diff --git a/RProject/.RData b/RProject/.RData
index efe36e3..65f4ac6 100644
Binary files a/RProject/.RData and b/RProject/.RData differ
diff --git a/RProject/.Rhistory b/RProject/.Rhistory
index 1a3e606..115104f 100644
--- a/RProject/.Rhistory
+++ b/RProject/.Rhistory
@@ -1,100 +1,133 @@
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
 pch=17,col='#9b6541')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9C" & plot.dat$N==x,]$h0.rejected.p))
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9A" & plot.dat$N==x,]$h0.rejected.p))
 lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#1a342b')
 points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
 pch=17,col='#1a342b')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11C" & plot.dat$N==x,]$h0.rejected.p))
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11A" & plot.dat$N==x,]$h0.rejected.p))
 lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#c0c23b')
 points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
 pch=17,col='#c0c23b')
-#### Scenarios with J=4 / M=2
-# B / Effect size 0.2 /
-plot.dat <- res.dat
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="1B" & plot.dat$N==x,]$h0.rejected.p))
-plot(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-xlab='N',ylab='Proportion of null hypothesis rejection',
-xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(0,1),lty=4,col='#03a18a',main='Scenarios with Effect size 0.2')
+## Plot 1 - baseline scenarios vs theoretical power
+par(mfrow=c(1,2))
+# theoretical
+plot.dat <- res.dat[res.dat$scenario %in% sapply(c('A','B','C','D','E'),function(x) paste0(1:4,x)),]
+plot(unique(plot.dat[plot.dat$scenario.type=="A",]$N),rep(unique(plot.dat[plot.dat$scenario.type=="A",]$theoretical.power),3),
+xlab='N',ylab='Theoretical power',
+xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(0,1),lty=4,col='#03a18a')
 axis(1,c(100,200,300))
 axis(2,seq(0,1,0.1))
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#03a18a')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5B" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#a12471')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#a12471')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7B" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#9b6541')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#9b6541')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9B" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#1a342b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#1a342b')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11B" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#c0c23b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#c0c23b')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5C" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='red')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#a12471')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7C" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='blue')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#9b6541')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9C" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='purple')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#1a342b')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11C" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='orange')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#c0c23b')
-# B / Effect size 0.2 /
-plot.dat <- res.dat
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="1B" & plot.dat$N==x,]$h0.rejected.p))
+lines(unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$theoretical.power),col='#c0c23b',lty=4)
+lines(unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$theoretical.power),col='#c0c23b',lty=4)
+lines(unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$theoretical.power),col='#a12471',lty=4)
+lines(unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$theoretical.power),col='#a12471',lty=4)
+lines(unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$theoretical.power),col='#9b6541',lty=4)
+lines(unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$theoretical.power),col='#9b6541',lty=4)
+lines(unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$theoretical.power),col='#1a342b',lty=4)
+lines(unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$theoretical.power),col='#1a342b',lty=4)
+points(unique(plot.dat[plot.dat$scenario %in% c("1A",'1A'),]$N),
+rep(unique(plot.dat[plot.dat$scenario %in% c("1A",'1A'),]$theoretical.power),3),col='#03a18a',pch=17)
+points(unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$theoretical.power),col='#c0c23b',pch=17)
+points(unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$theoretical.power),col='#c0c23b',pch=17)
+points(unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$theoretical.power),col='#a12471',pch=17)
+points(unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$theoretical.power),col='#a12471',pch=17)
+points(unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$theoretical.power),col='#9b6541',pch=17)
+points(unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$theoretical.power),col='#9b6541',pch=17)
+points(unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$theoretical.power),col='#1a342b',pch=17)
+points(unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$N),
+unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$theoretical.power),col='#1a342b',pch=17)
+legend("topleft",lty=rep(4,5),col=c("#03a18a","#c0c23b","#a12471","#9b6541","#1a342b"),
+pch=rep(17,5),
+legend=c("Scenario A",
+"Scenario 1-2 / B-D",
+"Scenario 3-4 / B-D",
+"Scenario 1-2 / C-E",
+"Scenario 3-4 / C-E"),cex=0.7)
+# real
+plot.dat <- res.dat[res.dat$scenario %in% sapply(c('A','B','C','D','E'),function(x) paste0(1:4,x)),]
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario.type=="A" & plot.dat$N==x,]$h0.rejected.p))
 plot(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
 xlab='N',ylab='Proportion of null hypothesis rejection',
-xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(0,1),lty=4,col='#03a18a',main='Scenarios with Effect size 0.2')
+xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(0,1),lty=4,col='#03a18a')
 axis(1,c(100,200,300))
 axis(2,seq(0,1,0.1))
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#03a18a')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5B" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#a12471')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#a12471')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7B" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#9b6541')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#9b6541')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9B" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#1a342b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#1a342b')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11B" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#c0c23b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#c0c23b')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5C" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='red')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='red')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7C" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='blue')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='blue')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9C" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='purple')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='purple')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11C" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='orange')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='orange')
-res.dat$bias <- res.dat$eff.size-res.dat$m.beta
-res.dat.dif$bias <- res.dat.dif$eff.size-res.dat.dif$m.beta
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("1B","1D") & plot.dat$N==x,]$h0.rejected.p))
+lines(unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$N),
+mean.A,col='#c6d18d',lty=4)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("2B","2D") & plot.dat$N==x,]$h0.rejected.p))
+lines(unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$N),
+mean.A,col='#c0c23b',lty=4)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("3B","3D") & plot.dat$N==x,]$h0.rejected.p))
+lines(unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$N),
+mean.A,col='#da77c7',lty=4)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("4B","4D") & plot.dat$N==x,]$h0.rejected.p))
+lines(unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$N),
+mean.A,col='#a12471',lty=4)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("1C","1E") & plot.dat$N==x,]$h0.rejected.p))
+lines(unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$N),
+mean.A,col='#b5a180',lty=4)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("2C","2E") & plot.dat$N==x,]$h0.rejected.p))
+lines(unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$N),
+mean.A,col='#9b6541',lty=4)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("3C","3E") & plot.dat$N==x,]$h0.rejected.p))
+lines(unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$N),
+mean.A,col='#30a466',lty=4)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("4C","4E") & plot.dat$N==x,]$h0.rejected.p))
+lines(unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$N),
+mean.A,col='#1a342b',lty=4)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario.type=="A" & plot.dat$N==x,]$h0.rejected.p))
+points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,pch=17,col='#03a18a')
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("1B","1D") & plot.dat$N==x,]$h0.rejected.p))
+points(unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$N),
+mean.A,col='#c6d18d',pch=17)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("2B","2D") & plot.dat$N==x,]$h0.rejected.p))
+points(unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$N),
+mean.A,col='#c0c23b',pch=17)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("3B","3D") & plot.dat$N==x,]$h0.rejected.p))
+points(unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$N),
+mean.A,col='#da77c7',pch=17)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("4B","4D") & plot.dat$N==x,]$h0.rejected.p))
+points(unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$N),
+mean.A,col='#a12471',pch=17)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("1C","1E") & plot.dat$N==x,]$h0.rejected.p))
+points(unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$N),
+mean.A,col='#b5a180',pch=17)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("2C","2E") & plot.dat$N==x,]$h0.rejected.p))
+points(unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$N),
+mean.A,col='#9b6541',pch=17)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("3C","3E") & plot.dat$N==x,]$h0.rejected.p))
+points(unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$N),
+mean.A,col='#30a466',pch=17)
+mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario%in% c("4C","4E") & plot.dat$N==x,]$h0.rejected.p))
+points(unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$N),
+mean.A,col='#1a342b',pch=17)
+legend("topleft",lty=rep(4,5),col=c("#03a18a","#c0c23b","#a12471","#9b6541","#1a342b"),
+pch=rep(17,5),
+legend=c("Scenario A",
+"Scenario 1-2 / B-D",
+"Scenario 3-4 / B-D",
+"Scenario 1-2 / C-E",
+"Scenario 3-4 / C-E"),cex=0.7)
+library(tinytex)
+tlmgr_install('soul')
+res.dat[res.dat$scenario=='2B',]$theoretical.power
+res.dat[res.dat$scenario=='2B',]$h0.rejected.p
+res.dat[res.dat$scenario=='1B',]$h0.rejected.p
+res.dat[res.dat$scenario=='1B',]$theoretical.power
 library(TAM)
 library(doMC)
 library(parallel)
@@ -102,84 +135,12 @@ library(pbmcapply)
 library(funprog)
 library(dplyr)
 library(readxl)
-res.dat$bias
-par(mfrow=c(1,1))
-#### Scenarios with J=4 / M=2
-# A / H=0
-plot.dat <- res.dat
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="1A" & plot.dat$N==x,]$bias))
-mean.A
-par(mfrow=c(1,1))
-#### Scenarios with J=4 / M=2
-# A / H=0
-plot.dat <- res.dat
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="1A" & plot.dat$N==x,]$bias))
-plot(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-xlab='N',ylab='Bias',
-xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(-1,1),lty=4,col='#03a18a',main='Scenarios where H0 is TRUE')
-axis(1,c(100,200,300))
-axis(2,seq(0,1,0.1))
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#03a18a')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5A" & plot.dat$N==x,]$bias))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#a12471')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#a12471')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7A" & plot.dat$N==x,]$bias))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#9b6541')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#9b6541')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9A" & plot.dat$N==x,]$bias))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#1a342b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#1a342b')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11A" & plot.dat$N==x,]$bias))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#c0c23b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#c0c23b')
-#### Scenarios with J=4 / M=2
-# B/ H=0
-plot.dat <- res.dat
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="1B" & plot.dat$N==x,]$bias))
-plot(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-xlab='N',ylab='Bias',
-xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(-1,1),lty=4,col='#03a18a',main='Scenarios where H0 is TRUE')
-axis(1,c(100,200,300))
-axis(2,seq(0,1,0.1))
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#03a18a')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5B" & plot.dat$N==x,]$bias))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#a12471')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#a12471')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7B" & plot.dat$N==x,]$bias))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#9b6541')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#9b6541')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9B" & plot.dat$N==x,]$bias))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#1a342b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#1a342b')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11B" & plot.dat$N==x,]$bias))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#c0c23b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#c0c23b')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5C" & plot.dat$N==x,]$bias))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='red')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='red')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7C" & plot.dat$N==x,]$bias))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='blue')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='blue')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9C" & plot.dat$N==x,]$bias))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='purple')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='purple')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11C" & plot.dat$N==x,]$bias))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='orange')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='orange')
+res.dat[res.dat$scenario=="2D",]$h0.rejected.p
+##############################################################################
+#----------------------------------------------------------------------------#
+################################# POWER PLOTS ################################
+#----------------------------------------------------------------------------#
+##############################################################################
 ## Plot 1 - baseline scenarios vs theoretical power
 par(mfrow=c(1,2))
 # theoretical
@@ -295,104 +256,145 @@ legend=c("Scenario A",
 "Scenario 3-4 / B-D",
 "Scenario 1-2 / C-E",
 "Scenario 3-4 / C-E"),cex=0.7)
-par(mfrow=c(1,1))
-#### Scenarios with J=4 / M=2
-# A / H=0
-plot.dat <- res.dat
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="1A" & plot.dat$N==x,]$h0.rejected.p))
-plot(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-xlab='N',ylab='Proportion of null hypothesis rejection',
-xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(0,1),lty=4,col='#03a18a',main='Scenarios where H0 is TRUE')
-axis(1,c(100,200,300))
-axis(2,seq(0,1,0.1))
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#03a18a')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5A" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#a12471')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#a12471')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7A" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#9b6541')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#9b6541')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9A" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#1a342b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#1a342b')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11A" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#c0c23b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#c0c23b')
-# B / Effect size 0.2
-plot.dat <- res.dat
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="1B" & plot.dat$N==x,]$h0.rejected.p))
-plot(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-xlab='N',ylab='Proportion of null hypothesis rejection',
-xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(0,1),lty=4,col='#03a18a',main='Scenarios with Effect size 0.2')
-axis(1,c(100,200,300))
-axis(2,seq(0,1,0.1))
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#03a18a')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5B" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#a12471')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#a12471')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7B" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#9b6541')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#9b6541')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9B" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#1a342b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#1a342b')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11B" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#c0c23b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#c0c23b')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5C" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='red')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='red')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7C" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='blue')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='blue')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9C" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='purple')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='purple')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11C" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='orange')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='orange')
-par(mfrow=c(1,1))
-#### Scenarios with J=4 / M=2
-# A / H=0
-plot.dat <- res.dat
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="1A" & plot.dat$N==x,]$h0.rejected.p))
-plot(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-xlab='N',ylab='Proportion of null hypothesis rejection',
-xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(0,1),lty=4,col='#03a18a',main='Scenarios where H0 is TRUE')
-axis(1,c(100,200,300))
-axis(2,seq(0,1,0.1))
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#03a18a')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="5A" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#a12471')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#a12471')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="7A" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#9b6541')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#9b6541')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="9A" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#1a342b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#1a342b')
-mean.A <- sapply(c(100,200,300),function(x) mean(plot.dat[plot.dat$scenario=="11A" & plot.dat$N==x,]$h0.rejected.p))
-lines(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,lty=4,col='#c0c23b')
-points(unique(plot.dat[plot.dat$scenario.type=="A",]$N),mean.A,
-pch=17,col='#c0c23b')
+###### Puissance théorique
+res.dat$theoretical.power <- 0
+### Scénarios N=100
+## Scénarios J=4 / M=2
+res.dat[res.dat$scenario %in% paste0(c(1,5,7,9,11),'A') & res.dat$N==100,]$theoretical.power <- 0.05
+res.dat[res.dat$scenario %in% paste0(c(1,5,7,9,11),'B') & res.dat$N==100,]$theoretical.power <- 0.1543
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'C') & res.dat$N==100,]$theoretical.power <- 0.1543
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'D') & res.dat$N==100,]$theoretical.power <- 0.4627
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'E') & res.dat$N==100,]$theoretical.power <- 0.4627
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'F') & res.dat$N==100,]$theoretical.power <- 0.1543
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'G') & res.dat$N==100,]$theoretical.power <- 0.4627
+res.dat[res.dat$scenario %in% paste0(1,'C') & res.dat$N==100,]$theoretical.power <- 0.4627
+res.dat[res.dat$scenario %in% paste0(1,'D') & res.dat$N==100,]$theoretical.power <- 0.1543
+res.dat[res.dat$scenario %in% paste0(1,'E') & res.dat$N==100,]$theoretical.power <- 0.4627
+## Scénarios J=4 / M=4
+res.dat[res.dat$scenario %in% paste0(c(2,6,8,10,12),'A') & res.dat$N==100,]$theoretical.power <- 0.05
+res.dat[res.dat$scenario %in% paste0(c(2,6,8,10,12),'B') & res.dat$N==100,]$theoretical.power <- 0.2177
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'C') & res.dat$N==100,]$theoretical.power <- 0.2177
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'D') & res.dat$N==100,]$theoretical.power <- 0.6586
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'E') & res.dat$N==100,]$theoretical.power <- 0.6586
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'F') & res.dat$N==100,]$theoretical.power <- 0.2177
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'G') & res.dat$N==100,]$theoretical.power <- 0.6586
+res.dat[res.dat$scenario %in% paste0(2,'C') & res.dat$N==100,]$theoretical.power <- 0.6586
+res.dat[res.dat$scenario %in% paste0(2,'D') & res.dat$N==100,]$theoretical.power <- 0.2177
+res.dat[res.dat$scenario %in% paste0(2,'E') & res.dat$N==100,]$theoretical.power <- 0.6586
+## Scénarios J=7 / M=2
+res.dat[res.dat$scenario %in% paste0(c(3,13,15,17,19),'A') & res.dat$N==100,]$theoretical.power <- 0.05
+res.dat[res.dat$scenario %in% paste0(c(3,13,15,17,19),'B') & res.dat$N==100,]$theoretical.power <- 0.1870
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'C') & res.dat$N==100,]$theoretical.power <- 0.1870
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'D') & res.dat$N==100,]$theoretical.power <- 0.5666
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'E') & res.dat$N==100,]$theoretical.power <- 0.5666
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'F') & res.dat$N==100,]$theoretical.power <- 0.1870
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'G') & res.dat$N==100,]$theoretical.power <- 0.5666
+res.dat[res.dat$scenario %in% paste0(3,'C') & res.dat$N==100,]$theoretical.power <- 0.5666
+res.dat[res.dat$scenario %in% paste0(3,'D') & res.dat$N==100,]$theoretical.power <- 0.1870
+res.dat[res.dat$scenario %in% paste0(3,'E') & res.dat$N==100,]$theoretical.power <- 0.5666
+## Scénarios J=7 / M=4
+res.dat[res.dat$scenario %in% paste0(c(4,14,16,18,20),'A') & res.dat$N==100,]$theoretical.power <- 0.05
+res.dat[res.dat$scenario %in% paste0(c(4,14,16,18,20),'B') & res.dat$N==100,]$theoretical.power <- 0.2450
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'C') & res.dat$N==100,]$theoretical.power <- 0.2450
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'D') & res.dat$N==100,]$theoretical.power <- 0.7136
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'E') & res.dat$N==100,]$theoretical.power <- 0.7136
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'F') & res.dat$N==100,]$theoretical.power <- 0.2450
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'G') & res.dat$N==100,]$theoretical.power <- 0.7136
+res.dat[res.dat$scenario %in% paste0(4,'C') & res.dat$N==100,]$theoretical.power <- 0.7136
+res.dat[res.dat$scenario %in% paste0(4,'D') & res.dat$N==100,]$theoretical.power <- 0.2450
+res.dat[res.dat$scenario %in% paste0(4,'E') & res.dat$N==100,]$theoretical.power <- 0.7136
+### Scénarios N=200
+## Scénarios J=4 / M=2
+res.dat[res.dat$scenario %in% paste0(c(1,5,7,9,11),'A') & res.dat$N==200,]$theoretical.power <- 0.05
+res.dat[res.dat$scenario %in% paste0(c(1,5,7,9,11),'B') & res.dat$N==200,]$theoretical.power <- 0.2618
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'C') & res.dat$N==200,]$theoretical.power <- 0.2618
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'D') & res.dat$N==200,]$theoretical.power <- 0.7507
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'E') & res.dat$N==200,]$theoretical.power <- 0.7507
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'F') & res.dat$N==200,]$theoretical.power <- 0.2618
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'G') & res.dat$N==200,]$theoretical.power <- 0.7507
+res.dat[res.dat$scenario %in% paste0(1,'C') & res.dat$N==200,]$theoretical.power <- 0.7507
+res.dat[res.dat$scenario %in% paste0(1,'D') & res.dat$N==200,]$theoretical.power <- 0.2618
+res.dat[res.dat$scenario %in% paste0(1,'E') & res.dat$N==200,]$theoretical.power <- 0.7507
+## Scénarios J=4 / M=4
+res.dat[res.dat$scenario %in% paste0(c(2,6,8,10,12),'A') & res.dat$N==200,]$theoretical.power <- 0.05
+res.dat[res.dat$scenario %in% paste0(c(2,6,8,10,12),'B') & res.dat$N==200,]$theoretical.power <- 0.3875
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'C') & res.dat$N==200,]$theoretical.power <- 0.3875
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'D') & res.dat$N==200,]$theoretical.power <- 0.9161
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'E') & res.dat$N==200,]$theoretical.power <- 0.9161
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'F') & res.dat$N==200,]$theoretical.power <- 0.3875
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'G') & res.dat$N==200,]$theoretical.power <- 0.9161
+res.dat[res.dat$scenario %in% paste0(2,'C') & res.dat$N==200,]$theoretical.power <- 0.9161
+res.dat[res.dat$scenario %in% paste0(2,'D') & res.dat$N==200,]$theoretical.power <- 0.3875
+res.dat[res.dat$scenario %in% paste0(2,'E') & res.dat$N==200,]$theoretical.power <- 0.9161
+## Scénarios J=7 / M=2
+res.dat[res.dat$scenario %in% paste0(c(3,13,15,17,19),'A') & res.dat$N==200,]$theoretical.power <- 0.05
+res.dat[res.dat$scenario %in% paste0(c(3,13,15,17,19),'B') & res.dat$N==200,]$theoretical.power <- 0.3258
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'C') & res.dat$N==200,]$theoretical.power <- 0.3258
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'D') & res.dat$N==200,]$theoretical.power <- 0.8538
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'E') & res.dat$N==200,]$theoretical.power <- 0.8538
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'F') & res.dat$N==200,]$theoretical.power <- 0.3258
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'G') & res.dat$N==200,]$theoretical.power <- 0.8538
+res.dat[res.dat$scenario %in% paste0(3,'C') & res.dat$N==200,]$theoretical.power <- 0.8538
+res.dat[res.dat$scenario %in% paste0(3,'D') & res.dat$N==200,]$theoretical.power <- 0.3258
+res.dat[res.dat$scenario %in% paste0(3,'E') & res.dat$N==200,]$theoretical.power <- 0.8538
+## Scénarios J=7 / M=4
+res.dat[res.dat$scenario %in% paste0(c(4,14,16,18,20),'A') & res.dat$N==200,]$theoretical.power <- 0.05
+res.dat[res.dat$scenario %in% paste0(c(4,14,16,18,20),'B') & res.dat$N==200,]$theoretical.power <- 0.4321
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'C') & res.dat$N==200,]$theoretical.power <- 0.4321
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'D') & res.dat$N==200,]$theoretical.power <- 0.9471
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'E') & res.dat$N==200,]$theoretical.power <- 0.9471
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'F') & res.dat$N==200,]$theoretical.power <- 0.4321
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'G') & res.dat$N==200,]$theoretical.power <- 0.9471
+res.dat[res.dat$scenario %in% paste0(4,'C') & res.dat$N==200,]$theoretical.power <- 0.9471
+res.dat[res.dat$scenario %in% paste0(4,'D') & res.dat$N==200,]$theoretical.power <- 0.4321
+res.dat[res.dat$scenario %in% paste0(4,'E') & res.dat$N==200,]$theoretical.power <- 0.9471
+### Scénarios N=300
+## Scénarios J=4 / M=2
+res.dat[res.dat$scenario %in% paste0(c(1,5,7,9,11),'A') & res.dat$N==300,]$theoretical.power <- 0.05
+res.dat[res.dat$scenario %in% paste0(c(1,5,7,9,11),'B') & res.dat$N==300,]$theoretical.power <- 0.3660
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'C') & res.dat$N==300,]$theoretical.power <- 0.3660
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'D') & res.dat$N==300,]$theoretical.power <- 0.8981
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'E') & res.dat$N==300,]$theoretical.power <- 0.8981
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'F') & res.dat$N==300,]$theoretical.power <- 0.3660
+res.dat[res.dat$scenario %in% paste0(c(5,7,9,11),'G') & res.dat$N==300,]$theoretical.power <- 0.8981
+res.dat[res.dat$scenario %in% paste0(1,'C') & res.dat$N==300,]$theoretical.power <- 0.8981
+res.dat[res.dat$scenario %in% paste0(1,'D') & res.dat$N==300,]$theoretical.power <- 0.3660
+res.dat[res.dat$scenario %in% paste0(1,'E') & res.dat$N==300,]$theoretical.power <- 0.8981
+## Scénarios J=4 / M=4
+res.dat[res.dat$scenario %in% paste0(c(2,6,8,10,12),'A') & res.dat$N==300,]$theoretical.power <- 0.05
+res.dat[res.dat$scenario %in% paste0(c(2,6,8,10,12),'B') & res.dat$N==300,]$theoretical.power <- 0.5373
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'C') & res.dat$N==300,]$theoretical.power <- 0.5373
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'D') & res.dat$N==300,]$theoretical.power <- 0.9834
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'E') & res.dat$N==300,]$theoretical.power <- 0.9834
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'F') & res.dat$N==300,]$theoretical.power <- 0.5373
+res.dat[res.dat$scenario %in% paste0(c(6,8,10,12),'G') & res.dat$N==300,]$theoretical.power <- 0.9834
+res.dat[res.dat$scenario %in% paste0(2,'C') & res.dat$N==300,]$theoretical.power <- 0.9834
+res.dat[res.dat$scenario %in% paste0(2,'D') & res.dat$N==300,]$theoretical.power <- 0.5373
+res.dat[res.dat$scenario %in% paste0(2,'E') & res.dat$N==300,]$theoretical.power <- 0.9834
+## Scénarios J=7 / M=2
+res.dat[res.dat$scenario %in% paste0(c(3,13,15,17,19),'A') & res.dat$N==300,]$theoretical.power <- 0.05
+res.dat[res.dat$scenario %in% paste0(c(3,13,15,17,19),'B') & res.dat$N==300,]$theoretical.power <- 0.4550
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'C') & res.dat$N==300,]$theoretical.power <- 0.4550
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'D') & res.dat$N==300,]$theoretical.power <- 0.9584
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'E') & res.dat$N==300,]$theoretical.power <- 0.9584
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'F') & res.dat$N==300,]$theoretical.power <- 0.4550
+res.dat[res.dat$scenario %in% paste0(c(13,15,17,19),'G') & res.dat$N==300,]$theoretical.power <- 0.9584
+res.dat[res.dat$scenario %in% paste0(3,'C') & res.dat$N==300,]$theoretical.power <- 0.9584
+res.dat[res.dat$scenario %in% paste0(3,'D') & res.dat$N==300,]$theoretical.power <- 0.4550
+res.dat[res.dat$scenario %in% paste0(3,'E') & res.dat$N==300,]$theoretical.power <- 0.9584
+## Scénarios J=7 / M=4
+res.dat[res.dat$scenario %in% paste0(c(4,14,16,18,20),'A') & res.dat$N==300,]$theoretical.power <- 0.05
+res.dat[res.dat$scenario %in% paste0(c(4,14,16,18,20),'B') & res.dat$N==300,]$theoretical.power <- 0.5907
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'C') & res.dat$N==300,]$theoretical.power <- 0.5907
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'D') & res.dat$N==300,]$theoretical.power <- 0.9919
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'E') & res.dat$N==300,]$theoretical.power <- 0.9919
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'F') & res.dat$N==300,]$theoretical.power <- 0.5907
+res.dat[res.dat$scenario %in% paste0(c(14,16,18,20),'G') & res.dat$N==300,]$theoretical.power <- 0.9919
+res.dat[res.dat$scenario %in% paste0(4,'C') & res.dat$N==300,]$theoretical.power <- 0.9919
+res.dat[res.dat$scenario %in% paste0(4,'D') & res.dat$N==300,]$theoretical.power <- 0.5907
+res.dat[res.dat$scenario %in% paste0(4,'E') & res.dat$N==300,]$theoretical.power <- 0.9919
+### DIF scenarios
+res.dat.dif$theoretical.power <- res.dat[61:nrow(res.dat),]$theoretical.power
 ## Plot 1 - baseline scenarios vs theoretical power
 par(mfrow=c(1,2))
 # theoretical
@@ -403,37 +405,37 @@ xaxt='n',yaxt='n',type='l',xlim=c(100,300),ylim=c(0,1),lty=4,col='#03a18a')
 axis(1,c(100,200,300))
 axis(2,seq(0,1,0.1))
 lines(unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$N),
-unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$theoretical.power),col='#c0c23b',lty=4)
+unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$theoretical.power),col='#c6d18d',lty=4)
 lines(unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$N),
 unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$theoretical.power),col='#c0c23b',lty=4)
 lines(unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$N),
-unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$theoretical.power),col='#a12471',lty=4)
+unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$theoretical.power),col='#da77c7',lty=4)
 lines(unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$N),
 unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$theoretical.power),col='#a12471',lty=4)
 lines(unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$N),
-unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$theoretical.power),col='#9b6541',lty=4)
+unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$theoretical.power),col='#b5a180',lty=4)
 lines(unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$N),
 unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$theoretical.power),col='#9b6541',lty=4)
 lines(unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$N),
-unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$theoretical.power),col='#1a342b',lty=4)
+unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$theoretical.power),col='#30a466',lty=4)
 lines(unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$N),
 unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$theoretical.power),col='#1a342b',lty=4)
 points(unique(plot.dat[plot.dat$scenario %in% c("1A",'1A'),]$N),
 rep(unique(plot.dat[plot.dat$scenario %in% c("1A",'1A'),]$theoretical.power),3),col='#03a18a',pch=17)
 points(unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$N),
-unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$theoretical.power),col='#c0c23b',pch=17)
+unique(plot.dat[plot.dat$scenario %in% c("1B",'1D'),]$theoretical.power),col='#c6d18d',pch=17)
 points(unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$N),
 unique(plot.dat[plot.dat$scenario %in% c("2B",'2D'),]$theoretical.power),col='#c0c23b',pch=17)
 points(unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$N),
-unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$theoretical.power),col='#a12471',pch=17)
+unique(plot.dat[plot.dat$scenario %in% c("3B",'3D'),]$theoretical.power),col='#da77c7',pch=17)
 points(unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$N),
 unique(plot.dat[plot.dat$scenario %in% c("4B",'4D'),]$theoretical.power),col='#a12471',pch=17)
 points(unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$N),
-unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$theoretical.power),col='#9b6541',pch=17)
+unique(plot.dat[plot.dat$scenario %in% c("1C",'1E'),]$theoretical.power),col='#b5a180',pch=17)
 points(unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$N),
 unique(plot.dat[plot.dat$scenario %in% c("2C",'2E'),]$theoretical.power),col='#9b6541',pch=17)
 points(unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$N),
-unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$theoretical.power),col='#1a342b',pch=17)
+unique(plot.dat[plot.dat$scenario %in% c("3C",'3E'),]$theoretical.power),col='#30a466',pch=17)
 points(unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$N),
 unique(plot.dat[plot.dat$scenario %in% c("4C",'4E'),]$theoretical.power),col='#1a342b',pch=17)
 legend("topleft",lty=rep(4,5),col=c("#03a18a","#c0c23b","#a12471","#9b6541","#1a342b"),
@@ -508,5 +510,3 @@ legend=c("Scenario A",
 "Scenario 3-4 / B-D",
 "Scenario 1-2 / C-E",
 "Scenario 3-4 / C-E"),cex=0.7)
-library(tinytex)
-tlmgr_install('soul')
diff --git a/Scripts/Analysis/DIF/item_merger.do b/Scripts/Analysis/DIF/item_merger.do
new file mode 100644
index 0000000..0ecfb8a
--- /dev/null
+++ b/Scripts/Analysis/DIF/item_merger.do
@@ -0,0 +1,108 @@
+// MERGE des modalités si non représentées
+
+  forvalues j = 1 / `nbitems' {
+  local recoda_`j' = 0
+  qui tab `item`j'' if `tt' == 0, matrow(rect1_g0_`j') matcell(nbrt1_g0_`j')					// Récupération des infos moda du temps 1pour chaque groupe
+  local minm`j'_t1_g0 = rect1_g0_`j'[1,1]
+  local maxm`j'_t1_g0 = rect1_g0_`j'[r(r),1]
+
+  qui tab `item`j'' if `tt' == 1, matrow(rect1_g1_`j') matcell(nbrt1_g1_`j')
+  local minm`j'_t1_g1 = rect1_g1_`j'[1,1]
+  local maxm`j'_t1_g1 = rect1_g1_`j'[r(r),1]
+
+  local minm_`j' = min(`minm`j'_t1_g0',`minm`j'_t1_g1')		// Info moda pour l'item j
+  local maxm_`j' = max(`maxm`j'_t1_g0',`maxm`j'_t1_g1')
+  local nbm_`j' = 4
+
+  if `minm_`j'' != 0 & `com_z' == 0 {
+    local com_z = 1
+  }
+  //Recodage des réponses en 0, 1, 2, etc...
+  //forvalues r = 0/`=`maxm_`j''-1'  {
+    //qui replace `item`j'' = `r' if `item`j'' == `=`r'+`minm_`j'''
+    //qui replace ``=`j'+`nbitems''' = `r' if ``=`j'+`nbitems''' == `=`r'+`minm_`j'''
+  //}
+
+  // Vérif. Que toutes les modas sont utilisées & concordance entre temps
+  forvalues m = 0/`=`nbm_`j''-1' {
+    qui count if `item`j'' == `m' & `tt' == 0
+    local nb_rn1_g0 = r(N)
+    qui count if `item`j'' == `m' & `tt' == 1
+    local nb_rn1_g1 = r(N)
+    local nb_rn = min(`nb_rn1_g0',`nb_rn1_g1')
+
+    if `nb_rn' == 0 {		// Une moda n'est pas utilisée
+      local recoda_`j' = 1
+      if  `m' == 0 | `m' < `minm`j'_t1_g0' | `m' < `minm`j'_t1_g1' { // La moda 0 n'est pas utilisée
+        local stop = 1
+        forvalues k = 1/`=`nbm_`j''-`m'' {
+          qui count if `item`j'' == `=`m' + `k'' & `tt' == 0
+          local v`k'1_0 = r(N)
+          qui count if `item`j'' == `=`m' + `k'' & `tt' == 1
+          local v`k'1_1 = r(N)
+          if (`v`k'1_0' != 0 | `v`k'1_1' != 0) & `stop' != 0 {
+            qui replace `item`j''= `=`m'+`k'' if `item`j''==`m'
+            qui replace ``=`j'+`nbitems'''=`=`m'+`k'' if ``=`j'+`nbitems'''==`m'
+            di  "WARNING: items `item`j'' & ``=`j'+`nbitems''': answers `m' and `=`m'+`k'' merged"
+            local stop = 0
+          }
+        }
+      }
+      else if `m' == `=`nbm_`j''-1' | `m' >= `maxm`j'_t1_g1' {	// La moda max n'est pas utilisée
+        local stop = 1
+        forvalues k = 1/`=`m'' {
+          qui count if `item`j'' == `=`m' - `k'' & `tt' == 0
+          local v`k'1_0 = r(N)
+          qui count if `item`j'' == `=`m' - `k'' & `tt' == 1
+          local v`k'1_1 = r(N)
+          if (`v`k'1_0' != 0 | `v`k'1_1' != 0) & `stop' != 0 {
+            qui replace `item`j''= `=`m' - `k'' if `item`j''==`m'
+            qui replace ``=`j'+`nbitems'''= `=`m' - `k'' if ``=`j'+`nbitems'''==`m'
+            di  "WARNING: items `item`j'' & ``=`j'+`nbitems''': answers `m' and `=`m'-`k'' merged"
+            local stop = 0
+          }
+        }
+      }
+      else {														// Moda central non utilisée
+        if runiform()>0.5{											// Tirage au sort pour regrouper
+          local stop = 1
+          forvalues k = 1/`m' {
+            qui count if `item`j'' == `=`m' - `k'' & `tt' == 0
+            local v`k'1_0 = r(N)
+            qui count if `item`j'' == `=`m' - `k'' & `tt' == 1
+            local v`k'1_1 = r(N)
+            if (`v`k'1_0' != 0 | `v`k'1_1' != 0) & `stop' != 0 {
+              qui replace `item`j''= `=`m'-`k'' if `item`j''==`m'
+              qui replace ``=`j'+`nbitems'''=`=`m'-`k'' if ``=`j'+`nbitems'''==`m'
+              di  "WARNING: items `item`j'' & ``=`j'+`nbitems''': answers `m' and `=`m'-`k'' merged"
+              local stop = 0
+            }
+          }
+        }
+        else {
+          local stop = 1
+          forvalues k = 1/`=`nbm_`j''-`m'' {
+            qui count if `item`j'' == `=`m' + `k'' & `tt' == 0
+            local v`k'1_0 = r(N)
+            qui count if `item`j'' == `=`m' + `k'' & `tt' == 1
+            local v`k'1_1 = r(N)
+            if (`v`k'1_0' != 0 | `v`k'1_1' != 0) & `stop' != 0{
+              qui replace `item`j''=`=`m' + `k'' if `item`j''==`m'
+              qui replace ``=`j'+`nbitems'''=`=`m' + `k'' if ``=`j'+`nbitems'''==`m'
+              di  "WARNING: items `item`j'' & ``=`j'+`nbitems''': answers `m' and `=`m'+`k'' merged"
+              local stop = 0
+            }
+            else {
+              if `stop' != 0 {
+                qui replace `item`j''= `nbm_`j'' if `item`j''==`m'
+                qui replace ``=`j'+`nbitems'''= `nbm_`j'' if ``=`j'+`nbitems'''==`m'
+                di  "WARNING: items `item`j'' & ``=`j'+`nbitems''': answers `m' and `nbm_`j'' merged"
+                local stop = 0
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+}