tests/test-nonlin_4_coxph.R

In Greg: Regression Helper Functions

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

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")),
                   # All variables should be in the same time unit
                   time = time/365.25,
                   sex = factor(sex,
                                levels = 0:1,
                                labels = c("Female", "Male")))

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

library(splines)
nl_model <- addNonlinearity(model, "age", "ns",
  flex_param = 2:7,
  workers = FALSE
)
if (!all.equal(model, nl_model)) {
  stop("Failed check coxph with ns")
}

nl_model <- addNonlinearity(model, "age", "ns",
  flex_param = 2:7, sig_level = .7,
  workers = FALSE
)
if (length(all.equal(model, nl_model)) == 1) {
  stop("Failed check coxph with ns with sensitivity increased")
}

nl_model <- addNonlinearity(model, "age", "pspline",
  flex_param = "Asdasdsadasda",
  workers = FALSE
)
if (!all.equal(model, nl_model)) {
  stop("Failed check coxph with pspline")
}

nl_model <- addNonlinearity(model, "age", "pspline",
  flex_param = "Asdasdsadasda", sig_level = .7,
  workers = FALSE
)
if (length(all.equal(model, nl_model)) == 1) {
  stop("Failed check coxph with pspline with sensitivity increased")
}