skip_if_not_installed("robustlmm", minimum_version = "3.0.1")
skip_if_not_installed("lme4")
skip_if_not(getRversion() >= "4.1.0")

data(sleepstudy, package = "lme4")

set.seed(123)
sleepstudy$mygrp <- sample(1:5, size = 180, replace = TRUE)
sleepstudy$mysubgrp <- NA
for (i in 1:5) {
  filter_group <- sleepstudy$mygrp == i
  sleepstudy$mysubgrp[filter_group] <-
    sample(1:30,
      size = sum(filter_group),
      replace = TRUE
    )
}

dat <<- sleepstudy

suppressPackageStartupMessages({
  suppressWarnings(suppressMessages(library(lme4, quietly = TRUE, warn.conflicts = FALSE)))
})

suppressMessages({
  m1 <- robustlmm::rlmer(
    Reaction ~ Days + (Days | Subject),
    data = dat,
    rho.sigma.e = robustlmm::psi2propII(robustlmm::smoothPsi, k = 2.28),
    rho.sigma.b = robustlmm::chgDefaults(robustlmm::smoothPsi, k = 5.11, s = 10)
  )

  m2 <- robustlmm::rlmer(
    Reaction ~ Days + (1 | mygrp / mysubgrp) + (1 | Subject),
    data = dat,
    rho.sigma.e = robustlmm::psi2propII(robustlmm::smoothPsi, k = 2.28),
    rho.sigma.b = robustlmm::chgDefaults(robustlmm::smoothPsi, k = 5.11, s = 10)
  )
})

test_that("model_info", {
  expect_true(model_info(m1)$is_linear)
  expect_true(model_info(m2)$is_linear)
})

test_that("find_predictors", {
  expect_identical(
    find_predictors(m1, effects = "all"),
    list(conditional = "Days", random = "Subject")
  )
  expect_identical(
    find_predictors(m1, effects = "all", flatten = TRUE),
    c("Days", "Subject")
  )
  expect_identical(
    find_predictors(m1, effects = "fixed"),
    list(conditional = "Days")
  )
  expect_identical(
    find_predictors(m1, effects = "fixed", flatten = TRUE),
    "Days"
  )
  expect_identical(
    find_predictors(m1, effects = "random"),
    list(random = "Subject")
  )
  expect_identical(
    find_predictors(m1, effects = "random", flatten = TRUE),
    "Subject"
  )
  expect_identical(
    find_predictors(m2, effects = "all"),
    list(
      conditional = "Days",
      random = c("mysubgrp", "mygrp", "Subject")
    )
  )
  expect_identical(
    find_predictors(m2, effects = "all", flatten = TRUE),
    c("Days", "mysubgrp", "mygrp", "Subject")
  )
  expect_identical(
    find_predictors(m2, effects = "fixed"),
    list(conditional = "Days")
  )
  expect_identical(find_predictors(m2, effects = "random"), list(random = c("mysubgrp", "mygrp", "Subject")))
  expect_null(find_predictors(m2, effects = "all", component = "zi"))
  expect_null(find_predictors(m2, effects = "fixed", component = "zi"))
  expect_null(find_predictors(m2, effects = "random", component = "zi"))
})

test_that("find_random", {
  expect_identical(find_random(m1), list(random = "Subject"))
  expect_identical(find_random(m1, flatten = TRUE), "Subject")
  expect_identical(find_random(m2), list(random = c(
    "mysubgrp:mygrp", "mygrp", "Subject"
  )))
  expect_identical(find_random(m2, split_nested = TRUE), list(random = c("mysubgrp", "mygrp", "Subject")))
  expect_identical(
    find_random(m2, flatten = TRUE),
    c("mysubgrp:mygrp", "mygrp", "Subject")
  )
  expect_identical(
    find_random(m2, split_nested = TRUE, flatten = TRUE),
    c("mysubgrp", "mygrp", "Subject")
  )
})

test_that("find_response", {
  expect_identical(find_response(m1), "Reaction")
  expect_identical(find_response(m2), "Reaction")
})

test_that("get_response", {
  expect_identical(get_response(m1), sleepstudy$Reaction)
})

test_that("link_inverse", {
  expect_identical(link_inverse(m1)(0.2), 0.2)
  expect_identical(link_inverse(m2)(0.2), 0.2)
})

test_that("get_data", {
  expect_identical(colnames(get_data(m1)), c("Reaction", "Days", "Subject"))
  expect_identical(colnames(get_data(m1, effects = "all")), c("Reaction", "Days", "Subject"))
  expect_identical(colnames(get_data(m1, effects = "random")), "Subject")
  expect_identical(
    colnames(get_data(m2)),
    c("Reaction", "Days", "mysubgrp", "mygrp", "Subject")
  )
  expect_identical(
    colnames(get_data(m2, effects = "all")),
    c("Reaction", "Days", "mysubgrp", "mygrp", "Subject")
  )
  expect_identical(colnames(get_data(m2, effects = "random")), c("mysubgrp", "mygrp", "Subject"))
})

test_that("find_formula", {
  expect_length(find_formula(m1), 2)
  expect_length(find_formula(m2), 2)
  expect_equal(
    find_formula(m1, component = "conditional"),
    list(
      conditional = as.formula("Reaction ~ Days"),
      random = as.formula("~Days | Subject")
    ),
    ignore_attr = TRUE
  )
  expect_equal(
    find_formula(m2, component = "conditional"),
    list(
      conditional = as.formula("Reaction ~ Days"),
      random = list(
        as.formula("~1 | mysubgrp:mygrp"),
        as.formula("~1 | mygrp"),
        as.formula("~1 | Subject")
      )
    ),
    ignore_attr = TRUE
  )
})

test_that("find_terms", {
  expect_identical(
    find_terms(m1),
    list(
      response = "Reaction",
      conditional = "Days",
      random = c("Days", "Subject")
    )
  )
  expect_identical(
    find_terms(m1, flatten = TRUE),
    c("Reaction", "Days", "Subject")
  )
  expect_identical(
    find_terms(m2),
    list(
      response = "Reaction",
      conditional = "Days",
      random = c("mysubgrp", "mygrp", "Subject")
    )
  )
  expect_identical(
    find_terms(m2, flatten = TRUE),
    c("Reaction", "Days", "mysubgrp", "mygrp", "Subject")
  )
})

test_that("find_variables", {
  expect_identical(
    find_variables(m1),
    list(
      response = "Reaction",
      conditional = "Days",
      random = "Subject"
    )
  )
})

test_that("get_response", {
  expect_identical(get_response(m1), sleepstudy$Reaction)
})

test_that("get_predictors", {
  expect_identical(colnames(get_predictors(m1)), "Days")
  expect_identical(colnames(get_predictors(m2)), "Days")
})

test_that("get_random", {
  expect_identical(colnames(get_random(m1)), "Subject")
  expect_identical(
    colnames(get_random(m2)),
    c("mysubgrp", "mygrp", "Subject")
  )
})

test_that("clean_names", {
  expect_identical(clean_names(m1), c("Reaction", "Days", "Subject"))
  expect_identical(
    clean_names(m2),
    c("Reaction", "Days", "mysubgrp", "mygrp", "Subject")
  )
})

test_that("linkfun", {
  expect_false(is.null(link_function(m1)))
  expect_false(is.null(link_function(m2)))
})

test_that("find_parameters", {
  expect_identical(
    find_parameters(m1),
    list(
      conditional = c("(Intercept)", "Days"),
      random = list(Subject = c("(Intercept)", "Days"))
    )
  )
  expect_identical(nrow(get_parameters(m1)), 2L)
  expect_identical(get_parameters(m1)$Parameter, c("(Intercept)", "Days"))

  expect_identical(
    find_parameters(m2),
    list(
      conditional = c("(Intercept)", "Days"),
      random = list(
        `mysubgrp:mygrp` = "(Intercept)",
        Subject = "(Intercept)",
        mygrp = "(Intercept)"
      )
    )
  )

  expect_identical(nrow(get_parameters(m2)), 2L)
  expect_identical(get_parameters(m2)$Parameter, c("(Intercept)", "Days"))
  expect_named(
    get_parameters(m2, effects = "random"),
    c("mysubgrp:mygrp", "Subject", "mygrp")
  )
})

test_that("is_multivariate", {
  expect_false(is_multivariate(m1))
  expect_false(is_multivariate(m2))
})

test_that("get_variance", {
  skip_on_cran()

  expect_equal(
    get_variance(m1),
    list(
      var.fixed = 944.68388146469, var.random = 1911.1173962696,
      var.residual = 399.07090932584, var.distribution = 399.07090932584,
      var.dispersion = 0, var.intercept = c(Subject = 782.758817383975),
      var.slope = c(Subject.Days = 41.8070895953001),
      cor.slope_intercept = c(Subject = -0.0387835013909591)
    ),
    tolerance = 1e-3
  )

  expect_equal(
    get_variance(m2),
    list(
      var.fixed = 914.841369705921, var.random = 1406.78220075798,
      var.residual = 809.318117542254, var.distribution = 809.318117542254,
      var.dispersion = 0,
      var.intercept = c(`mysubgrp:mygrp` = 0, Subject = 1390.66848960835, mygrp = 16.1137111496379)
    ),
    tolerance = 1e-3
  )
})

test_that("find_algorithm", {
  expect_identical(
    find_algorithm(m1),
    list(algorithm = "REML", optimizer = "rlmer.fit.DAS.nondiag")
  )
})

test_that("find_random_slopes", {
  expect_identical(find_random_slopes(m1), list(random = "Days"))
  expect_null(find_random_slopes(m2))
})

test_that("find_statistic", {
  expect_identical(find_statistic(m1), "t-statistic")
  expect_identical(find_statistic(m2), "t-statistic")
})