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############################################## # R Code for canonical correlation analysis # ############################################## # We will use the built-in iris data set.

# We will consider the entire data set (all three species) attach(iris) # We will standardize the variables first # by dividing by each column's standard deviation: # (we will remove column 5, the species labels) iris.std <- sweep(iris[,-5], 2, sqrt(apply(iris[,-5],2,var)), FUN="/") sepal.meas <- iris.std[,1:2] petal.meas <- iris.std[,3:4] ### Doing the CCA the long way: # Finding blocks of the correlation matrix: R11 <- cor(sepal.meas) R22 <- cor(petal.meas) R12 <- c(cor(sepal.meas[,1], petal.meas[,1]), cor(sepal.meas[,1], petal.meas[,2]), cor(sepal.meas[,2], petal.meas[,1]), cor(sepal.meas[,2], petal.meas[,2])) R12 <- matrix(R12, ncol=ncol(R22), byrow=T) # R12 has q2 columns, same as number of petal measurements R21 <- t(R12) # R21=transpose of R12 # Finding the E1 and E2 matrices: E1 <- solve(R11) %*% R12 %*% solve(R22) %*% R21 E2 <- solve(R22) %*% R21 %*% solve(R11) %*% R12 # print(E1) # print(E2) eigen(E1) eigen(E2) # The canonical correlations are: canon.corr <- sqrt(eigen(E1)$values) canon.corr # The canonical variates are based on the eigenvectors of E1 and E2: # # # # a1 b1 a2 b2 = = = = (0.922, -0.388) (0.943, -0.333) (0.457, 0.890) (-0.679, 0.734)

# Only the first canonical correlation is really substantial:

# u1 = 0.92*Sepal.Length - 0.39*Sepal.Width # v1 = 0.94*Petal.Length - 0.33*Petal.Width # Plotting the first set of canonical variables: u1 <- as.matrix(iris.std[,1:2]) %*% as.matrix(eigen(E1)$vectors[,1]) v1 <- as.matrix(iris.std[,3:4]) %*% as.matrix(eigen(E2)$vectors[,1]) plot(u1,v1) cor(u1,v1) # Plotting the second set of canonical variables: u2 <- as.matrix(iris.std[,1:2]) %*% as.matrix(eigen(E1)$vectors[,2]) v2 <- as.matrix(iris.std[,3:4]) %*% as.matrix(eigen(E2)$vectors[,2]) plot(u2,v2) cor(u2,v2) ### Doing CCA using the built-in cancor function: cancor(sepal.meas, petal.meas) # The canonical correlations are the same as the ones we found, # The canonical variates are a little different because the cancor # function works with the centered data rather than the original data. ### Doing CCA using Dr. Habing's cancor2 function: ### First copy this function into R: ############# ## cancor2<-function(x,y,dec=4){ #Canonical Correlation Analysis to mimic SAS PROC CANCOR output. #Basic formulas can be found in Chapter 10 of Mardia, Kent, and Bibby (1979). # The approximate F statistic is exercise 3.7.6b. x<-as.matrix(x);y<-as.matrix(y) n<-dim(x)[1];q1<-dim(x)[2];q2<-dim(y)[2];q<-min(q1,q2) S11<-cov(x);S12<-cov(x,y);S21<-t(S12);S22<-cov(y) E1<-eigen(solve(S11)%*%S12%*%solve(S22)%*%S21);E2<eigen(solve(S22)%*%S21%*%solve(S11)%*%S12) rsquared<-as.real(E1$values[1:q]) LR<-NULL;pp<-NULL;qq<-NULL;tt<-NULL for (i in 1:q){ LR<-c(LR,prod(1-rsquared[i:q])) pp<-c(pp,q1-i+1) qq<-c(qq,q2-i+1) tt<-c(tt,n-1-i+1)} m<-tt-0.5*(pp+qq+1);lambda<-(1/4)*(pp*qq-2);s<-sqrt((pp^2*qq^24)/(pp^2+qq^2-5)) F<-((m*s-2*lambda)/(pp*qq))*((1-LR^(1/s))/LR^(1/s));df1<-pp*qq;df2<(m*s-2*lambda);pval<-1-pf(F,df1,df2) outmat<-round(cbind(sqrt(rsquared),rsquared,LR,F,df1,df2,pval),dec) colnames(outmat)=list("R","RSquared","LR","ApproxF","NumDF","DenDF","pval ue") rownames(outmat)=as.character(1:q);xrels<round(cor(x,x%*%E1$vectors)[,1:q],dec)

colnames(xrels)<apply(cbind(rep("U",q),as.character(1:q)),1,paste,collapse="") yrels<-round(cor(y,y%*%E2$vectors)[,1:q],dec) colnames(yrels)<apply(cbind(rep("V",q),as.character(1:q)),1,paste,collapse="") list(Summary=outmat,a.Coefficients=E1$vectors,b.Coefficients=E2$vectors, XUCorrelations=xrels,YVCorrelations=yrels) } ## END FUNCTION ################################################# # Then use it as on the iris example: cancor2(sepal.meas, petal.meas) # It produces two other pieces of information: An F-test for the significance of # each canonical correlation, and the correlations between the original variables # and the corresponding canonical variates. ############################################################## ############################################################## # Doing canonical correlation given a sample correlation matrix # rather than the raw data matrix: # The Los Angeles Depression Study (n=294 individuals): # q1 = 2 "health variables": # CESD: A numerical measure of depression # Health: A measure of general perceived health status # # # # # q2 = 4 "personal (~demographic) variables": Gender: Low=Male, High=Female Age Income Education Level

# Suppose the sample correlation matrix R is as given in Table 8.4, page 165: R22 <- matrix( c( 1,.044,-.106,-.18, .044,1,-.208,-.192, -.106,-.208,1,.492, -.18,-.192,.492,1 ), ncol=4,byrow=T) R11 <- matrix( c( 1,.212,.212,1), ncol=2,byrow=T) R12 <- matrix( c( .124,-.164,-.101,-.158,

.098,.308,-.27,-.183), ncol=4, byrow=T) R21 <- t(R12) # Finding the E1 and E2 matrices: E1 <- solve(R11) %*% R12 %*% solve(R22) %*% R21 E2 <- solve(R22) %*% R21 %*% solve(R11) %*% R12 # print(E1) # print(E2) eigen(E1) eigen(E2) # The canonical correlations are: canon.corr <- sqrt(eigen(E1)$values) canon.corr # First canonical variate: # u1 = 0.46*CESD - 0.89*Health # v1 = 0.02*Gender + 0.90*Age - 0.41*Education + 0.13*Income # Second canonical variate: # u2 = - 0.95*CESD - 0.32*Health # v2 = - 0.45*Gender + 0.46*Age + 0.47*Education + 0.60*Income ## Bartlett's test for the significance of the first canonical correlation: ## The null hypothesis is that the first (and smaller) canonical correlations are zero. my.n <- 294; my.q1 <- 2; my.q2 <- 4 test.stat <- -( (my.n-1) - 0.5*(my.q1+my.q2+1) ) * sum(log(1eigen(E1)$values)) test.stat P.value <- pchisq(test.stat, df = my.q1*my.q2, lower.tail=F) P.value # Since the P-value is tiny, we conclude that there is at least one # nonzero canonical correlation. ## Bartlett's test for the significance of the second canonical correlation: ## The null hypothesis is that the second (and smaller) canonical correlations are zero in general, ## but there's only two here. my.n <- 294; my.q1 <- 2; my.q2 <- 4 test.stat <- -( (my.n-1) - 0.5*(my.q1+my.q2+1) ) * sum(log(1eigen(E1)$values[-1])) test.stat

P.value <- pchisq(test.stat, df = (my.q1-1)*(my.q2-1), lower.tail=F) P.value # The P-value is again very small, so we conclude there are at least two # nonzero canonical correlations. In this case, that means exactly two # nonzero canonical correlations! ######################################################################### ############ ######################################################################### ############ ######################################## # R Code for multivariate regression # ######################################## # Example 1: The Computer Data

comput <read.table("http://www.stat.sc.edu/~hitchcock/computerdata.txt", header=T) attach(comput) # Fitting the multivariate linear regression model: comp.mod.y1 <- lm(y1 ~ x1 + x2) comp.mod.y2 <- lm(y2 ~ x1 + x2) Beta.hat <- cbind(coef(comp.mod.y1), coef(comp.mod.y2) ) Beta.hat # A quicker way to get a summary: comp.mod <- lm(cbind(y1,y2) ~ x1 + x2) summary(comp.mod) # Getting the matrix of fitted values: X.mat <- cbind(rep(1,times=nrow(comput)),x1,x2) Y.hat <- X.mat %*% Beta.hat Y.hat # Getting the matrix of residuals: resid.mat <- cbind (y1,y2) - Y.hat resid.mat # Note we could get these matrices from the individual regression models as well: cbind(fitted(comp.mod.y1), fitted(comp.mod.y2)) cbind(resid(comp.mod.y1), resid(comp.mod.y2))

#### Testing about x2 in the model: ## Full model: my.n <- length(y1) # number of individuals my.p <- ncol(X.mat) - 1 # total number of predictors my.r <- ncol(resid.mat) # total number of responses E.mat.full <- (my.n-1)*var(resid.mat) ## Reduced model (without x2) Beta.hat.redu <- cbind(coef(lm(y1 ~ x1) ), coef(lm(y2 ~ x1) ) ) ## ## Note: If we were testing the null hypothesis that the *entire set* of predictors ## was useless in the model, our reduced model would contain ONLY an intercept term. ## We could fit such a reduced model using: ## Beta.hat.redu <- cbind(coef(lm(y1 ~ 1) ), coef(lm(y2 ~ 1) ) ) ## X.mat.redu <- cbind(rep(1,times=nrow(comput)),x1) my.p.redu <- ncol(X.mat.redu) - 1 # number of predictors in the reduced model Y.hat.redu <- X.mat.redu %*% Beta.hat.redu resid.mat.redu <- cbind (y1,y2) - Y.hat.redu E.mat.redu <- (my.n-1)*var(resid.mat.redu) my.test.stat <- -(my.n - my.p - 1 - 0.5*(my.r - my.p + my.p.redu + 1)) * log( det(E.mat.full)/det(E.mat.redu) ) my.test.stat p.value <- pchisq(my.test.stat, df = my.r*(my.p - my.p.redu), lower.tail=F ) p.value ############################## #### Prediction ellipse for (y1, y2) # Suppose we have a new site with 130 thousand orders and 7.5 thousand add-delete items. # Let's get a 95% prediction ellipse for that site's (CPU time, disk input/output capacity). # The predictor values of interest (including a "1" for the intercept term): x0 <- c(1, 130, 7.5) pt.est <- t(as.matrix(x0,nc=1)) %*% Beta.hat

pt.est # A point prediction for this site is: # predicted CPU time = 151.8 hours, predicted disk input/output capacity = 349.6. middle.mat <- solve((1/(my.n - my.p - 1))*E.mat.full) my.y1 <- runif(n=100000, min=min(y1), max=max(y1) ) my.y2 <- runif(n=100000, min=min(y2), max=max(y2) ) my.ys <- cbind(my.y1,my.y2) my.pts<-rep(0,times=length(my.y1)) for (i in 1:(length(my.pts)) ) { my.pts[i] <- (my.ys[i,] - pt.est) %*% middle.mat %*% t((my.ys[i,] pt.est)) } multiple.pred <- as.numeric( (1 + t(as.matrix(x0,nc=1)) %*% solve(t(X.mat) %*% X.mat) %*% as.matrix(x0,nc=1) ) * (my.r*(my.n-my.p-1)/(my.n-my.pmy.r) ) ) my.y1.inside.p <- my.y1[my.pts <= multiple.pred*qf(0.95, my.r, my.n-my.pmy.r)] my.y2.inside.p <- my.y2[my.pts <= multiple.pred*qf(0.95, my.r, my.n-my.pmy.r)] plot(my.y1.inside.p, my.y2.inside.p, xlab="CPU Time (hours)", ylab="Disk Input/output Capacity", type='n') conv.hull.p <- chull(my.y1.inside.p, my.y2.inside.p) polygon(my.y1.inside.p[conv.hull.p], my.y2.inside.p[conv.hull.p]) points(pt.est) #### Confidence ellipse for (y1, y2) # Let's consider all sites with 130 thousand orders and 7.5 thousand adddelete items. # Let's get a 95% confidence ellipse for (mean CPU time, mean disk input/output capacity) for those such sites. # The predictor values of interest (including a "1" for the intercept term): x0 <- c(1, 130, 7.5) pt.est <- t(as.matrix(x0,nc=1)) %*% Beta.hat pt.est # A point estimate for this mean vector is: # mean CPU time: 151.8 hours, mean disk input/output capacity: 349.6. middle.mat <- solve((1/(my.n - my.p - 1))*E.mat.full) my.y1 <- runif(n=100000, min=min(y1), max=max(y1) ) my.y2 <- runif(n=100000, min=min(y2), max=max(y2) )

my.ys <- cbind(my.y1,my.y2) my.pts<-rep(0,times=length(my.y1)) for (i in 1:(length(my.pts)) ) { my.pts[i] <- (my.ys[i,] - pt.est) %*% middle.mat %*% t((my.ys[i,] pt.est)) } multiple.conf <- as.numeric( (t(as.matrix(x0,nc=1)) %*% solve(t(X.mat) %*% X.mat) %*% as.matrix(x0,nc=1) ) * (my.r*(my.n-my.p-1)/(my.n-my.pmy.r) ) ) my.y1.inside.c <- my.y1[my.pts <= multiple.conf*qf(0.95, my.r, my.n-my.pmy.r)] my.y2.inside.c <- my.y2[my.pts <= multiple.conf*qf(0.95, my.r, my.n-my.pmy.r)] plot(my.y1.inside.c, my.y2.inside.c, xlab="CPU Time (hours)", ylab="Disk Input/output Capacity", type='n') conv.hull.c <- chull(my.y1.inside.c, my.y2.inside.c) polygon(my.y1.inside.c[conv.hull.c], my.y2.inside.c[conv.hull.c]) points(pt.est) # Prediction and Confidence ellipses on same plot: plot(my.y1.inside.p, my.y2.inside.p, xlab="CPU Time (hours)", ylab="Disk Input/output Capacity", type='n') polygon(my.y1.inside.c[conv.hull.c], my.y2.inside.c[conv.hull.c]) polygon(my.y1.inside.p[conv.hull.p], my.y2.inside.p[conv.hull.p], lty='dashed') points(pt.est) ### Checking model assumptions: qqnorm(resid.mat[,1], main = "Normal windows() plot(Y.hat[,1],resid.mat[,1], main = y1"); abline(h=0) windows() qqnorm(resid.mat[,2], main = "Normal windows() plot(Y.hat[,2],resid.mat[,2], main = y2"); abline(h=0) Q-Q plot, y1") "Residual plot vs. fitted values, Q-Q plot, y2") "Residual plot vs. fitted values,

######################################################################### ############ # Example 2: The sales performance data: salesdata <- read.table("http://www.stat.sc.edu/~hitchcock/salesmat.txt", header=T) attach(salesdata)

# # # # # # # # # # #

Recall the variables: X1 = Sales growth X2 = Sales profitability X3 = New account sales X4 = Creativity Test X5 = Mechanical Reasoning Test X6 = Abstract Reasoning Test X7 = Mathematics Test X8 = Historical Facts Test X9 = Sports Trivia Test X10 = Music Trivia Test

# We will try to predict the "performance" variables (x1, x2, x3) using the # "test score" variables (x4, x5, ..., x10). # Fitting the multivariate linear regression model: sales.mod.1 <- lm(x1 ~ x4 + x5 + x6 + x7 + x8 + x9 + x10) sales.mod.2 <- lm(x2 ~ x4 + x5 + x6 + x7 + x8 + x9 + x10) sales.mod.3 <- lm(x3 ~ x4 + x5 + x6 + x7 + x8 + x9 + x10) # A quick summary: sales.mod <- lm(cbind(x1,x2,x3) ~ x4 + x5 + x6 + x7 + x8 + x9 + x10) summary(sales.mod) Beta.hat <- cbind(coef(sales.mod.1), coef(sales.mod.2), coef(sales.mod.3) ) Beta.hat X.mat <- cbind(rep(1,times=nrow(salesdata)), x4, x5, x6, x7, x8, x9, x10) Y.hat <- cbind(fitted(sales.mod.1), fitted(sales.mod.2), fitted(sales.mod.3)) resid.mat <- cbind(resid(sales.mod.1), resid(sales.mod.2), resid(sales.mod.3)) #### Testing whether the set (x8, x9, x10) is useless, #### given the presence of x4, x5, x6, x7 as predictors in the model: ## Full model: my.n <- length(x1) # number of individuals my.p <- ncol(X.mat) - 1 # total number of predictors my.r <- ncol(resid.mat) # total number of responses E.mat.full <- (my.n-1)*var(resid.mat) ## Reduced model (without x8, x9, x10) Beta.hat.redu <- cbind(coef(lm(x1 ~ x4 + x5 + x6 + x7) ), coef(lm(x2 ~ x4 + x5 + x6 + x7) ), coef(lm(x3 ~ x4 + x5 + x6 + x7)) )

X.mat.redu <- cbind(rep(1,times=nrow(salesdata)), x4, x5, x6, x7) my.p.redu <- ncol(X.mat.redu) - 1 # number of predictors in the reduced model Y.hat.redu <- X.mat.redu %*% Beta.hat.redu resid.mat.redu <- cbind (x1,x2,x3) - Y.hat.redu E.mat.redu <- (my.n-1)*var(resid.mat.redu) my.test.stat <- -(my.n - my.p - 1 - 0.5*(my.r - my.p + my.p.redu + 1)) * log( det(E.mat.full)/det(E.mat.redu) ) my.test.stat p.value <- pchisq(my.test.stat, df = my.r*(my.p - my.p.redu), lower.tail=F ) p.value ### Checking model assumptions: qqnorm(resid.mat[,1], main = "Normal windows() plot(Y.hat[,1],resid.mat[,1], main = Sales growth"); abline(h=0) windows() qqnorm(resid.mat[,2], main = "Normal windows() plot(Y.hat[,2],resid.mat[,2], main = Sales profitability"); abline(h=0) windows() qqnorm(resid.mat[,3], main = "Normal windows() plot(Y.hat[,3],resid.mat[,3], main = New account sales"); abline(h=0) Q-Q plot, Sales growth") "Residual plot vs. fitted values, Q-Q plot, Sales profitability") "Residual plot vs. fitted values, Q-Q plot, New account sales") "Residual plot vs. fitted values,