test.art.con.R
In ARTool: Aligned Rank Transform

# Tests for art.con
#
# Author: lelkin
###############################################################################

library(testthat)
library(ARTool)

context("art.con")

# artlm.con tests if artlm.con and art.con match and if artlm.con and artlm are the
# same in the single-factor case (which of course by transitivity tests if art.con and artlm
# are the same in the single-factor case)

# Note: adjust method doesn't matter since t ratios don't get adjusted

test_that("art.con returns same result as ARTool.exe + JMP: no grouping term, two-factor model", {
    data(Higgins1990Table5, package = "ARTool")

    # run art without grouping term to use lm
    m = art(DryMatter ~ Moisture*Fertilizer, data = Higgins1990Table5)

    # single-factor contrasts
    expect_equal(
        summary(art.con(m, "Moisture"))$t,
        c(-7.400493839,-10.82021662,-4.862418335,-3.419722785,2.5380755044,5.9577982894),
        tolerance = 0.0001
    )

    # two-factor contrasts
    # compare "m1,f1 - m1,f2", "m1,f1 - m2,f1", and "m1,f1, m2,f2" to results from JMP.
    expect_equal(
        (summary(art.con(m, "Moisture:Fertilizer")) %>% filter(contrast %in% c("m1,f1 - m1,f2", "m1,f1 - m2,f1", "m1,f1 - m2,f2")) %>% select("t.ratio"))[[1]],
        c(-0.7886463535, -3.0362884611, -5.0079043449),
        tolerance = 0.0001
    )
})

test_that("art.con returns same result as ARTool.exe + JMP: no grouping term, three-factor model", {
    data(ElkinABC, package = "ARTool")

    m = art(Y ~ A*B*C, data = ElkinABC)

    # single-factor contrasts
    expect_equal(
        summary(art.con(m, "A"))$t,
        c(-5.772),
        tolerance = 0.0001
    )

    # two-factor contrasts
    # compare "A1,B1 - A1,B2", "A1,B1 - A2,B1", and "A1,B1, A2,B2" to results from JMP.
    expect_equal(
        (summary(art.con(m, "A:B")) %>% filter(contrast %in% c("A1,B1 - A1,B2", "A1,B1 - A2,B1", "A1,B1 - A2,B2")) %>% select("t.ratio"))[[1]],
        c(-0.022614705, -4.6247071, -3.177366003),
        tolerance = 0.0001
    )

    # three-factor contrasts
    # compare "A1,B1,C1 - A1,B1,C2", "A1,B1,C1 - A1,B2,C2", and "A1,B1,C1 - A2,B2,C2" to results from JMP.
    expect_equal(
        (summary(art.con(m, "A:B:C")) %>% filter(contrast %in% c("A1,B1,C1 - A1,B1,C2", "A1,B1,C1 - A1,B2,C2", "A1,B1,C1 - A2,B2,C2")) %>% select("t.ratio"))[[1]],
        c(-2.060574615, -2.060574615, -2.007739368),
        tolerance = 0.0001
    )
})

test_that("art.con returns same result as ARTool.exe + JMP: with grouping term, two-factor model", {
    data(Higgins1990Table5, package = "ARTool")

    #run with grouping term to force lmer
    m = art(DryMatter ~ Moisture*Fertilizer + (1|Tray), data = Higgins1990Table5)

    # single-factor contrasts
    expect_equal(
        summary(art.con(m, "Moisture"))$t,
        c(-5.606839446, -8.197725544, -3.68391617, -2.590886098, 1.9229232756, 4.5138093733),
        tolerance = 0.0001
    )

    # two-factor contrasts
    # compare "m1,f1 - m1,f2", "m1,f1 - m2,f1", and "m1,f1, m2,f2" to results from JMP.
    expect_equal(
        (summary(art.con(m, "Moisture:Fertilizer")) %>% filter(contrast %in% c("m1,f1 - m1,f2", "m1,f1 - m2,f1", "m1,f1 - m2,f2")) %>% select("t.ratio"))[[1]],
        c(-1.107980814, -3.036288461, -5.007904345),
        tolerance = 0.0001
    )
})

test_that("art.con returns same result as ARTool.exe + JMP: with grouping term, three-factor model", {
    data(ElkinABC, package = "ARTool")

    m = art(Y ~ A*B*C + (1|S), data = ElkinABC)

    # single-factor contrasts
    expect_equal(
        summary(art.con(m, "A"))$t,
        c(-16.98),
        tolerance = 0.001
    )

    # two-factor contrasts
    # compare "A1,B1 - A1,B2", "A1,B1 - A2,B1", and "A1,B1, A2,B2" to results from JMP.
    expect_equal(
        (summary(art.con(m, "A:B")) %>% filter(contrast %in% c("A1,B1 - A1,B2", "A1,B1 - A2,B1", "A1,B1 - A2,B2")) %>% select("t.ratio"))[[1]],
        c(-0.072115146, -14.74754746, -10.13217808),
        tolerance = 0.0001
    )

    # three-factor contrasts
    # compare "A1,B1,C1 - A1,B1,C2", "A1,B1,C1 - A1,B2,C2", and "A1,B1,C1 - A2,B2,C2" to results from JMP.
    expect_equal(
        (summary(art.con(m, "A:B:C")) %>% filter(contrast %in% c("A1,B1,C1 - A1,B1,C2", "A1,B1,C1 - A1,B2,C2", "A1,B1,C1 - A2,B2,C2")) %>% select("t.ratio"))[[1]],
        c(-8.041788515, -8.041788515, -7.835588809),
        tolerance = 0.0001
    )
})

test_that("art.con returns same result as ARTool.exe + JMP: with error term, two-factor model", {
    data(Higgins1990Table5, package = "ARTool")

    #run art with Error term to force aov
    m = art(DryMatter ~ Moisture*Fertilizer + Error(Tray), data = Higgins1990Table5)

    # single-factor contrasts
    expect_equal(
        summary(art.con(m, "Moisture"))$t,
        c(-5.606839446, -8.197725544, -3.68391617, -2.590886098, 1.9229232756, 4.5138093733),
        tolerance = 0.0001
    )

    # two-factor contrasts
    # can't use Higgins Table 5 because it's unbalanced with respect to Moisture:Fertilizer
    data(ElkinAB, package = "ARTool")
    m = art(Y ~ A*B + Error(S), data = ElkinAB)

    # compare "A1,B1 - A1,B2", "A1,B1 - A2,B1", and "A1,B1, A2,B2" to results from JMP.
    expect_equal(
        (summary(art.con(m, "A:B")) %>% filter(contrast %in% c("A1,B1 - A1,B2", "A1,B1 - A2,B1", "A1,B1 - A2,B2")) %>% select("t.ratio"))[[1]],
        c(-0.487275267, -16.40493399, -20.7904114),
        tolerance = 0.0001
    )

})

test_that("art.con returns same result as ARTool.exe + JMP: with error term, two-factor model", {
    data(ElkinABC, package = "ARTool")

    m = art(Y ~ A*B*C + Error(S), data = ElkinABC)

    # single-factor contrasts
    expect_equal(
        summary(art.con(m, "A"))$t,
        c(-16.98),
        tolerance = 0.001
    )

    # two-factor contrasts
    # compare "A1,B1 - A1,B2", "A1,B1 - A2,B1", and "A1,B1, A2,B2" to results from JMP.
    expect_equal(
        (summary(art.con(m, "A:B")) %>% filter(contrast %in% c("A1,B1 - A1,B2", "A1,B1 - A2,B1", "A1,B1 - A2,B2")) %>% select("t.ratio"))[[1]],
        c(-0.072115146, -14.74754746, -10.13217808),
        tolerance = 0.0001
    )

    # three-factor contrasts
    # compare "A1,B1,C1 - A1,B1,C2", "A1,B1,C1 - A1,B2,C2", and "A1,B1,C1 - A2,B2,C2" to results from JMP.
    expect_equal(
        (summary(art.con(m, "A:B:C")) %>% filter(contrast %in% c("A1,B1,C1 - A1,B1,C2", "A1,B1,C1 - A1,B2,C2", "A1,B1,C1 - A2,B2,C2")) %>% select("t.ratio"))[[1]],
        c(-8.041788515, -8.041788515, -7.835588809),
        tolerance = 0.0001
    )
})

test_that("art.con character format and formula format are equivalent", {
    data(Higgins1990Table5, package = "ARTool")

    #run with grouping term to force lmer
    m = art(DryMatter ~ Moisture*Fertilizer + (1|Tray), data = Higgins1990Table5)

    # single-factor contrasts
    expect_equal(
        summary(art.con(m, "Moisture")),
        summary(art.con(m, ~Moisture))
    )

    # two-factor contrasts
    # compare "m1,f1 - m1,f2", "m1,f1 - m2,f1", and "m1,f1, m2,f2" to results from JMP.
    expect_equal(
        summary(art.con(m, "Moisture:Fertilizer")),
        summary(art.con(m, ~Moisture*Fertilizer))
    )
})

test_that("art.con interaction contrasts equivalent to artlm interaction contrasts",{
    data(Higgins1990Table5, package = "ARTool")

    m = art(DryMatter ~ Moisture*Fertilizer + (1|Tray), data = Higgins1990Table5)

    expect_equal(
        summary(art.con(m, "Moisture:Fertilizer", interaction=TRUE)),
        summary(contrast(emmeans(artlm(m, "Moisture:Fertilizer"), ~ Moisture:Fertilizer), method="pairwise", interaction=TRUE))
    )

    data(ElkinABC, package = "ARTool")

    m = art(Y ~ A*B*C, data = ElkinABC)
    expect_equal(
        summary(art.con(m, "A:B:C", interaction=TRUE)),
        summary(contrast(emmeans(artlm(m, "A:B:C"), ~ A:B:C), method="pairwise", interaction=TRUE))
    )
})

test_that("throws error if vector of strings used",{
    data(Higgins1990Table5, package = "ARTool")

    m = art(DryMatter ~ Moisture*Fertilizer + (1|Tray), data = Higgins1990Table5)
    expect_error(art.con(m, c("Moisture:Fertilizer", "Moisture")))
})

test_that("throws error if contrast string term has a space in it",{
    data(Higgins1990Table5, package = "ARTool")

    m = art(DryMatter ~ Moisture*Fertilizer + (1|Tray), data = Higgins1990Table5)
    expect_error(art.con(m, "Moisture: Fertilizer"))
    expect_error(art.con(m, "Moisture :Fertilizer"))
    expect_error(art.con(m, " Moisture:Fertilizer"))
})

test_that("throws error if there is a grouping or error term in string contrast formula",{
    data(Higgins1990Table5, package = "ARTool")

    m = art(DryMatter ~ Moisture*Fertilizer + (1|Tray), data = Higgins1990Table5)
    expect_error(art.con(m, "Moisture:Fertilizer+(1|Tray)"))
    expect_error(art.con(m, ~ Moisture*Fertilizer + (1|Tray)))

    m = art(DryMatter ~ Moisture*Fertilizer + Error(Tray), data = Higgins1990Table5)
    expect_error(art.con(m, "Moisture:Fertilizer+Error(Tray)"))
})

test_that("throws error if try to use : in formula version (i.e., not with string version)",{
    data(Higgins1990Table5, package = "ARTool")

    m = art(DryMatter ~ Moisture*Fertilizer + (1|Tray), data = Higgins1990Table5)
    expect_error(art.con(m, ~ Moisture:Fertilizer))
})

test_that("throws error if dependent variables in contrast formula",{
    data(Higgins1990Table5, package = "ARTool")

    m = art(DryMatter ~ Moisture*Fertilizer + (1|Tray), data = Higgins1990Table5)
    expect_error(art.con(m, ~ DryMatter))
    expect_error(art.con(m, DryMatter ~Moisture*Fertilizer))
})

test_that("throws error if model is not an ART model",{
    data(Higgins1990Table5, package = "ARTool")

    m = aov(DryMatter ~ Moisture*Fertilizer, data = Higgins1990Table5)
    expect_error(art.con(m, ~ Moisture*Fertilizer))
})