R/TAB FUNCTION TWO DIRECTION.R
In AshZhong/Goahead:
Defines functions
Fix_SS_TAB_Bin_Prob
TAB_Bayesian
TAB_Bin_Cutoff
findtabcutoff
findbetacutoff
library(shiny)
####Two arms Binomial####
findbetacutoff<-function(a1=1,b1=1,a2=1,b2=1,n1=50,n2=50,p2=0.3,CT=0.2,rate=0.8,nsim=10000,stop.criterion=10^-3,direction='Greater',seed.num=369){
S=1
p1=p2
set.seed(seed.num)
upper=1
lower=0
while(S==1){
x1=rbeta(nsim,a1+n1,b1)
x0=rbeta(nsim,a1,b1+n1)
x=rbeta(nsim,a1+n1*p1,b1+n1*(1-p1))
y=rbeta(nsim,a2+n2*p2,b2+n2*(1-p2))
if(direction=='Greater'){
prob1=sum(x1>=y+CT)/nsim
prob0=sum(x0>=y+CT)/nsim
prob=sum(x>=y+CT)/nsim
if(prob1<=rate){
p1=Inf
S=0
}
if(prob0>=rate){
p1=0
S=0
}
if(abs(prob-rate)<=stop.criterion){
S=0
}else if(prob-rate>stop.criterion){
upper=p1
p1=(lower+p1)/2
}else{
lower=p1
p1=(upper+p1)/2
}
}
if(direction=='Less'){
prob1=sum(x1<=y+CT)/nsim
prob0=sum(x0<=y+CT)/nsim
prob=sum(x<=y+CT)/nsim
if(prob0<=rate){
p1=-Inf
S=0
}
if(prob1>=rate){
p1=1
S=0
}
if(abs(prob-rate)<=stop.criterion){
S=0
}else if(prob-rate>stop.criterion){
lower=p1
p1=(upper+p1)/2
}else{
upper=p1
p1=(lower+p1)/2
}
}
}
return(p1)
}
findtabcutoff<-function(n1=50,n2=50,p2=0.3,CT=0.2,rate=0.8,stop.criterion=10^-5,direction='Greater'){
upper=1
lower=0
S=1
p1=p2
if(direction=='Greater'){
while(S==1){
if((1-p2)<(CT+qnorm(rate)*sqrt(p2*(1-p2)/n2))){
p1=Inf
S=0
break
}else if((0-p2)>=(CT+qnorm(rate)*sqrt(p2*(1-p2)/n2))){
p1=0
S=0
break
}
sd=sqrt(p1*(1-p1)/n1+p2*(1-p2)/n2)
temp=p1-p2-CT-qnorm(rate)*sd
if(abs(temp)<=stop.criterion){
S=0
}else if(temp>stop.criterion){
upper=p1
p1=(lower+p1)/2
}else if(temp< -stop.criterion){
lower=p1
p1=(upper+p1)/2
}
}
}
if(direction=='Less'){
while(S==1){
if((1-p2)<=(CT+qnorm(1-rate)*sqrt(p2*(1-p2)/n2))){
p1=1
S=0
break
}else if((0-p2)>(CT+qnorm(1-rate)*sqrt(p2*(1-p2)/n2))){
p1=-Inf
S=0
break
}
sd=sqrt(p1*(1-p1)/n1+p2*(1-p2)/n2)
temp=p1-p2-CT-qnorm(1-rate)*sd
if(abs(temp)<=stop.criterion){
S=0
}else if(temp>stop.criterion){
upper=p1
p1=(lower+p1)/2
}else if(temp< -stop.criterion){
lower=p1
p1=(upper+p1)/2
}
}
}
return(p1)
}
TAB_Bin_Cutoff<-function(n=30,alloc.ratio=1,
prior.a1=1/3,prior.b1=1,
prior.a2=1/3,prior.b2=1,
control.mean=0,
CT1.go=0.25,
false.go.CT1=TRUE,FGR.CT1=0.25,
CT1.nogo=0.25,
false.nogo.CT1=TRUE,FNGR.CT1=0.25,
CT2.go=0.3,
false.go.CT2=TRUE, FGR.CT2=0.5,
CT2.nogo=0.3,
false.nogo.CT2=TRUE, FNGR.CT2=0.5,
method='Bayesian',direction='Greater',
seed.num=369,nsim=10000,stop.criterion=10^-3,
logic.go='and',logic.nogo='and'){
flag=rep(0,4)
overlap.flag=0
n1=round(n*alloc.ratio/(1+alloc.ratio))
n2=n-n1
var2=control.mean*(1-control.mean)
var11.go=(control.mean+CT1.go)*(1-control.mean-CT1.go)
var12.go=(control.mean+CT2.go)*(1-control.mean-CT2.go)
var11.nogo=(control.mean+CT1.nogo)*(1-control.mean-CT1.nogo)
var12.nogo=(control.mean+CT2.nogo)*(1-control.mean-CT2.nogo)
sd.n1.go=sqrt(var11.go/n1+var2/n2) ###for CT1.go###
sd.n2.go=sqrt(var12.go/n1+var2/n2) ###for CT2.go###
sd.n1.nogo=sqrt(var11.nogo/n1+var2/n2) ###for CT1.go###
sd.n2.nogo=sqrt(var12.nogo/n1+var2/n2) ###for CT2.go###
est1.go=NA
est2.go=NA
est1.nogo=NA
est2.nogo=NA
if(is.na(CT1.go)){
false.go.CT1=FALSE
}
if(is.na(CT1.nogo)){
false.nogo.CT1=FALSE
}
if(is.na(CT2.go)){
false.go.CT2=FALSE
}
if(is.na(CT2.nogo)){
false.nogo.CT2=FALSE
}
if(direction=='Greater'){
if(method=='Bayesian'){
if(false.go.CT1==TRUE){
p1.go<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT1.go,
rate=1-FGR.CT1,nsim=10000,
stop.criterion=10^-3,direction='Greater',seed.num=seed.num)
est1.go=p1.go-control.mean
}
if(false.go.CT2==TRUE){
p2.go<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT2.go,
rate=1-FGR.CT2,nsim=10000,
stop.criterion=10^-3,direction='Greater',seed.num=seed.num)
est2.go=p2.go-control.mean
}
if(false.nogo.CT1==TRUE){
p1.nogo<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT1.nogo,
rate=1-FNGR.CT1,nsim=nsim,
stop.criterion=stop.criterion,direction='Less',seed.num=seed.num)
est1.nogo=p1.nogo-control.mean
}
if(false.nogo.CT2==TRUE){
p2.nogo<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT2.nogo,
rate=1-FNGR.CT2,nsim=nsim,
stop.criterion=stop.criterion,direction='Less',seed.num=seed.num)
est2.nogo=p2.nogo-control.mean
}
}
if(method=='Frequentist'){
if(false.go.CT1==TRUE){
p1.go<-findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT1.go,rate=1-FGR.CT1,stop.criterion=10^-5,direction='Greater')
est1.go=p1.go-control.mean
}
if(false.go.CT2==TRUE){
p2.go<-findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT2.go,rate=1-FGR.CT2,stop.criterion=10^-5,direction='Greater')
est2.go=p2.go-control.mean
}
if(false.nogo.CT1==TRUE){
p1.nogo=findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT1.nogo,rate=1-FNGR.CT1,stop.criterion=10^-5,direction='Less')
est1.nogo=p1.nogo-control.mean
}
if(false.nogo.CT2==TRUE){
p2.nogo=findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT2.nogo,rate=1-FNGR.CT2,stop.criterion=10^-5,direction='Less')
est2.nogo=p2.nogo-control.mean
}
}
if(any(is.na(c(est1.go,est2.go)))){logic.go='and'}
if(any(is.na(c(est1.nogo,est2.nogo)))){logic.nogo='and'}
if(logic.go=='and'){
go_cutoff=max(est1.go,est2.go,na.rm=TRUE)
}
if(logic.go=='or'){
go_cutoff=min(est1.go,est2.go,na.rm=TRUE)
}
if(logic.nogo=='and')
{
nogo_cutoff=min(est1.nogo,est2.nogo,na.rm=TRUE)
}
if(logic.nogo=='or')
{
nogo_cutoff=max(est1.nogo,est2.nogo,na.rm=TRUE)
}
if(go_cutoff>=nogo_cutoff){return(list(cutoff=c(go_cutoff,nogo_cutoff),flag=flag,overlap=overlap.flag))}
else{
overlap.flag=1
return(list(cutoff=c(go_cutoff,nogo_cutoff),flag=flag,overlap=overlap.flag))}
if(all(flag==0)==FALSE){return(list(cutoff=c(NA,NA),flag=flag,overlap=overlap.flag))}
}
if(direction=='Less'){
if(method=='Bayesian'){
if(false.go.CT1==TRUE){
p1.go<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT1.go,
rate=1-FGR.CT1,nsim=nsim,
stop.criterion=stop.criterion,direction=direction,seed.num=seed.num)
est1.go=p1.go-control.mean
}
if(false.go.CT2==TRUE){
p2.go<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT2.go,
rate=1-FGR.CT2,nsim=nsim,
stop.criterion=stop.criterion,direction=direction,seed.num=seed.num)
est2.go=p2.go-control.mean
}
if(false.nogo.CT1==TRUE){
p1.nogo<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT1.nogo,
rate=1-FNGR.CT1,nsim=nsim,
stop.criterion=stop.criterion,direction='Greater',seed.num=seed.num)
est1.nogo=p1.nogo-control.mean
}
if(false.nogo.CT2==TRUE){
p2.nogo<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT2.nogo,
rate=1-FNGR.CT2,nsim=nsim,
stop.criterion=stop.criterion,direction='Greater',seed.num=seed.num)
est2.nogo=p2.nogo-control.mean
}
}
if(method=='Frequentist'){
if(false.go.CT1==TRUE){
p1.go<-findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT1.go,rate=1-FGR.CT1,stop.criterion=10^-5,direction='Less')
est1.go=p1.go-control.mean
}
if(false.go.CT2==TRUE){
p2.go<-findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT2.go,rate=1-FGR.CT2,stop.criterion=10^-5,direction='Less')
est2.go=p2.go-control.mean
}
if(false.nogo.CT1==TRUE){
p1.nogo=findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT1.nogo,rate=1-FNGR.CT1,stop.criterion=10^-5,direction='Greater')
est1.nogo=p1.nogo-control.mean
}
if(false.nogo.CT2==TRUE){
p2.nogo=findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT2.nogo,rate=1-FNGR.CT2,stop.criterion=10^-5,direction='Greater')
est2.nogo=p2.nogo-control.mean
}
}
if(any(is.na(c(est1.go,est2.go)))){logic.go='and'}
if(any(is.na(c(est1.nogo,est2.nogo)))){logic.nogo='and'}
if(logic.go=='and'){
go_cutoff=min(est1.go,est2.go,na.rm=TRUE)
}
if(logic.go=='or'){
go_cutoff=max(est1.go,est2.go,na.rm=TRUE)
}
if(logic.nogo=='and')
{
nogo_cutoff=max(est1.nogo,est2.nogo,na.rm=TRUE)
}
if(logic.nogo=='or')
{
nogo_cutoff=min(est1.nogo,est2.nogo,na.rm=TRUE)
}
if(go_cutoff<=nogo_cutoff){return(list(cutoff=c(go_cutoff,nogo_cutoff),flag=flag,overlap=overlap.flag))}
else{
overlap.flag=1
return(list(cutoff=c(go_cutoff,nogo_cutoff),flag=flag,overlap=overlap.flag))}
if(all(flag==0)==FALSE){return(list(cutoff=c(NA,NA),flag=flag,overlap=overlap.flag))}
}
}
TAB_Bayesian<-function(n=c(10,100),alloc.ratio=1,
prior.a1=1/3,prior.b1=1,
prior.a2=1/3,prior.b2=1,
control.mean=0,
mean=c(-0.5,0.8),
CT1.go=0.25,
false.go.CT1=TRUE,FGR.CT1=0.25,
CT1.nogo=0.25,
false.nogo.CT1=TRUE,FNGR.CT1=0.25,
CT2.go=0.3,
false.go.CT2=TRUE, FGR.CT2=0.5,
CT2.nogo=0.3,
false.nogo.CT2=TRUE, FNGR.CT2=0.5,
overlap.option='GO',
direction='Greater',
seed.num=369,nsim=10000,n_repeat=1000,
logic.go='and',logic.nogo='or'){
set.seed(seed.num)
go_prob<-matrix(NA,ncol=length(n),nrow=length(mean))
nogo_prob<-matrix(NA,ncol=length(n),nrow=length(mean))
inconclusive_prob<-matrix(NA,ncol=length(n),nrow=length(mean))
overlap.flag=rep(0,length(n))
for (ii in 1:length(mean)){
for (ii2 in 1:length(n)){
treatment.mean=control.mean+mean[ii]
i1=round(n[ii2]*alloc.ratio/(1+alloc.ratio))
i2=n[ii2]-i1
sum_x1=rbinom(n_repeat,i1,treatment.mean)
sum_x2=rbinom(n_repeat,i2,control.mean)
if(is.na(CT1.go)) false.go.CT1=FALSE
if(is.na(CT1.nogo)) false.nogo.CT1=FALSE
if(is.na(CT2.go)) false.go.CT2=FALSE
if(is.na(CT2.nogo)) false.nogo.CT2=FALSE
if(false.go.CT1==TRUE) pp_go_1 = rep(0,n_repeat)
if(false.nogo.CT1==TRUE) pp_nogo_1 = rep(0,n_repeat)
if(false.go.CT2==TRUE) pp_go_2 = rep(0,n_repeat)
if(false.nogo.CT2==TRUE) pp_nogo_2 = rep(0,n_repeat)
for (i in 1:n_repeat){
temp1 = rbeta(nsim,prior.a1+sum_x1[i],prior.b1+i1-sum_x1[i])
temp2 = rbeta(nsim,prior.a2+sum_x2[i],prior.b2+i2-sum_x2[i])
if(direction=='Greater'){
if(false.go.CT1==TRUE) pp_go_1[i] = sum(temp1-temp2>=CT1.go)/nsim
if(false.nogo.CT1==TRUE) pp_nogo_1[i] = sum(temp1-temp2>=CT1.nogo)/nsim
if(false.go.CT2==TRUE) pp_go_2[i] = sum(temp1-temp2>=CT2.go)/nsim
if(false.nogo.CT2==TRUE) pp_nogo_2[i] = sum(temp1-temp2>=CT2.nogo)/nsim
}
if(direction=='Less'){
if(false.go.CT1==TRUE) pp_go_1[i] = sum(temp1-temp2<=CT1.go)/nsim
if(false.nogo.CT1==TRUE) pp_nogo_1[i] = sum(temp1-temp2<=CT1.nogo)/nsim
if(false.go.CT2==TRUE) pp_go_2[i] = sum(temp1-temp2<=CT2.go)/nsim
if(false.nogo.CT2==TRUE) pp_nogo_2[i] = sum(temp1-temp2<=CT2.nogo)/nsim
}
}
if(false.go.CT1==TRUE & false.go.CT2==TRUE){
if(logic.go=='and')
go_prob[ii,ii2] = mean(pp_go_1>=1-FGR.CT1 & pp_go_2>=1-FGR.CT2)
if(logic.go=='or')
go_prob[ii,ii2] = mean(pp_go_1>=1-FGR.CT1 | pp_go_2>=1-FGR.CT2)
} else if(false.go.CT1==TRUE){
go_prob[ii,ii2] = mean(pp_go_1>=1-FGR.CT1)
} else if(false.go.CT2==TRUE){
go_prob[ii,ii2] = mean(pp_go_2>=1-FGR.CT2)
}
if(false.nogo.CT1==TRUE & false.nogo.CT2==TRUE){
if(logic.nogo=='and')
nogo_prob[ii,ii2] = mean(pp_nogo_1<FNGR.CT1 & pp_nogo_2<FNGR.CT2)
if(logic.nogo=='or')
nogo_prob[ii,ii2] = mean(pp_nogo_1<FNGR.CT1 | pp_nogo_2<FNGR.CT2)
} else if(false.nogo.CT1==TRUE){
nogo_prob[ii,ii2] = mean(pp_nogo_1<FNGR.CT1)
} else if(false.nogo.CT2==TRUE){
nogo_prob[ii,ii2] = mean(pp_nogo_2<FNGR.CT2)
}
if (go_prob[ii,ii2]+nogo_prob[ii,ii2]>1){
overlap.flag[ii2] = 1
if (overlap.option=='GO'){
nogo_prob[ii,ii2] = 1-go_prob[ii,ii2]
} else if (overlap.option=='NOGO'){
go_prob[ii,ii2] = 1-nogo_prob[ii,ii2]
}
}
inconclusive_prob[ii,ii2]=1-go_prob[ii,ii2]-nogo_prob[ii,ii2]
}
}
return(list(go_prob,nogo_prob,inconclusive_prob,overlap.flag))
}
###############################################################
Fix_SS_TAB_Bin_Prob<-function(n=100,alloc.ratio=1,
prior.a1=1/3,prior.b1=1,
prior.a2=1/3,prior.b2=1,
control.mean=0,
mean=c(-0.5,0.8),
CT1.go=0.25,
false.go.CT1=TRUE,FGR.CT1=0.25,
CT1.nogo=0.25,
false.nogo.CT1=TRUE,FNGR.CT1=0.25,
CT2.go=0.3,
false.go.CT2=TRUE, FGR.CT2=0.5,
CT2.nogo=0.3,
false.nogo.CT2=TRUE, FNGR.CT2=0.5,
overlap.option='GO',plot.figure=TRUE,
method='Bayesian',direction='Greater',seed.num=369,
nsim=nsim,stop.criterion=stop.criterion,
logic.go='and',logic.nogo='or'){
minmean=ifelse(min(mean)+control.mean>=0,min(mean),-control.mean)
maxmean=ifelse(max(mean)+control.mean<=1,max(mean),1-control.mean)
meanseq=round(seq(minmean,maxmean,0.05),3)
go_prob<-rep(NA,length(mean))
nogo_prob<-rep(NA,length(mean))
inconclusive_prob<-rep(NA,length(mean))
go_prob_plot<-rep(NA,length(meanseq))
nogo_prob_plot<-rep(NA,length(meanseq))
inconclusive_prob_plot<-rep(NA,length(meanseq))
index=1
unsatisfied.flag=0
overlap.flag=0
n1=round(n*alloc.ratio/(1+alloc.ratio))
n2=n-n1
if (abs(n*alloc.ratio/(1+alloc.ratio)-n1)>10^(-3))
stop ("Sample size for each arm must be an integer.")
var1=(mean+control.mean)*(1-mean-control.mean)
var2=control.mean*(1-control.mean)
var1seq=(meanseq+control.mean)*(1-meanseq-control.mean)
sd.n=sqrt(var1/n1+var2/n2)
sd.nseq=sqrt(var1seq/n1+var2/n2)
temp=TAB_Bin_Cutoff(n=n,alloc.ratio=alloc.ratio,
prior.a1=prior.a1,prior.b1=prior.b1,
prior.a2=prior.a2,prior.b2=prior.b2,
control.mean=control.mean,
CT1.go=CT1.go,
false.go.CT1 = false.go.CT1, FGR.CT1=FGR.CT1,
CT1.nogo = CT1.nogo,
false.nogo.CT1 = false.nogo.CT1, FNGR.CT1 = FNGR.CT1,
CT2.go=CT2.go,
false.go.CT2 = false.go.CT2, FGR.CT2=FGR.CT2,
CT2.nogo=CT2.nogo,
false.nogo.CT2 = false.nogo.CT2, FNGR.CT2 = FNGR.CT2,
method=method,direction=direction,seed.num=seed.num,
nsim=nsim,stop.criterion=stop.criterion,
logic.go=logic.go,logic.nogo = logic.nogo)
###TAB####
true_go_cutoff<-ifelse(temp$overlap==0,temp$cutoff[1],(overlap.option=='GO')*temp$cutoff[1]+(overlap.option=='NOGO')*(temp$cutoff[2]))
true_nogo_cutoff<-ifelse(temp$overlap==0,temp$cutoff[2],(overlap.option=='GO')*temp$cutoff[1]+(overlap.option=='NOGO')*(temp$cutoff[2]))
if(method=='Frequentist'){
if(direction=='Greater'){
if(all(temp$flag==0)&temp$overlap==0){
go_prob=1-pnorm(temp$cutoff[1],mean=mean,sd=sd.n)
nogo_prob=pnorm(temp$cutoff[2],mean=mean,sd=sd.n)
go_prob_plot=1-pnorm(temp$cutoff[1],mean=meanseq,sd=sd.nseq)
nogo_prob_plot=pnorm(temp$cutoff[2],mean=meanseq,sd=sd.nseq)
if(any(control.mean+temp$cutoff[1]>=1)){
go_prob[control.mean+temp$cutoff[1]>=1]=0
go_prob_plot[control.mean+temp$cutoff[1]>=1]=0
}
if(any(control.mean+temp$cutoff[1]<=0)){
go_prob[control.mean+temp$cutoff[1]<=0]=1
go_prob_plot[control.mean+temp$cutoff[1]<=0]=1
}
if(any(control.mean+temp$cutoff[2]<=0)){
nogo_prob[control.mean+temp$cutoff[2]<=0]=0
nogo_prob_plot[control.mean+temp$cutoff[2]<=0]=0
}
if(any(control.mean+temp$cutoff[2]>=1)){
nogo_prob[control.mean+temp$cutoff[2]>=1]=1
nogo_prob_plot[control.mean+temp$cutoff[2]>=1]=1
}
inconclusive_prob_plot=1-go_prob_plot-nogo_prob_plot
inconclusive_prob=1-go_prob-nogo_prob
}
if(all(temp$flag==0)&temp$overlap==1&overlap.option=="GO"){
go_prob=1-pnorm(temp$cutoff[1],mean=mean,sd=sd.n)
nogo_prob=pnorm(temp$cutoff[1],mean=mean,sd=sd.n)
go_prob_plot=1-pnorm(temp$cutoff[1],mean=meanseq,sd=sd.nseq)
nogo_prob_plot=pnorm(temp$cutoff[1],mean=meanseq,sd=sd.nseq)
if(any(control.mean+temp$cutoff[1]>=1)){
go_prob[control.mean+temp$cutoff[1]>=1]=0
go_prob_plot[control.mean+temp$cutoff[1]>=1]=0
}
if(any(control.mean+temp$cutoff[1]<=0)){
go_prob[control.mean+temp$cutoff[1]<=0]=1
go_prob_plot[control.mean+temp$cutoff[1]<=0]=1
}
if(any(control.mean+temp$cutoff[1]<=0)){
nogo_prob[control.mean+temp$cutoff[1]<=0]=0
nogo_prob_plot[control.mean+temp$cutoff[1]<=0]=0
}
if(any(control.mean+temp$cutoff[1]>=1)){
nogo_prob[control.mean+temp$cutoff[1]>=1]=1
nogo_prob_plot[control.mean+temp$cutoff[1]>=1]=1
}
inconclusive_prob_plot=1-go_prob_plot-nogo_prob_plot
inconclusive_prob=1-go_prob-nogo_prob
overlap.flag=1
}
if(all(temp$flag==0)&temp$overlap==1&overlap.option=="NOGO"){
go_prob=1-pnorm(temp$cutoff[2],mean=mean,sd=sd.n)
nogo_prob=pnorm(temp$cutoff[2],mean=mean,sd=sd.n)
go_prob_plot=1-pnorm(temp$cutoff[2],mean=meanseq,sd=sd.nseq)
nogo_prob_plot=pnorm(temp$cutoff[2],mean=meanseq,sd=sd.nseq)
if(any(control.mean+temp$cutoff[2]>=1)){
go_prob[control.mean+temp$cutoff[2]>=1]=0
go_prob_plot[control.mean+temp$cutoff[2]>=1]=0
}
if(any(control.mean+temp$cutoff[2]<=0)){
go_prob[control.mean+temp$cutoff[2]<=0]=1
go_prob_plot[control.mean+temp$cutoff[2]<=0]=1
}
if(any(control.mean+temp$cutoff[2]<=0)){
nogo_prob[control.mean+temp$cutoff[2]<=0]=0
nogo_prob_plot[control.mean+temp$cutoff[2]<=0]=0
}
if(any(control.mean+temp$cutoff[2]>=1)){
nogo_prob[control.mean+temp$cutoff[2]>=1]=1
nogo_prob_plot[control.mean+temp$cutoff[2]>=1]=1
}
inconclusive_prob_plot=1-go_prob_plot-nogo_prob_plot
inconclusive_prob=1-go_prob-nogo_prob
overlap.flag=1
}
if(all(temp$flag==0)==FALSE){
unsatisfied.flag=1
nogo_prob=rep(NA,length(mean))
go_prob=rep(NA,length(mean))
inconclusive_prob=rep(NA,length(mean))
}
}
if(direction=='Less'){
if(all(temp$flag==0)&temp$overlap==0){
go_prob=pnorm(temp$cutoff[1],mean=mean,sd=sd.n)
nogo_prob=1-pnorm(temp$cutoff[2],mean=mean,sd=sd.n)
go_prob_plot=pnorm(temp$cutoff[1],mean=meanseq,sd=sd.nseq)
nogo_prob_plot=1-pnorm(temp$cutoff[2],mean=meanseq,sd=sd.nseq)
if(any(control.mean+temp$cutoff[1]>=1)){
go_prob[control.mean+temp$cutoff[1]>=1]=1
go_prob_plot[control.mean+temp$cutoff[1]>=1]=1
}
if(any(control.mean+temp$cutoff[1]<=0)){
go_prob[control.mean+temp$cutoff[1]<=0]=0
go_prob_plot[control.mean+temp$cutoff[1]<=0]=0
}
if(any(control.mean+temp$cutoff[2]<=0)){
nogo_prob[control.mean+temp$cutoff[2]<=0]=1
nogo_prob_plot[control.mean+temp$cutoff[2]<=0]=1
}
if(any(control.mean+temp$cutoff[2]>=1)){
nogo_prob[control.mean+temp$cutoff[2]>=1]=0
nogo_prob_plot[control.mean+temp$cutoff[2]>=1]=0
}
inconclusive_prob_plot=1-go_prob_plot-nogo_prob_plot
inconclusive_prob=1-go_prob-nogo_prob
}
if(all(temp$flag==0)&temp$overlap==1&overlap.option=="GO"){
go_prob=pnorm(temp$cutoff[1],mean=mean,sd=sd.n)
nogo_prob=1-pnorm(temp$cutoff[1],mean=mean,sd=sd.n)
go_prob_plot=pnorm(temp$cutoff[1],mean=meanseq,sd=sd.nseq)
nogo_prob_plot=1-pnorm(temp$cutoff[1],mean=meanseq,sd=sd.nseq)
if(any(control.mean+temp$cutoff[1]>=1)){
go_prob[control.mean+temp$cutoff[1]>=1]=1
go_prob_plot[control.mean+temp$cutoff[1]>=1]=1
}
if(any(control.mean+temp$cutoff[1]<=0)){
go_prob[control.mean+temp$cutoff[1]<=0]=0
go_prob_plot[control.mean+temp$cutoff[1]<=0]=0
}
if(any(control.mean+temp$cutoff[1]<=0)){
nogo_prob[control.mean+temp$cutoff[1]<=0]=1
nogo_prob_plot[control.mean+temp$cutoff[1]<=0]=1
}
if(any(control.mean+temp$cutoff[1]>=1)){
nogo_prob[control.mean+temp$cutoff[1]>=1]=0
nogo_prob_plot[control.mean+temp$cutoff[1]>=1]=0
}
inconclusive_prob_plot=1-go_prob_plot-nogo_prob_plot
inconclusive_prob=1-go_prob-nogo_prob
overlap.flag=1
}
if(all(temp$flag==0)&temp$overlap==1&overlap.option=="NOGO"){
go_prob=pnorm(temp$cutoff[2],mean=mean,sd=sd.n)
nogo_prob=1-pnorm(temp$cutoff[2],mean=mean,sd=sd.n)
go_prob_plot=pnorm(temp$cutoff[2],mean=meanseq,sd=sd.nseq)
nogo_prob_plot=1-pnorm(temp$cutoff[2],mean=meanseq,sd=sd.nseq)
if(any(control.mean+temp$cutoff[2]>=1)){
go_prob[control.mean+temp$cutoff[2]>=1]=1
go_prob_plot[control.mean+temp$cutoff[2]>=1]=1
}
if(any(control.mean+temp$cutoff[2]<=0)){
go_prob[control.mean+temp$cutoff[2]<=0]=0
go_prob_plot[control.mean+temp$cutoff[2]<=0]=0
}
if(any(control.mean+temp$cutoff[2]<=0)){
nogo_prob[control.mean+temp$cutoff[2]<=0]=1
nogo_prob_plot[control.mean+temp$cutoff[2]<=0]=1
}
if(any(control.mean+temp$cutoff[2]>=1)){
nogo_prob[control.mean+temp$cutoff[2]>=1]=0
nogo_prob_plot[control.mean+temp$cutoff[2]>=1]=0
}
inconclusive_prob_plot=1-go_prob_plot-nogo_prob_plot
inconclusive_prob=1-go_prob-nogo_prob
overlap.flag=1
}
if(all(temp$flag==0)==FALSE){
unsatisfied.flag=1
nogo_prob=rep(NA,length(mean))
go_prob=rep(NA,length(mean))
inconclusive_prob=rep(NA,length(mean))
}
}
}
if(method=='Bayesian'){
n_repeat=1000
temp2 = TAB_Bayesian(n=n,alloc.ratio=alloc.ratio,
prior.a1=prior.a1,prior.b1=prior.b1,
prior.a2=prior.a2,prior.b2=prior.b2,
control.mean=control.mean,
mean=mean,
CT1.go=CT1.go,
false.go.CT1=false.go.CT1,FGR.CT1=FGR.CT1,
CT1.nogo=CT1.nogo,
false.nogo.CT1=false.nogo.CT1,FNGR.CT1=FNGR.CT1,
CT2.go=CT2.go,
false.go.CT2=false.go.CT2, FGR.CT2=FGR.CT2,
CT2.nogo=CT2.nogo,
false.nogo.CT2=false.nogo.CT2, FNGR.CT2=FNGR.CT2,
overlap.option=overlap.option,
direction=direction,
seed.num=seed.num,nsim=nsim,n_repeat=n_repeat,
logic.go=logic.go,logic.nogo=logic.nogo)
go_prob = as.numeric(temp2[[1]])
nogo_prob = as.numeric(temp2[[2]])
inconclusive_prob = as.numeric(temp2[[3]])
# plot
temp3 = TAB_Bayesian(n=n,alloc.ratio=alloc.ratio,
prior.a1=prior.a1,prior.b1=prior.b1,
prior.a2=prior.a2,prior.b2=prior.b2,
control.mean=control.mean,
mean=meanseq,
CT1.go=CT1.go,
false.go.CT1=false.go.CT1,FGR.CT1=FGR.CT1,
CT1.nogo=CT1.nogo,
false.nogo.CT1=false.nogo.CT1,FNGR.CT1=FNGR.CT1,
CT2.go=CT2.go,
false.go.CT2=false.go.CT2, FGR.CT2=FGR.CT2,
CT2.nogo=CT2.nogo,
false.nogo.CT2=false.nogo.CT2, FNGR.CT2=FNGR.CT2,
overlap.option=overlap.option,
direction=direction,
seed.num=seed.num,nsim=nsim,n_repeat=n_repeat,
logic.go=logic.go,logic.nogo=logic.nogo)
go_prob_plot = as.numeric(temp3[[1]])
nogo_prob_plot = as.numeric(temp3[[2]])
inconclusive_prob_plot = as.numeric(temp3[[3]])
}
#######################################################################################
if(plot.figure==TRUE){
delta=meanseq
p_nogo=nogo_prob_plot*100
p_grey=inconclusive_prob_plot*100
p_go=go_prob_plot*100
if(true_go_cutoff!=true_nogo_cutoff){
par(mfrow=c(1,1),pty="m",bty="l",cex=1.4)
plot(delta,p_go,xlab=expression(paste("True difference in Response Rates",sep="")),
ylab="Prob of GO/ NOGO/ Inconclusive (%)",xlim=range(delta),
ylim=c(0,100),type="n",axes=F)
axis(1, at=meanseq, labels=meanseq)
axis(2, at=seq(0,100,10),labels=T)
#text(rep(-0.6,6),seq(0,100,20),seq(0,100,20),adj=1,xpd=T)
box()
#abline(h=seq(0,100,10),lty=3,col=rgb(0.8,0.8,0.8),lwd=1)
points(delta,p_nogo,type="b",pch=16,col=rgb(0.9,0,0),lwd=3,lty=1)
points(delta,p_grey,type="b",pch=4,col=rgb(0.9,0.6,0),lwd=3,lty=6)
points(delta,p_go,type="b",pch=2,col=rgb(0,0.7,0),lwd=3,lty=2)
text(minmean,140,bquote(n==~.(n)),xpd=T,adj=0,cex=0.8,col=rgb(0, 0,0))
if(overlap.flag==0&unsatisfied.flag==0){
if(direction=='Greater'){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
text(minmean,110,bquote(Inconclusive~symbol("\336")~anything~between~GO~and~NOGO),xpd=T,adj=0,cex=0.8,col=rgb(0.9,0.6,0))
}
if(direction=='Less'){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
text(minmean,110,bquote(Inconclusive~symbol("\336")~anything~between~GO~and~NOGO),xpd=T,adj=0,cex=0.8,col=rgb(0.9,0.6,0))
}
}
if(overlap.flag==1&unsatisfied.flag==0&overlap.option=='GO'){
if(direction=="Greater"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
if(direction=="Less"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
}
if(overlap.flag==1&unsatisfied.flag==0&overlap.option=='NOGO'){
if(direction=="Greater"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
if(direction=="Less"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
}
if(unsatisfied.flag==1){
text(minmean,130,paste0('Warning: We could not find classification of zones to satisfy your both GO and NOGO criterions at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0,0))
text(minmean,120,paste0('Please check and modify your desicion rule or the range of sample size!'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0,0))
}
}
}
###########################################################################
if(plot.figure==TRUE){
delta=meanseq
p_nogo=nogo_prob_plot*100
p_grey=inconclusive_prob_plot*100
p_go=go_prob_plot*100
if(true_go_cutoff==true_nogo_cutoff){
par(mfrow=c(1,1),pty="m",bty="l",cex=1.4)
plot(delta,p_go,xlab=expression(paste("True difference in Response Rates",sep="")),
ylab="Prob of GO/ NOGO/ Inconclusive (%)",xlim=range(delta),
ylim=c(0,100),type="n",axes=F)
axis(1, at=meanseq, labels=meanseq)
axis(2, at=seq(0,100,10),labels=T)
#text(rep(-0.6,6),seq(0,100,20),seq(0,100,20),adj=1,xpd=T)
box()
#abline(h=seq(0,100,10),lty=3,col=rgb(0.8,0.8,0.8),lwd=1)
points(delta,p_nogo,type="b",pch=16,col=rgb(0.9,0,0),lwd=3,lty=1)
#points(delta,p_grey,type="b",pch=4,col=rgb(0.9,0.6,0),lwd=3,lty=6)
points(delta,p_go,type="b",pch=2,col=rgb(0,0.7,0),lwd=3,lty=2)
text(minmean,140,bquote(n==~.(n)),xpd=T,adj=0,cex=0.8,col=rgb(0, 0,0))
if(overlap.flag==0&unsatisfied.flag==0){
if(direction=='Greater'){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,110,bquote(Inconclusive~symbol("\336")~anything~between~GO~and~NOGO),xpd=T,adj=0,cex=0.8,col=rgb(0.9,0.6,0))
}
if(direction=='Less'){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,110,bquote(Inconclusive~symbol("\336")~anything~between~GO~and~NOGO),xpd=T,adj=0,cex=0.8,col=rgb(0.9,0.6,0))
}
}
if(overlap.flag==1&unsatisfied.flag==0&overlap.option=='GO'){
if(direction=="Greater"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
if(direction=="Less"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
}
if(overlap.flag==1&unsatisfied.flag==0&overlap.option=='NOGO'){
if(direction=="Greater"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
if(direction=="Less"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
}
if(unsatisfied.flag==1){
text(minmean,130,paste0('Warning: We could not find classification of zones to satisfy your both GO and NOGO criterions at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0,0))
text(minmean,120,paste0('Please check and modify your desicion rule or the range of sample size!'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0,0))
}
}
}
###########################################################################
return(list(go_prob=go_prob,nogo_prob=nogo_prob,
inconclusive_prob=inconclusive_prob,
overlap.flag=overlap.flag,overlap.option=overlap.option,
unsatisfied.flag=unsatisfied.flag,cutoff=temp$cutoff,true_cutoff=c(true_go_cutoff,true_nogo_cutoff))
)
}
Vary_SS_TAB_Bin_Prob<-function(nmin=10,nmax=50,
prior.a1=1/3,prior.b1=1,
prior.a2=1/3,prior.b2=1,
mean=0.3,alloc.ratio=1,
control.mean=0,
CT1.go=0.25,
false.go.CT1=TRUE,FGR.CT1=0.25,
CT1.nogo=0.25,
false.nogo.CT1=TRUE,FNGR.CT1=0.25,
CT2.go=0.3,
false.go.CT2=TRUE, FGR.CT2=0.5,
CT2.nogo=0.3,
false.nogo.CT2=TRUE, FNGR.CT2=0.5,
overlap.option='GO',plot.cutoff=TRUE,plot.prob=TRUE,
method="Bayesian",direction="Greater",seed.num=369,
nsim=10000,stop.criterion=10^-3,
logic.go='and',logic.nogo='or'){
nseq=unique(round(c(seq(nmin,(nmax+nmin)/2,length=6)[-6],seq((nmax+nmin)/2,nmax,length=6))))
go_prob<-matrix(NA,ncol=length(nseq),nrow=length(mean))
nogo_prob<-matrix(NA,ncol=length(nseq),nrow=length(mean))
inconclusive_prob<-matrix(NA,ncol=length(nseq),nrow=length(mean))
go_cutoff<-rep(NA,length(nseq))
nogo_cutoff<-rep(NA,length(nseq))
index=1
n_unsatisfied=NA
n_overlap=NA
ncore <- detectCores()
cl<-makeCluster(ncore)
registerDoParallel(cl)
results<-foreach(i = nseq,.export=c('TAB_Bin_Cutoff','findbetacutoff',"findtabcutoff"),.combine=rbind) %dopar% {
i1=round(i*alloc.ratio/(1+alloc.ratio))
i2=i-i1
var1=(mean+control.mean)*(1-mean-control.mean)
var2=control.mean*(1-control.mean)
sd.i=sqrt(var1/i1+var2/i2)
temp=TAB_Bin_Cutoff(n=i,alloc.ratio=alloc.ratio,
prior.a1=prior.a1,prior.b1=prior.b1,
prior.a2=prior.a2,prior.b2=prior.b2,
control.mean=control.mean,
CT1.go=CT1.go,
false.go.CT1 = false.go.CT1, FGR.CT1=FGR.CT1,
CT1.nogo=CT1.nogo,
false.nogo.CT1 = false.nogo.CT1, FNGR.CT1 = FNGR.CT1,
CT2.go = CT2.go,
false.go.CT2 = false.go.CT2, FGR.CT2=FGR.CT2,
CT2.nogo=CT2.nogo,
false.nogo.CT2 = false.nogo.CT2, FNGR.CT2 = FNGR.CT2,
method=method,direction=direction,seed.num = seed.num,
nsim=nsim,stop.criterion=stop.criterion,
logic.go = logic.go,logic.nogo = logic.nogo)
c(temp$overlap,temp$cutoff)
}
stopCluster(cl)
go_cutoff<-results[,2]
nogo_cutoff<-results[,3]
overlap<-results[,1]
for(mean.index in 1:length(mean)){
true_go_cutoff<-go_cutoff
true_nogo_cutoff<-nogo_cutoff
true_go_cutoff[overlap==1]<-(overlap.option=='GO')*go_cutoff[overlap==1]+(overlap.option=='NOGO')*nogo_cutoff[overlap==1]
true_nogo_cutoff[overlap==1]<-(overlap.option=='GO')*go_cutoff[overlap==1]+(overlap.option=='NOGO')*nogo_cutoff[overlap==1]
}
if(method=='Frequentist'){
for(mean.index in 1:length(mean)){
mean_temp=mean[mean.index]
i1=round(nseq*alloc.ratio/(1+alloc.ratio))
i2=nseq-i1
var1=(mean_temp+control.mean)*(1-mean_temp-control.mean)
var2=control.mean*(1-control.mean)
sd.i=sqrt(var1/nseq+var2/nseq)
if(direction=='Greater'){
go_prob[mean.index,]=1-pnorm(true_go_cutoff,mean=mean_temp,sd=sd.i)
nogo_prob[mean.index,]=pnorm(true_nogo_cutoff,mean=mean_temp,sd=sd.i)
if(any(control.mean+true_go_cutoff>=1)){
go_prob[mean.index,control.mean+true_go_cutoff>=1]=0
}
if(any(control.mean+true_go_cutoff<=0)){
go_prob[mean.index,control.mean+cutoff<=0]=1
}
if(any(control.mean+true_nogo_cutoff<=0)){
nogo_prob[mean.index,control.mean+true_nogo_cutoff<=0]=0
}
if(any(control.mean+true_nogo_cutoff>=1)){
nogo_prob[mean.index,control.mean+true_nogo_cutoff>=1]=1
}
}
if(direction=='Less'){
go_prob[mean.index,]=pnorm(true_go_cutoff,mean=mean_temp,sd=sd.i)
nogo_prob[mean.index,]=1-pnorm(true_nogo_cutoff,mean=mean_temp,sd=sd.i)
if(any(control.mean+true_go_cutoff>=1)){
go_prob[mean.index,control.mean+true_go_cutoff>=1]=1
}
if(any(control.mean+true_go_cutoff<=0)){
go_prob[mean.index,control.mean+cutoff<=0]=0
}
if(any(control.mean+true_nogo_cutoff<=0)){
nogo_prob[mean.index,control.mean+true_nogo_cutoff<=0]=1
}
if(any(control.mean+true_nogo_cutoff>=1)){
nogo_prob[mean.index,control.mean+true_nogo_cutoff>=1]=0
}
}
inconclusive_prob[mean.index,]=1-go_prob[mean.index,]-nogo_prob[mean.index,]
}
}
if(method=='Bayesian'){
n_repeat=1000
temp2 = TAB_Bayesian(n=nseq,alloc.ratio=alloc.ratio,
prior.a1=prior.a1,prior.b1=prior.b1,
prior.a2=prior.a2,prior.b2=prior.b2,
control.mean=control.mean,
mean=mean,
CT1.go=CT1.go,
false.go.CT1=false.go.CT1,FGR.CT1=FGR.CT1,
CT1.nogo=CT1.nogo,
false.nogo.CT1=false.nogo.CT1,FNGR.CT1=FNGR.CT1,
CT2.go=CT2.go,
false.go.CT2=false.go.CT2, FGR.CT2=FGR.CT2,
CT2.nogo=CT2.nogo,
false.nogo.CT2=false.nogo.CT2, FNGR.CT2=FNGR.CT2,
overlap.option=overlap.option,
direction=direction,
seed.num=seed.num,nsim=nsim,n_repeat=n_repeat,
logic.go=logic.go,logic.nogo=logic.nogo)
go_prob = temp2[[1]]
nogo_prob = temp2[[2]]
inconclusive_prob = temp2[[3]]
}
n_overlap=n_overlap[-1]
n_unsatisfied=n_unsatisfied[-1]
####plot figure
if(plot.prob==TRUE){
for(j in 1:length(mean)){
p_go=go_prob[j,]*100
p_nogo=nogo_prob[j,]*100
class(p_nogo)
dim(p_nogo)
p_grey=100-p_go-p_nogo
par(mfrow=c(1,1),pty="m",bty="l",cex=1.4)
cum_p_nogo=p_nogo
cum_p_grey=p_nogo+p_grey
cum_p_go=p_nogo+p_grey+p_go
delta=nseq
plot(delta,cum_p_go,xlab="Sample size",
ylab="Prob of GO/ NOGO/ Inconclusive (%)",xlim=c(nmin,nmax),
ylim=c(0,100),type="n",axes=F,pch=NA)
axis(1, at=nseq, labels=nseq)
axis(2, at=seq(0,100,10),labels=T)
#text(rep(-0.6,6),seq(0,100,20),seq(0,100,20),adj=1,xpd=T)
box()
#abline(h=seq(0,100,10),lty=3,col=rgb(0.8,0.8,0.8),lwd=1)
polygon(c(delta,rev(delta)),c(cum_p_nogo,rev(rep(0,length(delta)))),col=rgb(0.9,0,0),border=NA)
polygon(c(delta,rev(delta)),c(cum_p_grey,rev(cum_p_nogo)),col=rgb(0.9,0.6,0),border=NA)
polygon(c(delta,rev(delta)),c(cum_p_go,rev(cum_p_grey)),col=rgb(0,0.7,0),border=NA)
text((nmin+nmax)/2,120,paste0("True difference in RR=",round(mean[j],3),';Oberserved RR in control group=',round(control.mean,3)),xpd=T,adj=0.5,cex=0.8)
if(any(overlap!=0)){
text(nmin,115,paste0('Warning: GO and NOGO cut-offs are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(nmin,110,paste(n_overlap),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#print(n_overlap)
text(nmin,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
}
}
if(plot.cutoff==TRUE){
par(mfrow=c(1,1),pty="m",bty="l",cex=1.4)
ylim_max=max(c(go_cutoff,nogo_cutoff,round(CT1.go,3),round(CT1.nogo,3),round(CT2.go,3),round(CT2.nogo,3)),na.rm=TRUE)+0.1
ylim_min=min(c(go_cutoff,nogo_cutoff,round(CT1.go,3),round(CT1.nogo,3),round(CT2.go,3),round(CT2.nogo,3)),na.rm=TRUE)-0.1
plot(NA,NA,xlab='Sample size',ylab="Observed difference in RR",xlim=c(max(0,range(nseq)[1]-10),range(nseq)[2]+10),ylim=c(ylim_min,ylim_max),type="n",axes=F,col=rgb(1,0,0),lty=1,lwd=2)
axis(1, at=nseq,labels=nseq)
axis(2, at=round(c(seq(ylim_min,ylim_max,round((ylim_max-ylim_min)/10,digits=2)),CT1.go,CT2.go,CT1.nogo,CT2.nogo),digits=2),labels=T)
#text(rep(-0.6,6),seq(0,100,20),seq(0,300,20),adj=1,xpd=T)
box()
lines(nseq,nogo_cutoff,col=rgb(0.9,0,0),lwd=2)
lines(nseq,go_cutoff,col=rgb(0,0.7,0),lwd=2)
legend('bottomright',legend=c("Cut off of GO","Cut off of NOGO"),
col=c(rgb(0,0.7,0),rgb(0.9,0,0)),
lwd=c(2,2),
lty=c(1,1),cex=0.5)
text(nmin,ylim_max+3*abs(ylim_max-ylim_min)/20,paste0('Oberserved RR in control group=',round(control.mean,3)),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
if(any(overlap!=0)){
text(nmin,ylim_max+abs(ylim_max-ylim_min)/10,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(nmin,110,paste(n_overlap),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#print(n_overlap)
text(nmin,ylim_max+abs(ylim_max-ylim_min)/20,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
}
return(list(overlap))
}
Interim_TAB<-function(num_interim=3,interim_n=c(50,100,150),
alloc.ratio = 1,
prior.a1=1/3,prior.b1=1,
prior.a2=1/3,prior.b2=1,
control.mean=0,mean=c(0.25),
CT1.go=c(0.25,0.25,0.25),
false.go.CT1=c(TRUE,TRUE,TRUE),FGR.CT1=c(0.25,0.25,0.25),
CT1.nogo=c(0.25,0.25,0.25),
false.nogo.CT1=c(TRUE,TRUE,TRUE),FNGR.CT1=c(0.25,0.25,0.25),
CT2.go=c(0.3,0.3,0.3),
false.go.CT2=c(TRUE,TRUE,TRUE),FGR.CT2=c(0.25,0.25,0.25),
CT2.nogo=c(0.3,0.3,0.3),
false.nogo.CT2=c(TRUE,TRUE,TRUE),FNGR.CT2=c(0.25,0.25,0.25),
overlap.option=c('GO','GO','GO'),
method='Bayesian',direction=c("Greater",'Greater','Greater'),
task=c('Futility','Superiority','Futility and superiority'),
nsim=10000,seed.num=369,nsim_IA=10000,stop.criterion=10^-3,
logic.go=c('and','and','or'),logic.nogo=c('and','or','and')){
interim_n=sort(interim_n)
temptable=c()
for(meanindex in 1:length(mean)){
set.seed(seed.num)
diff_interim_n<-diff(interim_n)
generate_n<-c(interim_n[1],diff_interim_n)
sum_x1=matrix(NA,nrow=nsim_IA,ncol=num_interim)
sum_x2=sum_x1
treatment.mean=control.mean+mean[meanindex]
x1=c()
x2=c()
for(k in 1:num_interim){
i1=round(generate_n[k]*alloc.ratio/(1+alloc.ratio))
i2=generate_n[k]-i1
if (abs(generate_n[k]*alloc.ratio/(1+alloc.ratio)-i1)>10^(-3))
stop ("Sample size for each arm must be an integer in each interim.")
x1=cbind(x1,as.matrix(rbinom(nsim_IA,i1,treatment.mean)))
x2=cbind(x2,as.matrix(rbinom(nsim_IA,i2,control.mean)))
sum_x1[,k]=apply(x1,1,sum)
sum_x2[,k]=apply(x2,1,sum)
}
#####
go_matrix<-matrix(NA,nrow=nsim_IA,ncol=num_interim)
nogo_matrix<-matrix(NA,nrow=nsim_IA,ncol=num_interim)
inconclusive_matrix<-matrix(NA,nrow=nsim_IA,ncol=num_interim)
table<-matrix(NA,ncol=num_interim+1,nrow=6)
IA_go_matrix<-matrix(NA,nrow=nsim_IA,ncol=num_interim) ###whether continue to next stage
if(method=='Frequentist'){
go_cutoff<-rep(NA,num_interim)
nogo_cutoff<-rep(NA,num_interim)
true_go_cutoff<-rep(NA,num_interim)
true_nogo_cutoff<-rep(NA,num_interim)
overlap<-rep(NA,num_interim)
for(i in 1:num_interim){
temp<-TAB_Bin_Cutoff(n=interim_n[i],alloc.ratio = alloc.ratio,
prior.a1=prior.a1,prior.b1 = prior.b1,
prior.a2=prior.a2,prior.b2 = prior.b2,
control.mean=control.mean,
CT1.go=CT1.go[i],
false.go.CT1=false.go.CT1[i],FGR.CT1=FGR.CT1[i],
CT1.nogo=CT1.nogo[i],
false.nogo.CT1=false.nogo.CT1[i],FNGR.CT1=FNGR.CT1[i],
CT2.go=CT2.go[i],
false.go.CT2=false.go.CT2[i], FGR.CT2=FGR.CT2[i],
CT2.nogo=CT2.nogo[i],
false.nogo.CT2=false.nogo.CT2[i], FNGR.CT2=FNGR.CT2[i],
method=method,direction=direction[i],
seed.num=seed.num,nsim=nsim,stop.criterion=stop.criterion,
logic.go=logic.go[i],logic.nogo=logic.nogo[i])
go_cutoff[i]<-temp$cutoff[1]
nogo_cutoff[i]<-temp$cutoff[2]
overlap[i]<-temp$overlap
###TAB####
true_go_cutoff[i]<-ifelse(overlap[i]==0,go_cutoff[i],(overlap.option[i]=='GO')*go_cutoff[i]+(overlap.option[i]=='NOGO')*(nogo_cutoff[i]))
true_nogo_cutoff[i]<-ifelse(overlap[i]==0,nogo_cutoff[i],(overlap.option[i]=='GO')*(go_cutoff[i])+(overlap.option[i]=='NOGO')*(nogo_cutoff[i]))
####
}
for(j in 1:num_interim ){
i1 = round(interim_n[j]*alloc.ratio/(1+alloc.ratio))
i2 = interim_n[j]-i1
if(direction[j]=='Greater'){
go_matrix[,j]<-sum_x1[,j]/i1-sum_x2[,j]/i2>=(true_go_cutoff[j])
nogo_matrix[,j]<-sum_x1[,j]/i1-sum_x2[,j]/i2<(true_nogo_cutoff[j])
inconclusive_matrix[,j]<-rep(1,nsim_IA)-go_matrix[,j]-nogo_matrix[,j]
}
if(direction[j]=='Less'){
go_matrix[,j]<-sum_x1[,j]/i1-sum_x2[,j]/i2<=(true_go_cutoff[j])
nogo_matrix[,j]<-sum_x1[,j]/i1-sum_x2[,j]/i2>(true_nogo_cutoff[j])
inconclusive_matrix[,j]<-rep(1,nsim_IA)-go_matrix[,j]-nogo_matrix[,j]
}
}
}
if(method=='Bayesian'){
for(j in 1:num_interim ){
i1 = round(interim_n[j]*alloc.ratio/(1+alloc.ratio))
i2 = interim_n[j]-i1
if(is.na(CT1.go[j])) false.go.CT1[j]=FALSE
if(is.na(CT1.nogo[j])) false.nogo.CT1[j]=FALSE
if(is.na(CT2.go[j])) false.go.CT2[j]=FALSE
if(is.na(CT2.nogo[j])) false.nogo.CT2[j]=FALSE
if(false.go.CT1[j]==TRUE) pp_go_1 = rep(0,nsim_IA)
if(false.nogo.CT1[j]==TRUE) pp_nogo_1 = rep(0,nsim_IA)
if(false.go.CT2[j]==TRUE) pp_go_2 = rep(0,nsim_IA)
if(false.nogo.CT2[j]==TRUE) pp_nogo_2 = rep(0,nsim_IA)
for (i in 1:nsim_IA){
temp1 = rbeta(nsim,prior.a1+sum_x1[i,j],prior.b1+i1-sum_x1[i,j])
temp2 = rbeta(nsim,prior.a2+sum_x2[i,j],prior.b2+i2-sum_x2[i,j])
if(direction[j]=='Greater'){
if(false.go.CT1[j]==TRUE) pp_go_1[i] = sum(temp1-temp2>=CT1.go[j])/nsim
if(false.nogo.CT1[j]==TRUE) pp_nogo_1[i] = sum(temp1-temp2>=CT1.nogo[j])/nsim
if(false.go.CT2[j]==TRUE) pp_go_2[i] = sum(temp1-temp2>=CT2.go[j])/nsim
if(false.nogo.CT2[j]==TRUE) pp_nogo_2[i] = sum(temp1-temp2>=CT2.nogo[j])/nsim
}
if(direction[j]=='Less'){
if(false.go.CT1[j]==TRUE) pp_go_1[i] = sum(temp1-temp2<=CT1.go[j])/nsim
if(false.nogo.CT1[j]==TRUE) pp_nogo_1[i] = sum(temp1-temp2<=CT1.nogo[j])/nsim
if(false.go.CT2[j]==TRUE) pp_go_2[i] = sum(temp1-temp2<=CT2.go[j])/nsim
if(false.nogo.CT2[j]==TRUE) pp_nogo_2[i] = sum(temp1-temp2<=CT2.nogo[j])/nsim
}
}
if(false.go.CT1[j]==TRUE & false.go.CT2[j]==TRUE){
if(logic.go[j]=='and')
go_matrix[,j] = pp_go_1>=1-FGR.CT1[j] & pp_go_2>=1-FGR.CT2[j]
if(logic.go[j]=='or')
go_matrix[,j] = pp_go_1>=1-FGR.CT1[j] | pp_go_2>=1-FGR.CT2[j]
} else if(false.go.CT1[j]==TRUE){
go_matrix[,j] = pp_go_1>=1-FGR.CT1[j]
} else if(false.go.CT2[j]==TRUE){
go_matrix[,j] = pp_go_2>=1-FGR.CT2[j]
}
if(false.nogo.CT1[j]==TRUE & false.nogo.CT2[j]==TRUE){
if(logic.nogo[j]=='and')
nogo_matrix[,j] = pp_nogo_1<FNGR.CT1[j] & pp_nogo_2<FNGR.CT2[j]
if(logic.nogo[j]=='or')
nogo_matrix[,j] = pp_nogo_1<FNGR.CT1[j] | pp_nogo_2<FNGR.CT2[j]
} else if(false.nogo.CT1[j]==TRUE){
nogo_matrix[,j] = pp_nogo_1<FNGR.CT1[j]
} else if(false.nogo.CT2[j]==TRUE){
nogo_matrix[,j] = pp_nogo_2<FNGR.CT2[j]
}
if (overlap.option[j]=='GO'){
nogo_matrix[nogo_matrix[,j]==go_matrix[,j] & nogo_matrix[,j]==1,j] = 0
} else if (overlap.option[j]=='NOGO'){
go_matrix[go_matrix[,j]==nogo_matrix[,j] & go_matrix[,j]==1,j] = 0
}
inconclusive_matrix[,j] = rep(1,nsim_IA)-go_matrix[,j]-nogo_matrix[,j]
}
}
for(ii in 1:(num_interim)){
if(task[ii]=='Futility'){
IA_go_matrix[,ii]=inconclusive_matrix[,ii]+go_matrix[,ii]
}
if(task[ii]=='Superiority'){
IA_go_matrix[,ii]=inconclusive_matrix[,ii]+nogo_matrix[,ii]
}
if(task[ii]=='Futility and superiority'){
IA_go_matrix[,ii]=inconclusive_matrix[,ii]
}
}
cum_IA_go_matrix<-t(apply(IA_go_matrix,1,cumprod))
for(j in 1:(num_interim)){
table[1,j]=interim_n[j]
table[2,j]=mean[meanindex]
table[3,j]=task[j]
if(j==1){
if(task[j]=='Superiority'|task[j]=='Futility and superiority'){
table[4,j]=round(sum(go_matrix[,j]==1)/nsim_IA,3)}else{table[4,j]=0}
if(task[j]=='Futility'|task[j]=='Futility and superiority'){
table[6,j]=round(sum(nogo_matrix[,j]==1)/nsim_IA,3)
}else{table[6,j]=0}
}else{
if(task[j]=='Superiority'|task[j]=='Futility and superiority'){
table[4,j]=round(sum(go_matrix[,j]==1&cum_IA_go_matrix[,j-1]==1)/nsim_IA,3)}else{table[4,j]=0}
if(task[j]=='Futility'|task[j]=='Futility and superiority'){
table[6,j]=round(sum(nogo_matrix[,j]==1&cum_IA_go_matrix[,j-1]==1)/nsim_IA,3)
}else{table[6,j]=0}
}
table[5,j]=round(sum(cum_IA_go_matrix[,j]==1)/nsim_IA,3)
# if(task[j]=='Futility'){
# table[7,j]=ifelse(direction[j]=='Greater',HTML(paste0('-/<',round(true_nogo_cutoff[1,j],3))),HTML(paste0('-/>',round(true_nogo_cutoff[1,j],3))))
# }
# if(task[j]=='Superiority'){
# table[7,j]=ifelse(direction[j]=='Greater',HTML(paste0('>=',round(true_go_cutoff[1,j],3),'/-')),HTML(paste0('<=',round(true_go_cutoff[1,j],3),'/-')))
# }
# if(task[j]=='Futility and superiority'){
# table[7,j]=ifelse(direction[j]=='Greater',HTML(paste0('>=',round(true_go_cutoff[1,j],3),' /','<',round(true_nogo_cutoff[1,j],3))),HTML(paste0('<=',round(true_go_cutoff[1,j],3),' / ','>',round(true_nogo_cutoff[1,j],3))))
# }
# table[10,j]=ifelse(direction[j]=='Greater',HTML(paste0('>=',round(go_cutoff[1,j],3))),HTML(paste0('<=',round(go_cutoff[1,j],3))))
# table[9,j]=ifelse(direction[j]=='Greater',HTML(paste0('<',round(nogo_cutoff[1,j],3))),HTML(paste0('>',round(nogo_cutoff[1,j],3))))
# table[8,j]<-ifelse(overlap[j]==1,paste0('GO/NOGO zones overlapped, classified by criterion of ',overlap.option[j]),'None')
}
expectss<-round(sum(as.numeric(table[1,1:num_interim])*(c(as.numeric(table[4,1:num_interim-1])+as.numeric(table[6,1:num_interim-1]),as.numeric(table[5,num_interim-1])))),3)
table[1,num_interim+1]=HTML(paste0(expectss,' (expected)'))
table[2,num_interim+1]=mean[meanindex]
table[3,num_interim+1]=''
table[4,num_interim+1]=round(sum(as.numeric(table[4,1:num_interim])),3)
table[5,num_interim+1]=round(as.numeric(table[5,num_interim]),3)
table[6,num_interim+1]=round(sum(as.numeric(table[6,1:num_interim])),3)
# table[7,num_interim+1]=''
# table[8,num_interim+1]=''
# table[9,num_interim+1]=''
# table[10,num_interim+1]=''
table<-as.table(table)
tablecolname<-c(paste0('Interim analysis ',1:(num_interim-1)),'Final analysis',"Summary")
tablerowname<-c('Sample size','True difference of RR','Task','Success','To next interim/final or inconclusive',
'Stop')
table<-cbind(tablerowname,rep(meanindex,6),table)
colnames(table)<-c(" ",'Setting',tablecolname)
temptable=rbind(temptable,table)
}
return(temptable)
}
#Interim_TAB(direction=c('Greater','Greater','Greater'),logic.go=c('and','or','or'),logic.nogo=c('and','or','or'))
# Fix_SS_TAB_Bin_Prob(n=45,alloc.ratio=1,
# prior.a1=1/3,prior.b1=1,
# prior.a2=1/3,prior.b2=1,
# control.mean=0,
# mean=c(-0.5,0.8),
# CT1.go=0.15,
# false.go.CT1=TRUE,FGR.CT1=0.8,
# CT1.nogo=0.25,
# false.nogo.CT1=TRUE,FNGR.CT1=0.2,
# CT2.go=0.3,
# false.go.CT2=FALSE, FGR.CT2=0.5,
# CT2.nogo=0.3,
# false.nogo.CT2=FALSE, FNGR.CT2=0.5,
# overlap.option='GO',plot.figure=TRUE,
# method='Frequentist',direction='Less',seed.num=369,
# nsim=2000,stop.criterion=0.00001,
# logic.go='and',logic.nogo='or')
#
AshZhong/Goahead documentation built on May 5, 2022, 12:30 a.m.
R Package Documentation
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Defines functions Fix_SS_TAB_Bin_Prob TAB_Bayesian TAB_Bin_Cutoff findtabcutoff findbetacutoff
library(shiny)
####Two arms Binomial####
findbetacutoff<-function(a1=1,b1=1,a2=1,b2=1,n1=50,n2=50,p2=0.3,CT=0.2,rate=0.8,nsim=10000,stop.criterion=10^-3,direction='Greater',seed.num=369){
S=1
p1=p2
set.seed(seed.num)
upper=1
lower=0
while(S==1){
x1=rbeta(nsim,a1+n1,b1)
x0=rbeta(nsim,a1,b1+n1)
x=rbeta(nsim,a1+n1*p1,b1+n1*(1-p1))
y=rbeta(nsim,a2+n2*p2,b2+n2*(1-p2))
if(direction=='Greater'){
prob1=sum(x1>=y+CT)/nsim
prob0=sum(x0>=y+CT)/nsim
prob=sum(x>=y+CT)/nsim
if(prob1<=rate){
p1=Inf
S=0
}
if(prob0>=rate){
p1=0
S=0
}
if(abs(prob-rate)<=stop.criterion){
S=0
}else if(prob-rate>stop.criterion){
upper=p1
p1=(lower+p1)/2
}else{
lower=p1
p1=(upper+p1)/2
}
}
if(direction=='Less'){
prob1=sum(x1<=y+CT)/nsim
prob0=sum(x0<=y+CT)/nsim
prob=sum(x<=y+CT)/nsim
if(prob0<=rate){
p1=-Inf
S=0
}
if(prob1>=rate){
p1=1
S=0
}
if(abs(prob-rate)<=stop.criterion){
S=0
}else if(prob-rate>stop.criterion){
lower=p1
p1=(upper+p1)/2
}else{
upper=p1
p1=(lower+p1)/2
}
}
}
return(p1)
}
findtabcutoff<-function(n1=50,n2=50,p2=0.3,CT=0.2,rate=0.8,stop.criterion=10^-5,direction='Greater'){
upper=1
lower=0
S=1
p1=p2
if(direction=='Greater'){
while(S==1){
if((1-p2)<(CT+qnorm(rate)*sqrt(p2*(1-p2)/n2))){
p1=Inf
S=0
break
}else if((0-p2)>=(CT+qnorm(rate)*sqrt(p2*(1-p2)/n2))){
p1=0
S=0
break
}
sd=sqrt(p1*(1-p1)/n1+p2*(1-p2)/n2)
temp=p1-p2-CT-qnorm(rate)*sd
if(abs(temp)<=stop.criterion){
S=0
}else if(temp>stop.criterion){
upper=p1
p1=(lower+p1)/2
}else if(temp< -stop.criterion){
lower=p1
p1=(upper+p1)/2
}
}
}
if(direction=='Less'){
while(S==1){
if((1-p2)<=(CT+qnorm(1-rate)*sqrt(p2*(1-p2)/n2))){
p1=1
S=0
break
}else if((0-p2)>(CT+qnorm(1-rate)*sqrt(p2*(1-p2)/n2))){
p1=-Inf
S=0
break
}
sd=sqrt(p1*(1-p1)/n1+p2*(1-p2)/n2)
temp=p1-p2-CT-qnorm(1-rate)*sd
if(abs(temp)<=stop.criterion){
S=0
}else if(temp>stop.criterion){
upper=p1
p1=(lower+p1)/2
}else if(temp< -stop.criterion){
lower=p1
p1=(upper+p1)/2
}
}
}
return(p1)
}
TAB_Bin_Cutoff<-function(n=30,alloc.ratio=1,
prior.a1=1/3,prior.b1=1,
prior.a2=1/3,prior.b2=1,
control.mean=0,
CT1.go=0.25,
false.go.CT1=TRUE,FGR.CT1=0.25,
CT1.nogo=0.25,
false.nogo.CT1=TRUE,FNGR.CT1=0.25,
CT2.go=0.3,
false.go.CT2=TRUE, FGR.CT2=0.5,
CT2.nogo=0.3,
false.nogo.CT2=TRUE, FNGR.CT2=0.5,
method='Bayesian',direction='Greater',
seed.num=369,nsim=10000,stop.criterion=10^-3,
logic.go='and',logic.nogo='and'){
flag=rep(0,4)
overlap.flag=0
n1=round(n*alloc.ratio/(1+alloc.ratio))
n2=n-n1
var2=control.mean*(1-control.mean)
var11.go=(control.mean+CT1.go)*(1-control.mean-CT1.go)
var12.go=(control.mean+CT2.go)*(1-control.mean-CT2.go)
var11.nogo=(control.mean+CT1.nogo)*(1-control.mean-CT1.nogo)
var12.nogo=(control.mean+CT2.nogo)*(1-control.mean-CT2.nogo)
sd.n1.go=sqrt(var11.go/n1+var2/n2) ###for CT1.go###
sd.n2.go=sqrt(var12.go/n1+var2/n2) ###for CT2.go###
sd.n1.nogo=sqrt(var11.nogo/n1+var2/n2) ###for CT1.go###
sd.n2.nogo=sqrt(var12.nogo/n1+var2/n2) ###for CT2.go###
est1.go=NA
est2.go=NA
est1.nogo=NA
est2.nogo=NA
if(is.na(CT1.go)){
false.go.CT1=FALSE
}
if(is.na(CT1.nogo)){
false.nogo.CT1=FALSE
}
if(is.na(CT2.go)){
false.go.CT2=FALSE
}
if(is.na(CT2.nogo)){
false.nogo.CT2=FALSE
}
if(direction=='Greater'){
if(method=='Bayesian'){
if(false.go.CT1==TRUE){
p1.go<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT1.go,
rate=1-FGR.CT1,nsim=10000,
stop.criterion=10^-3,direction='Greater',seed.num=seed.num)
est1.go=p1.go-control.mean
}
if(false.go.CT2==TRUE){
p2.go<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT2.go,
rate=1-FGR.CT2,nsim=10000,
stop.criterion=10^-3,direction='Greater',seed.num=seed.num)
est2.go=p2.go-control.mean
}
if(false.nogo.CT1==TRUE){
p1.nogo<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT1.nogo,
rate=1-FNGR.CT1,nsim=nsim,
stop.criterion=stop.criterion,direction='Less',seed.num=seed.num)
est1.nogo=p1.nogo-control.mean
}
if(false.nogo.CT2==TRUE){
p2.nogo<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT2.nogo,
rate=1-FNGR.CT2,nsim=nsim,
stop.criterion=stop.criterion,direction='Less',seed.num=seed.num)
est2.nogo=p2.nogo-control.mean
}
}
if(method=='Frequentist'){
if(false.go.CT1==TRUE){
p1.go<-findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT1.go,rate=1-FGR.CT1,stop.criterion=10^-5,direction='Greater')
est1.go=p1.go-control.mean
}
if(false.go.CT2==TRUE){
p2.go<-findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT2.go,rate=1-FGR.CT2,stop.criterion=10^-5,direction='Greater')
est2.go=p2.go-control.mean
}
if(false.nogo.CT1==TRUE){
p1.nogo=findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT1.nogo,rate=1-FNGR.CT1,stop.criterion=10^-5,direction='Less')
est1.nogo=p1.nogo-control.mean
}
if(false.nogo.CT2==TRUE){
p2.nogo=findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT2.nogo,rate=1-FNGR.CT2,stop.criterion=10^-5,direction='Less')
est2.nogo=p2.nogo-control.mean
}
}
if(any(is.na(c(est1.go,est2.go)))){logic.go='and'}
if(any(is.na(c(est1.nogo,est2.nogo)))){logic.nogo='and'}
if(logic.go=='and'){
go_cutoff=max(est1.go,est2.go,na.rm=TRUE)
}
if(logic.go=='or'){
go_cutoff=min(est1.go,est2.go,na.rm=TRUE)
}
if(logic.nogo=='and')
{
nogo_cutoff=min(est1.nogo,est2.nogo,na.rm=TRUE)
}
if(logic.nogo=='or')
{
nogo_cutoff=max(est1.nogo,est2.nogo,na.rm=TRUE)
}
if(go_cutoff>=nogo_cutoff){return(list(cutoff=c(go_cutoff,nogo_cutoff),flag=flag,overlap=overlap.flag))}
else{
overlap.flag=1
return(list(cutoff=c(go_cutoff,nogo_cutoff),flag=flag,overlap=overlap.flag))}
if(all(flag==0)==FALSE){return(list(cutoff=c(NA,NA),flag=flag,overlap=overlap.flag))}
}
if(direction=='Less'){
if(method=='Bayesian'){
if(false.go.CT1==TRUE){
p1.go<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT1.go,
rate=1-FGR.CT1,nsim=nsim,
stop.criterion=stop.criterion,direction=direction,seed.num=seed.num)
est1.go=p1.go-control.mean
}
if(false.go.CT2==TRUE){
p2.go<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT2.go,
rate=1-FGR.CT2,nsim=nsim,
stop.criterion=stop.criterion,direction=direction,seed.num=seed.num)
est2.go=p2.go-control.mean
}
if(false.nogo.CT1==TRUE){
p1.nogo<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT1.nogo,
rate=1-FNGR.CT1,nsim=nsim,
stop.criterion=stop.criterion,direction='Greater',seed.num=seed.num)
est1.nogo=p1.nogo-control.mean
}
if(false.nogo.CT2==TRUE){
p2.nogo<-findbetacutoff(a1=prior.a1,b1=prior.b1,
a2=prior.a2,b2=prior.b2,
n1=n1,n2=n2,p2=control.mean,CT=CT2.nogo,
rate=1-FNGR.CT2,nsim=nsim,
stop.criterion=stop.criterion,direction='Greater',seed.num=seed.num)
est2.nogo=p2.nogo-control.mean
}
}
if(method=='Frequentist'){
if(false.go.CT1==TRUE){
p1.go<-findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT1.go,rate=1-FGR.CT1,stop.criterion=10^-5,direction='Less')
est1.go=p1.go-control.mean
}
if(false.go.CT2==TRUE){
p2.go<-findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT2.go,rate=1-FGR.CT2,stop.criterion=10^-5,direction='Less')
est2.go=p2.go-control.mean
}
if(false.nogo.CT1==TRUE){
p1.nogo=findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT1.nogo,rate=1-FNGR.CT1,stop.criterion=10^-5,direction='Greater')
est1.nogo=p1.nogo-control.mean
}
if(false.nogo.CT2==TRUE){
p2.nogo=findtabcutoff(n1=n1,n2=n2,p2=control.mean,CT=CT2.nogo,rate=1-FNGR.CT2,stop.criterion=10^-5,direction='Greater')
est2.nogo=p2.nogo-control.mean
}
}
if(any(is.na(c(est1.go,est2.go)))){logic.go='and'}
if(any(is.na(c(est1.nogo,est2.nogo)))){logic.nogo='and'}
if(logic.go=='and'){
go_cutoff=min(est1.go,est2.go,na.rm=TRUE)
}
if(logic.go=='or'){
go_cutoff=max(est1.go,est2.go,na.rm=TRUE)
}
if(logic.nogo=='and')
{
nogo_cutoff=max(est1.nogo,est2.nogo,na.rm=TRUE)
}
if(logic.nogo=='or')
{
nogo_cutoff=min(est1.nogo,est2.nogo,na.rm=TRUE)
}
if(go_cutoff<=nogo_cutoff){return(list(cutoff=c(go_cutoff,nogo_cutoff),flag=flag,overlap=overlap.flag))}
else{
overlap.flag=1
return(list(cutoff=c(go_cutoff,nogo_cutoff),flag=flag,overlap=overlap.flag))}
if(all(flag==0)==FALSE){return(list(cutoff=c(NA,NA),flag=flag,overlap=overlap.flag))}
}
}
TAB_Bayesian<-function(n=c(10,100),alloc.ratio=1,
prior.a1=1/3,prior.b1=1,
prior.a2=1/3,prior.b2=1,
control.mean=0,
mean=c(-0.5,0.8),
CT1.go=0.25,
false.go.CT1=TRUE,FGR.CT1=0.25,
CT1.nogo=0.25,
false.nogo.CT1=TRUE,FNGR.CT1=0.25,
CT2.go=0.3,
false.go.CT2=TRUE, FGR.CT2=0.5,
CT2.nogo=0.3,
false.nogo.CT2=TRUE, FNGR.CT2=0.5,
overlap.option='GO',
direction='Greater',
seed.num=369,nsim=10000,n_repeat=1000,
logic.go='and',logic.nogo='or'){
set.seed(seed.num)
go_prob<-matrix(NA,ncol=length(n),nrow=length(mean))
nogo_prob<-matrix(NA,ncol=length(n),nrow=length(mean))
inconclusive_prob<-matrix(NA,ncol=length(n),nrow=length(mean))
overlap.flag=rep(0,length(n))
for (ii in 1:length(mean)){
for (ii2 in 1:length(n)){
treatment.mean=control.mean+mean[ii]
i1=round(n[ii2]*alloc.ratio/(1+alloc.ratio))
i2=n[ii2]-i1
sum_x1=rbinom(n_repeat,i1,treatment.mean)
sum_x2=rbinom(n_repeat,i2,control.mean)
if(is.na(CT1.go)) false.go.CT1=FALSE
if(is.na(CT1.nogo)) false.nogo.CT1=FALSE
if(is.na(CT2.go)) false.go.CT2=FALSE
if(is.na(CT2.nogo)) false.nogo.CT2=FALSE
if(false.go.CT1==TRUE) pp_go_1 = rep(0,n_repeat)
if(false.nogo.CT1==TRUE) pp_nogo_1 = rep(0,n_repeat)
if(false.go.CT2==TRUE) pp_go_2 = rep(0,n_repeat)
if(false.nogo.CT2==TRUE) pp_nogo_2 = rep(0,n_repeat)
for (i in 1:n_repeat){
temp1 = rbeta(nsim,prior.a1+sum_x1[i],prior.b1+i1-sum_x1[i])
temp2 = rbeta(nsim,prior.a2+sum_x2[i],prior.b2+i2-sum_x2[i])
if(direction=='Greater'){
if(false.go.CT1==TRUE) pp_go_1[i] = sum(temp1-temp2>=CT1.go)/nsim
if(false.nogo.CT1==TRUE) pp_nogo_1[i] = sum(temp1-temp2>=CT1.nogo)/nsim
if(false.go.CT2==TRUE) pp_go_2[i] = sum(temp1-temp2>=CT2.go)/nsim
if(false.nogo.CT2==TRUE) pp_nogo_2[i] = sum(temp1-temp2>=CT2.nogo)/nsim
}
if(direction=='Less'){
if(false.go.CT1==TRUE) pp_go_1[i] = sum(temp1-temp2<=CT1.go)/nsim
if(false.nogo.CT1==TRUE) pp_nogo_1[i] = sum(temp1-temp2<=CT1.nogo)/nsim
if(false.go.CT2==TRUE) pp_go_2[i] = sum(temp1-temp2<=CT2.go)/nsim
if(false.nogo.CT2==TRUE) pp_nogo_2[i] = sum(temp1-temp2<=CT2.nogo)/nsim
}
}
if(false.go.CT1==TRUE & false.go.CT2==TRUE){
if(logic.go=='and')
go_prob[ii,ii2] = mean(pp_go_1>=1-FGR.CT1 & pp_go_2>=1-FGR.CT2)
if(logic.go=='or')
go_prob[ii,ii2] = mean(pp_go_1>=1-FGR.CT1 | pp_go_2>=1-FGR.CT2)
} else if(false.go.CT1==TRUE){
go_prob[ii,ii2] = mean(pp_go_1>=1-FGR.CT1)
} else if(false.go.CT2==TRUE){
go_prob[ii,ii2] = mean(pp_go_2>=1-FGR.CT2)
}
if(false.nogo.CT1==TRUE & false.nogo.CT2==TRUE){
if(logic.nogo=='and')
nogo_prob[ii,ii2] = mean(pp_nogo_1<FNGR.CT1 & pp_nogo_2<FNGR.CT2)
if(logic.nogo=='or')
nogo_prob[ii,ii2] = mean(pp_nogo_1<FNGR.CT1 | pp_nogo_2<FNGR.CT2)
} else if(false.nogo.CT1==TRUE){
nogo_prob[ii,ii2] = mean(pp_nogo_1<FNGR.CT1)
} else if(false.nogo.CT2==TRUE){
nogo_prob[ii,ii2] = mean(pp_nogo_2<FNGR.CT2)
}
if (go_prob[ii,ii2]+nogo_prob[ii,ii2]>1){
overlap.flag[ii2] = 1
if (overlap.option=='GO'){
nogo_prob[ii,ii2] = 1-go_prob[ii,ii2]
} else if (overlap.option=='NOGO'){
go_prob[ii,ii2] = 1-nogo_prob[ii,ii2]
}
}
inconclusive_prob[ii,ii2]=1-go_prob[ii,ii2]-nogo_prob[ii,ii2]
}
}
return(list(go_prob,nogo_prob,inconclusive_prob,overlap.flag))
}
###############################################################
Fix_SS_TAB_Bin_Prob<-function(n=100,alloc.ratio=1,
prior.a1=1/3,prior.b1=1,
prior.a2=1/3,prior.b2=1,
control.mean=0,
mean=c(-0.5,0.8),
CT1.go=0.25,
false.go.CT1=TRUE,FGR.CT1=0.25,
CT1.nogo=0.25,
false.nogo.CT1=TRUE,FNGR.CT1=0.25,
CT2.go=0.3,
false.go.CT2=TRUE, FGR.CT2=0.5,
CT2.nogo=0.3,
false.nogo.CT2=TRUE, FNGR.CT2=0.5,
overlap.option='GO',plot.figure=TRUE,
method='Bayesian',direction='Greater',seed.num=369,
nsim=nsim,stop.criterion=stop.criterion,
logic.go='and',logic.nogo='or'){
minmean=ifelse(min(mean)+control.mean>=0,min(mean),-control.mean)
maxmean=ifelse(max(mean)+control.mean<=1,max(mean),1-control.mean)
meanseq=round(seq(minmean,maxmean,0.05),3)
go_prob<-rep(NA,length(mean))
nogo_prob<-rep(NA,length(mean))
inconclusive_prob<-rep(NA,length(mean))
go_prob_plot<-rep(NA,length(meanseq))
nogo_prob_plot<-rep(NA,length(meanseq))
inconclusive_prob_plot<-rep(NA,length(meanseq))
index=1
unsatisfied.flag=0
overlap.flag=0
n1=round(n*alloc.ratio/(1+alloc.ratio))
n2=n-n1
if (abs(n*alloc.ratio/(1+alloc.ratio)-n1)>10^(-3))
stop ("Sample size for each arm must be an integer.")
var1=(mean+control.mean)*(1-mean-control.mean)
var2=control.mean*(1-control.mean)
var1seq=(meanseq+control.mean)*(1-meanseq-control.mean)
sd.n=sqrt(var1/n1+var2/n2)
sd.nseq=sqrt(var1seq/n1+var2/n2)
temp=TAB_Bin_Cutoff(n=n,alloc.ratio=alloc.ratio,
prior.a1=prior.a1,prior.b1=prior.b1,
prior.a2=prior.a2,prior.b2=prior.b2,
control.mean=control.mean,
CT1.go=CT1.go,
false.go.CT1 = false.go.CT1, FGR.CT1=FGR.CT1,
CT1.nogo = CT1.nogo,
false.nogo.CT1 = false.nogo.CT1, FNGR.CT1 = FNGR.CT1,
CT2.go=CT2.go,
false.go.CT2 = false.go.CT2, FGR.CT2=FGR.CT2,
CT2.nogo=CT2.nogo,
false.nogo.CT2 = false.nogo.CT2, FNGR.CT2 = FNGR.CT2,
method=method,direction=direction,seed.num=seed.num,
nsim=nsim,stop.criterion=stop.criterion,
logic.go=logic.go,logic.nogo = logic.nogo)
###TAB####
true_go_cutoff<-ifelse(temp$overlap==0,temp$cutoff[1],(overlap.option=='GO')*temp$cutoff[1]+(overlap.option=='NOGO')*(temp$cutoff[2]))
true_nogo_cutoff<-ifelse(temp$overlap==0,temp$cutoff[2],(overlap.option=='GO')*temp$cutoff[1]+(overlap.option=='NOGO')*(temp$cutoff[2]))
if(method=='Frequentist'){
if(direction=='Greater'){
if(all(temp$flag==0)&temp$overlap==0){
go_prob=1-pnorm(temp$cutoff[1],mean=mean,sd=sd.n)
nogo_prob=pnorm(temp$cutoff[2],mean=mean,sd=sd.n)
go_prob_plot=1-pnorm(temp$cutoff[1],mean=meanseq,sd=sd.nseq)
nogo_prob_plot=pnorm(temp$cutoff[2],mean=meanseq,sd=sd.nseq)
if(any(control.mean+temp$cutoff[1]>=1)){
go_prob[control.mean+temp$cutoff[1]>=1]=0
go_prob_plot[control.mean+temp$cutoff[1]>=1]=0
}
if(any(control.mean+temp$cutoff[1]<=0)){
go_prob[control.mean+temp$cutoff[1]<=0]=1
go_prob_plot[control.mean+temp$cutoff[1]<=0]=1
}
if(any(control.mean+temp$cutoff[2]<=0)){
nogo_prob[control.mean+temp$cutoff[2]<=0]=0
nogo_prob_plot[control.mean+temp$cutoff[2]<=0]=0
}
if(any(control.mean+temp$cutoff[2]>=1)){
nogo_prob[control.mean+temp$cutoff[2]>=1]=1
nogo_prob_plot[control.mean+temp$cutoff[2]>=1]=1
}
inconclusive_prob_plot=1-go_prob_plot-nogo_prob_plot
inconclusive_prob=1-go_prob-nogo_prob
}
if(all(temp$flag==0)&temp$overlap==1&overlap.option=="GO"){
go_prob=1-pnorm(temp$cutoff[1],mean=mean,sd=sd.n)
nogo_prob=pnorm(temp$cutoff[1],mean=mean,sd=sd.n)
go_prob_plot=1-pnorm(temp$cutoff[1],mean=meanseq,sd=sd.nseq)
nogo_prob_plot=pnorm(temp$cutoff[1],mean=meanseq,sd=sd.nseq)
if(any(control.mean+temp$cutoff[1]>=1)){
go_prob[control.mean+temp$cutoff[1]>=1]=0
go_prob_plot[control.mean+temp$cutoff[1]>=1]=0
}
if(any(control.mean+temp$cutoff[1]<=0)){
go_prob[control.mean+temp$cutoff[1]<=0]=1
go_prob_plot[control.mean+temp$cutoff[1]<=0]=1
}
if(any(control.mean+temp$cutoff[1]<=0)){
nogo_prob[control.mean+temp$cutoff[1]<=0]=0
nogo_prob_plot[control.mean+temp$cutoff[1]<=0]=0
}
if(any(control.mean+temp$cutoff[1]>=1)){
nogo_prob[control.mean+temp$cutoff[1]>=1]=1
nogo_prob_plot[control.mean+temp$cutoff[1]>=1]=1
}
inconclusive_prob_plot=1-go_prob_plot-nogo_prob_plot
inconclusive_prob=1-go_prob-nogo_prob
overlap.flag=1
}
if(all(temp$flag==0)&temp$overlap==1&overlap.option=="NOGO"){
go_prob=1-pnorm(temp$cutoff[2],mean=mean,sd=sd.n)
nogo_prob=pnorm(temp$cutoff[2],mean=mean,sd=sd.n)
go_prob_plot=1-pnorm(temp$cutoff[2],mean=meanseq,sd=sd.nseq)
nogo_prob_plot=pnorm(temp$cutoff[2],mean=meanseq,sd=sd.nseq)
if(any(control.mean+temp$cutoff[2]>=1)){
go_prob[control.mean+temp$cutoff[2]>=1]=0
go_prob_plot[control.mean+temp$cutoff[2]>=1]=0
}
if(any(control.mean+temp$cutoff[2]<=0)){
go_prob[control.mean+temp$cutoff[2]<=0]=1
go_prob_plot[control.mean+temp$cutoff[2]<=0]=1
}
if(any(control.mean+temp$cutoff[2]<=0)){
nogo_prob[control.mean+temp$cutoff[2]<=0]=0
nogo_prob_plot[control.mean+temp$cutoff[2]<=0]=0
}
if(any(control.mean+temp$cutoff[2]>=1)){
nogo_prob[control.mean+temp$cutoff[2]>=1]=1
nogo_prob_plot[control.mean+temp$cutoff[2]>=1]=1
}
inconclusive_prob_plot=1-go_prob_plot-nogo_prob_plot
inconclusive_prob=1-go_prob-nogo_prob
overlap.flag=1
}
if(all(temp$flag==0)==FALSE){
unsatisfied.flag=1
nogo_prob=rep(NA,length(mean))
go_prob=rep(NA,length(mean))
inconclusive_prob=rep(NA,length(mean))
}
}
if(direction=='Less'){
if(all(temp$flag==0)&temp$overlap==0){
go_prob=pnorm(temp$cutoff[1],mean=mean,sd=sd.n)
nogo_prob=1-pnorm(temp$cutoff[2],mean=mean,sd=sd.n)
go_prob_plot=pnorm(temp$cutoff[1],mean=meanseq,sd=sd.nseq)
nogo_prob_plot=1-pnorm(temp$cutoff[2],mean=meanseq,sd=sd.nseq)
if(any(control.mean+temp$cutoff[1]>=1)){
go_prob[control.mean+temp$cutoff[1]>=1]=1
go_prob_plot[control.mean+temp$cutoff[1]>=1]=1
}
if(any(control.mean+temp$cutoff[1]<=0)){
go_prob[control.mean+temp$cutoff[1]<=0]=0
go_prob_plot[control.mean+temp$cutoff[1]<=0]=0
}
if(any(control.mean+temp$cutoff[2]<=0)){
nogo_prob[control.mean+temp$cutoff[2]<=0]=1
nogo_prob_plot[control.mean+temp$cutoff[2]<=0]=1
}
if(any(control.mean+temp$cutoff[2]>=1)){
nogo_prob[control.mean+temp$cutoff[2]>=1]=0
nogo_prob_plot[control.mean+temp$cutoff[2]>=1]=0
}
inconclusive_prob_plot=1-go_prob_plot-nogo_prob_plot
inconclusive_prob=1-go_prob-nogo_prob
}
if(all(temp$flag==0)&temp$overlap==1&overlap.option=="GO"){
go_prob=pnorm(temp$cutoff[1],mean=mean,sd=sd.n)
nogo_prob=1-pnorm(temp$cutoff[1],mean=mean,sd=sd.n)
go_prob_plot=pnorm(temp$cutoff[1],mean=meanseq,sd=sd.nseq)
nogo_prob_plot=1-pnorm(temp$cutoff[1],mean=meanseq,sd=sd.nseq)
if(any(control.mean+temp$cutoff[1]>=1)){
go_prob[control.mean+temp$cutoff[1]>=1]=1
go_prob_plot[control.mean+temp$cutoff[1]>=1]=1
}
if(any(control.mean+temp$cutoff[1]<=0)){
go_prob[control.mean+temp$cutoff[1]<=0]=0
go_prob_plot[control.mean+temp$cutoff[1]<=0]=0
}
if(any(control.mean+temp$cutoff[1]<=0)){
nogo_prob[control.mean+temp$cutoff[1]<=0]=1
nogo_prob_plot[control.mean+temp$cutoff[1]<=0]=1
}
if(any(control.mean+temp$cutoff[1]>=1)){
nogo_prob[control.mean+temp$cutoff[1]>=1]=0
nogo_prob_plot[control.mean+temp$cutoff[1]>=1]=0
}
inconclusive_prob_plot=1-go_prob_plot-nogo_prob_plot
inconclusive_prob=1-go_prob-nogo_prob
overlap.flag=1
}
if(all(temp$flag==0)&temp$overlap==1&overlap.option=="NOGO"){
go_prob=pnorm(temp$cutoff[2],mean=mean,sd=sd.n)
nogo_prob=1-pnorm(temp$cutoff[2],mean=mean,sd=sd.n)
go_prob_plot=pnorm(temp$cutoff[2],mean=meanseq,sd=sd.nseq)
nogo_prob_plot=1-pnorm(temp$cutoff[2],mean=meanseq,sd=sd.nseq)
if(any(control.mean+temp$cutoff[2]>=1)){
go_prob[control.mean+temp$cutoff[2]>=1]=1
go_prob_plot[control.mean+temp$cutoff[2]>=1]=1
}
if(any(control.mean+temp$cutoff[2]<=0)){
go_prob[control.mean+temp$cutoff[2]<=0]=0
go_prob_plot[control.mean+temp$cutoff[2]<=0]=0
}
if(any(control.mean+temp$cutoff[2]<=0)){
nogo_prob[control.mean+temp$cutoff[2]<=0]=1
nogo_prob_plot[control.mean+temp$cutoff[2]<=0]=1
}
if(any(control.mean+temp$cutoff[2]>=1)){
nogo_prob[control.mean+temp$cutoff[2]>=1]=0
nogo_prob_plot[control.mean+temp$cutoff[2]>=1]=0
}
inconclusive_prob_plot=1-go_prob_plot-nogo_prob_plot
inconclusive_prob=1-go_prob-nogo_prob
overlap.flag=1
}
if(all(temp$flag==0)==FALSE){
unsatisfied.flag=1
nogo_prob=rep(NA,length(mean))
go_prob=rep(NA,length(mean))
inconclusive_prob=rep(NA,length(mean))
}
}
}
if(method=='Bayesian'){
n_repeat=1000
temp2 = TAB_Bayesian(n=n,alloc.ratio=alloc.ratio,
prior.a1=prior.a1,prior.b1=prior.b1,
prior.a2=prior.a2,prior.b2=prior.b2,
control.mean=control.mean,
mean=mean,
CT1.go=CT1.go,
false.go.CT1=false.go.CT1,FGR.CT1=FGR.CT1,
CT1.nogo=CT1.nogo,
false.nogo.CT1=false.nogo.CT1,FNGR.CT1=FNGR.CT1,
CT2.go=CT2.go,
false.go.CT2=false.go.CT2, FGR.CT2=FGR.CT2,
CT2.nogo=CT2.nogo,
false.nogo.CT2=false.nogo.CT2, FNGR.CT2=FNGR.CT2,
overlap.option=overlap.option,
direction=direction,
seed.num=seed.num,nsim=nsim,n_repeat=n_repeat,
logic.go=logic.go,logic.nogo=logic.nogo)
go_prob = as.numeric(temp2[[1]])
nogo_prob = as.numeric(temp2[[2]])
inconclusive_prob = as.numeric(temp2[[3]])
# plot
temp3 = TAB_Bayesian(n=n,alloc.ratio=alloc.ratio,
prior.a1=prior.a1,prior.b1=prior.b1,
prior.a2=prior.a2,prior.b2=prior.b2,
control.mean=control.mean,
mean=meanseq,
CT1.go=CT1.go,
false.go.CT1=false.go.CT1,FGR.CT1=FGR.CT1,
CT1.nogo=CT1.nogo,
false.nogo.CT1=false.nogo.CT1,FNGR.CT1=FNGR.CT1,
CT2.go=CT2.go,
false.go.CT2=false.go.CT2, FGR.CT2=FGR.CT2,
CT2.nogo=CT2.nogo,
false.nogo.CT2=false.nogo.CT2, FNGR.CT2=FNGR.CT2,
overlap.option=overlap.option,
direction=direction,
seed.num=seed.num,nsim=nsim,n_repeat=n_repeat,
logic.go=logic.go,logic.nogo=logic.nogo)
go_prob_plot = as.numeric(temp3[[1]])
nogo_prob_plot = as.numeric(temp3[[2]])
inconclusive_prob_plot = as.numeric(temp3[[3]])
}
#######################################################################################
if(plot.figure==TRUE){
delta=meanseq
p_nogo=nogo_prob_plot*100
p_grey=inconclusive_prob_plot*100
p_go=go_prob_plot*100
if(true_go_cutoff!=true_nogo_cutoff){
par(mfrow=c(1,1),pty="m",bty="l",cex=1.4)
plot(delta,p_go,xlab=expression(paste("True difference in Response Rates",sep="")),
ylab="Prob of GO/ NOGO/ Inconclusive (%)",xlim=range(delta),
ylim=c(0,100),type="n",axes=F)
axis(1, at=meanseq, labels=meanseq)
axis(2, at=seq(0,100,10),labels=T)
#text(rep(-0.6,6),seq(0,100,20),seq(0,100,20),adj=1,xpd=T)
box()
#abline(h=seq(0,100,10),lty=3,col=rgb(0.8,0.8,0.8),lwd=1)
points(delta,p_nogo,type="b",pch=16,col=rgb(0.9,0,0),lwd=3,lty=1)
points(delta,p_grey,type="b",pch=4,col=rgb(0.9,0.6,0),lwd=3,lty=6)
points(delta,p_go,type="b",pch=2,col=rgb(0,0.7,0),lwd=3,lty=2)
text(minmean,140,bquote(n==~.(n)),xpd=T,adj=0,cex=0.8,col=rgb(0, 0,0))
if(overlap.flag==0&unsatisfied.flag==0){
if(direction=='Greater'){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
text(minmean,110,bquote(Inconclusive~symbol("\336")~anything~between~GO~and~NOGO),xpd=T,adj=0,cex=0.8,col=rgb(0.9,0.6,0))
}
if(direction=='Less'){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
text(minmean,110,bquote(Inconclusive~symbol("\336")~anything~between~GO~and~NOGO),xpd=T,adj=0,cex=0.8,col=rgb(0.9,0.6,0))
}
}
if(overlap.flag==1&unsatisfied.flag==0&overlap.option=='GO'){
if(direction=="Greater"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
if(direction=="Less"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
}
if(overlap.flag==1&unsatisfied.flag==0&overlap.option=='NOGO'){
if(direction=="Greater"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
if(direction=="Less"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
}
if(unsatisfied.flag==1){
text(minmean,130,paste0('Warning: We could not find classification of zones to satisfy your both GO and NOGO criterions at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0,0))
text(minmean,120,paste0('Please check and modify your desicion rule or the range of sample size!'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0,0))
}
}
}
###########################################################################
if(plot.figure==TRUE){
delta=meanseq
p_nogo=nogo_prob_plot*100
p_grey=inconclusive_prob_plot*100
p_go=go_prob_plot*100
if(true_go_cutoff==true_nogo_cutoff){
par(mfrow=c(1,1),pty="m",bty="l",cex=1.4)
plot(delta,p_go,xlab=expression(paste("True difference in Response Rates",sep="")),
ylab="Prob of GO/ NOGO/ Inconclusive (%)",xlim=range(delta),
ylim=c(0,100),type="n",axes=F)
axis(1, at=meanseq, labels=meanseq)
axis(2, at=seq(0,100,10),labels=T)
#text(rep(-0.6,6),seq(0,100,20),seq(0,100,20),adj=1,xpd=T)
box()
#abline(h=seq(0,100,10),lty=3,col=rgb(0.8,0.8,0.8),lwd=1)
points(delta,p_nogo,type="b",pch=16,col=rgb(0.9,0,0),lwd=3,lty=1)
#points(delta,p_grey,type="b",pch=4,col=rgb(0.9,0.6,0),lwd=3,lty=6)
points(delta,p_go,type="b",pch=2,col=rgb(0,0.7,0),lwd=3,lty=2)
text(minmean,140,bquote(n==~.(n)),xpd=T,adj=0,cex=0.8,col=rgb(0, 0,0))
if(overlap.flag==0&unsatisfied.flag==0){
if(direction=='Greater'){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,110,bquote(Inconclusive~symbol("\336")~anything~between~GO~and~NOGO),xpd=T,adj=0,cex=0.8,col=rgb(0.9,0.6,0))
}
if(direction=='Less'){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,110,bquote(Inconclusive~symbol("\336")~anything~between~GO~and~NOGO),xpd=T,adj=0,cex=0.8,col=rgb(0.9,0.6,0))
}
}
if(overlap.flag==1&unsatisfied.flag==0&overlap.option=='GO'){
if(direction=="Greater"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
if(direction=="Less"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[1],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
}
if(overlap.flag==1&unsatisfied.flag==0&overlap.option=='NOGO'){
if(direction=="Greater"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
if(direction=="Less"){
text(minmean,130,bquote(GO~symbol("\336")~Observed~difference~'in'~RR~symbol("\243")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0, 0.7,0))
text(minmean,120,bquote(NOGO~symbol("\336")~Observed~difference~'in'~RR~symbol("\263")~.(round(temp$cutoff[2],digits=3))),xpd=T,adj=0,cex=0.8,col=rgb(0.9, 0,0))
#text(minmean,115,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(minmean,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
}
if(unsatisfied.flag==1){
text(minmean,130,paste0('Warning: We could not find classification of zones to satisfy your both GO and NOGO criterions at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0,0))
text(minmean,120,paste0('Please check and modify your desicion rule or the range of sample size!'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0,0))
}
}
}
###########################################################################
return(list(go_prob=go_prob,nogo_prob=nogo_prob,
inconclusive_prob=inconclusive_prob,
overlap.flag=overlap.flag,overlap.option=overlap.option,
unsatisfied.flag=unsatisfied.flag,cutoff=temp$cutoff,true_cutoff=c(true_go_cutoff,true_nogo_cutoff))
)
}
Vary_SS_TAB_Bin_Prob<-function(nmin=10,nmax=50,
prior.a1=1/3,prior.b1=1,
prior.a2=1/3,prior.b2=1,
mean=0.3,alloc.ratio=1,
control.mean=0,
CT1.go=0.25,
false.go.CT1=TRUE,FGR.CT1=0.25,
CT1.nogo=0.25,
false.nogo.CT1=TRUE,FNGR.CT1=0.25,
CT2.go=0.3,
false.go.CT2=TRUE, FGR.CT2=0.5,
CT2.nogo=0.3,
false.nogo.CT2=TRUE, FNGR.CT2=0.5,
overlap.option='GO',plot.cutoff=TRUE,plot.prob=TRUE,
method="Bayesian",direction="Greater",seed.num=369,
nsim=10000,stop.criterion=10^-3,
logic.go='and',logic.nogo='or'){
nseq=unique(round(c(seq(nmin,(nmax+nmin)/2,length=6)[-6],seq((nmax+nmin)/2,nmax,length=6))))
go_prob<-matrix(NA,ncol=length(nseq),nrow=length(mean))
nogo_prob<-matrix(NA,ncol=length(nseq),nrow=length(mean))
inconclusive_prob<-matrix(NA,ncol=length(nseq),nrow=length(mean))
go_cutoff<-rep(NA,length(nseq))
nogo_cutoff<-rep(NA,length(nseq))
index=1
n_unsatisfied=NA
n_overlap=NA
ncore <- detectCores()
cl<-makeCluster(ncore)
registerDoParallel(cl)
results<-foreach(i = nseq,.export=c('TAB_Bin_Cutoff','findbetacutoff',"findtabcutoff"),.combine=rbind) %dopar% {
i1=round(i*alloc.ratio/(1+alloc.ratio))
i2=i-i1
var1=(mean+control.mean)*(1-mean-control.mean)
var2=control.mean*(1-control.mean)
sd.i=sqrt(var1/i1+var2/i2)
temp=TAB_Bin_Cutoff(n=i,alloc.ratio=alloc.ratio,
prior.a1=prior.a1,prior.b1=prior.b1,
prior.a2=prior.a2,prior.b2=prior.b2,
control.mean=control.mean,
CT1.go=CT1.go,
false.go.CT1 = false.go.CT1, FGR.CT1=FGR.CT1,
CT1.nogo=CT1.nogo,
false.nogo.CT1 = false.nogo.CT1, FNGR.CT1 = FNGR.CT1,
CT2.go = CT2.go,
false.go.CT2 = false.go.CT2, FGR.CT2=FGR.CT2,
CT2.nogo=CT2.nogo,
false.nogo.CT2 = false.nogo.CT2, FNGR.CT2 = FNGR.CT2,
method=method,direction=direction,seed.num = seed.num,
nsim=nsim,stop.criterion=stop.criterion,
logic.go = logic.go,logic.nogo = logic.nogo)
c(temp$overlap,temp$cutoff)
}
stopCluster(cl)
go_cutoff<-results[,2]
nogo_cutoff<-results[,3]
overlap<-results[,1]
for(mean.index in 1:length(mean)){
true_go_cutoff<-go_cutoff
true_nogo_cutoff<-nogo_cutoff
true_go_cutoff[overlap==1]<-(overlap.option=='GO')*go_cutoff[overlap==1]+(overlap.option=='NOGO')*nogo_cutoff[overlap==1]
true_nogo_cutoff[overlap==1]<-(overlap.option=='GO')*go_cutoff[overlap==1]+(overlap.option=='NOGO')*nogo_cutoff[overlap==1]
}
if(method=='Frequentist'){
for(mean.index in 1:length(mean)){
mean_temp=mean[mean.index]
i1=round(nseq*alloc.ratio/(1+alloc.ratio))
i2=nseq-i1
var1=(mean_temp+control.mean)*(1-mean_temp-control.mean)
var2=control.mean*(1-control.mean)
sd.i=sqrt(var1/nseq+var2/nseq)
if(direction=='Greater'){
go_prob[mean.index,]=1-pnorm(true_go_cutoff,mean=mean_temp,sd=sd.i)
nogo_prob[mean.index,]=pnorm(true_nogo_cutoff,mean=mean_temp,sd=sd.i)
if(any(control.mean+true_go_cutoff>=1)){
go_prob[mean.index,control.mean+true_go_cutoff>=1]=0
}
if(any(control.mean+true_go_cutoff<=0)){
go_prob[mean.index,control.mean+cutoff<=0]=1
}
if(any(control.mean+true_nogo_cutoff<=0)){
nogo_prob[mean.index,control.mean+true_nogo_cutoff<=0]=0
}
if(any(control.mean+true_nogo_cutoff>=1)){
nogo_prob[mean.index,control.mean+true_nogo_cutoff>=1]=1
}
}
if(direction=='Less'){
go_prob[mean.index,]=pnorm(true_go_cutoff,mean=mean_temp,sd=sd.i)
nogo_prob[mean.index,]=1-pnorm(true_nogo_cutoff,mean=mean_temp,sd=sd.i)
if(any(control.mean+true_go_cutoff>=1)){
go_prob[mean.index,control.mean+true_go_cutoff>=1]=1
}
if(any(control.mean+true_go_cutoff<=0)){
go_prob[mean.index,control.mean+cutoff<=0]=0
}
if(any(control.mean+true_nogo_cutoff<=0)){
nogo_prob[mean.index,control.mean+true_nogo_cutoff<=0]=1
}
if(any(control.mean+true_nogo_cutoff>=1)){
nogo_prob[mean.index,control.mean+true_nogo_cutoff>=1]=0
}
}
inconclusive_prob[mean.index,]=1-go_prob[mean.index,]-nogo_prob[mean.index,]
}
}
if(method=='Bayesian'){
n_repeat=1000
temp2 = TAB_Bayesian(n=nseq,alloc.ratio=alloc.ratio,
prior.a1=prior.a1,prior.b1=prior.b1,
prior.a2=prior.a2,prior.b2=prior.b2,
control.mean=control.mean,
mean=mean,
CT1.go=CT1.go,
false.go.CT1=false.go.CT1,FGR.CT1=FGR.CT1,
CT1.nogo=CT1.nogo,
false.nogo.CT1=false.nogo.CT1,FNGR.CT1=FNGR.CT1,
CT2.go=CT2.go,
false.go.CT2=false.go.CT2, FGR.CT2=FGR.CT2,
CT2.nogo=CT2.nogo,
false.nogo.CT2=false.nogo.CT2, FNGR.CT2=FNGR.CT2,
overlap.option=overlap.option,
direction=direction,
seed.num=seed.num,nsim=nsim,n_repeat=n_repeat,
logic.go=logic.go,logic.nogo=logic.nogo)
go_prob = temp2[[1]]
nogo_prob = temp2[[2]]
inconclusive_prob = temp2[[3]]
}
n_overlap=n_overlap[-1]
n_unsatisfied=n_unsatisfied[-1]
####plot figure
if(plot.prob==TRUE){
for(j in 1:length(mean)){
p_go=go_prob[j,]*100
p_nogo=nogo_prob[j,]*100
class(p_nogo)
dim(p_nogo)
p_grey=100-p_go-p_nogo
par(mfrow=c(1,1),pty="m",bty="l",cex=1.4)
cum_p_nogo=p_nogo
cum_p_grey=p_nogo+p_grey
cum_p_go=p_nogo+p_grey+p_go
delta=nseq
plot(delta,cum_p_go,xlab="Sample size",
ylab="Prob of GO/ NOGO/ Inconclusive (%)",xlim=c(nmin,nmax),
ylim=c(0,100),type="n",axes=F,pch=NA)
axis(1, at=nseq, labels=nseq)
axis(2, at=seq(0,100,10),labels=T)
#text(rep(-0.6,6),seq(0,100,20),seq(0,100,20),adj=1,xpd=T)
box()
#abline(h=seq(0,100,10),lty=3,col=rgb(0.8,0.8,0.8),lwd=1)
polygon(c(delta,rev(delta)),c(cum_p_nogo,rev(rep(0,length(delta)))),col=rgb(0.9,0,0),border=NA)
polygon(c(delta,rev(delta)),c(cum_p_grey,rev(cum_p_nogo)),col=rgb(0.9,0.6,0),border=NA)
polygon(c(delta,rev(delta)),c(cum_p_go,rev(cum_p_grey)),col=rgb(0,0.7,0),border=NA)
text((nmin+nmax)/2,120,paste0("True difference in RR=",round(mean[j],3),';Oberserved RR in control group=',round(control.mean,3)),xpd=T,adj=0.5,cex=0.8)
if(any(overlap!=0)){
text(nmin,115,paste0('Warning: GO and NOGO cut-offs are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(nmin,110,paste(n_overlap),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#print(n_overlap)
text(nmin,110,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
}
}
if(plot.cutoff==TRUE){
par(mfrow=c(1,1),pty="m",bty="l",cex=1.4)
ylim_max=max(c(go_cutoff,nogo_cutoff,round(CT1.go,3),round(CT1.nogo,3),round(CT2.go,3),round(CT2.nogo,3)),na.rm=TRUE)+0.1
ylim_min=min(c(go_cutoff,nogo_cutoff,round(CT1.go,3),round(CT1.nogo,3),round(CT2.go,3),round(CT2.nogo,3)),na.rm=TRUE)-0.1
plot(NA,NA,xlab='Sample size',ylab="Observed difference in RR",xlim=c(max(0,range(nseq)[1]-10),range(nseq)[2]+10),ylim=c(ylim_min,ylim_max),type="n",axes=F,col=rgb(1,0,0),lty=1,lwd=2)
axis(1, at=nseq,labels=nseq)
axis(2, at=round(c(seq(ylim_min,ylim_max,round((ylim_max-ylim_min)/10,digits=2)),CT1.go,CT2.go,CT1.nogo,CT2.nogo),digits=2),labels=T)
#text(rep(-0.6,6),seq(0,100,20),seq(0,300,20),adj=1,xpd=T)
box()
lines(nseq,nogo_cutoff,col=rgb(0.9,0,0),lwd=2)
lines(nseq,go_cutoff,col=rgb(0,0.7,0),lwd=2)
legend('bottomright',legend=c("Cut off of GO","Cut off of NOGO"),
col=c(rgb(0,0.7,0),rgb(0.9,0,0)),
lwd=c(2,2),
lty=c(1,1),cex=0.5)
text(nmin,ylim_max+3*abs(ylim_max-ylim_min)/20,paste0('Oberserved RR in control group=',round(control.mean,3)),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
if(any(overlap!=0)){
text(nmin,ylim_max+abs(ylim_max-ylim_min)/10,paste0('Warning: GO and NOGO zones are overlaped at some sample sizes'),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#text(nmin,110,paste(n_overlap),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
#print(n_overlap)
text(nmin,ylim_max+abs(ylim_max-ylim_min)/20,paste0('The zones are classfied by cutoff of ', overlap.option),xpd=T,adj=0,cex=0.5,col=rgb(0.9,0.6,0))
}
}
return(list(overlap))
}
Interim_TAB<-function(num_interim=3,interim_n=c(50,100,150),
alloc.ratio = 1,
prior.a1=1/3,prior.b1=1,
prior.a2=1/3,prior.b2=1,
control.mean=0,mean=c(0.25),
CT1.go=c(0.25,0.25,0.25),
false.go.CT1=c(TRUE,TRUE,TRUE),FGR.CT1=c(0.25,0.25,0.25),
CT1.nogo=c(0.25,0.25,0.25),
false.nogo.CT1=c(TRUE,TRUE,TRUE),FNGR.CT1=c(0.25,0.25,0.25),
CT2.go=c(0.3,0.3,0.3),
false.go.CT2=c(TRUE,TRUE,TRUE),FGR.CT2=c(0.25,0.25,0.25),
CT2.nogo=c(0.3,0.3,0.3),
false.nogo.CT2=c(TRUE,TRUE,TRUE),FNGR.CT2=c(0.25,0.25,0.25),
overlap.option=c('GO','GO','GO'),
method='Bayesian',direction=c("Greater",'Greater','Greater'),
task=c('Futility','Superiority','Futility and superiority'),
nsim=10000,seed.num=369,nsim_IA=10000,stop.criterion=10^-3,
logic.go=c('and','and','or'),logic.nogo=c('and','or','and')){
interim_n=sort(interim_n)
temptable=c()
for(meanindex in 1:length(mean)){
set.seed(seed.num)
diff_interim_n<-diff(interim_n)
generate_n<-c(interim_n[1],diff_interim_n)
sum_x1=matrix(NA,nrow=nsim_IA,ncol=num_interim)
sum_x2=sum_x1
treatment.mean=control.mean+mean[meanindex]
x1=c()
x2=c()
for(k in 1:num_interim){
i1=round(generate_n[k]*alloc.ratio/(1+alloc.ratio))
i2=generate_n[k]-i1
if (abs(generate_n[k]*alloc.ratio/(1+alloc.ratio)-i1)>10^(-3))
stop ("Sample size for each arm must be an integer in each interim.")
x1=cbind(x1,as.matrix(rbinom(nsim_IA,i1,treatment.mean)))
x2=cbind(x2,as.matrix(rbinom(nsim_IA,i2,control.mean)))
sum_x1[,k]=apply(x1,1,sum)
sum_x2[,k]=apply(x2,1,sum)
}
#####
go_matrix<-matrix(NA,nrow=nsim_IA,ncol=num_interim)
nogo_matrix<-matrix(NA,nrow=nsim_IA,ncol=num_interim)
inconclusive_matrix<-matrix(NA,nrow=nsim_IA,ncol=num_interim)
table<-matrix(NA,ncol=num_interim+1,nrow=6)
IA_go_matrix<-matrix(NA,nrow=nsim_IA,ncol=num_interim) ###whether continue to next stage
if(method=='Frequentist'){
go_cutoff<-rep(NA,num_interim)
nogo_cutoff<-rep(NA,num_interim)
true_go_cutoff<-rep(NA,num_interim)
true_nogo_cutoff<-rep(NA,num_interim)
overlap<-rep(NA,num_interim)
for(i in 1:num_interim){
temp<-TAB_Bin_Cutoff(n=interim_n[i],alloc.ratio = alloc.ratio,
prior.a1=prior.a1,prior.b1 = prior.b1,
prior.a2=prior.a2,prior.b2 = prior.b2,
control.mean=control.mean,
CT1.go=CT1.go[i],
false.go.CT1=false.go.CT1[i],FGR.CT1=FGR.CT1[i],
CT1.nogo=CT1.nogo[i],
false.nogo.CT1=false.nogo.CT1[i],FNGR.CT1=FNGR.CT1[i],
CT2.go=CT2.go[i],
false.go.CT2=false.go.CT2[i], FGR.CT2=FGR.CT2[i],
CT2.nogo=CT2.nogo[i],
false.nogo.CT2=false.nogo.CT2[i], FNGR.CT2=FNGR.CT2[i],
method=method,direction=direction[i],
seed.num=seed.num,nsim=nsim,stop.criterion=stop.criterion,
logic.go=logic.go[i],logic.nogo=logic.nogo[i])
go_cutoff[i]<-temp$cutoff[1]
nogo_cutoff[i]<-temp$cutoff[2]
overlap[i]<-temp$overlap
###TAB####
true_go_cutoff[i]<-ifelse(overlap[i]==0,go_cutoff[i],(overlap.option[i]=='GO')*go_cutoff[i]+(overlap.option[i]=='NOGO')*(nogo_cutoff[i]))
true_nogo_cutoff[i]<-ifelse(overlap[i]==0,nogo_cutoff[i],(overlap.option[i]=='GO')*(go_cutoff[i])+(overlap.option[i]=='NOGO')*(nogo_cutoff[i]))
####
}
for(j in 1:num_interim ){
i1 = round(interim_n[j]*alloc.ratio/(1+alloc.ratio))
i2 = interim_n[j]-i1
if(direction[j]=='Greater'){
go_matrix[,j]<-sum_x1[,j]/i1-sum_x2[,j]/i2>=(true_go_cutoff[j])
nogo_matrix[,j]<-sum_x1[,j]/i1-sum_x2[,j]/i2<(true_nogo_cutoff[j])
inconclusive_matrix[,j]<-rep(1,nsim_IA)-go_matrix[,j]-nogo_matrix[,j]
}
if(direction[j]=='Less'){
go_matrix[,j]<-sum_x1[,j]/i1-sum_x2[,j]/i2<=(true_go_cutoff[j])
nogo_matrix[,j]<-sum_x1[,j]/i1-sum_x2[,j]/i2>(true_nogo_cutoff[j])
inconclusive_matrix[,j]<-rep(1,nsim_IA)-go_matrix[,j]-nogo_matrix[,j]
}
}
}
if(method=='Bayesian'){
for(j in 1:num_interim ){
i1 = round(interim_n[j]*alloc.ratio/(1+alloc.ratio))
i2 = interim_n[j]-i1
if(is.na(CT1.go[j])) false.go.CT1[j]=FALSE
if(is.na(CT1.nogo[j])) false.nogo.CT1[j]=FALSE
if(is.na(CT2.go[j])) false.go.CT2[j]=FALSE
if(is.na(CT2.nogo[j])) false.nogo.CT2[j]=FALSE
if(false.go.CT1[j]==TRUE) pp_go_1 = rep(0,nsim_IA)
if(false.nogo.CT1[j]==TRUE) pp_nogo_1 = rep(0,nsim_IA)
if(false.go.CT2[j]==TRUE) pp_go_2 = rep(0,nsim_IA)
if(false.nogo.CT2[j]==TRUE) pp_nogo_2 = rep(0,nsim_IA)
for (i in 1:nsim_IA){
temp1 = rbeta(nsim,prior.a1+sum_x1[i,j],prior.b1+i1-sum_x1[i,j])
temp2 = rbeta(nsim,prior.a2+sum_x2[i,j],prior.b2+i2-sum_x2[i,j])
if(direction[j]=='Greater'){
if(false.go.CT1[j]==TRUE) pp_go_1[i] = sum(temp1-temp2>=CT1.go[j])/nsim
if(false.nogo.CT1[j]==TRUE) pp_nogo_1[i] = sum(temp1-temp2>=CT1.nogo[j])/nsim
if(false.go.CT2[j]==TRUE) pp_go_2[i] = sum(temp1-temp2>=CT2.go[j])/nsim
if(false.nogo.CT2[j]==TRUE) pp_nogo_2[i] = sum(temp1-temp2>=CT2.nogo[j])/nsim
}
if(direction[j]=='Less'){
if(false.go.CT1[j]==TRUE) pp_go_1[i] = sum(temp1-temp2<=CT1.go[j])/nsim
if(false.nogo.CT1[j]==TRUE) pp_nogo_1[i] = sum(temp1-temp2<=CT1.nogo[j])/nsim
if(false.go.CT2[j]==TRUE) pp_go_2[i] = sum(temp1-temp2<=CT2.go[j])/nsim
if(false.nogo.CT2[j]==TRUE) pp_nogo_2[i] = sum(temp1-temp2<=CT2.nogo[j])/nsim
}
}
if(false.go.CT1[j]==TRUE & false.go.CT2[j]==TRUE){
if(logic.go[j]=='and')
go_matrix[,j] = pp_go_1>=1-FGR.CT1[j] & pp_go_2>=1-FGR.CT2[j]
if(logic.go[j]=='or')
go_matrix[,j] = pp_go_1>=1-FGR.CT1[j] | pp_go_2>=1-FGR.CT2[j]
} else if(false.go.CT1[j]==TRUE){
go_matrix[,j] = pp_go_1>=1-FGR.CT1[j]
} else if(false.go.CT2[j]==TRUE){
go_matrix[,j] = pp_go_2>=1-FGR.CT2[j]
}
if(false.nogo.CT1[j]==TRUE & false.nogo.CT2[j]==TRUE){
if(logic.nogo[j]=='and')
nogo_matrix[,j] = pp_nogo_1<FNGR.CT1[j] & pp_nogo_2<FNGR.CT2[j]
if(logic.nogo[j]=='or')
nogo_matrix[,j] = pp_nogo_1<FNGR.CT1[j] | pp_nogo_2<FNGR.CT2[j]
} else if(false.nogo.CT1[j]==TRUE){
nogo_matrix[,j] = pp_nogo_1<FNGR.CT1[j]
} else if(false.nogo.CT2[j]==TRUE){
nogo_matrix[,j] = pp_nogo_2<FNGR.CT2[j]
}
if (overlap.option[j]=='GO'){
nogo_matrix[nogo_matrix[,j]==go_matrix[,j] & nogo_matrix[,j]==1,j] = 0
} else if (overlap.option[j]=='NOGO'){
go_matrix[go_matrix[,j]==nogo_matrix[,j] & go_matrix[,j]==1,j] = 0
}
inconclusive_matrix[,j] = rep(1,nsim_IA)-go_matrix[,j]-nogo_matrix[,j]
}
}
for(ii in 1:(num_interim)){
if(task[ii]=='Futility'){
IA_go_matrix[,ii]=inconclusive_matrix[,ii]+go_matrix[,ii]
}
if(task[ii]=='Superiority'){
IA_go_matrix[,ii]=inconclusive_matrix[,ii]+nogo_matrix[,ii]
}
if(task[ii]=='Futility and superiority'){
IA_go_matrix[,ii]=inconclusive_matrix[,ii]
}
}
cum_IA_go_matrix<-t(apply(IA_go_matrix,1,cumprod))
for(j in 1:(num_interim)){
table[1,j]=interim_n[j]
table[2,j]=mean[meanindex]
table[3,j]=task[j]
if(j==1){
if(task[j]=='Superiority'|task[j]=='Futility and superiority'){
table[4,j]=round(sum(go_matrix[,j]==1)/nsim_IA,3)}else{table[4,j]=0}
if(task[j]=='Futility'|task[j]=='Futility and superiority'){
table[6,j]=round(sum(nogo_matrix[,j]==1)/nsim_IA,3)
}else{table[6,j]=0}
}else{
if(task[j]=='Superiority'|task[j]=='Futility and superiority'){
table[4,j]=round(sum(go_matrix[,j]==1&cum_IA_go_matrix[,j-1]==1)/nsim_IA,3)}else{table[4,j]=0}
if(task[j]=='Futility'|task[j]=='Futility and superiority'){
table[6,j]=round(sum(nogo_matrix[,j]==1&cum_IA_go_matrix[,j-1]==1)/nsim_IA,3)
}else{table[6,j]=0}
}
table[5,j]=round(sum(cum_IA_go_matrix[,j]==1)/nsim_IA,3)
# if(task[j]=='Futility'){
# table[7,j]=ifelse(direction[j]=='Greater',HTML(paste0('-/<',round(true_nogo_cutoff[1,j],3))),HTML(paste0('-/>',round(true_nogo_cutoff[1,j],3))))
# }
# if(task[j]=='Superiority'){
# table[7,j]=ifelse(direction[j]=='Greater',HTML(paste0('>=',round(true_go_cutoff[1,j],3),'/-')),HTML(paste0('<=',round(true_go_cutoff[1,j],3),'/-')))
# }
# if(task[j]=='Futility and superiority'){
# table[7,j]=ifelse(direction[j]=='Greater',HTML(paste0('>=',round(true_go_cutoff[1,j],3),' /','<',round(true_nogo_cutoff[1,j],3))),HTML(paste0('<=',round(true_go_cutoff[1,j],3),' / ','>',round(true_nogo_cutoff[1,j],3))))
# }
# table[10,j]=ifelse(direction[j]=='Greater',HTML(paste0('>=',round(go_cutoff[1,j],3))),HTML(paste0('<=',round(go_cutoff[1,j],3))))
# table[9,j]=ifelse(direction[j]=='Greater',HTML(paste0('<',round(nogo_cutoff[1,j],3))),HTML(paste0('>',round(nogo_cutoff[1,j],3))))
# table[8,j]<-ifelse(overlap[j]==1,paste0('GO/NOGO zones overlapped, classified by criterion of ',overlap.option[j]),'None')
}
expectss<-round(sum(as.numeric(table[1,1:num_interim])*(c(as.numeric(table[4,1:num_interim-1])+as.numeric(table[6,1:num_interim-1]),as.numeric(table[5,num_interim-1])))),3)
table[1,num_interim+1]=HTML(paste0(expectss,' (expected)'))
table[2,num_interim+1]=mean[meanindex]
table[3,num_interim+1]=''
table[4,num_interim+1]=round(sum(as.numeric(table[4,1:num_interim])),3)
table[5,num_interim+1]=round(as.numeric(table[5,num_interim]),3)
table[6,num_interim+1]=round(sum(as.numeric(table[6,1:num_interim])),3)
# table[7,num_interim+1]=''
# table[8,num_interim+1]=''
# table[9,num_interim+1]=''
# table[10,num_interim+1]=''
table<-as.table(table)
tablecolname<-c(paste0('Interim analysis ',1:(num_interim-1)),'Final analysis',"Summary")
tablerowname<-c('Sample size','True difference of RR','Task','Success','To next interim/final or inconclusive',
'Stop')
table<-cbind(tablerowname,rep(meanindex,6),table)
colnames(table)<-c(" ",'Setting',tablecolname)
temptable=rbind(temptable,table)
}
return(temptable)
}
#Interim_TAB(direction=c('Greater','Greater','Greater'),logic.go=c('and','or','or'),logic.nogo=c('and','or','or'))
# Fix_SS_TAB_Bin_Prob(n=45,alloc.ratio=1,
# prior.a1=1/3,prior.b1=1,
# prior.a2=1/3,prior.b2=1,
# control.mean=0,
# mean=c(-0.5,0.8),
# CT1.go=0.15,
# false.go.CT1=TRUE,FGR.CT1=0.8,
# CT1.nogo=0.25,
# false.nogo.CT1=TRUE,FNGR.CT1=0.2,
# CT2.go=0.3,
# false.go.CT2=FALSE, FGR.CT2=0.5,
# CT2.nogo=0.3,
# false.nogo.CT2=FALSE, FNGR.CT2=0.5,
# overlap.option='GO',plot.figure=TRUE,
# method='Frequentist',direction='Less',seed.num=369,
# nsim=2000,stop.criterion=0.00001,
# logic.go='and',logic.nogo='or')
#
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