inst/tinytest/test_binreg.R

In kkholst/mets: Analysis of Multivariate Event Times

# binreg simple-icpw versus prodlim
library("tinytest")

test_binreg_cif <- function() {
  data(bmt)
  bmt$time <-  bmt$time + runif(nrow(bmt)) * 0.001
  out <- binreg(Event(time, cause) ~ -1+factor(platelet),
                bmt, time=50, cens.model=~strata(platelet))
  summary(out)
  pp <- predict(out, data.frame(platelet = 0:1, tcell = 0:1))

  cif1 <- cif(Event(time,cause) ~ strata(platelet), bmt)
  cifs <- cbind(cif1$cumhaz[, 1],
                vecAllStrata(cif1$cumhaz[,2],
                             cif1$strata,
                             cif1$nstrata))
  pcif50 <- cpred(cifs, 50)[, 2]

  se.cifs <- cbind(cif1$cumhaz[, 1],
                   vecAllStrata(cif1$se.cumhaz[,2],
                                cif1$strata,
                                cif1$nstrata))
  se.pcif50 <- cpred(se.cifs,50)[, 2]
  ## estimate (same) and standard errors (close)
  expect_true( ((sum(abs(pcif50 - pp[, 1]))) < 0.0001) &
                         (sum(abs(pp[, 2] - cpred(se.cifs, 50)[, 2])) < 0.0002))
}
test_binreg_cif()