pseudoPoisPHMM: Pseudo poisson data for fitting PHMM via GLMM

In phmm: Proportional Hazards Mixed-Effects Model

Description

Function for generating a pseudo Poisson data set which can be used to fit a PHMM using GLMM software. This follows the mixed-model extension Whitehead (1980), who described how to fit Cox (fixed effects) models with GLM software.

Usage

pseudoPoisPHMM(x)

Arguments

x	an object of class phmm.

Value

A data.frame with columns:

References

Whitehead, J. (1980). Fitting Cox's Regression Model to Survival Data using GLIM. Journal of the Royal Statistical Society. Series C, Applied statistics, 29(3). 268-.

See Also

phmm, traceHat

Examples

n <- 50      # total sample size
nclust <- 5  # number of clusters
clusters <- rep(1:nclust,each=n/nclust)
beta0 <- c(1,2)
set.seed(13)
#generate phmm data set
Z <- cbind(Z1=sample(0:1,n,replace=TRUE),
           Z2=sample(0:1,n,replace=TRUE),
           Z3=sample(0:1,n,replace=TRUE))
b <- cbind(rep(rnorm(nclust),each=n/nclust),rep(rnorm(nclust),each=n/nclust))
Wb <- matrix(0,n,2)
for( j in 1:2) Wb[,j] <- Z[,j]*b[,j]
Wb <- apply(Wb,1,sum)
T <- -log(runif(n,0,1))*exp(-Z[,c('Z1','Z2')]%*%beta0-Wb)
C <- runif(n,0,1)
time <- ifelse(T<C,T,C)
event <- ifelse(T<=C,1,0)
mean(event)
phmmd <- data.frame(Z)
phmmd$cluster <- clusters
phmmd$time <- time
phmmd$event <- event

fit.phmm <- phmm(Surv(time, event) ~ Z1 + Z2 + (-1 + Z1 + Z2 | cluster),
   phmmd, Gbs = 100, Gbsvar = 1000, VARSTART = 1,
   NINIT = 10, MAXSTEP = 100, CONVERG=90)

# Same data can be fit with glmer,
# though the correlation structures are different.
poisphmmd <- pseudoPoisPHMM(fit.phmm)

library(lme4)
fit.lmer <- glmer(m~-1+as.factor(time)+z1+z2+
  (-1+w1+w2|cluster)+offset(log(N)),
  as.data.frame(as(poisphmmd, "matrix")), family=poisson, nAGQ=0)

fixef(fit.lmer)[c("z1","z2")]
fit.phmm$coef

VarCorr(fit.lmer)$cluster
fit.phmm$Sigma

logLik(fit.lmer)
fit.phmm$loglik

traceHat(fit.phmm)

phmm documentation built on March 26, 2020, 5:10 p.m.