R Under development (unstable) (2024-11-18 r87347 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 
> set.seed(290875)
> 
> ret <- TRUE
> 
> if (require("survival") && require("tram") && require("coin")) {
+ 
+     d <- ovarian
+     d$y <- with(d, Surv(futime, fustat))
+     d$Ry <- with(d, R(y, as.R.ordered = TRUE))
+     d$x <- d$rx
+     tm <- sort(unique(d$futime[d$fustat == 1]))
+ 
+     tol <- 1e-4
+ 
+     ### nonpara ML, unconditional
+     mP0 <- Polr(Ry ~ 1, data = d, method = "cloglog")
+     s1 <- summary(survfit(y ~ 1, data = d), times = tm)$surv
+     s2 <- predict(mP0, newdata = data.frame(1), type = "survivor")
+     ret <- isTRUE(all.equal(s1, s2[-length(s2)], 
+                      check.attributes = FALSE, tol = tol))  &&
+                   cor(resid(mP0), logrank_trafo(d$y)) > .9999 &&
+            isTRUE(all.equal(logLik(mP0, parm = coef(as.mlt(mP0))),
+                             logLik(mP0, parm = log(-log(s1)))))
+ 
+     ### conditional: estimate HR
+     mP1 <- Polr(Ry ~ x, data = d, method = "cloglog")
+     sf <- survdiff(y ~ x, data = d)
+     mc1 <- coxph(y ~ x, data = d)
+ 
+     ### see Survival Analysis: A Practical Approach, 
+     ### Second Edition David Machin, Yin Bun Cheung, Mahesh K.B. Parmar
+     ### Page 12
+     oe <- sf$obs / sf$exp
+     HR <- oe[1] / oe[2]
+ 
+     ### compare: mP1 is nonpara ML, mc1 partial likelihood
+     ### what is HR?
+     #exp(coef(mP1))
+     #exp(-coef(mc1))
+ }
Loading required package: survival
Loading required package: tram
Loading required package: mlt
Loading required package: basefun
Loading required package: variables
Loading required package: mvtnorm
Loading required package: coin

Attaching package: 'coin'

The following object is masked from 'package:variables':

    support

> 
> ret
[1] TRUE
> 
> proc.time()
   user  system elapsed 
   1.95    0.37    2.29