tests/testthat/test-stratified_cox.R

In XuemeiDing/survival19: Deal with Stratified Cox Proportional Hazard Model

test_that("results match coxph in survival", {
  set.seed(2019)
  testdata = generate_data(F_pre = 1, gamma = 1)
  beta1 = stratified_cox(testdata$delta, testdata$z, testdata$facility, testdata$time, testdata$num_facility, tol= 1.0e-6)
  require(survival)
  beta2 = coxph(Surv(testdata$time, testdata$delta) ~ testdata$z + strata(testdata$facility))$coef
  expect_equal(as.numeric(beta1), as.vector(beta2))
  set.seed(2020)
  testdata2 = generate_data(order = F)
  beta3 = stratified_cox(testdata2$delta, testdata2$z, testdata2$facility, testdata2$time, testdata2$num_facility, tol= 1.0e-6)
  require(survival)
  beta4 = coxph(Surv(testdata2$time, testdata2$delta) ~ testdata2$z + strata(testdata2$facility))$coef
  expect_equal(as.numeric(beta3), as.vector(beta4))
})