R Under development (unstable) (2024-01-28 r85838 ucrt) -- "Unsuffered Consequences"
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> library(Greg)
Loading required package: Gmisc
Loading required package: Rcpp
Loading required package: htmlTable
Loading required package: forestplot
Loading required package: grid
Loading required package: checkmate
Loading required package: abind
> library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

> 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")
+ }
> 
> proc.time()
   user  system elapsed 
   4.18    0.60    4.73