Question

I want to override the default predict.lm function due to a bug:

library(datasets)
# Just a regular linear regression
fit <- lm(mpg~disp+hp+wt+drat, data=mtcars)
termplot(fit, terms=2, se=T)

Gives this error:

Error in predict.lm(model, type = "terms", se.fit = se, terms = terms) : 
  subscript out of bounds

I know where the bug is and I’ve sent an email that awaits approval by the core mailing list but in the meantime I would like to test my own predict.lm function to fix this. I’ve understood that I need to redefine the S3 function for predict but when running this code:

setMethod("predict", "lm", predict.lm2)
getMethod("predict", "lm")

The getMethod returns my new function as expected but the termplot still runs the old function. The methods("predict") shows also that the old predict.lm is still there and I think it might be the call-order or something that I need to adjust. Anyone familiar with how to do this?

Answer 1

@James’s comment suggests to define your own lm2 class,
that extends lm, and to implement predict.lm2.

class(fit) <- c("lm2", class(fit))
predict.lm2 <- function(...) { 
  # The function with your bugfix
  cat("Inside predict.lm2\n")
  predict.lm(...) 
}
termplot(fit, terms=2, se=T)