m00=855,m01=280,m10=60,m11=211)

# initial values

list( g00=1, g01=1, g10=1, g11=1)