inst/examples/addNonlinearity_example.R

In Greg: Regression Helper Functions

library(Greg)
data("melanoma", package = "boot", envir = environment())

library(dplyr)
melanoma <- mutate(melanoma, 
                   status = factor(status,
                                   levels = 1:3,
                                   labels = c("Died from melanoma", 
                                              "Alive", 
                                              "Died from other causes")),
                   ulcer = factor(ulcer,
                                  levels = 0:1,
                                  labels = c("Absent", "Present")),
                   time = time/365.25, # All variables should be in the same time unit
                   sex = factor(sex,
                                levels = 0:1,
                                labels = c("Female", "Male")))

library(survival)
model <- coxph(Surv(time, status == "Died from melanoma") ~ sex + age,
  data = melanoma
)

nl_model <- addNonlinearity(model, "age",
  spline_fn = "pspline",
  verbal = TRUE,
  workers = FALSE
)
# Note that there is no support for nonlinearity in this case