source("http://192.38.117.59/~linearpredictors/datafiles/readPbc3.R")
library(survival)

model1 <- coxph(Surv(followup, status != 0) ~ tment + alb + log(bili) + log(alkph) +
                log(asptr) + age,
                data = pbc3)

pbc3$event <- ifelse(pbc3$status != 0, 1, 0)

eventtimes <- survfit(model1)$time

## we need to record the status for each patient at each event time,
## such that the covariate which includes time, has an observation for
## each patient and is used for the estimation of the effect.
pbc3.split <- survSplit(pbc3,         
                        cut = eventtimes,
                        start = "start",
                        end = "followup",
                        event = "event",
                        id = "ptno")

pbc3.split$end <- pbc3.split$followup

## note that the extended data set still fits model1 correctly
coxph(Surv(start, end, event) ~ tment + alb + log(bili) + log(alkph) +
                log(asptr) + age,
                data = pbc3.split)

## now including interactions with functions of time. 

coxph(Surv(start, end, event) ~ tment + alb + log(bili) + log(alkph) +
                log(asptr) + age + ifelse(tment == "1", log(end), 0),
                data = pbc3.split)

coxph(Surv(start, end, event) ~ tment + alb + log(bili) + log(alkph) +
                log(asptr) + age + ifelse(tment == "1", end, 0),
                data = pbc3.split)

coxph(Surv(start, end, event) ~ tment + alb + log(bili) + log(alkph) +
                log(asptr) + age + I(log(alb)*log(end)),
                data = pbc3.split)

coxph(Surv(start, end, event) ~ tment + alb + log(bili) + log(alkph) +
                log(asptr) + age + I(log(bili)*log(end)),
                data = pbc3.split)

coxph(Surv(start, end, event) ~ tment + alb + log(bili) + log(alkph) +
                log(asptr) + age + I(log(bili)*end),
                data = pbc3.split)

coxph(Surv(start, end, event) ~ tment + alb + log(bili) + log(alkph) +
                log(asptr) + age + I(log(alkph)*log(end)),
                data = pbc3.split)

coxph(Surv(start, end, event) ~ tment + alb + log(bili) + log(alkph) +
                log(asptr) + age + I(log(asptr)*log(end)),
                data = pbc3.split)

coxph(Surv(start, end, event) ~ tment + alb + log(bili) + log(alkph) +
                log(asptr) + age + I(age*log(end)),
                data = pbc3.split)