CVSummary1SAMP<-function(CVRes){

CVRes<-CVRes[with(CVRes,order(id)),]
p<-seq(0,1,0.01)  ##sets up a grid of different cutoff values.
l_p<-length(p)

AUC<-Sensitivity<-Specificity<-New_Sensitivity<-New_Specificity<-PCC<-New_PCC<-PPV<-NPV<-Unclass<-WidthCI<-Cutoff<-Mean_Lead_time<-Median_Lead_time<-ProbPredREF<-vector(length=6)
Mean_Pred_time<-Median_Pred_time<-Mean_Obs<-Median_Obs<-Mean_TotalObs<-Median_TotalObs<-My_Specificity<-My_Sensitivity<-My_PCC<-My_PPV<-My_NPV<-vector(length=6)

SensMtot<-SpecMtot<-SensCtot<-SpecCtot<-SensREtot<-SpecREtot<-SensMCItot<-SpecMCItot<-SensCCItot<-SpecCCItot<-SensRECItot<-SpecRECItot<-vector(length=6)
PCCMtot<-PCCCtot<-PCCREtot<-PCCMCItot<-PCCCCItot<-PCCRECItot<-PPVMtot<-PPVCtot<-PPVREtot<-PPVMCItot<-PPVCCItot<-PPVRECItot<-NPVMtot<-NPVCtot<-NPVREtot<-NPVMCItot<-NPVCCItot<-NPVRECItot<-vector(length=6)
SensMtotNew<-SpecMtotNew<-SensCtotNew<-SpecCtotNew<-SensREtotNew<-SpecREtotNew<-SensMCItotNew<-SpecMCItotNew<-SensCCItotNew<-SpecCCItotNew<-SensRECItotNew<-SpecRECItotNew<-vector(length=6)
PCCMtotNew<-PCCCtotNew<-PCCREtotNew<-PCCMCItotNew<-PCCCCItotNew<-PCCRECItotNew<-vector(length=6)
MyPCCMCItot<-MyPCCCCItot<-MyPCCRECItot<-MySpecMCItot<-MySpecCCItot<-MySpecRECItot<-MyNPVMCItot<-MyNPVCCItot<-MyNPVRECItot<-vector(length=6)

Resul<-CVRes ##Label the number of the observation.
for(i in unique(Resul$id)){Resul$Ob[Resul$id == i] <- 1:sum(Resul$id == i)}

IndProf <- getProfiles(t="time", y=c("Marg2","Cond2","RanEf2","Marg2L","Marg2H","Cond2L","Cond2H","RanEf2L","RanEf2H","Status","Ob"),id="id", data=Resul)
l<-length(unique(Resul$id))
SANAD_status<-1-aggregate(Status~id,max,data=Resul)$Status
Allocation_Marg<-matrix(nrow=l,ncol=l_p)
Allocation_Cond<-matrix(nrow=l,ncol=l_p)
Allocation_RE<-matrix(nrow=l,ncol=l_p)

Allocation_Marg_CI<-matrix(nrow=l,ncol=l_p)
Allocation_Cond_CI<-matrix(nrow=l,ncol=l_p)
Allocation_RE_CI<-matrix(nrow=l,ncol=l_p)

Pred_timeM<-matrix(nrow=l,ncol=l_p)
Pred_timeC<-matrix(nrow=l,ncol=l_p)
Pred_timeRE<-matrix(nrow=l,ncol=l_p)
Pred_timeMCI<-matrix(nrow=l,ncol=l_p)
Pred_timeCCI<-matrix(nrow=l,ncol=l_p)
Pred_timeRECI<-matrix(nrow=l,ncol=l_p)

Ob_timeM<-matrix(nrow=l,ncol=l_p)
Ob_timeC<-matrix(nrow=l,ncol=l_p)
Ob_timeRE<-matrix(nrow=l,ncol=l_p)
Ob_timeMCI<-matrix(nrow=l,ncol=l_p)
Ob_timeCCI<-matrix(nrow=l,ncol=l_p)
Ob_timeRECI<-matrix(nrow=l,ncol=l_p)
Final_timeM<-vector(length=l)
 for(k in 1:l_p){
 for(i in 1:l){
  Prof<-IndProf[[i]]
  l_prof<-dim(Prof)[1] ##Number of visits for patient i
 Final_timeM[i]<-Prof[l_prof,"time"]
  for(j in 1:l_prof){ifelse(Prof[j,"Marg2"]>p[k],{Allocation_Marg[i,k]<-1;Pred_timeM[i,k]<-Prof[j,"time"];Ob_timeM[i,k]<-Prof[j,"Ob"];break},{Allocation_Marg[i,k]<-0;Pred_timeM[i,k]<-Prof[j,"time"];Ob_timeM[i,k]<-Prof[j,"Ob"]})}
  for(j in 1:l_prof){ifelse(Prof[j,"Cond2"]>p[k],{Allocation_Cond[i,k]<-1;Pred_timeC[i,k]<-Prof[j,"time"];Ob_timeC[i,k]<-Prof[j,"Ob"];break},{Allocation_Cond[i,k]<-0;Pred_timeC[i,k]<-Prof[j,"time"];Ob_timeC[i,k]<-Prof[j,"Ob"]})}
  for(j in 1:l_prof){ifelse(Prof[j,"RanEf2"]>p[k],{Allocation_RE[i,k]<-1;Pred_timeRE[i,k]<-Prof[j,"time"];Ob_timeRE[i,k]<-Prof[j,"Ob"];break},{Allocation_RE[i,k]<-0;Pred_timeRE[i,k]<-Prof[j,"time"];Ob_timeRE[i,k]<-Prof[j,"Ob"]})}
 for(j in 1:l_prof){ifelse(Prof[j,"Marg2L"]>p[k],{Allocation_Marg_CI[i,k]<-1;Pred_timeMCI[i,k]<-Prof[j,"time"];Ob_timeMCI[i,k]<-Prof[j,"Ob"];break},{ifelse(Prof[j,"Marg2H"]<p[k],Allocation_Marg_CI[i,k]<-0,Allocation_Marg_CI[i,k]<-2);Pred_timeMCI[i,k]<-Prof[j,"time"];Ob_timeMCI[i,k]<-Prof[j,"Ob"]})}
 for(j in 1:l_prof){ifelse(Prof[j,"Cond2L"]>p[k],{Allocation_Cond_CI[i,k]<-1;Pred_timeCCI[i,k]<-Prof[j,"time"];Ob_timeCCI[i,k]<-Prof[j,"Ob"];break},{ifelse(Prof[j,"Cond2H"]<p[k],Allocation_Cond_CI[i,k]<-0,Allocation_Cond_CI[i,k]<-2);Pred_timeCCI[i,k]<-Prof[j,"time"];Ob_timeCCI[i,k]<-Prof[j,"Ob"]})}
 for(j in 1:l_prof){ifelse(Prof[j,"RanEf2L"]>p[k],{Allocation_RE_CI[i,k]<-1;Pred_timeRECI[i,k]<-Prof[j,"time"];Ob_timeRECI[i,k]<-Prof[j,"Ob"];break},{ifelse(Prof[j,"RanEf2H"]<p[k],Allocation_RE_CI[i,k]<-0,Allocation_RE_CI[i,k]<-2);Pred_timeRECI[i,k]<-Prof[j,"time"];Ob_timeRECI[i,k]<-Prof[j,"Ob"]})}
              }
                }

SensNewM<-SensNewMCI<-SensNewC<-SensNewCCI<-SensNewRE<-SensNewRECI<-SpecNewM<-SpecNewMCI<-SpecNewC<-SpecNewCCI<-SpecNewRE<-SpecNewRECI<-SensM<-SensC<-SensRE<-SpecM<-SpecC<-SpecRE<-PCC_M<-PCC_C<-PCC_RE<-vector(length=l_p)
SensMCI<-SensCCI<-SensRECI<-SpecMCI<-SpecCCI<-SpecRECI<-PCC_MCI<-PCC_CCI<-PCC_RECI<-PPVM<-PPVMCI<-PPVC<-PPVCCI<-PPVRE<-PPVRECI<-NPVM<-NPVMCI<-NPVC<-NPVCCI<-NPVRE<-NPVRECI<-UnclassM<-UnclassMCI<-vector(length=l_p)
UnclassC<-UnclassCCI<-UnclassRE<-UnclassRECI<-PPRM<-PPRC<-PPRre<-PPRMCI<-PPRCCI<-PPRreCI<-PCC_MNew<-PCC_CNew<-PCC_RENew<-PCC_MNewCI<-PCC_CNewCI<-PCC_RENewCI<-vector(length=l_p)
MyPCCMCI<-MyPCCCCI<-MyPCCRECI<-MySpecMCI<-MySpecCCI<-MySpecRECI<-MyNPVMCI<-MyNPVCCI<-MyNPVRECI<-vector(length=l_p)

for(k in 1:l_p){
Marg_ClassT<-table(factor(SANAD_status,levels=c(0,1)),factor(Allocation_Marg[,k],levels=c(0,1,2)))
Marg_ClassT<-addmargins(Marg_ClassT,c(1,2),sum)
Cond_ClassT<-table(factor(SANAD_status,levels=c(0,1)),factor(Allocation_Cond[,k],levels=c(0,1,2)))
Cond_ClassT<-addmargins(Cond_ClassT,c(1,2),sum)
RE_ClassT<-table(factor(SANAD_status,levels=c(0,1)),factor(Allocation_RE[,k],levels=c(0,1,2)))
RE_ClassT<-addmargins(RE_ClassT,c(1,2),sum) 
SensM[k]<-Marg_ClassT[2,2]/Marg_ClassT[2,4]
SensC[k]<-Cond_ClassT[2,2]/Cond_ClassT[2,4]
SensRE[k]<-RE_ClassT[2,2]/RE_ClassT[2,4]
SpecM[k]<-Marg_ClassT[1,1]/Marg_ClassT[1,4]
SpecC[k]<-Cond_ClassT[1,1]/Cond_ClassT[1,4]
SpecRE[k]<-RE_ClassT[1,1]/RE_ClassT[1,4]
SensNewM[k]<-Marg_ClassT[2,2]/(Marg_ClassT[2,4]-Marg_ClassT[2,3])
SensNewC[k]<-Cond_ClassT[2,2]/(Cond_ClassT[2,4]-Cond_ClassT[2,3])
SensNewRE[k]<-RE_ClassT[2,2]/(RE_ClassT[2,4]-RE_ClassT[2,3])
SpecNewM[k]<-Marg_ClassT[1,1]/(Marg_ClassT[1,4]-Marg_ClassT[1,3])
SpecNewC[k]<-Cond_ClassT[1,1]/(Cond_ClassT[1,4]-Cond_ClassT[1,3])
SpecNewRE[k]<-RE_ClassT[1,1]/(RE_ClassT[1,4]-RE_ClassT[1,3])
PCC_M[k]<-sum(Marg_ClassT[1,1]+Marg_ClassT[2,2])/Marg_ClassT[3,4]
PCC_C[k]<-sum(Cond_ClassT[1,1]+Cond_ClassT[2,2])/Cond_ClassT[3,4]
PCC_RE[k]<-sum(RE_ClassT[1,1]+RE_ClassT[2,2])/RE_ClassT[3,4]
PCC_MNew[k]<-sum(Marg_ClassT[1,1]+Marg_ClassT[2,2])/(Marg_ClassT[3,4]-Marg_ClassT[3,3])
PCC_CNew[k]<-sum(Cond_ClassT[1,1]+Cond_ClassT[2,2])/(Cond_ClassT[3,4]-Cond_ClassT[3,3])
PCC_RENew[k]<-sum(RE_ClassT[1,1]+RE_ClassT[2,2])/(RE_ClassT[3,4]-RE_ClassT[3,3])
PPVM[k]<-Marg_ClassT[2,2]/Marg_ClassT[3,2]
PPVC[k]<-Cond_ClassT[2,2]/Cond_ClassT[3,2]
PPVRE[k]<-RE_ClassT[2,2]/RE_ClassT[3,2]
NPVM[k]<-Marg_ClassT[1,1]/Marg_ClassT[3,1]
NPVC[k]<-Cond_ClassT[1,1]/Cond_ClassT[3,1]
NPVRE[k]<-RE_ClassT[1,1]/RE_ClassT[3,1]
PPRM[k]<-(Marg_ClassT[1,2]+Marg_ClassT[2,2])/Marg_ClassT[3,4]
PPRC[k]<-(Cond_ClassT[1,2]+Cond_ClassT[2,2])/Cond_ClassT[3,4]
PPRre[k]<-(RE_ClassT[1,2]+RE_ClassT[2,2])/RE_ClassT[3,4]
UnclassM[k]<-Marg_ClassT[3,3]/Marg_ClassT[3,4]
UnclassC[k]<-Cond_ClassT[3,3]/Cond_ClassT[3,4]
UnclassRE[k]<-RE_ClassT[3,3]/RE_ClassT[3,4]
Marg_ClassTCI<-table(factor(SANAD_status,levels=c(0,1)),factor(Allocation_Marg_CI[,k],levels=c(0,1,2)))
Marg_ClassTCI<-addmargins(Marg_ClassTCI,c(1,2),sum)
Cond_ClassTCI<-table(factor(SANAD_status,levels=c(0,1)),factor(Allocation_Cond_CI[,k],levels=c(0,1,2)))
Cond_ClassTCI<-addmargins(Cond_ClassTCI,c(1,2),sum)
RE_ClassTCI<-table(factor(SANAD_status,levels=c(0,1)),factor(Allocation_RE_CI[,k],levels=c(0,1,2)))
RE_ClassTCI<-addmargins(RE_ClassTCI,c(1,2),sum) 
SensMCI[k]<-Marg_ClassTCI[2,2]/Marg_ClassTCI[2,4]
SensCCI[k]<-Cond_ClassTCI[2,2]/Cond_ClassTCI[2,4]
SensRECI[k]<-RE_ClassTCI[2,2]/RE_ClassTCI[2,4]
SpecMCI[k]<-Marg_ClassTCI[1,1]/Marg_ClassTCI[1,4]
SpecCCI[k]<-Cond_ClassTCI[1,1]/Cond_ClassTCI[1,4]
SpecRECI[k]<-RE_ClassTCI[1,1]/RE_ClassTCI[1,4]
SensNewMCI[k]<-Marg_ClassTCI[2,2]/(Marg_ClassTCI[2,4]-Marg_ClassTCI[2,3])
SensNewCCI[k]<-Cond_ClassTCI[2,2]/(Cond_ClassTCI[2,4]-Cond_ClassTCI[2,3])
SensNewRECI[k]<-RE_ClassTCI[2,2]/(RE_ClassTCI[2,4]-RE_ClassTCI[2,3])
SpecNewMCI[k]<-Marg_ClassTCI[1,1]/(Marg_ClassTCI[1,4]-Marg_ClassTCI[1,3])
SpecNewCCI[k]<-Cond_ClassTCI[1,1]/(Cond_ClassTCI[1,4]-Cond_ClassTCI[1,3])
SpecNewRECI[k]<-RE_ClassTCI[1,1]/(RE_ClassTCI[1,4]-RE_ClassTCI[1,3])
MySpecMCI[k]<-(Marg_ClassTCI[1,1]+Marg_ClassTCI[1,3])/Marg_ClassTCI[1,4]
MySpecCCI[k]<-(Cond_ClassTCI[1,1]+Cond_ClassTCI[1,3])/Cond_ClassTCI[1,4]
MySpecRECI[k]<-(RE_ClassTCI[1,1]+RE_ClassTCI[1,3])/RE_ClassTCI[1,4]
PCC_MCI[k]<-sum(Marg_ClassTCI[1,1]+Marg_ClassTCI[2,2])/Marg_ClassTCI[3,4]
PCC_CCI[k]<-sum(Cond_ClassTCI[1,1]+Cond_ClassTCI[2,2])/Cond_ClassTCI[3,4]
PCC_RECI[k]<-sum(RE_ClassTCI[1,1]+RE_ClassTCI[2,2])/RE_ClassTCI[3,4]
PCC_MNewCI[k]<-sum(Marg_ClassTCI[1,1]+Marg_ClassTCI[2,2])/(Marg_ClassTCI[3,4]-Marg_ClassTCI[3,3])
PCC_CNewCI[k]<-sum(Cond_ClassTCI[1,1]+Cond_ClassTCI[2,2])/(Cond_ClassTCI[3,4]-Cond_ClassTCI[3,3])
PCC_RENewCI[k]<-sum(RE_ClassTCI[1,1]+RE_ClassTCI[2,2])/(RE_ClassTCI[3,4]-RE_ClassTCI[3,3])
MyPCCMCI[k]<-(Marg_ClassTCI[1,1]+Marg_ClassTCI[1,3]+Marg_ClassTCI[2,2])/Marg_ClassTCI[3,4]
MyPCCCCI[k]<-(Cond_ClassTCI[1,1]+Cond_ClassTCI[1,3]+Cond_ClassTCI[2,2])/Cond_ClassTCI[3,4]
MyPCCRECI[k]<-(RE_ClassTCI[1,1]+RE_ClassTCI[1,3]+RE_ClassTCI[2,2])/RE_ClassTCI[3,4]
PPVMCI[k]<-Marg_ClassTCI[2,2]/Marg_ClassTCI[3,2]
PPVCCI[k]<-Cond_ClassTCI[2,2]/Cond_ClassTCI[3,2]
PPVRECI[k]<-RE_ClassTCI[2,2]/RE_ClassTCI[3,2]
MyNPVMCI[k]<-(Marg_ClassTCI[1,1]+Marg_ClassTCI[1,3])/(Marg_ClassTCI[3,1]+Marg_ClassTCI[3,3])
MyNPVCCI[k]<-(Cond_ClassTCI[1,1]+Cond_ClassTCI[1,3])/(Cond_ClassTCI[3,1]+Cond_ClassTCI[3,3])
MyNPVRECI[k]<-(RE_ClassTCI[1,1]+RE_ClassTCI[1,3])/(RE_ClassTCI[3,1]+RE_ClassTCI[3,3])
NPVMCI[k]<-Marg_ClassTCI[1,1]/Marg_ClassTCI[3,1]
NPVCCI[k]<-Cond_ClassTCI[1,1]/Cond_ClassTCI[3,1]
NPVRECI[k]<-RE_ClassTCI[1,1]/RE_ClassTCI[3,1]
PPRMCI[k]<-(Marg_ClassTCI[1,2]+Marg_ClassTCI[2,2])/Marg_ClassTCI[3,4]
PPRCCI[k]<-(Cond_ClassTCI[1,2]+Cond_ClassTCI[2,2])/Cond_ClassTCI[3,4]
PPRreCI[k]<-(RE_ClassTCI[1,2]+RE_ClassTCI[2,2])/RE_ClassTCI[3,4]
UnclassMCI[k]<-Marg_ClassTCI[3,3]/Marg_ClassTCI[3,4]
UnclassCCI[k]<-Cond_ClassTCI[3,3]/Cond_ClassTCI[3,4]
UnclassRECI[k]<-RE_ClassTCI[3,3]/RE_ClassTCI[3,4]
}


UNCLASS<-cbind(UnclassM,UnclassC,UnclassRE,UnclassMCI,UnclassCCI,UnclassRECI)
SensMtot<-SensM
SpecMtot<-SpecM
SensCtot<-SensC
SpecCtot<-SpecC
SensREtot<-SensRE
SpecREtot<-SpecRE
SensMCItot<-SensMCI
SpecMCItot<-SpecMCI
SensCCItot<-SensCCI
SpecCCItot<-SpecCCI
SensRECItot<-SensRECI
SpecRECItot<-SpecRECI

SensMtotNew<-SensNewM
SpecMtotNew<-SpecNewM
SensCtotNew<-SensNewC
SpecCtotNew<-SpecNewC
SensREtotNew<-SensNewRE
SpecREtotNew<-SpecNewRE
SensMCItotNew<-SensNewMCI
SpecMCItotNew<-SpecNewMCI
SensCCItotNew<-SensNewCCI
SpecCCItotNew<-SpecNewCCI
SensRECItotNew<-SensNewRECI
SpecRECItotNew<-SpecNewRECI

PCCMtot<-PCC_M
PCCCtot<-PCC_C
PCCREtot<-PCC_RE
PCCMCItot<-PCC_MCI
PCCCCItot<-PCC_CCI
PCCRECItot<-PCC_RECI
PCCMtotNew<-PCC_MNew
PCCCtotNew<-PCC_CNew
PCCREtotNew<-PCC_RENew
PCCMCItotNew<-PCC_MNewCI
PCCCCItotNew<-PCC_CNewCI
PCCRECItotNew<-PCC_RENewCI

PPVMtot<-PPVM
PPVCtot<-PPVC
PPVREtot<-PPVRE
PPVMCItot<-PPVMCI
PPVCCItot<-PPVCCI
PPVRECItot<-PPVRECI

NPVMtot<-NPVM
NPVCtot<-NPVC
NPVREtot<-NPVRE
NPVMCItot<-NPVMCI
NPVCCItot<-NPVCCI
NPVRECItot<-NPVRECI
MyPCCMCItot<-MyPCCMCI
MyPCCCCItot<-MyPCCCCI
MyPCCRECItot<-MyPCCRECI
MyNPVMCItot<-MyNPVMCI
MyNPVCCItot<-MyNPVCCI
MyNPVRECItot<-MyNPVRECI
MySpecMCItot<-MySpecMCI
MySpecCCItot<-MySpecCCI
MySpecRECItot<-MySpecRECI

aucM<-trapz(SpecM,SensM)
aucC<-trapz(SpecC,SensC)
aucRE<-trapz(SpecRE,SensRE)
aucMCI<-trapz(SpecNewMCI,SensNewMCI)
aucCCI<-trapz(SpecNewCCI,SensNewCCI)
aucRECI<-trapz(SpecNewRECI,SensNewRECI)
D_M<-sqrt((1-SensM)^2+(1-SpecM)^2)
D_C<-sqrt((1-SensC)^2+(1-SpecC)^2)
D_RE<-sqrt((1-SensRE)^2+(1-SpecRE)^2)
D_MCI<-sqrt((1-SensMCI)^2+(1-SpecMCI)^2)
D_CCI<-sqrt((1-SensCCI)^2+(1-SpecCCI)^2)
D_RECI<-sqrt((1-SensRECI)^2+(1-SpecRECI)^2)
m_opt<-which.min(D_M)
c_opt<-which.min(D_C)
r_opt<-which.min(D_RE)
m_optCI<-which.min(D_MCI)
c_optCI<-which.min(D_CCI)
r_optCI<-which.min(D_RECI)
SensMm<-SensM[m_opt]
SpecMm<-SpecM[m_opt]
SensMmNew<-SensNewM[m_opt]
SpecMmNew<-SpecNewM[m_opt]
PCC_Mopt<-PCC_M[m_opt]
PCC_MoptNew<-PCC_MNew[m_opt]
MyPCCMCIopt<-MyPCCMCI[m_opt]
MyNPVMCIopt<-MyNPVMCI[m_opt]
MySpecMCIopt<-MySpecMCI[m_opt]
PPV_M<-PPVM[m_opt]
NPV_M<-NPVM[m_opt]
PPR_M<-PPRM[m_opt]
UnclassM<-UnclassM[m_opt]

SensCc<-SensC[c_opt]
SpecCc<-SpecC[c_opt]
PCC_Copt<-PCC_C[c_opt]
PCC_CoptNew<-PCC_CNew[c_opt]
PPV_C<-PPVC[c_opt]
MyPCCCCIopt<-MyPCCCCI[c_opt]
MyNPVCCIopt<-MyNPVCCI[c_opt]
MySpecCCIopt<-MySpecCCI[c_opt]
NPV_C<-NPVC[c_opt]
PPR_C<-PPRC[c_opt]
UnclassC<-UnclassC[c_opt]
SensCcNew<-SensNewC[c_opt]
SpecCcNew<-SpecNewC[c_opt]

SensREr<-SensRE[r_opt]
SpecREr<-SpecRE[r_opt]
PCC_REopt<-PCC_RE[r_opt]
PCC_REoptNew<-PCC_RENew[r_opt]
PPV_RE<-PPVRE[r_opt]
NPV_RE<-NPVRE[r_opt]
PPR_RE<-PPRre[r_opt]
UnclassRE<-UnclassRE[r_opt]
SensRErNew<-SensNewRE[r_opt]
SpecRErNew<-SpecNewRE[r_opt]

SensMmCI<-SensMCI[m_opt]
SpecMmCI<-SpecMCI[m_opt]
PCC_MoptCI<-PCC_MCI[m_opt]
PCC_MoptCINew<-PCC_MNewCI[m_opt]
PPV_MCI<-PPVMCI[m_opt]
NPV_MCI<-NPVMCI[m_opt]
PPR_MCI<-PPRMCI[m_opt]
UnclassMCI<-UnclassMCI[m_opt]
SensMmCINew<-SensNewMCI[m_opt]
SpecMmCINew<-SpecNewMCI[m_opt]

SensCcCI<-SensCCI[c_opt]
SpecCcCI<-SpecCCI[c_opt]
PCC_CoptCI<-PCC_CCI[c_opt]
PCC_CoptCINew<-PCC_CNewCI[c_opt]
PPV_CCI<-PPVCCI[c_opt]
NPV_CCI<-NPVCCI[c_opt]
PPR_CCI<-PPRCCI[c_opt]
UnclassCCI<-UnclassCCI[c_opt]
SensCcCINew<-SensNewCCI[c_opt]
SpecCcCINew<-SpecNewCCI[c_opt]

SensRErCI<-SensRECI[r_opt]
SpecRErCI<-SpecRECI[r_opt]
PCC_REoptCI<-PCC_RECI[r_opt]
PCC_REoptCINew<-PCC_RENewCI[r_opt]
PPV_RECI<-PPVRECI[r_opt]
NPV_RECI<-NPVRECI[r_opt]
PPR_RECI<-PPRreCI[r_opt]
MyPCCRECIopt<-MyPCCRECI[r_opt]
MyNPVRECIopt<-MyNPVRECI[r_opt]
MySpecRECIopt<-MySpecRECI[r_opt]
UnclassRECI<-UnclassRECI[r_opt]
SensRErCINew<-SensNewRECI[r_opt]
SpecRErCINew<-SpecNewRECI[r_opt]
AUC<-c(aucM,aucC,aucRE,aucMCI,aucCCI,aucRECI)
Cutoff<-c(p[m_opt],p[c_opt],p[r_opt],p[m_opt],p[c_opt],p[r_opt])
Sensitivity<-c(SensMm,SensCc,SensREr,SensMmCI,SensCcCI,SensRErCI)
Specificity<-c(SpecMm,SpecCc,SpecREr,SpecMmCI,SpecCcCI,SpecRErCI)
New_Sensitivity<-c(SensMmNew,SensCcNew,SensRErNew,SensMmCINew,SensCcCINew,SensRErCINew)
New_Specificity<-c(SpecMmNew,SpecCcNew,SpecRErNew,SpecMmCINew,SpecCcCINew,SpecRErCINew)
PCC<-c(PCC_Mopt,PCC_Copt,PCC_REopt,PCC_MoptCI,PCC_CoptCI,PCC_REoptCI)
New_PCC<-c(PCC_MoptNew,PCC_CoptNew,PCC_REoptNew,PCC_MoptCINew,PCC_CoptCINew,PCC_REoptCINew)
My_PCC<-c(0,0,0,MyPCCMCIopt,MyPCCCCIopt,MyPCCRECIopt)
My_Specificity<-c(0,0,0,MySpecMCIopt,MySpecCCIopt,MySpecRECIopt)
My_NPV<-c(0,0,0,MyNPVMCIopt,MyNPVCCIopt,MyNPVRECIopt)
PPV<-c(PPV_M,PPV_C,PPV_RE,PPV_MCI,PPV_CCI,PPV_RECI)
NPV<-c(NPV_M,NPV_C,NPV_RE,NPV_MCI,NPV_CCI,NPV_RECI)
ProbPredREF<-c(PPR_M,PPR_C,PPR_RE,PPR_MCI,PPR_CCI,PPR_RECI)
Unclass<-c(UnclassM,UnclassC,UnclassRE,UnclassMCI,UnclassCCI,UnclassRECI)

ObsEnd<-aggregate(End_Date1~id,max,data=Resul)
randAV<-aggregate(rand~id,max,data=Resul)
TotalObs<-aggregate(Ob~id,max,data=Resul)$Ob

Diagtime<-as.numeric(ObsEnd$End_Date1-randAV$rand)
Lead_time<-Diagtime - cbind(Pred_timeM[,m_opt],Pred_timeC[,c_opt],Pred_timeRE[,r_opt],Pred_timeMCI[,m_opt],Pred_timeCCI[,c_opt],Pred_timeRECI[,r_opt]) ##Calculates the lead time for each patient.
Pred_time<-cbind(Pred_timeM[,m_opt],Pred_timeC[,c_opt],Pred_timeRE[,r_opt],Pred_timeMCI[,m_opt],Pred_timeCCI[,c_opt],Pred_timeRECI[,r_opt])
Ob_time<-cbind(Ob_timeM[,m_opt],Ob_timeC[,c_opt],Ob_timeRE[,r_opt],Ob_timeMCI[,m_opt],Ob_timeCCI[,c_opt],Ob_timeRECI[,r_opt])
Allocation<-cbind(Allocation_Marg[,m_opt],Allocation_Cond[,c_opt],Allocation_RE[,r_opt],Allocation_Marg_CI[,m_opt],Allocation_Cond_CI[,c_opt],Allocation_RE_CI[,r_opt])
M0<-which(Allocation[,1]==1&SANAD_status==1)
C0<-which(Allocation[,2]==1&SANAD_status==1)
RE0<-which(Allocation[,3]==1&SANAD_status==1)
M0CI<-which(Allocation[,4]==1&SANAD_status==1)
C0CI<-which(Allocation[,5]==1&SANAD_status==1)
RE0CI<-which(Allocation[,6]==1&SANAD_status==1)

M_Lead<-mean(Lead_time[M0,1])
C_Lead<-mean(Lead_time[C0,2])
Re_Lead<-mean(Lead_time[RE0,3])
M_LeadCI<-mean(Lead_time[M0CI,4])
C_LeadCI<-mean(Lead_time[C0CI,5])
Re_LeadCI<-mean(Lead_time[RE0CI,6])
Mean_Lead_time<-c(M_Lead,C_Lead,Re_Lead,M_LeadCI,C_LeadCI,Re_LeadCI)

M_LeadMed<-median(Lead_time[M0,1])
C_LeadMed<-median(Lead_time[C0,2])
Re_LeadMed<-median(Lead_time[RE0,3])
M_LeadMedCI<-median(Lead_time[M0CI,4])
C_LeadMedCI<-median(Lead_time[C0CI,5])
Re_LeadMedCI<-median(Lead_time[RE0CI,6])
Median_Lead_time<-c(M_LeadMed,C_LeadMed,Re_LeadMed,M_LeadMedCI,C_LeadMedCI,Re_LeadMedCI)

M_pred<-mean(Pred_time[M0,1])
C_pred<-mean(Pred_time[C0,2])
RE_pred<-mean(Pred_time[RE0,3])
M_predCI<-mean(Pred_time[M0CI,4])
C_predCI<-mean(Pred_time[C0CI,5])
RE_predCI<-mean(Pred_time[RE0CI,6])
Mean_Pred_time<-c(M_pred,C_pred,RE_pred,M_predCI,C_predCI,RE_predCI)

M_predMed<-median(Pred_time[M0,1])
C_predMed<-median(Pred_time[C0,2])
RE_predMed<-median(Pred_time[RE0,3])
M_predCIMed<-median(Pred_time[M0CI,4])
C_predCIMed<-median(Pred_time[C0CI,5])
RE_predCIMed<-median(Pred_time[RE0CI,6])
Median_Pred_time<-c(M_predMed,C_predMed,RE_predMed,M_predCIMed,C_predCIMed,RE_predCIMed)

M_Ob<-mean(Ob_time[M0,1])
C_Ob<-mean(Ob_time[C0,2])
RE_Ob<-mean(Ob_time[RE0,3])
M_ObCI<-mean(Ob_time[M0CI,4])
C_ObCI<-mean(Ob_time[C0CI,5])
RE_ObCI<-mean(Ob_time[RE0CI,6])
Mean_Obs<-c(M_Ob,C_Ob,RE_Ob,M_ObCI,C_ObCI,RE_ObCI)

M_ObMed<-median(Ob_time[M0,1])
C_ObMed<-median(Ob_time[C0,2])
RE_ObMed<-median(Ob_time[RE0,3])
M_ObCIMed<-median(Ob_time[M0CI,4])
C_ObCIMed<-median(Ob_time[C0CI,5])
RE_ObCIMed<-median(Ob_time[RE0CI,6])
Median_Obs<-c(M_ObMed,C_ObMed,RE_ObMed,M_ObCIMed,C_ObCIMed,RE_ObCIMed)

M_TOb<-mean(TotalObs[M0])
C_TOb<-mean(TotalObs[C0])
RE_TOb<-mean(TotalObs[RE0])
M_TObCI<-mean(TotalObs[M0CI])
C_TObCI<-mean(TotalObs[C0CI])
RE_TObCI<-mean(TotalObs[RE0CI])
Mean_TotalObs<-c(M_TOb,C_TOb,RE_TOb,M_TObCI,C_TObCI,RE_TObCI)

M_TObMed<-median(TotalObs[M0])
C_TObMed<-median(TotalObs[C0])
RE_TObMed<-median(TotalObs[RE0])
M_TObCIMed<-median(TotalObs[M0CI])
C_TObCIMed<-median(TotalObs[C0CI])
RE_TObCIMed<-median(TotalObs[RE0CI])
Median_TotalObs<-c(M_TObMed,C_TObMed,RE_TObMed,M_TObCIMed,C_TObCIMed,RE_TObCIMed)


Comp_Table1<-rbind(Cutoff,Sensitivity,New_Sensitivity,Specificity,New_Specificity,PCC,New_PCC,AUC,PPV,NPV,ProbPredREF,Unclass,Mean_Lead_time,Median_Lead_time,Mean_Pred_time,Median_Pred_time,Mean_Obs,Median_Obs,Mean_TotalObs,Median_TotalObs)
colnames(Comp_Table1)<-c("Marginal","Conditional","Random effects","Marginal (with CI)","Conditional (with CI)","Random effects (with CI)")
rownames(Comp_Table1)<-c("Cutoff","Sensitivity","New Sensitivity","Specificity","New Specificity","PCC","New PCC","AUC","PPV","NPV","Proportion Predicted Refractory","Unclassified","Mean Lead Time","Median Lead Time","Mean Prediction Time","Median Prediction Time","Mean Predicted Observations","Median Predicted Observations","Mean Total Observations","Median Total Observations")

RET <- list()
RET$SummaryTable<-Comp_Table1
RET$Unclassified<-UNCLASS
RET$SensitivityMNew<-SensMtotNew
RET$SpecificityMNew<-SpecMtotNew
RET$SensitivityCNew<-SensCtotNew
RET$SpecificityCNew<-SpecCtotNew
RET$SensitivityRENew<-SensREtotNew
RET$SpecificityRENew<-SpecREtotNew
RET$SensitivityMCINew<-SensMCItotNew
RET$SpecificityMCINew<-SpecMCItotNew
RET$SensitivityCCINew<-SensCCItotNew
RET$SpecificityCCINew<-SpecCCItotNew
RET$SensitivityRECINew<-SensRECItotNew
RET$SpecificityRECINew<-SpecRECItotNew

RET$SensitivityM<-SensMtot
RET$SpecificityM<-SpecMtot
RET$SensitivityC<-SensCtot
RET$SpecificityC<-SpecCtot
RET$SensitivityRE<-SensREtot
RET$SpecificityRE<-SpecREtot
RET$SensitivityMCI<-SensMCItot
RET$SpecificityMCI<-SpecMCItot
RET$SensitivityCCI<-SensCCItot
RET$SpecificityCCI<-SpecCCItot
RET$SensitivityRECI<-SensRECItot
RET$SpecificityRECI<-SpecRECItot

RET$PCCM<-PCCMtot
RET$PCCC<-PCCCtot
RET$PCCRE<-PCCREtot
RET$PCCMCI<-PCCMCItot
RET$PCCCCI<-PCCCCItot
RET$PCCRECI<-PCCRECItot

RET$PCCMNew<-PCCMtotNew
RET$PCCCNew<-PCCCtotNew
RET$PCCRENew<-PCCREtotNew
RET$PCCMCINew<-PCCMCItotNew
RET$PCCCCINew<-PCCCCItotNew
RET$PCCRECINew<-PCCRECItotNew

RET$PPVM<-PPVMtot
RET$PPVC<-PPVCtot
RET$PPVRE<-PPVREtot
RET$PPVMCI<-PPVMCItot
RET$PPVCCI<-PPVCCItot
RET$PPVRECI<-PPVRECItot

RET$NPVM<-NPVMtot
RET$NPVC<-NPVCtot
RET$NPVRE<-NPVREtot
RET$NPVMCI<-NPVMCItot
RET$NPVCCI<-NPVCCItot
RET$NPVRECI<-NPVRECItot

RET$MyPCCMCI<-MyPCCMCItot
RET$MyPCCCCI<-MyPCCCCItot
RET$MyPCCRECI<-MyPCCRECItot

RET$MyNPVMCI<-MyNPVMCItot
RET$MyNPVCCI<-MyNPVCCItot
RET$MyNPVRECI<-MyNPVRECItot

RET$MySpecMCI<-MySpecMCItot
RET$MySpecCCI<-MySpecCCItot
RET$MySpecRECI<-MySpecRECItot
RET$MarginalAllocation<-Allocation_Marg
RET$MarginalCIAllocation<-Allocation_Marg_CI
RET$MarginalPredictionTime<-Pred_timeM
RET$MarginalCIPredictionTime<-Pred_timeMCI
RET$KnownStatusTime<-Diagtime
RET$status<-SANAD_status
return(RET)
}