skip_if_offline()
skip_if_not(getRversion() >= "4.4.0")
suppressWarnings(skip_if_not_installed("glmmTMB"))
suppressWarnings(skip_if_not_installed("geoR"))
skip_if_not_installed("TMB")

data(ca20, package = "geoR")
d <- data.frame(
  x = ca20$coords[, 1],
  y = ca20$coords[, 2],
  calcium = ca20$data,
  elevation = ca20$covariate[, 1],
  region = factor(ca20$covariate[, 2]),
  pos = glmmTMB::numFactor(scale(ca20$coords[, 1]), scale(ca20$coords[, 2])),
  ID = factor(rep(1, length(ca20$coords[, 1])))
)
dat <<- d

m1 <- download_model("glmmTMB_spatial_1")
skip_if(is.null(m1))

test_that("find_weights", {
  expect_null(find_weights(m1))
})

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

test_that("clean_names", {
  expect_identical(clean_names(m1), c("calcium", "elevation", "region", "pos", "ID"))
})

test_that("find_predictors", {
  expect_identical(
    find_predictors(m1, effects = "all"),
    list(conditional = c("elevation", "region"), random = c("pos", "ID"))
  )
  expect_identical(
    find_predictors(m1, effects = "all", flatten = TRUE),
    c("elevation", "region", "pos", "ID")
  )

  expect_identical(
    find_predictors(m1, effects = "random"),
    list(random = "ID")
  )
  expect_identical(find_predictors(m1, effects = "random", flatten = TRUE), "ID")
})

test_that("find_response", {
  expect_identical(find_response(m1), "calcium")
})

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

test_that("get_data", {
  expect_identical(
    colnames(get_data(m1)),
    c("calcium", "elevation", "region", "pos", "ID")
  )
  expect_identical(
    colnames(get_data(m1, effects = "all")),
    c("calcium", "elevation", "region", "pos", "ID")
  )
})

test_that("find_predictors", {
  expect_identical(
    find_predictors(m1, effects = "fixed", component = "conditional"),
    list(conditional = c("elevation", "region"))
  )
  expect_identical(
    find_predictors(m1),
    list(conditional = c("elevation", "region"))
  )
  expect_identical(
    find_predictors(m1, effects = "all"),
    list(
      conditional = c("elevation", "region"),
      random = c("pos", "ID")
    )
  )
})

test_that("find_formula", {
  expect_length(find_formula(m1), 2)
  expect_equal(
    find_formula(m1),
    list(
      conditional = as.formula("calcium ~ elevation + region"),
      random = as.formula("~pos + 0 | ID")
    ),
    ignore_attr = TRUE
  )
})

test_that("find_random", {
  expect_identical(
    find_random(m1),
    list(random = "ID")
  )
})

test_that("find_terms", {
  expect_identical(
    find_terms(m1),
    list(
      response = "calcium",
      conditional = c("elevation", "region"),
      random = c("pos", "ID")
    )
  )
})

test_that("find_variables", {
  expect_identical(
    find_variables(m1),
    list(
      response = "calcium",
      conditional = c("elevation", "region"),
      random = c("pos", "ID")
    )
  )
})


test_that("get_predictors", {
  expect_identical(
    colnames(get_predictors(m1)),
    c("elevation", "region")
  )
})

test_that("get_random", {
  expect_identical(colnames(get_random(m1)), "ID")
})

test_that("get_data", {
  expect_identical(
    colnames(get_data(m1)),
    c("calcium", "elevation", "region", "pos", "ID")
  )
})


test_that("get_parameters", {
  expect_identical(nrow(get_parameters(m1)), 4L)
  expect_identical(
    get_parameters(m1)$Parameter,
    c("(Intercept)", "elevation", "region2", "region3")
  )
})

test_that("find_random_slopes", {
  skip_on_cran()
  expect_identical(
    find_random_slopes(m1),
    list(random = "pos")
  )
})