tests/testthat/test-nlme.R

In strengejacke/ggeffects: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs

skip_on_os(c("mac", "solaris"))
skip_if_not_installed("lme4")
skip_if_not_installed("nlme")

test_that("ggpredict, lme", {
  skip_if_not_installed("effects")
  data(Orthodont, package = "nlme")
  fit <- nlme::lme(distance ~ age + Sex, data = Orthodont, random = ~ 1 | Subject)
  expect_s3_class(ggpredict(fit, "age"), "data.frame")
  expect_s3_class(ggpredict(fit, c("age", "Sex")), "data.frame")
  expect_s3_class(ggpredict(fit, "age", type = "re"), "data.frame")
  expect_s3_class(ggpredict(fit, c("age", "Sex"), type = "re"), "data.frame")
  expect_s3_class(ggeffect(fit, "age"), "data.frame")
  expect_s3_class(ggeffect(fit, c("age", "Sex")), "data.frame")
})

test_that("ggpredict, lme", {
  data(Orthodont, package = "nlme")
  m5 <- lme4::lmer(distance ~ age * Sex + (age | Subject), data = Orthodont)
  m6 <- nlme::lme(distance ~ age * Sex, data = Orthodont, random = ~ age | Subject)
  expect_s3_class(ggpredict(m5, c("age", "Sex")), "data.frame")
  expect_s3_class(ggpredict(m6, c("age", "Sex")), "data.frame")
  expect_s3_class(ggpredict(m5, c("age", "Sex"), type = "re"), "data.frame")
  expect_s3_class(ggpredict(m6, c("age", "Sex"), type = "re"), "data.frame")
})

test_that("ggpredict, lme, type=re", {
  data(sleepstudy, package = "lme4")
  m7 <- nlme::lme(Reaction ~ Days, random = ~ Days | Subject, sleepstudy, method = "REML")
  out1 <- ggpredict(m7, "Days", type = "fe")
  out2 <- ggpredict(m7, "Days", type = "re")
  expect_equal(
    out1$predicted,
    c(251.4051, 261.87239, 272.33968, 282.80696, 293.27425, 303.74153,
      314.20882, 324.67611, 335.14339, 345.61068),
    tolerance = 1e-3
  )
  expect_equal(
    out1$conf.low,
    c(237.928, 248.46965, 258.32998, 267.5903, 276.37872, 284.82043,
      293.01462, 301.03256, 308.92359, 316.72167),
    tolerance = 1e-3
  )
  expect_equal(
    out2$predicted,
    c(
      251.4051, 261.87239, 272.33968, 282.80696, 293.27425, 303.74153,
      314.20882, 324.67611, 335.14339, 345.61068
    ),
    tolerance = 1e-3
  )
  expect_equal(
    out2$conf.low,
    c(199.10003, 209.58643, 219.89485, 230.0269, 239.98591, 249.77677,
      259.4057, 268.88, 278.20776, 287.39759),
    tolerance = 1e-3
  )
})