"sci.ratioI" <-
function(Response, Treatment, Num.Contrast, Den.Contrast, alternative = 'two.sided', conf.level = 0.95,
method="Plug") {
CMat <- Num.Contrast
DMat <- Den.Contrast
n.Treat <- tapply(Response,Treatment,length)
Mean.Treat <- tapply(Response,Treatment,mean)
Var.Treat <- tapply(Response,Treatment,var)
if(!is.numeric(conf.level) | length(conf.level)!=1 | conf.level<=0.5 | conf.level>=1)
{stop("Argument 'conf.level' must be a single numeric value between 0.5 and 1")}
if(any( sqrt(Var.Treat) < 10 * .Machine$double.eps * abs(Mean.Treat)))
{warning("Data are essentially constant in a least one group")}
if(any( n.Treat < 2 ))
{warning("There are less than 2 observations in a least one group")}
degree.f <- sum(n.Treat-1)
Pooled.Var <- sum( (n.Treat - 1)*Var.Treat)/degree.f
M <- diag(1/n.Treat) # Diagonal matrix containing reciprocals of the ni"s
n.comp <- nrow (CMat) # Number of comparisons
# print(cbind(n.Treat,Mean.Treat))
gammaC.vec <- CMat%*%Mean.Treat/DMat%*%Mean.Treat # MLE of the ratios
CorrMat.plug <- matrix(as.numeric(rep(NA,n.comp*n.comp)),nrow=n.comp)
for(i in 1:n.comp) {
for(j in 1:n.comp) {
CorrMat.plug[i,j] <- (gammaC.vec[i]*DMat[i,] - CMat[i,])%*%M%*%(gammaC.vec[j]*DMat[j,] - CMat[j,])/
(sqrt((gammaC.vec[i]*DMat[i,] - CMat[i,])%*%M%*%(gammaC.vec[i]*DMat[i,] - CMat[i,]))*
sqrt((gammaC.vec[j]*DMat[j,] - CMat[j,])%*%M%*%(gammaC.vec[j]*DMat[j,] - CMat[j,])))
}
}
Quad.root <- function(Aj, Bj, Cj){
Discrimi <- Bj^2 - 4*Aj*Cj
if ((Aj > 0)&(Discrimi >= 0)) Limit.s <- (-Bj + plus.minus*sqrt(Discrimi))/(2*Aj)
else Limit.s <- as.numeric(NA)
return(Limit.s)}
switch(method,
# UNADJUSTED CI:
Unadj =
{
if (alternative=="two.sided"){
side <- 2
plus.minus <- c(-1,1)
cpUAd <- qt(1- (1-conf.level)/(side), degree.f, lower.tail = TRUE)
}
if ((alternative=="less")|(alternative=="greater")){
side <- 1
if (alternative=="less") plus.minus <- 1
else plus.minus <- -1
cpUAd <- qt(1- (1-conf.level)/(side), degree.f, lower.tail = TRUE)
}
UAdCL <- matrix(as.numeric(rep(NA,side*n.comp)),nrow=n.comp)
for(j in 1:n.comp)
{
AjUAd <- (DMat[j,]%*%Mean.Treat)^2 - (cpUAd^2)*Pooled.Var*DMat[j,]%*%M%*%DMat[j,]
BjUAd <- -2*((CMat[j,]%*%Mean.Treat)*(DMat[j,]%*%Mean.Treat) -
(cpUAd^2)*Pooled.Var*CMat[j,]%*%M%*%DMat[j,])
CjUAd <- (CMat[j,]%*%Mean.Treat)^2 - (cpUAd^2)*Pooled.Var*CMat[j,]%*%M%*%CMat[j,]
UAdCL[j,] <- Quad.root(AjUAd, BjUAd, CjUAd)
}
sci.table <- data.frame( UAdCL)
df <- degree.f; critp <- cpUAd
},
# Bonferroni-adjustment
Bonf =
{
if (alternative=="two.sided"){
side <- 2
plus.minus <- c(-1,1)
cpBon <- qt(1- (1-conf.level)/(side*n.comp), degree.f, lower.tail = TRUE)
} # End of two-sided CI
if ((alternative=="less")|(alternative=="greater")){
side <- 1
if (alternative=="less") plus.minus <- 1
else plus.minus <- -1
cpBon <- qt(1- (1-conf.level)/(side*n.comp), degree.f, lower.tail = TRUE)
} # End of one-sided CI
BonCL <- matrix(as.numeric(rep(NA,side*n.comp)),nrow=n.comp)
for(j in 1:n.comp)
{
AjBon <- (DMat[j,]%*%Mean.Treat)^2 - (cpBon^2)*Pooled.Var*DMat[j,]%*%M%*%DMat[j,]
BjBon <- -2*((CMat[j,]%*%Mean.Treat)*(DMat[j,]%*%Mean.Treat) -
(cpBon^2)*Pooled.Var*CMat[j,]%*%M%*%DMat[j,])
CjBon <- (CMat[j,]%*%Mean.Treat)^2 - (cpBon^2)*Pooled.Var*CMat[j,]%*%M%*%CMat[j,]
BonCL[j,] <- Quad.root(AjBon, BjBon, CjBon)
}
sci.table <- data.frame(BonCL)
df <- degree.f; critp <- cpBon
},
# MtI: Sidak or Slepian for two-sided or one-sided CI
MtI =
{
if (alternative=="two.sided"){
side <- 2
plus.minus <- c(-1,1)
cpMtI <- qmvt(conf.level, interval=c(0,10),df=as.integer(degree.f),corr=diag(n.comp),delta=rep(0,n.comp), tail="both", abseps=1e-05)$quantile
} # End of two-sided CI
if ((alternative=="less")|(alternative=="greater")){
side <- 1
if (alternative=="less") plus.minus <- 1
else plus.minus <- -1
cpMtI <- qmvt(conf.level, interval=c(0,10),df=as.integer(degree.f),corr=diag(n.comp),delta=rep(0,n.comp),
tail="lower.tail", abseps=1e-05)$quantile
} # End of one-sided CI
MtICL <- matrix(as.numeric(rep(NA,side*n.comp)),nrow=n.comp)
for(j in 1:n.comp)
{
AjMtI <- (DMat[j,]%*%Mean.Treat)^2 - (cpMtI^2)*Pooled.Var*DMat[j,]%*%M%*%DMat[j,]
BjMtI <- -2*((CMat[j,]%*%Mean.Treat)*(DMat[j,]%*%Mean.Treat) -
(cpMtI^2)*Pooled.Var*CMat[j,]%*%M%*%DMat[j,])
CjMtI <- (CMat[j,]%*%Mean.Treat)^2 - (cpMtI^2)*Pooled.Var*CMat[j,]%*%M%*%CMat[j,]
MtICL[j,] <- Quad.root(AjMtI, BjMtI, CjMtI)
}
sci.table <- data.frame(MtICL)
df <- as.integer(degree.f); critp <- cpMtI
},
# Plug in of ratio estimates
Plug =
{
if (alternative=="two.sided"){
side <- 2
plus.minus <- c(-1,1)
Cplug <- qmvt(conf.level, interval=c(0,10),df=as.integer(degree.f),corr=CorrMat.plug,delta=rep(0,n.comp), tail="both", abseps=1e-05)$quantile
} # End of two-sided CI
if ((alternative=="less")|(alternative=="greater")){
side <- 1
if (alternative=="less") plus.minus <- 1
else plus.minus <- -1
Cplug <- qmvt(conf.level, interval=c(0,10),df=as.integer(degree.f),corr=CorrMat.plug,delta=rep(0,n.comp),
tail="lower.tail", abseps=1e-05)$quantile
} # End of one-sided CI
PlugCL <- matrix(as.numeric(rep(NA,side*n.comp)),nrow=n.comp)
for(j in 1:n.comp)
{
AjPlug <- (DMat[j,]%*%Mean.Treat)^2 - (Cplug^2)*Pooled.Var*DMat[j,]%*%M%*%DMat[j,]
BjPlug <- -2*((CMat[j,]%*%Mean.Treat)*(DMat[j,]%*%Mean.Treat) -
(Cplug^2)*Pooled.Var*CMat[j,]%*%M%*%DMat[j,])
CjPlug <- (CMat[j,]%*%Mean.Treat)^2 - (Cplug^2)*Pooled.Var*CMat[j,]%*%M%*%CMat[j,]
PlugCL[j,] <- Quad.root(AjPlug, BjPlug, CjPlug)
}
sci.table <- data.frame(PlugCL)
df <- as.integer(degree.f); critp <- Cplug
}
)
if (alternative=="two.sided")
{
names(sci.table) <- c("lower","upper")
}
if (alternative=="less")
{
names(sci.table) <- c("upper")
}
if (alternative=="greater")
{
names(sci.table) <- c("lower")
}
if( any(CorrMat.plug<0) && method=="MtI" && alternative!="two.sided")
{
warning(paste("At least one element of the estimated correlation matrix is negative, therefore, according to Slepian inequality, the MtI method might yield incorrect estimates."))
}
if (any(is.na(sci.table))){NSD <- TRUE}
else{NSD <- FALSE}
list(
estimate=gammaC.vec,
CorrMat.est=CorrMat.plug,
Num.Contrast=CMat,
Den.Contrast=DMat,
conf.int=sci.table,
NSD=NSD,
method=method,
alternative=alternative,
conf.level=conf.level,
df=df,
quantile=critp
)
} # END OF sci.ratioI
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.