Nothing
CreateWeights <- function(formula,Gorder=3,dif=TRUE,facCons=FALSE,data,side,type.ind,fac.level,ord.fac,
indTwo=NULL, indThree=NULL){
## Make the difference in three-way interactions
D3function <- function(alevel,blevel,clevel,type="A",ordABC=c(FALSE,FALSE,FALSE)){
if(type=="A"){
D3 <- D3Afunction(alevel=alevel,blevel=blevel,clevel=clevel,ord=ordABC[1])
}else if(type=="B"){
D3 <- D3Bfunction(alevel=alevel,blevel=blevel,clevel=clevel,ord=ordABC[2])
}else if(type=="C"){
D3 <- D3Cfunction(alevel=alevel,blevel=blevel,clevel=clevel,ord=ordABC[3])
}
return(D3)
}
D3Afunction <- function(alevel,blevel,clevel,ord=FALSE){
D3a <- matrix(0,nrow=0,ncol=(alevel*blevel*clevel))
if(ord==FALSE){
for(i in 1:(alevel-1)){
for(j in (i+1):alevel){
base.v <- rep(0,alevel)
base.v[i] <- -1
base.v[j] <- 1
base.mat <- diag((blevel*clevel)) %x% t(base.v)
D3a <- rbind(D3a,base.mat)
}
}
}else if(ord==TRUE){
for(i in 1:(alevel-1)){
base.v <- rep(0,alevel)
base.v[i] <- -1
base.v[(i+1)] <- 1
base.mat <- diag((blevel*clevel)) %x% t(base.v)
D3a <- rbind(D3a,base.mat)
}
}
return(D3a)
}
## (B): Make the difference in two-way interactions
D3Bfunction <- function(alevel,blevel,clevel,ord=FALSE){
if(ord==FALSE){
D3b <- matrix(0,nrow=0,ncol=(alevel*blevel*clevel))
for(i in 1:(blevel-1)){
left.temp <- matrix(0,ncol=((i-1)*(alevel)),nrow=(alevel))
left.main <- -diag((alevel))
left.final <- cbind(left.temp,left.main)
for(j in (i+1):blevel){
middle.temp <- matrix(0,ncol=((j-i-1)*(alevel)),nrow=(alevel))
right.main <- diag((alevel))
right.temp <- matrix(0,ncol=((blevel-j)*(alevel)),nrow=(alevel))
right.final <- cbind(middle.temp,right.main,right.temp)
D2b <- cbind(left.final,right.final) ## The base
D3base <- diag(clevel) %x% D2b
D3b <- rbind(D3b, D3base)
}
}
}else if (ord==TRUE){
D3b <- matrix(0,nrow=0,ncol=(alevel*blevel*clevel))
for(i in 1:(blevel-1)){
left <- matrix(0,ncol=((i-1)*(alevel)),nrow=(alevel))
Main <- cbind(-diag((alevel)),diag((alevel)))
right <- matrix(0,ncol=((blevel-(i+1))*(alevel)),nrow=(alevel))
D2b <- cbind(left,Main,right)
D3base <- diag(clevel) %x% D2b
D3b <- rbind(D3b, D3base)
}
}
return(D3b)
## psy_B(2,3), psy_B(2,4), psy_B(2,5)
}
D3Cfunction <- function(alevel,blevel,clevel,ord=FALSE){
if(ord==FALSE){
D3c <- matrix(0,nrow=0,ncol=(alevel*blevel*clevel))
for(i in 1:(clevel-1)){
left.temp <- matrix(0,ncol=((i-1)*(alevel*blevel)),nrow=(alevel*blevel))
left.main <- -diag((alevel*blevel))
left.final <- cbind(left.temp,left.main)
for(j in (i+1):clevel){
middle.temp <- matrix(0,ncol=((j-i-1)*(alevel*blevel)),nrow=(alevel*blevel))
right.main <- diag((alevel*blevel))
right.temp <- matrix(0,ncol=((clevel-j)*(alevel*blevel)),
nrow=(alevel*blevel))
right.final <- cbind(middle.temp,right.main,right.temp)
D3c <- rbind(D3c,cbind(left.final,right.final))
}
}
}else if (ord==TRUE){
Left <- cbind(-diag((alevel*blevel)*(clevel-1)),
matrix(0,ncol=(alevel*blevel),nrow=(alevel*blevel)*(clevel-1)))
Right <- cbind(matrix(0,ncol=(alevel*blevel),nrow=(alevel*blevel)*(clevel-1)),
diag((alevel*blevel)*(clevel-1)))
D3c <- Left + Right
}
return(D3c)
}
## From this version, I use D2 rather than D3
## Make the difference in two-way interactions
D2function <- function(alevel,blevel,type,ordAB){
if(type=="A"){
D2 <- D2Afunction(alevel=alevel,blevel=blevel,ord=ordAB[1])
}else if(type=="B"){
D2 <- D2Bfunction(alevel=alevel,blevel=blevel,ord=ordAB[2])
}
return(D2)
## D2 matrix
## nrow = differences between two-way interactions fixing the sublevel
## ncol = alevel*blevel (coefficients for two-ways)
}
## (A): Make the difference in two-way interactions
D2Afunction <- function(alevel,blevel,ord=FALSE){
D2a <- matrix(0,nrow=0,ncol=(alevel*blevel))
if(ord==FALSE){
for(i in 1:(alevel-1)){
for(j in (i+1):alevel){
base.v <- rep(0,alevel)
base.v[i] <- -1
base.v[j] <- 1
base.mat <- diag(blevel) %x% t(base.v)
D2a <- rbind(D2a,base.mat)
}
}
}else if(ord==TRUE){
for(i in 1:(alevel-1)){
base.v <- rep(0,alevel)
base.v[i] <- -1
base.v[(i+1)] <- 1
base.mat <- diag(blevel) %x% t(base.v)
D2a <- rbind(D2a,base.mat)
}
}
return(D2a)
}
## (B): Make the difference in two-way interactions
D2Bfunction <- function(alevel,blevel,ord=FALSE){
if(ord==FALSE){
D2b <- matrix(0,nrow=0,ncol=(alevel*blevel))
for(i in 1:(blevel-1)){
left.temp <- matrix(0,ncol=((i-1)*(alevel)),nrow=(alevel))
left.main <- -diag((alevel))
left.final <- cbind(left.temp,left.main)
for(j in (i+1):blevel){
middle.temp <- matrix(0,ncol=((j-i-1)*(alevel)),nrow=(alevel))
right.main <- diag((alevel))
right.temp <- matrix(0,ncol=((blevel-j)*(alevel)),nrow=(alevel))
right.final <- cbind(middle.temp,right.main,right.temp)
D2b <- rbind(D2b,cbind(left.final,right.final))
}
}
}else if (ord==TRUE){
Left <- cbind(-diag((alevel)*(blevel-1)),matrix(0,ncol=alevel,nrow=(alevel)*(blevel-1)))
Right <- cbind(matrix(0,ncol=alevel,nrow=(alevel)*(blevel-1)), diag((alevel)*(blevel-1)))
D2b <- Left + Right
}
return(D2b)
## psy_B(2,3), psy_B(2,4), psy_B(2,5)
}
## (Main): Making the difference between all levels
D1function <- function(nlevel,ord=FALSE){
if(ord==FALSE){
qp = (nlevel)*(nlevel-1)/2
D1.mat <- matrix(0,ncol=(nlevel),nrow=0)
if (qp==1) D1.mat <- matrix(c(-1,1),ncol=2,nrow=1)
if (qp>1){
for(i in 1 : (nlevel-1)){
w.diag <- diag((nlevel-i))
left.v <- c(rep(0,(i-1)),-1)
left.mat <- matrix(rep(left.v,(nlevel-i)),nrow=(nlevel-i),byrow=TRUE)
w.mat <- cbind(left.mat,w.diag)
D1.mat <- rbind(D1.mat,w.mat)
}
}
}else if(ord==TRUE){
if(nlevel==2){
D1.mat <- matrix(c(-1,1),ncol=2,nrow=1)
}else{
D1.mat <- cbind(0,diag(nlevel-1)) + cbind(-diag(nlevel-1),0)
}
}
return(D1.mat)
## nrow = differences between main effects
## ncol = mainlevel (coefficients for the main factor)
}
if(dif==TRUE){
data1 <- data[side==1,]
data2 <- data[side==0,]
model.frame <- model.frame(formula,data=data1)
contr <- rep(list("contr.sum"), ncol(model.frame) - 1)
names(contr) <- colnames(model.frame)[-1]
y <- model.frame[,1]
x1 <- model.matrix(formula, data=data1,contrast=contr)[,-1]
x2 <- model.matrix(formula, data=data2,contrast=contr)[,-1]
X <- x1-x2
}else if (dif==FALSE){
model.frame <- model.frame(formula,data=data)
contr <- rep(list("contr.sum"), ncol(model.frame) - 1)
names(contr) <- colnames(model.frame)[-1]
y <- model.frame[,1]
X <- model.matrix(formula, data=data,contrast=contr)[,-1]
}
lm.fit <- lm(y ~ X)
coef.use <- coef(lm.fit)[-1]
levelIndex <- CreatelevelIndex(fac.level=(fac.level-1),ord.fac=ord.fac,Gorder=Gorder,
indTwo=indTwo, indThree=indThree)
use.ind <- (levelIndex$plus==1)*(levelIndex$dif==0)
Index.use <- levelIndex[use.ind==1,]
Fac.index <- levelIndex[,regexpr("Fac",colnames(levelIndex))>0]
Fac.Ind.use <- Fac.index[use.ind==1,]
Fac.level.useC <- (rep(1,nrow(Fac.Ind.use)) %x% t((fac.level-1))) * Fac.Ind.use
Fac.level.use <- (rep(1,nrow(Fac.Ind.use)) %x% t((fac.level))) * Fac.Ind.use
Index.use$start <- c(1,cumsum(Index.use$length)[-nrow(Index.use)]+1)
Index.use$end <- cumsum(Index.use$length)
if(Gorder==2){
Index.use$seq.order <- c(seq(1:sum(Index.use$order==1)),
seq(1:sum(Index.use$order==2)))
}else if(Gorder==3){
Index.use$seq.order <- c(seq(1:sum(Index.use$order==1)),
seq(1:sum(Index.use$order==2)),
seq(1:sum(Index.use$order==3)))
}
## Need to change?
Coef.list <- CreateCoef(coef.use=coef.use,
Index.use=Index.use,
Fac.level.use=Fac.level.useC,
Gorder=Gorder)
if(facCons==TRUE){
n.fac <- length(fac.level)
MainDif <- list()
IntDif <- list()
ThreeDif <- list()
for(z in 1:n.fac){
Maincoef <- Coef.list$One.coef[[z]]
MainD1 <- D1function(nlevel=fac.level[z],ord=ord.fac[z])
MainDif[[z]] <- t(MainD1 %*% Maincoef)
}
ind.use.Two <- (Index.use$order==2)
Index.useTwo <- Index.use[ind.use.Two==1,]
Fac.useTwo <- Fac.Ind.use[ind.use.Two==1,]
Fac.level.useTwo <- Fac.level.use[ind.use.Two==1,]
## IntDif <- matrix(0,nrow=0,ncol=qp)
for(z in 1:nrow(Index.useTwo)){
level.use <- as.numeric(Fac.level.useTwo[z,Fac.useTwo[z, ]==1])
ord.use <- ord.fac[Fac.useTwo[z, ]==1]
coef.int <- c(Coef.list$Two.coef[[z]])
D2A <- D2function(alevel=level.use[1],blevel=level.use[2],
type="A",ordAB=ord.use)
D2B <- D2function(alevel=level.use[1],blevel=level.use[2],
type="B",ordAB=ord.use)
IntDif.A <- D2A %*% coef.int
IntDif.B <- D2B %*% coef.int
IntDif[[z]] <- c(IntDif.A, IntDif.B)
if(Gorder>2){
## Three-ways
ind.use.Three <- (Index.use$order==3)
Index.useThree <- Index.use[ind.use.Three==1,]
Fac.useThree <- Fac.Ind.use[ind.use.Three==1,]
Fac.level.useThree <- Fac.level.use[ind.use.Three==1,]
ThreeDif <- list()
for(z in 1:nrow(Index.useThree)){
level.use <- as.numeric(Fac.level.useThree[z,Fac.useThree[z, ]==1])
ord.use <- ord.fac[Fac.useThree[z, ]==1]
D3A <- D3function(alevel=level.use[1],blevel=level.use[2],clevel=level.use[3],
type="A",ordABC=ord.use)
D3B <- D3function(alevel=level.use[1],blevel=level.use[2],clevel=level.use[3],
type="B",ordABC=ord.use)
D3C <- D3function(alevel=level.use[1],blevel=level.use[2],clevel=level.use[3],
type="C",ordABC=ord.use)
coef.three <- c(Coef.list$Three.coef[[z]])
ThreeDif.A <- D3A %*% coef.three
ThreeDif.B <- D3B %*% coef.three
ThreeDif.C <- D3C %*% coef.three
ThreeDif[[z]] <- c(ThreeDif.A, ThreeDif.B, ThreeDif.C)
}
}
}
Main.max <- unlist(lapply(1:length(MainDif),function(x) 1/max(abs(MainDif[[x]]))))
Int.max <- unlist(lapply(1:length(IntDif),function(x) 1/max(abs(IntDif[[x]]))))
if(Gorder > 2){
Three.max <- unlist(lapply(1:length(ThreeDif),function(x) 1/max(abs(ThreeDif[[x]]))))
weight <- c(Main.max,Int.max, Three.max)
}else if(Gorder==2){
weight <- c(Main.max,Int.max)
}
}
else if(facCons==FALSE){
## Main Effects
Maincoef <- Coef.list$One.coef[[type.ind]]
MainD1 <- D1function(nlevel=fac.level[type.ind],ord=ord.fac[type.ind])
MainDif <- t(MainD1 %*% Maincoef)
qp <- ncol(MainDif)
## Two-ways
onlyOne <- sum(Fac.Ind.use[type.ind])==1
yesTwo <- sum((Index.use$order==2)*(Fac.Ind.use[type.ind]==1))>0
yesThree <- sum((Index.use$order==3)*(Fac.Ind.use[type.ind]==1))>0
if(onlyOne==TRUE){
## No Interaction
Dif <- abs(MainDif)
## print(Dif)
}else if(yesTwo==TRUE){
ind.use.Two <- (Index.use$order==2)*(Fac.Ind.use[type.ind]==1)
Index.useTwo <- Index.use[ind.use.Two==1,]
Fac.useTwo <- Fac.Ind.use[ind.use.Two==1,]
Fac.level.useTwo <- Fac.level.use[ind.use.Two==1,]
IntDif <- matrix(0,nrow=0,ncol=qp)
for(z in 1:nrow(Index.useTwo)){
level.use <- as.numeric(Fac.level.useTwo[z,Fac.useTwo[z, ]==1])
ord.use <- ord.fac[Fac.useTwo[z, ]==1]
if(min(which(Fac.useTwo[z,]==1))==type.ind){
type.d2 <- "A"}else{ type.d2 <- "B" }
D2 <- D2function(alevel=level.use[1],blevel=level.use[2],
type=type.d2,ordAB=ord.use)
coef.int <- c(Coef.list$Two.coef[[Index.useTwo[z,"seq.order"]]])
IntDif.t <- D2 %*% coef.int
IntDif.mat <- matrix(IntDif.t,ncol=qp)
IntDif <- rbind(IntDif, IntDif.mat)
}
if(yesThree==FALSE){
Dif <- abs(rbind(MainDif,IntDif))
}else if(yesThree==TRUE){
## Three-ways
ind.use.Three <- (Index.use$order==3)*(Fac.Ind.use[type.ind]==1)
Index.useThree <- Index.use[ind.use.Three==1,]
Fac.useThree <- Fac.Ind.use[ind.use.Three==1,]
Fac.level.useThree <- Fac.level.use[ind.use.Three==1,]
ThreeDif <- matrix(0,nrow=0,ncol=qp)
for(z in 1:nrow(Index.useThree)){
level.use <- as.numeric(Fac.level.useThree[z,Fac.useThree[z, ]==1])
ord.use <- ord.fac[Fac.useThree[z, ]==1]
if(min(which(Fac.useThree[z,]==1))==type.ind){
type.d3 <- "A"
}else if (max(which(Fac.useThree[z,]==1))==type.ind){
type.d3 <- "C"
}else{ type.d3 <- "B"}
D3 <- D3function(alevel=level.use[1],blevel=level.use[2],clevel=level.use[3],
type=type.d3,ordABC=ord.use)
coef.three <- c(Coef.list$Three.coef[[Index.useThree[z,"seq.order"]]])
ThreeDif.t <- D3 %*% coef.three
ThreeDif.mat <- matrix(ThreeDif.t,ncol=qp)
ThreeDif <- rbind(ThreeDif, ThreeDif.mat)
}
Dif <- abs(rbind(MainDif,IntDif,ThreeDif))
}
}
## if(Gorder == 2){
## Dif <- abs(rbind(MainDif,IntDif))
## }else if(Gorder > 2){
## Dif <- abs(rbind(MainDif,IntDif,ThreeDif))
## }
weight <- apply(Dif,2,function(x) 1/max(abs(x)))
}
levelIndex <- CreatelevelIndex(fac.level=(fac.level),ord.fac=ord.fac, Gorder=Gorder,
indTwo=indTwo, indThree=indThree)
use.ind <- (levelIndex$plus==1)*(levelIndex$dif==1) * (levelIndex$order==1)
Index.use <- levelIndex[use.ind==1,]
temp.w <- 1/(sqrt(fac.level[type.ind])*(fac.level[type.ind]+1))
weight.u <- rep(temp.w, times=Index.use$length[type.ind])
## Combine two weights.
output <- list("weight.ols"=weight, "weight.fac"=weight.u)
return(output)
}
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