Nothing
lm.main=function(x, y, nsteps=8, backfit=F, mincut=0.1, maxnumcut=1, dirp=0)
{n=length(y)
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)
num.cut=rep(0, p.true)
x.out=x
order.index=matrix(0, n, p)
for(i in 1:p)
{order.index[,i]=order(x.out[,i])}
y.pool=x.replicate=matrix(0, n, p)
for(i in 1:p)
{y.pool[,i]=y[order.index[,i]]
x.replicate[,i]=rep((1:n)[cumsum(table(x[,i]))], table(x[,i]))}
id.in=NULL
zvalue=NULL
cut.value=NULL
direction=NULL
res=as.list(NULL)
p.out=p
muhat=mean(y)
sigma=sum((y-muhat)^2)/(n-1)
loop=1
count=1
while(loop==1)
{score.pool=matrix(0, n, p.out)
for(i in 1:p.out)
{score.pool[,i]=score.current[order.index[,i]]}
score.stat=apply(y.pool-muhat,2,cumsum)+sum((y-muhat)*score.current)
v.stat=sigma*(2*apply(score.pool,2,cumsum)+1:n+sum(score.current^2)-(sum(score.current)+1:n)^2/n)
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+1*(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]
y.pool=y.pool[,-id.exclude,drop=F]
x.replicate=x.replicate[, -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.lm.main( x.adj, y,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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