Getting the prediction standard error from a natural spline fit

I’m fitting a natural spline fit to some data points. I’d like to estimate the prediction error for the predicted value. In linear regression (I agree that natural spline is also a linear regression with a specific type of design matrix), we know:

ˆβ=(XTX)1XTY assuming var(Y) = σ2I then : var(ˆβ)=(XTX)1σ2

Now consider ˆY=XiTˆβ+ϵi. We can then write:


This is easy to calculate for linear regression. How should I do it with natural spline? I can get the design matrix for natural spline. I can get (XTX)1σ2 but how can I get the rest of it:

Here is an example in R:

x <- c(1:100)
y <- sin(pi*x/50)
epsilon <- rnorm(100, 0, 3)
knots <- c(10, 20, 30, 40, 50, 60, 70, 80, 90)
myFit <- lm(y ~ ns(x, knots = knots))

Now consider x = 32.5 . How can I get the variance for the ˆY corresponding to x = 32.5 ? I know we can use the predict function. however, what I do really want is to get calculate it similar to linear regression by getting the design matrix and multiplying them together.

I really appreciate your help.


You can get the design matrix for a linear model in R using model.matrix():

X <- model.matrix(myFit)
sigma <- summary(myFit)$sigma
var.Yhat <- (diag(X %*% solve(t(X) %*% X) %*% t(X)) + 1) * sigma^2

Or, if you want to get the prediction variance for new values of X, use ns() to transform into the natural spline basis first: <- cbind(1, ns(, knots=knots))
var.Yhat <- (diag( %*% solve(t(X) %*% X) %*% t( + 1) * sigma^2

Source : Link , Question Author : Sam , Answer Author : Michael Culbertson

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