tests/testthat/test-rstanarm.R

In ggeffects: Create Tidy Data Frames of Marginal Effects for 'ggplot' from Model Outputs

.runThisTest <- Sys.getenv("RunAllggeffectsTests") == "yes"

if (.runThisTest && suppressWarnings(
  requiet("testthat") &&
  requiet("lme4") &&
  requiet("sjmisc") &&
  requiet("rstanarm") &&
  requiet("ggeffects")
)) {
  # fit linear model
  data(sleepstudy)
  data(efc, package = "ggeffects")
  sleepstudy$age <- round(runif(nrow(sleepstudy), min = 20, max = 60))
  sleepstudy$Rdicho <- dicho(sleepstudy$Reaction)
  efc <- to_label(efc, e42dep, c161sex, c172code)
  d <<- sleepstudy
  d2 <<- efc

  m <- suppressWarnings(rstanarm::stan_glmer(
    Reaction ~ Days + age + (1 | Subject),
    data = d, QR = TRUE,
    # this next line is only to keep the example small in size!
    chains = 2, cores = 1, seed = 12345, iter = 500, refresh = 0
  ))

  m2 <- suppressWarnings(rstanarm::stan_glmer(
    Rdicho ~ Days + age + (1 | Subject),
    data = d, QR = TRUE,
    family = binomial,
    chains = 2, iter = 500, refresh = 0
  ))

  m3 <- suppressWarnings(rstanarm::stan_glm(
    tot_sc_e ~ neg_c_7 + e42dep + barthtot + c172code + c161sex,
    data = d2,
    family = poisson("log"),
    chains = 2, iter = 500
  ))

  test_that("ggpredict, rstan", {
    expect_s3_class(ggpredict(m, "Days", verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m, c("Days", "age"), verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m, "Days", type = "re", verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m, c("Days", "age"), type = "re", verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m, "Days", ppd = TRUE, verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m, c("Days", "age"), ppd = TRUE, verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m, "Days", type = "re", ppd = TRUE, verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m, c("Days", "age"), type = "re", ppd = TRUE, verbose = FALSE), "data.frame")
  })

  test_that("ggpredict, rstan", {
    expect_s3_class(ggpredict(m2, "Days", verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m2, c("Days", "age"), verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m2, "Days", type = "re", verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m2, c("Days", "age"), type = "re", verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m2, "Days", ppd = TRUE, verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m2, c("Days", "age"), ppd = TRUE, verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m2, "Days", type = "re", ppd = TRUE, verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m2, c("Days", "age"), type = "re", ppd = TRUE, verbose = FALSE), "data.frame")
  })

  test_that("ggpredict, rstan", {
    expect_s3_class(ggpredict(m3, "neg_c_7", verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m3, c("neg_c_7", "e42dep"), verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m3, "neg_c_7", ppd = TRUE, verbose = FALSE), "data.frame")
    expect_s3_class(ggpredict(m3, c("neg_c_7", "e42dep"), ppd = TRUE, verbose = FALSE), "data.frame")
  })
}