\[ \newcommand{\Expect}[1]{\mathbb{E}\left[ #1 \right]} \]

The general problem

• You have a parametric regression model for your data
  • e.g., linear with such-and-such variables
• You are worried that it might be misspecified, that the true \(\mu(x)\) isn’t in the model
• Now that we know nonparametric regression, we can test this

First case: linear specification is wrong

# Make up sample data
x <- sort(runif(300, 0, 3)) # Sorting simplifies plotting later
# Impose true regression function $\log{(x+1)} +$ Gaussian noise:
yg <- log(x+1) + rnorm(length(x), 0, 0.15)
# Bind into a data frame:
gframe <- data.frame(x=x, y=yg)

What this looks like

Plot it, plus the true regression curve

plot(y~x, data=gframe, xlab="x", ylab="y", pch=16, cex=0.5)
curve(log(1+x), col="grey", add=TRUE, lwd=4)

What linear fit do we get?

Fit the linear model

glinfit <- lm(y~x, data=gframe)
print(summary(glinfit), signif.stars=FALSE, digits=2)

## 
## Call:
## lm(formula = y ~ x, data = gframe)
## 
## Residuals:
##    Min     1Q Median     3Q    Max 
## -0.571 -0.098  0.011  0.105  0.401 
## 
## Coefficients:
##             Estimate Std. Error t value Pr(>|t|)
## (Intercept)    0.228      0.018      13   <2e-16
## x              0.428      0.011      40   <2e-16
## 
## Residual standard error: 0.16 on 298 degrees of freedom
## Multiple R-squared:  0.84,   Adjusted R-squared:  0.84 
## F-statistic: 1.6e+03 on 1 and 298 DF,  p-value: <2e-16

(N.B.: everything is crazily significant, but the linear model is wrong.)

MSE of linear model, in-sample: 0.0251.

We’ll need to do that a lot, so make it a function:

(mse.residuals <- function(model) { mean(residuals(model)^2) })

## function(model) { mean(residuals(model)^2) }

• OFFLINE: Write comments giving the inputs and outputs of the function ms.residuals
• OFFLINE: Check that the function works (how?)

Fit the non-parametric alternative; use splines as implemented in gam():

library(mgcv)

gnpr <- gam(y~s(x),data=gframe)

Add the fitted values from the spline to the plot:

plot(x,yg,xlab="x",ylab="y")
curve(log(1+x),col="grey",add=TRUE,lwd=4)
abline(glinfit, lwd=4)
lines(x,fitted(gnpr),col="blue",lwd=4)
legend("bottomright", legend=c("Truth", "Linear", "Spline"),
       col=c("grey", "black", "blue"), lwd=4)

Calculate the difference in MSEs:

(D.hat <- mse.residuals(glinfit) - mse.residuals(gnpr))

## [1] 0.003589289

• OFFLINE: Why do we believe this code works?

How do we test the linear model?

• \(H_0\): \(\mu(x)\) is a linear function vs. \(H_A\): \(\mu(x)\) is not linear
• Test statistic: Difference in MSEs \(=D\)
  • If the linear model is right, it will predict at least as well as a non-parametric model
  • If the linear model is wrong, eventually the non-parametric model will beat it
• Need the sampling distribution of \(D\) under the null hypothesis
  • Need to simulate the linear model
  • And need to calculate \(D\) over and over

Simulate the parametric model

Simulate from the parametric model, assuming Gaussian noise

sim.lm <- function(linfit, test.x) {
  n <- length(test.x)
  sim.frame <- data.frame(x=test.x)
  sigma <- sqrt(mse.residuals(linfit))  # There are other ways to get sigma
  y.sim <- predict(linfit,newdata=sim.frame)
  y.sim <- y.sim + rnorm(n,0,sigma)
  sim.frame <- data.frame(sim.frame,y=y.sim)
  return(sim.frame)
}

• OFFLINE: Write comments describing input and output of the sim.lm function
• OFFLINE: How can we check that sim.lm is working?
• OFFLINE: How can we switch to non-Gaussian noise?

Calculate the test statistic

Calculate difference in MSEs between parametric and nonparametric models on a data frame:

calc.D <- function(df) {
  MSE.p <- mse.residuals(lm(y~x,data=df))
  MSE.np <- mse.residuals(gam(y~s(x),data=df))
  return(MSE.p - MSE.np)
}

• OFFLINE: Comments once again (with feeling this time)
• OFFLINE: Check that this function works properly (how?)

Put the pieces together

Calculate the MSE difference on one simulation run:

calc.D(sim.lm(glinfit,x))

## [1] 0.0001258959

Calculate the MSE difference on 200 simulation runs, so we get a sample from the null hypothesis:

null.samples.D <- replicate(200,calc.D(sim.lm(glinfit,x)))

How often does the simulation produce gaps bigger than what we really saw?

mean(null.samples.D >= D.hat)

## [1] 0

Look at the distribution

Plot histogram of the sampling distribution, and the observed value:

hist(null.samples.D,n=31,xlim=c(min(null.samples.D),1.2*D.hat),probability=TRUE,
     main="Distribution of D under the null model",
     xlab="D")
abline(v=D.hat, col="red")

Second case: linear model is properly specified

Deliberately left uncommented so that you can explore

y2 <- 0.2+0.5*x + rnorm(length(x),0,0.15)
  # Why don't I have to make up x values again?
y2.frame <- data.frame(x=x,y=y2)
plot(x,y2,xlab="x",ylab="y",pch=16)
abline(0.2,0.5,col="grey",lwd=4)

y2.fit <- lm(y~x,data=y2.frame)
null.samples.D.y2 <- replicate(200,calc.D(sim.lm(y2.fit,x)))
(D.hat2 <- calc.D(y2.frame))

## [1] 7.64804e-11

hist(null.samples.D.y2,n=31,probability=TRUE, main="Distribution of D when the linear model is right", xlab="D")
abline(v=D.hat2, col="red")

mean(null.samples.D.y2 >= D.hat2)

## [1] 0.42

Extensions/lessons

• Don’t need to guess at specific nonlinearities; let the smoother figure it out
• Extends to testing a linear model with multiple predictors easily
  • Choice of whether the alternative then is an additive model vs. a general nonparametric regression
  • Additive: more power to detect additive nonlinearities, can easily miss nonlinear interactions
  • General model: sensitive to more mis-specifications but less power over-all (curse of dimensionality again)
• Nothing special about linear models — the same idea works for testing any parametric regression model

Another approach, based on residuals

\[ Y = \mu(X) + \epsilon, ~ \Expect{\epsilon|X} = 0 \]

• \(\Rightarrow\) if we’ve got the right model, \(\Expect{Y-\mu(X)|X=x} = 0\) for all \(x\)
• \(\Rightarrow\) smooth the residuals and see if we get (close to) 0

par(mfrow=c(1,2))
plot(gam(residuals(glinfit) ~ s(x)),residuals=TRUE,
  lwd=4,ylab="Residuals of the linear model", main="Reality nonlinear")
abline(h=0,col="grey")
plot(gam(residuals(y2.fit) ~ s(x)), residuals=TRUE,
     lwd=4, ylab="Residuals of the linear model", main="Reality linear")
abline(h=0,col="grey")

Smoothing residuals, cont’d

• We’d need to calculate how far the smoothed-residuals curve is from 0
  • Once common choice is the \(L_2\) norm, \(\|r\|^2_2 \equiv \int{r^2(x) dx}\), or \(\int{r^2(x) f(x) dx}\) to weight by the pdf \(f(x)\)
  • Could approximate the weighted version by \(\frac{1}{n}\sum_{i=1}^{n}{r^2(x_i)}\) (why?)
• Then simulate to get a null distribution for that test statistic

Backup: Interactions in gam()

• Can extend the additive model to include interaction terms: \[ Y = \alpha + \sum_{j=1}^{p}{f_j(x_j)} + \sum_{j=1}^{p}{\sum_{k=j+1}^{p}{f_{jk}(x_j, x_k)}} + \epsilon \]
• Estimate \(f_{jk}\) by taking partial residuals and doing a 2D smooth against \(x_j\) and \(x_k\)
• How do we do this in R?
  • s(xj, xk) fits a 2D (“thin plate”) spline, good if xj and xk are on the same scale
  • te(xj, xk) fits a “tensor-product” spline, good if xj and xk are measured on different scales
• When do you want interactions?
  • When it makes sense (location interacts latitude and longitude)
  • Diagonstic: scatter-plot residuals vs. xj and xk, look for patterns
• Reading: textbook, section 8.5

Convergence when we add interactions to a GAM

• Convergence rate for a \(k\)-dimensional smoother is \(O(n^{-4/(4+k)})\)
• MSE of true regression function \(\mu\) is \(\sigma^2\)
• For the additive model (w/ no interactions), \[ MSE = \sigma^2 + (\text{approximation bias of best additive model})^2 + O(pn^{-4/5}) \]
• For the model with all two-way interactions, \[ MSE = \sigma^2 + (\text{approximation bias of best two-way model})^2 + O(p^2 n^{-4/6}) \]
  • There are \({p \choose 2} = O(p^2)\) possible interactions, each converging at rate \(O(n^{-4/6})\), and these dominate the \(O(n^{-4/5})\) of the additive terms
• For the model with all \(k\)-way interactions, \[ MSE = \sigma^2 + (\text{approximation bias})^2 + O\left({p \choose k} n^{-4/(4+k)}\right) \]