if (suppressWarnings(requiet("testthat") && requiet("ggeffects") && requiet("marginaleffects") && requiet("ggplot2"))) { set.seed(123) n <- 200 d <- data.frame( outcome = rnorm(n), groups = as.factor(sample(c("treatment", "control"), n, TRUE)), episode = as.factor(sample(1:3, n, TRUE)), ID = as.factor(rep(1:10, n / 10)), sex = as.factor(sample(c("female", "male"), n, TRUE, prob = c(0.4, 0.6))) ) model1 <- lm(outcome ~ groups * episode, data = d) test_that("hypothesis_test, categorical, pairwise", { out <- hypothesis_test(model1, c("groups", "episode")) expect_identical(colnames(out), c("groups", "episode", "Contrast", "conf.low", "conf.high", "p.value")) expect_equal( out$Contrast, c( 0.4183, -0.2036, -0.1482, 0.0709, 0.1211, -0.6219, -0.5666, -0.3475, -0.2972, 0.0554, 0.2745, 0.3247, 0.2191, 0.2694, 0.0503 ), tolerance = 1e-3, ignore_attr = FALSE ) expect_identical( out$groups, c( "control-treatment", "control-control", "control-treatment", "control-control", "control-treatment", "treatment-control", "treatment-treatment", "treatment-control", "treatment-treatment", "control-treatment", "control-control", "control-treatment", "treatment-control", "treatment-treatment", "control-treatment" ) ) expect_equal( attributes(out)$standard_error, c( 0.23286, 0.21745, 0.23533, 0.22247, 0.21449, 0.23558, 0.25218, 0.24022, 0.23286, 0.23803, 0.22532, 0.21745, 0.24262, 0.23533, 0.22247 ), tolerance = 1e-3 ) }) test_that("hypothesis_test, categorical, pairwise, p_adjust", { out1 <- hypothesis_test(model1, c("groups", "episode")) out2 <- hypothesis_test(model1, c("groups", "episode"), p_adjust = "tukey") expect_equal( out1$p.value, c( 0.074, 0.3503, 0.5295, 0.7504, 0.5729, 0.009, 0.0258, 0.1497, 0.2033, 0.8163, 0.2247, 0.137, 0.3676, 0.2538, 0.8215 ), tolerance = 1e-3, ignore_attr = FALSE ) expect_equal( out2$p.value, c( 0.4704, 0.9366, 0.9887, 0.9996, 0.9931, 0.0927, 0.2215, 0.6985, 0.7976, 0.9999, 0.8276, 0.6689, 0.9453, 0.862, 0.9999 ), tolerance = 1e-3, ignore_attr = FALSE ) }) test_that("hypothesis_test, categorical, NULL", { out <- hypothesis_test(model1, c("groups", "episode"), test = NULL) expect_identical(colnames(out), c("groups", "episode", "Predicted", "conf.low", "conf.high", "p.value")) expect_equal(out$Predicted, c(0.028, -0.3903, 0.2316, 0.1763, -0.0428, -0.0931), tolerance = 1e-3, ignore_attr = FALSE ) expect_identical( out$groups, structure(c(1L, 2L, 1L, 2L, 1L, 2L), levels = c("control", "treatment"), class = "factor") ) }) data(iris) model2 <- lm(Sepal.Width ~ Sepal.Length * Species, data = iris) test_that("hypothesis_test, interaction", { out <- hypothesis_test(model2, c("Sepal.Length", "Species")) expect_identical(colnames(out), c( "Sepal.Length", "Species", "Contrast", "conf.low", "conf.high", "p.value" )) expect_equal(out$Contrast, c(0.4788, 0.5666, 0.0878), tolerance = 1e-3, ignore_attr = FALSE ) expect_identical(out$Sepal.Length, c("slope", "slope", "slope")) }) test_that("hypothesis_test, by-argument", { skip_if_not_installed("datawizard") data(efc) efc$c161sex <- datawizard::to_factor(efc$c161sex) efc$c172code <- datawizard::to_factor(efc$c172code) mfilter <- lm(neg_c_7 ~ c161sex * c172code + e42dep + c12hour, data = efc) prfilter <- ggpredict(mfilter, "c172code") out <- hypothesis_test(prfilter, by = "c161sex") expect_identical(nrow(out), 6L) expect_identical( out$c172code, c( "low level of education-intermediate level of education", "low level of education-high level of education", "intermediate level of education-high level of education", "low level of education-intermediate level of education", "low level of education-high level of education", "intermediate level of education-high level of education" ) ) expect_equal(out$p.value, c(0.3962, 0.6512, 0.7424, 0.9491, 0.0721, 0.0288), tolerance = 1e-3) out <- hypothesis_test(prfilter, by = "c161sex", p_adjust = "tukey") expect_equal(out$p.value, c(0.6727, 0.8934, 0.9422, 0.9978, 0.1699, 0.0734), tolerance = 1e-3) prfilter <- ggpredict(mfilter, c("c172code", "c161sex")) out <- hypothesis_test(prfilter, p_adjust = "tukey") out <- out[out$c161sex %in% c("Male-Male", "Female-Female"), , drop = FALSE] expect_equal(out$p.value, c(0.9581, 0.9976, 0.9995, 1, 0.4657, 0.2432), tolerance = 1e-3) expect_error(hypothesis_test(mfilter, "c161sex", by = "c12hour"), regex = "categorical") }) if (suppressWarnings(requiet("lme4"))) { model3 <- suppressMessages(lme4::lmer(outcome ~ groups * episode + sex + (1 | ID), data = d)) test_that("hypothesis_test, categorical, pairwise", { out <- hypothesis_test(model3, c("groups", "episode")) expect_identical(colnames(out), c("groups", "episode", "Contrast", "conf.low", "conf.high", "p.value")) expect_equal( out$Contrast, c( 0.4199, -0.2051, -0.1528, 0.0666, 0.1187, -0.6251, -0.5727, -0.3533, -0.3012, 0.0524, 0.2718, 0.3239, 0.2194, 0.2715, 0.0521 ), tolerance = 1e-3, ignore_attr = FALSE ) expect_identical( out$groups, c( "control-treatment", "control-control", "control-treatment", "control-control", "control-treatment", "treatment-control", "treatment-treatment", "treatment-control", "treatment-treatment", "control-treatment", "control-control", "control-treatment", "treatment-control", "treatment-treatment", "control-treatment" ), ) expect_identical( out$episode, c( "1-1", "1-2", "1-2", "1-3", "1-3", "1-2", "1-2", "1-3", "1-3", "2-2", "2-3", "2-3", "2-3", "2-3", "3-3" ) ) }) test_that("hypothesis_test, categorical, NULL", { out <- hypothesis_test(model3, c("groups", "episode"), test = NULL) out <- out[order(out$groups, out$episode), ] expect_identical(colnames(out), c("groups", "episode", "Predicted", "conf.low", "conf.high", "p.value")) expect_equal(out$Predicted, c(0.0559, 0.2611, -0.0107, -0.364, 0.2087, -0.0628), tolerance = 1e-3, ignore_attr = FALSE ) expect_identical( out$groups, structure(c(1L, 1L, 1L, 2L, 2L, 2L), levels = c("control", "treatment"), class = "factor") ) expect_identical( out$episode, structure(c(1L, 2L, 3L, 1L, 2L, 3L), levels = c("1", "2", "3"), class = "factor") ) }) if (suppressWarnings(requiet("nlme"))) { d <- nlme::Orthodont m <- lme4::lmer(distance ~ age * Sex + (1 | Subject), data = d) test_that("hypothesis_test, numeric, one focal, pairwise", { out <- hypothesis_test(m, "age") expect_identical(colnames(out), c("age", "Slope", "conf.low", "conf.high", "p.value")) expect_equal(out$Slope, 0.6602, tolerance = 1e-3, ignore_attr = FALSE) }) test_that("hypothesis_test, numeric, one focal, NULL", { out <- hypothesis_test(m, "age", test = NULL) expect_identical(colnames(out), c("age", "Slope", "conf.low", "conf.high", "p.value")) expect_equal(out$Slope, 0.6602, tolerance = 1e-3, ignore_attr = FALSE) }) test_that("hypothesis_test, categorical, one focal, pairwise", { out <- hypothesis_test(m, "Sex") expect_identical(colnames(out), c("Sex", "Contrast", "conf.low", "conf.high", "p.value")) expect_equal(out$Contrast, 2.321023, tolerance = 1e-3, ignore_attr = FALSE) }) test_that("hypothesis_test, categorical, one focal, NULL", { out <- hypothesis_test(m, "Sex", test = NULL) expect_identical(colnames(out), c("Sex", "Predicted", "conf.low", "conf.high", "p.value")) expect_equal(out$Predicted, c(24.9688, 22.6477), tolerance = 1e-3, ignore_attr = FALSE) }) } } if (suppressWarnings(requiet("lme4"))) { set.seed(123) n <- 200 d <- data.frame( outcome = rnorm(n), groups = as.factor(sample(c("ta-ca", "tb-cb"), n, TRUE)), episode = as.factor(sample(1:3, n, TRUE)), ID = as.factor(rep(1:10, n / 10)), sex = as.factor(sample(c("1", "2"), n, TRUE, prob = c(0.4, 0.6))) ) model <- suppressMessages(lme4::lmer(outcome ~ groups * sex + episode + (1 | ID), data = d)) test_that("hypothesis_test, masked chars in levels", { out <- hypothesis_test(model, c("groups", "sex")) expect_identical(colnames(out), c("groups", "sex", "Contrast", "conf.low", "conf.high", "p.value")) expect_equal( out$Contrast, c(-0.1854, -0.4473, -0.2076, -0.2619, -0.0222, 0.2397), tolerance = 1e-3, ignore_attr = FALSE ) expect_identical( out$groups, c( "ta-ca-ta-ca", "ta-ca-tb-cb", "ta-ca-tb-cb", "ta-ca-tb-cb", "ta-ca-tb-cb", "tb-cb-tb-cb" ) ) }) } if (suppressWarnings(requiet("lme4"))) { test_that("hypothesis_test, don't drop single columns", { data(iris) iris$Sepal.Width.factor <- factor(as.numeric(iris$Sepal.Width >= 3)) m <- lme4::lmer(Petal.Length ~ Petal.Width * Sepal.Width.factor + (1 | Species), data = iris) expect_s3_class( hypothesis_test(m, c("Sepal.Width.factor", "Petal.Width [0.5]")), "ggcomparisons" ) }) } if (suppressWarnings(requiet("lme4"))) { test_that("hypothesis_test, make sure random effects group is categorical", { data(sleepstudy) set.seed(123) sleepstudy$grp <- as.factor(sample(letters[1:3], nrow(sleepstudy), replace = TRUE)) sleepstudy$ID <- as.numeric(sleepstudy$Subject) m <- lmer(Reaction ~ Days + (1 | ID), sleepstudy) out <- hypothesis_test(ggpredict(m, "Days")) expect_equal(out$Slope, 10.467285959584, tolerance = 1e-4) m <- lmer(Reaction ~ Days * grp + (1 | ID), sleepstudy) out <- hypothesis_test(ggpredict(m, c("Days", "grp"))) expect_equal(out$Contrast, c(-0.0813, -1.26533, -1.18403), tolerance = 1e-4) }) } }