Prediction using a natural spline fit

Question

I have a fitted a simple natural spline (df = 3) model and I'm trying to predict for some out of sample observations. Using the function predict(), I'm able to get fitted values for in-sample observations but I've not been able to get the predicted value for new observations.

Here is my code:

library(splines)

set.seed(12345)
x <- seq(0, 2, by = 0.01)
y <- rnorm(length(x)) + 2*sin(2*pi*(x-1/4))

# My n.s fit:
fit.temp <- lm(y ~ ns(x, knots = seq(0.01, 2, by = 0.1)))

# Getting fitted values:
fit.temp.values <- predict(fit.temp,interval="prediction", level = 1 - 0.05)

# Plotting the data, the fit, and the 95% CI:
plot(x, y, ylim = c(-6, +6))
lines(x, fit.temp.values[,1], col = "darkred")
lines(x, fit.temp.values[,2], col = "darkblue", lty = 2)
lines(x, fit.temp.values[,3], col = "darkblue", lty = 2)

# Consider the points for which we want to get the predicted values:
x.new <- c(0.275, 0.375, 0.475, 0.575, 1.345)

How can I get the predicted values for x.new?

Thanks very much for your help,

p.s. I searched all related questions on SO and I didn't find the answer.

Answer 1

Create a data frame with a column called x, and pass it as the newdata argument to predict:

predict(fit.temp, newdata=data.frame(x=x.new))

Answer 2

You are sending individual vectors to lm. If you want to see what is going wrong here, then type:

 fit.temp$terms

... and notice that the name of the x-predictor is:

attr(,"term.labels")
[1] "ns(x, knots = seq(0.01, 2, by = 0.1))"

You would need to give predict a list with that as a name for x. Much easier would be to use lm and lm.predict with a dataframe argument so that the predictions could be done with internal re-evaluation of the new values.

 df <- data.frame(x,y)
 # My n.s fit:
 fit.temp <- lm(y ~ ns(x, knots = seq(0.01, 2, by = 0.1)) , data=df)
 predict(fit.temp, newdata=list(x =c(0.275, 0.375, 0.475, 0.575, 1.345) )  )
#        1         2         3         4         5 
#0.9264572 1.6549046 2.0743470 1.9507962 0.8220687 
points(x.new, predict(fit.temp, 
               newdata=list(x =c(0.275, 0.375, 0.475, 0.575, 1.345) )), 
       col="red", cex=2)