PCDSpline (version 1.0)

PCDReg.wf: Regression analysis of panel count data under the Gamma frailty non-homogeneous Poisson process model

Description

Fits the Gamma frailty non-homogeneous Poisson process model to panel count data using EM algorithm.

Usage

PCDReg.wf(DATA, order, placement, nknot, myknots, binit, ninit, ginit, t.seq, tol)

Arguments

DATA

use specified data structure.

order

the order of basis functions.

placement

logical, if TRUE knots are placed evenly across the observed intervals based on the input data set; if FALSE knots should be specified by the user. see myknots.

nknot

the number of knots to be used.

myknots

knots specified by the user whose length is nknot.

binit

initial estimate of regression coefficients.

ninit

initial estimate of gamma frailty variance parameter.

ginit

initial estimate of spline coefficients whose length should be (order+nknot-2) or (order+length(myknots)-2).

t.seq

an increasing sequence of points at which the baseline mean function is evaluated.

tol

the convergence criterion of the EM algorithm.

Value

beta

estimates of regression coefficients.

nu

estimates of gamma frailty variance parameter.

gamma

estimates of spline coefficients.

var.bn

the variance covariance matrix of regression coefficients estimates and gamma frailty variance parameter estimates.

knots

the knots used in the analysis; equally spaced knots or knots specified by the user.

bmf

estimated baseline mean function evaluated at the points t.seq; use pmf to plot the baseline mean function.

AIC

the Akaike information criterion.

BIC

the Bayesian information/Schwarz criterion.

flag

the indicator whether the Hessian matrix is non-singular. When flag="TRUE",the variance estimate may not be accurate.

Details

The above function fits the Gamma frailty non-homogeneous Poisson process model to panel count data via EM algorithm. To use this function, the data must have the same structure as in BladTumor1. For a discussion of order, number of interior knots and further details please see Yao et al. (2014+). The EM algorithm converges when the maximum of the absolute difference in the parameter estimates is less than tol.

References

Yao, B., Wang, L., and He, X. (2014+). Semiparametric regression analysis of panel count data allowing for within-subject correlation.

See Also

PCDHess.wf

Examples

##Simulated Data

n=13; #the number of subjects

##generate the number of observations for each subject
k=rpois(n,6)+1; K=max(k);
  
##generate random time gaps for each subject
y=matrix(,n,K);
for (i in 1:n){y[i,1:k[i]]=rexp(k[i],1)} 

##get observation time points for each subject
t=matrix(,n,K);
for (i in 1:n){
  for (j in 2:K){
    t[i,1] = y[i,1]
    t[i,j] = y[i,j]+t[i,j-1]
  }
}

##covariate x1 and x2 generated from Normal(0,0.5^2) and Bernoulli(0.5) respectively
x1=rnorm(n,0,0.5); x2=rbinom(n,1,0.5); x=cbind(x1,x2)

##true regression parameters and frailty variance parameter
beta1=1; beta2=-1; nu=0.5; 
parms=c(beta1,beta2)
phi=rgamma(n,nu,nu) 

##true baseline mean function
mu=function(t){2*t^(0.5)} 

##get the number of events between time intervals
z=matrix(,n,K);
xparms=c();for (s in 1:nrow(x)){xparms[s]=sum(x[s,]*parms)}
for (i in 1:n){
 z[i,1]=rpois(1,mu(t[i,1])*exp(xparms[i])*phi[i]) 
 if (k[i]>1){
 z[i,2:k[i]]=rpois(k[i]-1,(mu(t[i,2:k[i]])-mu(t[i,1:(k[i]-1)]))*exp(xparms[i])*phi[i])
 }
}

TestD<-list(t=t, x=x, z=z, k=k, K=K)

fit<-PCDReg.wf(DATA = TestD, order = 1, placement = TRUE, nknot = 3, myknots, 
               binit = c(0.5,-0.5), ninit = 0.1, ginit = seq(0.1,2),
               t.seq = seq(0,15,0.2), tol = 10^(-3))