# VIF for generalized linear model

Is the variance inflation factor useful for GLM models. Below example shows OLS is showing VIF>5, but GLM lower. GLM shows instability in the coefficients between train and test set.

> library(MASS)
> set.seed(1)
> mu <- rep(0,4)
> Sigma <- matrix(.9, nrow=4, ncol=4)
> diag(Sigma) <- 1
> rawvars <- mvrnorm(n=1000, mu=mu, Sigma=Sigma)
> d  <- as.ordered( as.numeric(rawvars[,1]>0.5) )
> d[1:200]  <- 1
> #
> df  <- data.frame(rawvars, d)
>
> ind  <- sample(1:nrow(df), 500)
> train  <- df[ind,]
> test  <- df[-ind,]
>
> fit.lm = lm(X4~X1+X2+X3, train)
>
> fit.lm.test = lm(X4~X1+X2+X3, test)
> summary(fit.lm)

Call:
lm(formula = X4 ~ X1 + X2 + X3, data = train)

Residuals:
Min       1Q   Median       3Q      Max
-1.16108 -0.24883  0.01356  0.25803  1.43455

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept)  0.02638    0.01698   1.554    0.121
X1           0.30456    0.04243   7.178  2.6e-12 ***
X2           0.33006    0.04285   7.703  7.3e-14 ***
X3           0.33138    0.04477   7.402  5.8e-13 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.3788 on 496 degrees of freedom
Multiple R-squared:  0.8553,    Adjusted R-squared:  0.8544
F-statistic: 977.1 on 3 and 496 DF,  p-value: < 2.2e-16

> summary(fit.lm.test)

Call:
lm(formula = X4 ~ X1 + X2 + X3, data = test)

Residuals:
Min       1Q   Median       3Q      Max
-1.06717 -0.25019  0.00594  0.26794  1.14282

Coefficients:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -0.02660    0.01669  -1.594    0.112
X1           0.33038    0.04216   7.836 2.85e-14 ***
X2           0.35636    0.04044   8.811  < 2e-16 ***
X3           0.27625    0.04125   6.697 5.78e-11 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.3727 on 496 degrees of freedom
Multiple R-squared:  0.8806,    Adjusted R-squared:  0.8799
F-statistic:  1219 on 3 and 496 DF,  p-value: < 2.2e-16

>
> car::vif(fit.lm)
X1       X2       X3
6.260418 6.329868 6.480232
> car::vif(fit.lm.test)
X1       X2       X3
7.252877 7.097506 7.138707
>
> fit.glm  <- glm(d~X1+X2+X3, train,            family = binomial(link="probit"))
> fit.glm.test  <- glm(d~X1+X2+X3, test,          family = binomial(link="probit"))
> summary(fit.glm)

Call:
glm(formula = d ~ X1 + X2 + X3, family = binomial(link = "probit"),
data = train)

Deviance Residuals:
Min       1Q   Median       3Q      Max
-1.7122  -0.8662  -0.2447   0.7068   3.7270

Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.08018    0.06551  -1.224   0.2210
X1           0.78783    0.17028   4.627 3.71e-06 ***
X2           0.31422    0.16544   1.899   0.0575 .
X3          -0.03526    0.17270  -0.204   0.8382
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for binomial family taken to be 1)

Null deviance: 689.62  on 499  degrees of freedom
Residual deviance: 475.49  on 496  degrees of freedom
AIC: 483.49

Number of Fisher Scoring iterations: 5

> summary(fit.glm.test)

Call:
glm(formula = d ~ X1 + X2 + X3, family = binomial(link = "probit"),
data = test)

Deviance Residuals:
Min       1Q   Median       3Q      Max
-1.4552  -0.9145  -0.3013   0.7889   2.8701

Coefficients:
Estimate Std. Error z value Pr(>|z|)
(Intercept) -0.10849    0.06398  -1.696   0.0899 .
X1           0.77867    0.16649   4.677 2.91e-06 ***
X2           0.01052    0.15355   0.068   0.9454
X3           0.09631    0.15826   0.609   0.5428
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

(Dispersion parameter for binomial family taken to be 1)

Null deviance: 690.83  on 499  degrees of freedom
Residual deviance: 505.10  on 496  degrees of freedom
AIC: 513.1

Number of Fisher Scoring iterations: 5

>
> car::vif(fit.glm)
X1       X2       X3
3.826678 3.734214 4.022859
> car::vif(fit.glm.test)
X1       X2       X3
4.633032 4.617873 4.717568

• Why do you say X3 is definitely showing instability? BTW illustrative code is useful, but considerably less so without explanation or comments. Feb 2 '15 at 17:46
• VIF is a function of the independent variables only, and so ought to have the same value for any dependent variable and any GLM based on those independent variables (although its interpretation in terms of standard errors of coefficients may vary). See the Wikipedia article for a description. What, then, is your question? What do you mean by "instability"? In what sense do you believe it "is not possible to understand the multicollinearity from VIF"?
– whuber
Feb 2 '15 at 20:25
• @whuber I read the page again. Are the steps of VIF calculation same regardless of the model. If that was the case, I would think I should get same for lm vs glm numbers on above example. GLM VIF numbers seem to be a little bit muted
Feb 2 '15 at 20:47
• You are correct (+1). car::vif is computing something called a generalized variance inflation factor, as proposed in a 1992 JASA article referenced at inside-r.org/packages/cran/car/docs/vif.
– whuber
Feb 2 '15 at 20:57

If we look at the function

library(car)
getS3method("vif", "default")
#R function (mod, ...)
#R {
#R     v <- vcov(mod)
#R     assign <- attr(model.matrix(mod), "assign")
#R     [...]
#R     terms <- labels(terms(mod))
#R     n.terms <- length(terms)
#R     [...]
#R     R <- cov2cor(v)
#R     detR <- det(R)
#R     result <- matrix(0, n.terms, 3)
#R     rownames(result) <- terms
#R     colnames(result) <- c("GVIF", "Df", "GVIF^(1/(2*Df))")
#R     for (term in 1:n.terms) {
#R      subs <- which(assign == term)
#R      result[term, 1] <- det(as.matrix(R[subs, subs])) * det(as.matrix(R[-subs,
#R          -subs]))/detR
#R      result[term, 2] <- length(subs)
#R     }
#R     if (all(result[, 2] == 1))
#R      result <- result[, 1]
#R     else result[, 3] <- result[, 1]^(1/(2 * result[, 2]))
#R     result
#R }


then it calls vcov which will differ for a glm then lm. In the glm case it depends on the outcome. Thus, you get the different results. All the above is consistent with the 1992 article

Fox, J., & Monette, G. (1992). Generalized collinearity diagnostics. Journal of the American Statistical Association, 87(417), 178-183.

in the linear model case. See particularly Equation (10) and

#R      result[term, 1] <- det(as.matrix(R[subs, subs])) * det(as.matrix(R[-subs,
#R          -subs]))/detR


To the question

Is the variance inflation factor useful for GLM models

Then I gather that the results in the 1992 article may still hold asymptotically. However, some pen and paper is likely need to justify this claim and I am may be wrong.