tests/testthat/test-brokenstick_edge.R

In stefvanbuuren/brokenstick: Broken Stick Model for Irregular Longitudinal Data

knots <- seq(0, 2, by = 0.25)
boundary <- c(0, 3)

# low n - method kr - EDGE cases
test_that("brokenstick handles low number of cases - 1", {
  expect_error(
    brokenstick(hgt_z ~ age | id, smocc_200[1:10, ],
      knots = knots, boundary = boundary,
      method = "kr", seed = 1L
    ),
    "`Sigma` is symmetric but not positive"
  )
})

# OUTCOMMENTED because this did NOT error on LINUX (R-develop) but
# did on Window & Mac
# test_that("brokenstick handles low number of cases - 2", {
#   expect_error(
#     brokenstick(hgt_z ~ age | id, smocc_200[1:95, ],
#       knots = knots, boundary = boundary,
#       method = "kr", seed = 2L
#     ),
#     "`Sigma` is symmetric but not positive"
#   )
# })

test_that("brokenstick handles low number of cases - 3", {
  expect_error(
    brokenstick(hgt_z ~ age | id, smocc_200[1:100, ],
      knots = knots, boundary = boundary,
      method = "kr", seed = 3L
    ),
    "`Sigma` is symmetric but not positive"
  )
})

test_that("brokenstick handles low number of cases - 4", {
  expect_silent(brokenstick(hgt_z ~ age | id, smocc_200[1:200, ],
    knots = knots, boundary = boundary,
    method = "kr", seed = 4L
  ))
})


# # low n - method lmer - EDGE cases
test_that("brokenstick handles low number of cases - 1", {
  expect_error(brokenstick(hgt_z ~ age | id, smocc_200[1:10, ],
    knots = knots, boundary = boundary,
    method = "lmer"
  ),
  regexp = "grouping factors must have > 1 sampled level",
  fixed = TRUE
  )
})

test_that("brokenstick handles low number of cases - 2", {
  expect_warning(brokenstick(hgt_z ~ age | id, smocc_200[1:11, ],
    knots = knots, boundary = boundary,
    method = "lmer"
  ),
  regexp = "number of observations (=11) <= number of random effects (=20)",
  fixed = TRUE
  )
})

test_that("brokenstick handles low number of cases - 3", {
  expect_warning(brokenstick(hgt_z ~ age | id, smocc_200[1:30, ],
    knots = knots, boundary = boundary,
    method = "lmer"
  ),
  regexp = "number of observations (=30) <= number of random effects (=40)",
  fixed = TRUE
  )
})

test_that("brokenstick handles low number of cases - 4", {
  expect_warning(brokenstick(hgt_z ~ age | id, smocc_200[1:200, ],
    knots = knots, boundary = boundary,
    method = "lmer"
  ),
  regexp = "number of observations (=199) <= number of random effects (=210)",
  fixed = TRUE
  )
})

test_that("warns that right boundary is lower than max(age)", {
  expect_warning(brokenstick(hgt_z ~ age | id, smocc_200,
    knots = 1:2, boundary = c(0, 1),
    warn_splines = TRUE
  ),
  regexp = "some 'x' values beyond boundary knots may cause ill-conditioned bases",
  fixed = TRUE
  )
})