Nothing
cox.main=function(x, y, delta, nsteps=8, mincut=0.1, backfit=F, maxnumcut=1, dirp=0)
{
n=length(x[,1])
id=order(y)
y=y[id]
delta=delta[id]
x=x[id,]
x0=x
p.true=length(x0[1,])
x=cbind(x0, -x0)
marker.x=rep(1:p.true, 2)
direction.x=c(rep(-1, p.true), rep(1, p.true))
if(sum(abs(dirp))>0)
{index1=(1:p.true)[dirp==-1 | dirp==0]
index2=(1:p.true)[dirp==1 | dirp==0]
x=cbind(x0[,index1], x0[,index2])
marker.x=c((1:p.true)[index1], (1:p.true)[index2])
direction.x=c(rep(-1, length(index1)), rep(1, length(index2)))
}
p=length(x[1,])
if(mincut>0)
{effect.range=ceiling(n*mincut):floor(n*(1-mincut))}
if(mincut==0)
{effect.range=1:n}
score.current=rep(0,n)
x.out=x
order.index=delta.pool=x.replicate=matrix(0, n, p)
for(i in 1:p)
{idx=order(x[,i])
order.index[,i]=idx
delta.pool[,i]=delta[idx]
x.replicate[,i]=rep((1:n)[cumsum(table(x[,i]))], table(x[,i]))
}
id.in=NULL
id.out=1:p.true
p.out=p
zvalue=NULL
cut.value=NULL
direction=NULL
imax=NULL
res=as.list(NULL)
num.cut=rep(0, p.true)
tby=table(y)
ntime=length(unique(y))
time.index=rep(c(1, cumsum(tby)+1)[-(ntime+1)], tby)
num.risk=(n:1)[time.index]
time.index.plus=rep(cumsum(tby), tby)
risk.set=matrix(0, n, n)
for(i in 1:n)
{risk.set[(n-num.risk[i]+1):n,i]=1}
i1.pool=i3.pool=u.pool=matrix(0, n, p.out)
u0=(cumsum(delta/num.risk))[time.index.plus]
i10=(cumsum(delta*(num.risk-1)/num.risk^2))[time.index.plus]
for(i in 1:p.out)
{idx=order.index[,i]
idy=order(idx)
u.pool[,i]=u0[idx]
i1.pool[,i]=i10[idx]
risk.set.sub=risk.set[idx,]
w=apply(risk.set.sub,2,cumsum)
w=rbind(0, w[-n,])
w=t(w[idy,])
i3.pool[,i]=2*(diag((apply(delta/num.risk^2*w,2,cumsum))[time.index.plus,]))[idx]
}
count=1
loop=1
while(loop==1)
{score.bar=(rev(cumsum(rev(score.current)))/(n:1))
u0.stat=sum(delta*(score.current-score.bar[time.index]))
i0.stat=sum(delta/num.risk*((rev(cumsum(rev(score.current^2)))-score.bar^2*(n:1)))[time.index])
i.pool=matrix(0, n, p.out)
for(i in 1:p.out)
{
idx=order.index[,i]
i.pool[,i]=i1.pool[,i]+2*u.pool[,i]*score.current[idx]-2*(cumsum(delta/num.risk*score.bar[time.index]))[time.index.plus][idx]-i3.pool[,i]
}
score.stat=u0.stat+apply(delta.pool-u.pool,2,cumsum)
v.stat=i0.stat+apply(i.pool,2,cumsum)
for(i in 1:p.out)
{idx=x.replicate[,i]
v.stat[,i]=v.stat[idx ,i]
score.stat[,i]=score.stat[idx, i]
}
test=score.stat/sqrt(v.stat+1e-8)
if(mincut==0)
{mtest=apply(test,2,max)}
if(mincut>0)
{mtest=rep(0, p.out)
for(i in 1:p.out)
{test.post=test[max(effect.range)+1,i]
test0=test[effect.range,i]
test0=test0[test0!=test.post]
mtest[i]=max(test0)}
}
mcut=rep(0, p.out)
i0=rep(0, p.out)
for(i in 1:p.out)
{i0[i]=max(effect.range[test[effect.range,i]==mtest[i]])+1
if(i0[i]>n)
mcut[i]=Inf
if(i0[i]<=n)
mcut[i]=x.out[order.index[,i],i][i0[i]]
}
i.sel=(1:p.out)[mtest==max(mtest)][1]
score.current=score.current+(x.out[,i.sel]<mcut[i.sel])
marker.sel=marker.x[i.sel]
id.in=c(id.in, marker.sel)
direction=c(direction, direction.x[i.sel])
cut.value=c(cut.value, -mcut[i.sel]*direction.x[i.sel])
num.cut[marker.sel]=num.cut[marker.sel]+1
if(num.cut[marker.sel]==maxnumcut)
{id.exclude=(1:p.out)[marker.x==marker.sel]
x.out=x.out[,-id.exclude,drop=F]
order.index=order.index[, -id.exclude,drop=F]
delta.pool=delta.pool[,-id.exclude,drop=F]
x.replicate=x.replicate[, -id.exclude,drop=F]
i1.pool=i1.pool[,-id.exclude,drop=F]
i3.pool=i3.pool[,-id.exclude,drop=F]
u.pool=u.pool[,-id.exclude,drop=F]
direction.x=direction.x[-id.exclude]
marker.x=marker.x[-id.exclude]
p.out=p.out-length(id.exclude)
}
if(backfit==T)
{if(count>1)
{x.adj=x0[, id.in]
x.adj=-t(t(x.adj)*direction)
cutp=-cut.value*direction
fit=backfit.cox.main(x.adj, y, delta, cutp, mincut=mincut)
jmax=id.in
cutp=-fit$cutp*direction
maxdir=direction
res[[count]]=cbind(jmax, cutp, maxdir)
zvalue=c(zvalue, max(fit$zscore))
score.current=apply((t(x.adj)<fit$cutp),2,sum)
}
if(count==1)
{jmax=id.in
cutp=cut.value
maxdir=direction
res[[count]]=cbind(jmax, cutp, maxdir)
zvalue=c(zvalue, max(mtest))
}
}
if(backfit==F)
{cutp=cut.value
maxdir=direction
jmax=id.in
zvalue=c(zvalue, max(mtest))
maxsc=zvalue
res[[count]]=cbind(jmax, cutp, maxdir, maxsc)
}
count=count+1
loop=(length(id.in)<nsteps)
}
return(list(res=res, maxsc=zvalue))
}
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