R/LogL_pss1I.R

In cold: Count Longitudinal Data

LogL.pss1I<- function(parameters, X, data, integrate, trace)
{
  
  loglik1 <- function(param, X, y,integrate, trace)
  {
    npar <-as.integer(length(param)-1)
    beta<- as.double(param[1:(npar-1)])
    bt<- as.double(param[1:(npar-1)])
    rho<-as.double(param[npar])
    omega<-as.double(param[npar+1])
    y[is.na(y)]<-(-1)
    y<- as.integer(y)
    n <- as.integer(length(y))
    x<-matrix(as.double(X),nrow=n,ncol=npar-1)
    theta<- work<- as.double(rep(0,n))
    logL <- as.double(0)
    
    li<-as.double(integrate$li)
    ls<-as.double(integrate$ls)
    epsabs<-as.double(integrate$epsabs)
    epsrel<-as.double(integrate$epsrel)
    limit<-as.integer(integrate$limit)
    key<-as.integer(integrate$key)
    
    m <- max(y)
    link <- as.integer(1)
    
    results <- .Fortran("intp",logL,bt,beta,rho,omega,
                        npar,link,m,x,y,theta,work,n,li,ls,epsabs,epsrel,key,limit,PACKAGE="cold")
    
    return(results[[1]])}
  
  if(trace)	cat(paste(format(parameters[length(parameters)-1], digit=4), collapse=" "), "\t")
  if(trace)	cat(paste("\t",(format(parameters[length(parameters)], digit=4)), collapse=" "), "\t")
  
  nparam<-length(parameters)
  omega1<-as.double(parameters[nparam])
  ti.repl<-data[[1]]
  cumti.repl<-cumsum(ti.repl)
  n.cases<- as.integer(length(ti.repl))
  y<-data[[2]]
  logL1<-0
  k1<-1
  npar <- as.integer(length(parameters))
  rho<- as.double(parameters[npar-1])
  
  if (rho < 0 |  rho >= 1 )
  { logL1<-NaN
  if(trace)	cat(paste("\t",(format( logL1,digit=6)), collapse=" "), "\n")
  return(NaN)}
  
  else if (rho > 0 &  rho < 1 )
  {
    for (i in 1:n.cases)
    {
      k2<-cumti.repl[i]
      
      z<-loglik1(param=parameters,X=X[k1:k2,], y=y[k1:k2],integrate=integrate,trace=trace)
      #logL1 gives the log-likelihood
      
      if  (z=="Inf" )  z<-(1e+150)
      
      logL1<-logL1+ log(z*(1/(sqrt(2*pi)*exp(omega1/2))))
      k1<-k2+1
    }
    
    if(trace)	cat(paste("\t",(format( logL1,digit=6)), collapse=" "), "\n")
    return(-logL1)}
}