Outcome model for time-to-event end-points (proportional hazards)

Outcome model for time-to-event end-points (proportional hazards)

Usage

outcome_phreg(
  data,
  lp = NULL,
  par = NULL,
  outcome.name = c("time", "status"),
  remove = c("id", "num"),
  model = NULL,
  cens.model = NULL,
  cens.lp = NULL,
  cens.par = NULL,
  ...
)

Arguments

data

(data.table) Covariate data, usually the output of the covariate model of a Trial object.

lp

linear predictor (formula or function)

par

optional list of model parameter

outcome.name

names of outcome (time and censoring status)

remove

Variables that will be removed from input data (if formula is not specified).

model

optional mets::phreg object

cens.model

optional model for censoring mechanism

cens.lp

censoring linear predictor argument (formula or function)

cens.par

list of censoring model parameters

...

Additional arguments to outcome_lp

Value

function (random generator)

See also

outcome_count outcome_lp outcome_binary outcome_continuous

Author

Klaus Kähler Holst

Examples

if (FALSE) { # \dontrun{
outcome_phreg <- carts:::outcome_phreg
library("survival")
data(pbc, package = "survival")
pbc0 <- na.omit(pbc) |>
  transform(trt = factor(trt, labels = c("Active", "Placebo")) |>
    relevel(ref = "Placebo"))

fit1 <- mets::phreg(Surv(time, status > 0) ~ age + sex * trt, data = pbc0)

covar <- covar_bootstrap(pbc0, subset = c("age", "sex")) %join%
  function(n, ...) data.frame(trt = sample(pbc0$trt, n, replace = TRUE))

outcome <- setargs(
  outcome_phreg,
  model = fit1,
  par = list("trtActive" = 0)
)

xx <- covar(5e3)
pbc1 <- outcome(xx) |> cbind(xx)
mets::phreg(formula(fit1), data = pbc1)


## Introducing additional interactions
fit2 <- mets::phreg(Surv(time, status > 0) ~ age + sex + trt, data = pbc0)

outcome <- setallargs(
  outcome_phreg,
  model = fit2,
  par = list("trtActive" = -.5, "age:trtActive" = 0),
  treatment = "trt",
  default.parameter = -0.2
)

xx <- covar(1e4)
attr(outcome(xx), "par")
pbc1 <- outcome(xx) |> cbind(xx)
mets::phreg(Surv(time, status) ~ (age + sex) * trt, pbc1)
rm(pbc1, xx)
} # }