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# --------------------------------------------------------------------------------
# Summary function for samon differences in treatment for pairs of alpha
# --------------------------------------------------------------------------------
samonCrossSummaryIM <- function(trt1,trt2, CIlevel=0.95) {
Nalpha <- trt1$Nalpha
alphaList <- trt1$alphaList
NSamples <- trt1$NSamples
n10 <- trt1$n0
n20 <- trt2$n0
TM1 <- trt1$TM[, c("alpha","IFEst","MIIFVar")]
TM2 <- trt2$TM[, c("alpha","IFEst","MIIFVar")]
TS1 <- trt1$TS[, c("alpha","Sample","IFEst","MIIFVar","mIFEst")]
TS2 <- trt2$TS[, c("alpha","Sample","IFEst","MIIFVar","mIFEst")]
colnames(TM1) <- c("alpha1","IFEst1","IFVar1")
colnames(TM2) <- c("alpha2","IFEst2","IFVar2")
colnames(TS1) <- c("alpha1","Sample","IFEst1","IFVar1","MIFEst1")
colnames(TS2) <- c("alpha2","Sample","IFEst2","IFVar2","MIFEst2")
for ( i1 in 1:Nalpha ) {
for ( i2 in 1:Nalpha ) {
alpha1 <- alphaList[i1]
alpha2 <- alphaList[i2]
TMA1 <- TM1[TM1[,"alpha1"] == alpha1,, drop=FALSE ]
TMA2 <- TM2[TM2[,"alpha2"] == alpha2,, drop=FALSE ]
TSA1 <- TS1[TS1[,"alpha1"] == alpha1,, drop=FALSE ]
TSA2 <- TS2[TS2[,"alpha2"] == alpha2,, drop=FALSE ]
TM <- cbind(TMA1,TMA2)
TM[,"Difference"] <- TM[,"IFEst2" ] - TM[,"IFEst1" ]
TM[,"DIFSE"] <- sqrt(TM[,"IFVar2"] + TM[,"IFVar1"])
TS <- merge(TSA1,TSA2,by=c("Sample"))
TS[,"Difference"] <- TS[,"IFEst2" ] - TS[,"IFEst1" ]
TS[,"DIFSE"] <- sqrt(TS[,"IFVar2"] + TS[,"IFVar1"])
TS[,"TIF"] <- (TS[,"Difference"] - TS[,"MIFEst2"] + TS[,"MIFEst1"]) / TS[,"DIFSE"]
TS <- data.frame(TS)
## quantiles
cicut <- CIlevel
cicut1 <- (1 - CIlevel)/2
cicut2 <- 1 - cicut1
myq <- function(x) {
x1 <- as.vector(quantile(x, c(cicut1,cicut2)))
x2 <- as.vector(quantile(abs(x), c(cicut)))
return(c(x1,x2))
}
## ag1 <- matrix(myq( TS[,c("TVals")]), nrow=1 )
## ag2 <- matrix(myq( TS[,c("Difference")]), nrow=1)
ag3 <- matrix(myq( TS[,c("TIF") ]), nrow=1)
## colnames(ag1) <- c("tLow", "tHigh", "tSym")
## colnames(ag2) <- c("DIFLow", "DIFHigh", "DIFSym")
colnames(ag3) <- c("tIFLow", "tIFHigh", "tIFSym")
## TM <- merge(TM,ag1)
## TM <- merge(TM,ag2)
TM <- merge(TM,ag3)
zcut <- qnorm( cicut2 )
## IF CI
lb1 <- TM[,"Difference"] - zcut * TM[,"DIFSE"]
ub1 <- TM[,"Difference"] + zcut * TM[,"DIFSE"]
## Bootstrap CI
## lb2 <- TM[,"Difference"] - 1.96 * TM[,"DIFSE" ]
## ub2 <- TM[,"Difference"] + 1.96 * TM[,"DIFSE" ]
## jk CI
## lb3 <- TM[,"Difference"] - 1.96 * TM[,"DjkSE" ]
## ub3 <- TM[,"Difference"] + 1.96 * TM[,"DjkSE" ]
## quantiles
## lb4 <- TM[,"DIFLow" ]
## ub4 <- TM[,"DIFHigh"]
## t using IF se
lb5 <- TM[,"Difference"] - TM[,"tIFHigh"] * TM[,"DIFSE"]
ub5 <- TM[,"Difference"] - TM[,"tIFLow" ] * TM[,"DIFSE"]
## t using jk se
## lb6 <- TM[,"Difference"] - TM[,"tHigh"] * TM[,"DjkSE"]
## ub6 <- TM[,"Difference"] - TM[,"tLow" ] * TM[,"DjkSE"]
## t using IF se symmetric
lb7 <- TM[,"Difference"] - TM[,"tIFSym"] * TM[,"DIFSE"]
ub7 <- TM[,"Difference"] + TM[,"tIFSym"] * TM[,"DIFSE"]
## t using jk se symmetric
## lb8 <- TM[,"Difference"] - TM[,"tIFSym"] * TM[,"DjkSE"]
## ub8 <- TM[,"Difference"] + TM[,"tIFSym"] * TM[,"DjkSE"]
Difference <- TM[,"Difference"]
CI <- cbind( alpha1, alpha2,Difference,lb1, ub1, lb5, ub5, lb7, ub7)
if ( i1 == 1 & i2 == 1) {
CIout <- CI
TMout <- TM
}
else {
CIout <- rbind(CIout,CI)
TMout <- rbind(TMout,TM)
}
}
}
Ret <- list( TM = TMout, CI = CIout, Nalpha = Nalpha, alphaList = alphaList, CIlevel=CIlevel )
return(Ret)
}
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