Ridge Regression Estimates

The function ridge fits linear models by ridge regression, returning an object of class ridge designed to be used with the plotting methods in this package.

It is also designed to facilitate an alternative representation of the effects of shrinkage in the space of uncorrelated (PCA/SVD) components of the predictors.

The standard formulation of ridge regression is that it regularizes the estimates of coefficients by adding small positive constants $\lambda$ to the diagonal elements of $\mathbf{X}^\top\mathbf{X}$ in the least squares solution to achieve a more favorable tradeoff between bias and variance (inverse of precision) of the coefficients.

$$\widehat{\mathbf{\beta}}^{\text{RR}}_k = (\mathbf{X}^\top \mathbf{X} + \lambda \mathbf{I})^{-1} \mathbf{X}^\top \mathbf{y} $$

Ridge regression shrinkage can be parameterized in several ways.

If a vector of lambda values is supplied, these are used directly in the ridge regression computations.
Otherwise, if a vector df can be supplied the equivalent values for effective degrees of freedom corresponding to shrinkage, going down from the number of predictors in the model.

In either case, both lambda and df are returned in the ridge object, but the rownames of the coefficients are given in terms of lambda.

Usage

ridge(y, ...)

# S3 method for class 'formula'
ridge(formula, data, lambda = 0, df, svd = TRUE, contrasts = NULL, ...)

# Default S3 method
ridge(y, X, lambda = 0, df, svd = TRUE, ...)

# S3 method for class 'ridge'
coef(object, ...)

# S3 method for class 'ridge'
print(x, digits = max(5, getOption("digits") - 5), ...)

# S3 method for class 'ridge'
vcov(object, ...)

Arguments

y: A numeric vector containing the response variable. NAs not allowed.
...: Other arguments, passed down to methods
formula: For the formula method, a two-sided formula.
data: For the formula method, data frame within which to evaluate the formula.
lambda: A scalar or vector of ridge constants. A value of 0 corresponds to ordinary least squares.
df: A scalar or vector of effective degrees of freedom corresponding to lambda
svd: If TRUE the SVD of the centered and scaled X matrix is returned in the ridge object.
contrasts: a list of contrasts to be used for some or all of factor terms in the formula. See the contrasts.arg of model.matrix.default.
X: A matrix of predictor variables. NA's not allowed. Should not include a column of 1's for the intercept.
x, object: An object of class ridge
digits: For the print method, the number of digits to print.

Value

A list with the following components:

lambda: The vector of ridge constants
df: The vector of effective degrees of freedom corresponding to lambda
coef: The matrix of estimated ridge regression coefficients
scales: scalings used on the X matrix
kHKB: HKB estimate of the ridge constant
kLW: L-W estimate of the ridge constant
GCV: vector of GCV values
kGCV: value of lambda with the minimum GCV
criteria: Collects the criteria kHKB, kLW, and kGCV in a named vector

If svd==TRUE (the default), the following are also included:

svd.D: Singular values of the svd of the scaled X matrix
svd.U: Left singular vectors of the svd of the scaled X matrix. Rows correspond to observations and columns to dimensions.
svd.V: Right singular vectors of the svd of the scaled X matrix. Rows correspond to variables and columns to dimensions.

Details

If an intercept is present in the model, its coefficient is not penalized. (If you want to penalize an intercept, put in your own constant term and remove the intercept.)

References

Hoerl, A. E., Kennard, R. W., and Baldwin, K. F. (1975), "Ridge Regression: Some Simulations," Communications in Statistics, 4, 105-123.

Lawless, J.F., and Wang, P. (1976), "A Simulation Study of Ridge and Other Regression Estimators," Communications in Statistics, 5, 307-323.

Author

Michael Friendly

Examples



#\donttest{
# Longley data, using number Employed as response
longley.y <- longley[, "Employed"]
longley.X <- data.matrix(longley[, c(2:6,1)])

lambda <- c(0, 0.005, 0.01, 0.02, 0.04, 0.08)
lridge <- ridge(longley.y, longley.X, lambda=lambda)

# same, using formula interface
lridge <- ridge(Employed ~ GNP + Unemployed + Armed.Forces + Population + Year + GNP.deflator, 
    data=longley, lambda=lambda)


coef(lridge)
#>              GNP Unemployed Armed.Forces  Population     Year GNP.deflator
#> 0.000 -3.4471925  -1.827886   -0.6962102 -0.34419721 8.431972   0.15737965
#> 0.005 -1.0424783  -1.491395   -0.6234680 -0.93558040 6.566532  -0.04175039
#> 0.010 -0.1797967  -1.361047   -0.5881396 -1.00316772 5.656287  -0.02612152
#> 0.020  0.4994945  -1.245137   -0.5476331 -0.86755299 4.626116   0.09766305
#> 0.040  0.9059471  -1.155229   -0.5039108 -0.52347060 3.576502   0.32123994
#> 0.080  1.0907048  -1.086421   -0.4582525 -0.08596324 2.641649   0.57025165

# standard trace plot
traceplot(lridge)

# plot vs. equivalent df
traceplot(lridge, X="df")

pairs(lridge, radius=0.5)

#}

# \donttest{
data(prostate)
py <- prostate[, "lpsa"]
pX <- data.matrix(prostate[, 1:8])
pridge <- ridge(py, pX, df=8:1)
pridge
#> Ridge Coefficients:
#>            lcavol      lweight     age         lbph        svi       
#>   0.00000   0.6617092   0.2651031  -0.1573777   0.1395860   0.3136993
#>   7.08544   0.5774912   0.2574888  -0.1240459   0.1239824   0.2825540
#>  17.80389   0.4966273   0.2435259  -0.0910692   0.1087544   0.2542261
#>  34.68940   0.4182786   0.2224269  -0.0591493   0.0936983   0.2271752
#>  62.98554   0.3413151   0.1935614  -0.0296600   0.0784146   0.1988651
#> 115.28893   0.2641305   0.1565931  -0.0049775   0.0622832   0.1660546
#> 230.11308   0.1842675   0.1116128   0.0112850   0.0444562   0.1249585
#> 601.44017   0.0979221   0.0591504   0.0144649   0.0239578   0.0711874
#>            lcp         gleason     pgg45     
#>   0.00000  -0.1475193   0.0353655   0.1250701
#>   7.08544  -0.0556184   0.0457910   0.0958079
#>  17.80389   0.0159166   0.0518160   0.0800300
#>  34.68940   0.0670223   0.0559538   0.0738953
#>  62.98554   0.0979877   0.0592922   0.0732073
#> 115.28893   0.1087550   0.0607835   0.0729838
#> 230.11308   0.0981548   0.0564920   0.0666687
#> 601.44017   0.0633002   0.0392473   0.0455834

plot(pridge)

pairs(pridge)

traceplot(pridge)

traceplot(pridge, X="df")

# }

# Hospital manpower data from Table 3.8 of Myers (1990) 
data(Manpower)
str(Manpower)
#> 'data.frame':	17 obs. of  6 variables:
#>  $ Hours  : num  567 697 1033 1604 1611 ...
#>  $ Load   : num  15.6 44 20.4 18.7 49.2 ...
#>  $ Xray   : int  2463 2048 3940 6505 5723 11520 5779 5969 8461 20106 ...
#>  $ BedDays: num  473 1340 620 568 1498 ...
#>  $ AreaPop: num  18 9.5 12.8 36.7 35.7 ...
#>  $ Stay   : num  4.45 6.92 4.28 3.9 5.5 4.6 5.62 5.15 6.18 6.15 ...

mmod <- lm(Hours ~ ., data=Manpower)
vif(mmod)
#>        Load        Xray     BedDays     AreaPop        Stay 
#> 9597.570761    7.940593 8933.086501   23.293856    4.279835 
# ridge regression models, specified in terms of equivalent df
mridge <- ridge(Hours ~ ., data=Manpower, df=seq(5, 3.75, -.25))
vif(mridge)
#>                     Load     Xray     BedDays   AreaPop     Stay
#> 0.0000000000 9597.570762 7.940593 8933.086501 23.293856 4.279835
#> 0.0002836352 5602.507260 7.927390 5215.176404 19.045017 3.923247
#> 0.0009043689 2438.603928 7.912946 2270.761610 15.667945 3.638481
#> 0.0026667276  634.529233 7.890568  591.831974 13.699280 3.467754
#> 0.0203643899   23.623930 7.715258   23.249737 12.530582 3.312552
#> 0.1364900421    7.336948 6.733109    8.136369  9.838466 2.795880

# univariate ridge trace plots
traceplot(mridge)

traceplot(mridge, X="df")


# \donttest{
# bivariate ridge trace plots
plot(mridge, radius=0.25, labels=mridge$df)

pairs(mridge, radius=0.25)


# 3D views
# ellipsoids for Load, Xray & BedDays are nearly 2D
plot3d(mridge, radius=0.2, labels=mridge$df)
# variables in model selected by AIC & BIC
plot3d(mridge, variables=c(2,3,5), radius=0.2, labels=mridge$df)

# plots in PCA/SVD space
mpridge <- pca(mridge)
traceplot(mpridge, X="df")

biplot(mpridge, radius=0.25)

#> Vector scale factor set to  8774.365 
# }