tests/testthat/test-posthoc_vsRef.R

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

test_that("Check post-hoc vsRef comparisonss", {
  #make a mixed effects model with grafify
  mmod5 <- mixed_model(data_2w_Festing,         #grafify model
                       "GST",
                       c("Treatment", "Strain"),
                       "Block")
  #fit same model with lmer call
  mmod6 <- lmerTest::lmer(GST ~ Treatment*Strain + 
                            (1|Block),          #native call
                          data = data_2w_Festing)
  
  #compare posthoc_ tests from grafify with native emmeans call on grafify model 
  em1 <- posthoc_vsRef(mmod5, c("Treatment", "Strain"))
  em2 <- emmeans(mmod5, trt.vs.ctrl ~Treatment|Strain, Ref = 1, adjust = "fdr")
  expect_equal(em1$contrasts@grid, em2$contrasts@grid)
  expect_equal(em1$emmeans@misc$sigma, em2$emmeans@misc$sigma)
  expect_equal(em1$emmeans@levels$Treatment, em2$emmeans@levels$Treatment)
  expect_equal(em1$emmeans@V[[1]], em2$emmeans@V[[1]])
  expect_equal(em1$contrasts@levels$contrast, em2$contrasts@levels$contrast)
  expect_equal(em1$contrasts@misc$adjust, em2$contrasts@misc$adjust)
  expect_equal(em1$emmeans@grid[,3], em2$emmeans@grid[,3])
  expect_equal(em1$contrasts@model.info$call, em2$contrasts@model.info$call)
  
  #compare posthoc_ tests from grafify with native emmeans call on native model
  em3 <- posthoc_vsRef(mmod6, c("Treatment", "Strain"))
  em4 <- emmeans(mmod6, trt.vs.ctrl ~Treatment|Strain, Ref = 1)
  expect_equal(em3$contrasts@grid, em4$contrasts@grid)
  expect_equal(em3$emmeans@misc$sigma, em4$emmeans@misc$sigma)
  expect_equal(em3$emmeans@levels$Treatment, em4$emmeans@levels$Treatment)
  expect_equal(em3$emmeans@V[[1]], em4$emmeans@V[[1]])
  expect_equal(em3$contrasts@levels$contrast, em4$contrasts@levels$contrast)
  expect_no_match(em3$contrasts@misc$adjust, em4$contrasts@misc$adjust)   #different from default in grafify
  expect_equal(em3$contrasts@misc$orig.grid[,2], em4$contrasts@misc$orig.grid[,2])
  expect_equal(em3$contrasts@model.info$call, em4$contrasts@model.info$call)
})