tests/testthat/test-boot.R

In graemeleehickey/joineRML: Joint Modelling of Multivariate Longitudinal Data and Time-to-Event Outcomes

library(joineRML)
context("Bootstrap")

test_that("bootstrap MV models", {
  skip_on_cran()
  skip_on_os("mac")
  # load data + fit model
  data(heart.valve)
  hvd <- heart.valve[!is.na(heart.valve$log.grad) & !is.na(heart.valve$log.lvmi), ]
  set.seed(12345)
  fit <- mjoint(
    formLongFixed = list("grad" = log.grad ~ time + sex + hs,
                         "lvmi" = log.lvmi ~ time + sex),
    formLongRandom = list("grad" = ~ 1 | num,
                          "lvmi" = ~ time | num),
    formSurv = Surv(fuyrs, status) ~ age,
    data = list(hvd, hvd),
    inits = list("gamma" = c(0.11, 1.51, 0.80)),
    timeVar = "time",
    control = list(convCrit = "abs", tol0 = 0.1, tol.em = 1e-02,
                   burnin = 40, mcmaxIter = 200),
    verbose = FALSE)
  set.seed(1)
  fit.boot1 <- bootSE(fit, nboot = 1, verbose = TRUE)
  set.seed(1)
  fit.boot2 <- bootSE(fit, nboot = 1, ncores = 1)
  # tests
  expect_is(fit.boot1, "bootSE")
  expect_is(fit.boot2, "bootSE")
  expect_output(str(fit.boot1), "List of 11")
  expect_output(print(fit.boot1))
  expect_is(summary(fit, bootSE = fit.boot1), "summary.mjoint")
  expect_output(print(summary(fit.boot1, bootSE = fit.boot)))
  expect_output(str(summary(fit, bootSE = fit.boot1)), "List of 22")
  expect_equal(summary(fit, bootSE = fit.boot1)$se.type, "boot")
  expect_equal(dim(confint(fit, bootSE = fit.boot1)), c(10, 2))
  expect_equal(dim(confint(fit, parm = "Longitudinal", bootSE = fit.boot1)), c(7, 2))
  expect_equal(dim(confint(fit, parm = "Event", bootSE = fit.boot1)), c(3, 2))
})


test_that("non-convergence", {
  skip_on_cran()
  skip_on_os("mac")
  # load data + fit model
  data(pbc2)
  pbc2$log.b <- log(pbc2$serBilir)
  fit <- mjoint(
    formLongFixed = list("log.bil" = log.b ~ year),
    formLongRandom = list("log.bil" = ~ year | id),
    formSurv = Surv(years, status2) ~ age,
    data = pbc2,
    timeVar = "year",
    control = list(convCrit = "abs", tol0 = 1e-3,
                   burnin = 5, mcmaxIter = 10),
    verbose = FALSE)
  set.seed(1)
  # tests
  expect_error(bootSE(fit, nboot = 1, progress = FALSE),
               "Cannot estimate SEs: fewer than 10% of bootstrap models converged.")
})


test_that("univariate intercept only + non-MLE inits", {
  skip_on_cran()
  skip_on_appveyor()
  skip_on_os("mac")
  # load data + fit model
  data(pbc2)
  pbc2$log.b <- log(pbc2$serBilir)
  fit <- mjoint(
    formLongFixed = list("log.bil" = log.b ~ year),
    formLongRandom = list("log.bil" = ~ 1 | id),
    formSurv = Surv(years, status2) ~ age,
    data = pbc2,
    timeVar = "year",
    control = list(convCrit = "abs", tol0 = 0.05, burnin = 100),
    verbose = FALSE)
  set.seed(12345)
  fit.boot <- bootSE(fit, nboot = 1,
                     progress = FALSE,
                     use.mle = FALSE,
                     control = list(convCrit = "abs", tol0 = 0.05, gammaOpt = "GN"))
  # tests
  expect_is(fit.boot, "bootSE")
  expect_warning(bootSE(fit, control = list("fake" = TRUE), nboot = 1),
                 "Unknown arguments passed to 'control': fake")
})