R Under development (unstable) (2023-12-17 r85691 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2023 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.

> 
> library("tram")
Loading required package: mlt
Loading required package: basefun
Loading required package: variables
Loading required package: mvtnorm
> library("survival")
> library("trtf")
Loading required package: partykit
Loading required package: grid

Attaching package: 'grid'

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

    unit

Loading required package: libcoin
> 
> ### Windows diffs...
> options(digits = 3)
> 
> chk <- function(x, y, tol = 1e-1) 
+     stopifnot(isTRUE(all.equal(x, y, check.attributes = FALSE, tol = tol)))
> 
> data("GBSG2", package = "TH.data")
> 
> cmod <- coxph(Surv(time, cens) ~ progrec + pnodes + strata(horTh, tgrade),
+                data = GBSG2)
> Cmod <- Coxph(Surv(time, cens) | 0 + horTh:tgrade ~ progrec + pnodes, 
+               data = GBSG2)
> 
> chk(coef(cmod), coef(Cmod))
> chk(diag(vcov(cmod)), diag(vcov(Cmod)))
> 
> Cmod_lf <- Coxph(Surv(time, cens) | 0 + horTh:tgrade ~ progrec + pnodes, 
+                 data = GBSG2, log_first = TRUE)
> 
> chk(coef(cmod), coef(Cmod_lf))
> chk(diag(vcov(cmod)), diag(vcov(Cmod_lf)))
> 
> cmod_2 <- coxph(Surv(time, cens) ~ ., data = GBSG2)
> Cmod_2 <- Coxph(Surv(time, cens) ~ ., data = GBSG2)
> 
> chk(coef(cmod_2), coef(Cmod_2))
> chk(diag(vcov(cmod_2)), diag(vcov(Cmod_2)))
> 
> cmod <- Coxph(Surv(time, cens) ~ horTh, data = GBSG2)
> (tmod <- trafotree(cmod, formula = Surv(time, cens) ~ horTh | ., data = GBSG2))

Model formula:
Surv(time, cens) ~ horTh + (age + menostat + tsize + tgrade + 
    pnodes + progrec + estrec)

Fitted party:
[1] root
|   [2] pnodes <= 4: 2372 (n = 433)
|   [3] pnodes > 4
|   |   [4] tgrade <= II: 1146 (n = 179)
|   |   [5] tgrade > II: 600 (n = 74)

Number of inner nodes:    2
Number of terminal nodes: 3
> logLik(tmod)
'log Lik.' -2579 (df=24)
> 
> ### check residuals
> library("sandwich")
> GBSG2$y <- with(GBSG2, Surv(time, cens))
> ORDER <- 12
> ### indirect computation: score wrt to int
> GBSG2$int <- 1
> m <- Coxph(y ~ int, data = GBSG2, fixed = c("int" = 0), 
+            LRtest = FALSE, order = ORDER)
> m1 <- mlt(m$model, data = GBSG2, dofit = FALSE)
> coef(m1) <- coef(as.mlt(m))
> LR1 <- estfun(m1)[, length(coef(m1))]
> 
> ### direct computation
> m2 <- Coxph(y ~ 1, data = GBSG2, 
+             LRtest = FALSE, order = ORDER)
> LR2 <- resid(as.mlt(m2))
> 
> chk(LR1, LR2)
> 
> ## interval-censoring
> load(system.file("rda", "Primary_endpoint_data.rda", package = "TH.data"))
> 
> ## [tram] Parametric distribution-free PH model (interval censoring)
> mci <- Coxph(iDFS ~ randarm, data = CAOsurv, log_first = TRUE)
> logLik(mci)
'log Lik.' -2256 (df=8)
> 
> proc.time()
   user  system elapsed 
   11.1     1.9    13.0