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`scoresFromFit` <- function(icFIT, scores, dqfunc=NULL){
A<-icFIT$A
k<-dim(A)[[2]]
n<-dim(A)[[1]]
if (is.null(dqfunc) & scores=="general") stop("must provide dqfunc for general scores")
phat<-c(0,icFIT$pf)
Shat<- 1-cumsum(phat)
## ckstar gives scores associated with each element of the pf vector
if (scores=="logrank1"){
Stilde<- exp( - c(0,cumsum(phat[2:(k+1)]/Shat[1:k])) )
ckstar<- (1/phat[2:(k+1)])*( Shat[1:k]* log(Stilde[1:k]) - Shat[2:(k+1)]* log(Stilde[2:(k+1)]) )
} else if (scores=="logrank2"){
ckstar<- (1/phat[2:(k+1)])*c(
Shat[1:(k-1)]* log( Shat[1:(k-1)]) - Shat[2:(k)]* log( Shat[2:(k)]),
Shat[k]* log( Shat[k]))
} else if (scores=="wmw"){
ckstar<-Shat[1:k] + Shat[2:(k+1)] - 1
} else if (scores=="normal"){
ckstar<- (-1/phat[2:(k+1)])*(
dnorm( qnorm( Shat[1:k])) - dnorm( qnorm( Shat[2:(k+1)] )))
} else if (scores=="general"){
if (is.null(dqfunc)) stop("must provide dqfunc for general scores")
ckstar<- (-1/phat[2:(k+1)])*c(
dqfunc( Shat[1:k]) - dqfunc(Shat[2:(k+1)]))
}
p<-phat[2:(k+1)]
tempfunc<-function(Arow){
sum(Arow*p*ckstar)/sum(Arow*p)
}
## cc is the vector of ci values for each individual
## it is just the weighted average of the ckstar values for the possible intervals
## (for the ith individual it is intervals with A[i,j]=1) weighted by the pf values
cc<- apply(A,1,tempfunc)
cc
}
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