#This function takes delta, leta(:=log(1/lambda)),data, pos as arguments.
#Computes log(likelihood) under null hypothesis and returns -log(likelihood).

mloglik.null <- function(leta,delta,data,pos) {
  lambda<-1/exp(leta)

  ntumor<-nrow(data)
  nmark<-ncol(data)
  
  lik.null<-1
  
  for(i in 1:ntumor){

    #subtract informative maker cases

    newpos<-pos[data[i,]>=0]
    newdata<-data[i,data[i,]>=0]
    m<-length(newdata)
    
    if(m>=1){ 
      if(newdata[1] == 1)
	lik.null<-lik.null*delta
      else 
	lik.null<-lik.null*(1-delta)
    
      if(m>=2){
	for(j in 1:(m-1)) {
	  
	  dist<-newpos[j+1]-newpos[j]
	  
	  if(newdata[j]==1){
	    if(newdata[j+1]==1)
	      lik.null<-lik.null*(1-(1-delta)*(1-exp(-lambda*dist)))
	    else 
	      lik.null<-lik.null*(1-delta)*(1-exp(-lambda*dist)) 
	  }     

	  else {
	    if(newdata[j+1]==0)
	      lik.null<-lik.null*(1-delta*(1-exp(-lambda*dist)))
            else
	      lik.null<-lik.null*delta*(1-exp(-lambda*dist))
	  }
	}
      }
    }
  }
  return(-log(lik.null))
}