Get fitted effects from a model with an rcs term

Question

I would like to get fitted values from a linear model that includes a restricted cubic spline term fit via rms::rcs(), to pass into an effects plot. The issue is that the package I typically use to get fitted values, effects, throws an error when I try to pass a model with an rcs term.

Here's a minimal reprex:

library(rms)
library(effects)
mod <- lm(Sepal.Length ~ rcs(Sepal.Width, 3), iris)
Effect("Sepal.Width", mod)
##Error in rcspline.eval(x, nk = nknots, inclx = TRUE, pc = pc, fractied = fractied) : knots not specified, and < 6 non-missing observations

I have tried debugging this error, but I can't arrive at how rcspline.eval() got 6+ NAs in x and non-specified nknots. How do I deal with this error? Alternatively, is there another package out there that can get fitted effects from a model with an rcs term?

Answer 1

Users of the rms environment will need to use the specialized functions that support its activities:

 library(rms)
 ddist <- datadist(iris)  # need both datadist and options 
 options(datadist='ddist')
 mod <- ols(Sepal.Length ~ rcs(Sepal.Width, 3), iris)  # need ols rather than lm
 plot( Predict(mod, Sepal.Width))  # Predict can be done in 2 or 3 dimension
        # gives a lattice output