R/jung.rstat.R

In PROMISE: PRojection Onto the Most Interesting Statistical Evidence

`jung.rstat` <-
function(x,time.cens,strat=NULL)
#  x: matrix of array data; row:probe, clumn: subject
#  time.cens: matrix of time and censor variable; first column is time and the second is censor variable
#  strat=NULL: stratification vector, entries for subjects, same order as columns of Y

{
  if (is.null (strat)) strat<-rep(1, dim(time.cens)[1])
	ustrat<-unique(strat)
	nstrat<-length(ustrat)
	stat.sum<-0
	sum.n<-0
	for (i in 1:nstrat)
	{
    this.strat<-(strat==ustrat[i])
		this.x<-x[,this.strat]
    this.n<-sum(this.strat)
    this.time.cens<-time.cens[this.strat,]
    
         time<-this.time.cens[,1]
         cens<-this.time.cens[,2]

         miss.tc<-is.na(time)|is.na(cens)
         time<-time[!miss.tc]
         cens<-cens[!miss.tc]
         this.x<-this.x[,!miss.tc]

         miss.this.x<-is.na(this.x)

       	 tR<-apply(this.x,1,rank)
         R<-t(tR)
         n<-length(time)
       	 Y<-matrix(0,n,n)
       	 for (i in 1:n)
         {
       	  	ind<-(time>=time[i])
       		  Y[i,]<-ind/sum(ind)
       	 }
         # Compute observed statistic
       	 I.Y<-diag(1,n)-Y
         s<-t(I.Y)%*%cens
         mn.s<-mean(s)
         sd.s<-sqrt(apply(s, 2, var))
         s.cnt<-(s-mn.s)/sd.s

         mn.R<-(n+1)/2
         sd.R<-sqrt(var(1:n))
         cnt.R<-(R-mn.R)/sd.R

         n<-rowSums(!miss.this.x)
         cnt.R[miss.this.x]<-0

         res<-as.vector((cnt.R%*%s.cnt)/n)
    
		stat.sum<-stat.sum+this.n*res
		sum.n<-sum.n+this.n
	}
  stat.sum<-as.vector(stat.sum/sum.n)
	return(stat.sum)
}