# 10. Gram-Schmidt Orthogonalization and Regression

#### Michael Friendly

#### 2025-10-05

This vignette illustrates the process of transforming a set of variables to a new set of uncorrelated (orthogonal) variables. It carries out the Gram-Schmidt process directly by successively projecting each successive variable on the previous ones and subtracting (taking residuals). This is equivalent by replacing each successive variable by its residuals from a least squares regression on the previous variables.

When this method is used on the predictors in a regression problem, the resulting orthogonal variables have exactly the same `anova()` summary (based on “Type I”, sequential sums of squares) as do original variables.

## Setup

We use the `class` data set, but convert the character factor `sex` to a dummy (0/1) variable `male`.

    library(matlib)
    data(class)
    class$male <- as.numeric(class$sex=="M")

For later use in regression, we create a variable `IQ` as a response variable

    class <- transform(class,
                       IQ = round(20 + height + 3*age -.1*weight -3*male + 10*rnorm(nrow(class))))
    head(class)

    ##         sex age height weight male  IQ
    ## Alfred    M  14   69.0  112.5    1 115
    ## Alice     F  13   56.5   84.0    0 112
    ## Barbara   F  13   65.3   98.0    0 118
    ## Carol     F  14   62.8  102.5    0 118
    ## Henry     M  14   63.5  102.5    1  99
    ## James     M  12   57.3   83.0    1  97

Reorder the predictors we want, forming a numeric matrix, `X`.

    X <- as.matrix(class[,c(3,4,2,5)])
    head(X)

    ##         height weight age male
    ## Alfred    69.0  112.5  14    1
    ## Alice     56.5   84.0  13    0
    ## Barbara   65.3   98.0  13    0
    ## Carol     62.8  102.5  14    0
    ## Henry     63.5  102.5  14    1
    ## James     57.3   83.0  12    1

## Orthogonalization by projections

The Gram-Schmidt process treats the variables in a given order, according to the columns in `X`. We start with a new matrix `Z` consisting of `X[,1]`. Then, find a new variable `Z[,2]` orthogonal to `Z[,1]` by subtracting the projection of `X[,2]` on `Z[,1]`.

    Z <- cbind(X[,1], 0, 0, 0)
    Z[,2] <- X[,2] - Proj(X[,2], Z[,1])
    crossprod(Z[,1], Z[,2])     # verify orthogonality

    ##           [,1]
    ## [1,] 7.276e-12

Continue in the same way, subtracting the projections of `X[,3]` on the previous columns, and so forth

    Z[,3] <- X[,3] - Proj(X[,3], Z[,1]) - Proj(X[,3], Z[,2])
    Z[,4] <- X[,4] - Proj(X[,4], Z[,1]) - Proj(X[,4], Z[,2]) - Proj(X[,4], Z[,3])

Note that if any column of `X` is a linear combination of the previous columns, the corresponding column of `Z` will be all zeros.

These computations are similar to the following set of linear regressions:

    z2 <- residuals(lm(X[,2] ~ X[,1]), type="response")
    z3 <- residuals(lm(X[,3] ~ X[,1:2]), type="response")
    z4 <- residuals(lm(X[,4] ~ X[,1:3]), type="response")

The columns of `Z` are now orthogonal, but not of unit length,

    zapsmall(crossprod(Z))     # check orthogonality

    ##       [,1] [,2] [,3] [,4]
    ## [1,] 57888    0    0    0
    ## [2,]     0 3249    0    0
    ## [3,]     0    0    7    0
    ## [4,]     0    0    0    2

We make standardize column to unit length, giving `Z` as an orthonormal matrix, such that \(Z' Z = I\).

    Z <- Z %*% diag(1 / len(Z))    # make each column unit length
    zapsmall(crossprod(Z))         # check orthonormal

    ##      [,1] [,2] [,3] [,4]
    ## [1,]    1    0    0    0
    ## [2,]    0    1    0    0
    ## [3,]    0    0    1    0
    ## [4,]    0    0    0    1

    colnames(Z) <- colnames(X)

### Relationship to QR factorization

The QR method uses essentially the same process, factoring the matrix \(\mathbf{X}\) as \(\mathbf{X = Q R}\), where \(\mathbf{Q}\) is the orthonormal matrix corresponding to `Z` and \(\mathbf{R}\) is an upper triangular matrix. However, the signs of the columns of \(\mathbf{Q}\) are arbitrary, and `QR()` returns `QR(X)$Q` with signs reversed, compared to `Z`.

    # same result as QR(X)$Q, but with signs reversed
    head(Z, 5)

    ##         height   weight     age     male
    ## Alfred  0.2868  0.07545 -0.3687  0.12456
    ## Alice   0.2348 -0.08067  0.3569 -0.02177
    ## Barbara 0.2714 -0.07715 -0.3862 -0.45170
    ## Carol   0.2610  0.07058  0.1559 -0.20548
    ## Henry   0.2639  0.05132  0.1047  0.40538

    head(-QR(X)$Q, 5)

    ##        [,1]     [,2]    [,3]     [,4]
    ## [1,] 0.2868  0.07545 -0.3687  0.12456
    ## [2,] 0.2348 -0.08067  0.3569 -0.02177
    ## [3,] 0.2714 -0.07715 -0.3862 -0.45170
    ## [4,] 0.2610  0.07058  0.1559 -0.20548
    ## [5,] 0.2639  0.05132  0.1047  0.40538

    all.equal( unname(Z), -QR(X)$Q )

    ## [1] TRUE

## Regression with X and Z

We carry out two regressions of `IQ` on the variables in `X` and in `Z`. These are equivalent, in the sense that

- The \(R^2\) and MSE are the same in both models
- Residuals are the same
- The Type I tests given by `anova()` are the same.

    class2 <- data.frame(Z, IQ=class$IQ)

Regression of IQ on the original variables in `X`

    mod1 <- lm(IQ ~ height + weight + age + male, data=class)
    anova(mod1)

    ## Analysis of Variance Table
    ##
    ## Response: IQ
    ##           Df Sum Sq Mean Sq F value Pr(>F)
    ## height     1  160.2   160.2    6.38  0.030 *
    ## weight     1   14.5    14.5    0.58  0.465
    ## age        1  176.4   176.4    7.03  0.024 *
    ## male       1  273.8   273.8   10.91  0.008 **
    ## Residuals 10  251.0    25.1
    ## ---
    ## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Regression of IQ on the orthogonalized variables in `Z`

    mod2 <- lm(IQ ~ height + weight + age + male, data=class2)
    anova(mod2)

    ## Analysis of Variance Table
    ##
    ## Response: IQ
    ##           Df Sum Sq Mean Sq F value Pr(>F)
    ## height     1  160.2   160.2    6.38  0.030 *
    ## weight     1   14.5    14.5    0.58  0.465
    ## age        1  176.4   176.4    7.03  0.024 *
    ## male       1  273.8   273.8   10.91  0.008 **
    ## Residuals 10  251.0    25.1
    ## ---
    ## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

This illustrates that `anova()` tests for linear models are sequential tests. They test hypotheses about the extra contribution of each variable over and above all previous ones, in a given order. These usually do not make substantive sense, except in testing ordered (“hierarchical”) models.