inst/tinytest/test-pkg-afex.R

In marginaleffects: Predictions, Comparisons, Slopes, Marginal Means, and Hypothesis Tests

source("helpers.R")
using("marginaleffects")

requiet("afex")
requiet("emmeans")

data(md_12.1, package = "afex")
mod <- aov_ez("id", "rt", md_12.1, within = c("angle", "noise"))

# no validity
expect_slopes(mod)
pre <- predictions(mod)
expect_inherits(pre, "predictions")
cmp <- comparisons(mod)
expect_inherits(cmp, "comparisons")

# marginalmeans vs. emmeans
mm <- marginal_means(
    mod,
    variables = c("angle", "noise"),
    cross = FALSE)
em1 <- data.frame(emmeans(mod, ~angle))
em2 <- data.frame(emmeans(mod, ~noise))
expect_equal(mm$estimate, c(em1$emmean, em2$emmean))
expect_equal(mm$std.error, c(em1$SE, em2$SE))

# contrasts vs emmeans
cmp <- comparisons(mod,
    variables = "angle",
    newdata = "marginalmeans")
em <- emmeans(mod, ~angle)
em <- emmeans::contrast(em, method = "trt.vs.ctrl1")
em <- data.frame(em)
expect_equal(cmp$estimate, em$estimate)
expect_equal(cmp$std.error, em$SE)

# predictions vs emmeans
pre <- predictions(
    mod,
    newdata = datagrid(angle = c("X0", "X4", "X8"),
                       noise = md_12.1$noise))
emm <- emmeans(mod, c("noise", "angle"))
emm <- data.frame(emm)
expect_equivalent(pre$estimate, emm$emmean)
expect_equivalent(pre$std.error, emm$SE)


# coefficient matrix (ANOVA on full design)
data(obk.long, package = "afex")
mod <- suppressMessages(aov_car(
    value ~ treatment * gender + Error(id/(phase*hour)), 
    data = obk.long, observed = "gender"))

em <- data.frame(emmeans(mod, ~ phase))
mm <- marginal_means(mod, "phase")
expect_equivalent(mm$estimate, em$emmean)
expect_equivalent(mm$std.error, em$SE)



# data from https://github.com/mattansb/Analysis-of-Factorial-Designs-foR-Psychologists/03 Main and simple effects analysis
Phobia <- readRDS("stata/databases/Phobia.rds")
mod <- suppressMessages(aov_ez(
  id = "ID", dv = "BehavioralAvoidance",
  between = c("Condition", "Gender"),
  data = Phobia,
  anova_table = list(es = "pes")))

pre <- predictions(mod)
mfx <- slopes(mod)
expect_inherits(pre, "predictions")
expect_inherits(cmp, "comparisons")
expect_false(anyNA(pre$std.error))
expect_false(anyNA(cmp$std.error))




rm(list = ls())