tests/testthat/test-mixed_anova_slopes.R

In ashenoy-cmbi/grafify: Easy Graphs for Data Visualisation and Linear Models for ANOVA

test_that("Mixed effects models with slopes", {
  mmod5 <- mixed_model_slopes(data_2w_Tdeath, 
                              "PI",
                              c("Genotype", "Time"),
                              "Time",
                              "Experiment")
  mmod6 <- lmer(PI ~ Genotype*Time+
                  (Time|Experiment),          #native call
                data = data_2w_Tdeath)
  mmod6 <- lmerTest::as_lmerModLmerTest(mmod6)
  expect_equal(mmod5@call$formula[2], mmod6@call$formula[2]) #compare models
  #expect_equal(mmod5@call$data , mmod6@call$data)
  expect_equal(mmod5@sigma, mmod6@sigma, tolerance = 1e-5)
  #expect_equal(mmod5@frame[[1]], mmod6@frame[[1]])
  expect_equal(mmod5@beta, mmod6@beta, tolerance = 1e-5)
  #expect_equal(mmod5@call, mmod6@call) #only difference is lmerTest:: in native call
})

test_that("Mixed effects slopes ANOVA table - defaults", {
  mmod1 <- mixed_anova(data_2w_Festing,        #fit with grafify call
                       "GST",
                       c("Treatment", "Strain"),
                       "Block")
  mmod2 <- anova(lmerTest::lmer(GST ~ Treatment*Strain + #fit with native call
                                  (1|Block),
                                data = data_2w_Festing),
                 type = "II",                 #default in grafify
                 ddf = "Kenward-Roger")       #default in grafify
  expect_equal(mmod1$`Sum Sq`, mmod2$`Sum Sq`, tolerance = 1e-5)    #check some cells in ANOVA table
  expect_equal(mmod1$`F value`, mmod2$`F value`, tolerance = 1e-5)
  expect_equal(mmod1$`Pr(>F)`[1], mmod2$`Pr(>F)`[1], tolerance = 1e-5)
})

test_that("Mixed effects ANOVA table - custom", {
  mmod3 <- mixed_anova_slopes(data_2w_Tdeath, 
                       "PI",
                       c("Genotype", "Time"),
                       "Time",
                       "Experiment",
                       Df_method = "Satterthwaite") #change ddf method
  mmod4 <- anova(lmerTest::lmer(PI ~ Genotype*Time+
                                  (Time|Experiment),          #native call
                                data = data_2w_Tdeath),
                 type = "II",
                 ddf = "Satterthwaite")        #change ddf method
  expect_equal(mmod3$`Sum Sq`, mmod4$`Sum Sq`, tolerance = 1e-5) #check cells from ANOVA table
  expect_equal(mmod3$`F value`, mmod4$`F value`, tolerance = 1e-5)
  expect_equal(mmod3$`Pr(>F)`[1], mmod4$`Pr(>F)`[1], tolerance = 1e-5)
  expect_equal(class(mmod3), class(mmod4))
})