tests/testthat/test_apa_print_model_comp.R

In crsh/papaja: Prepare American Psychological Association Journal Articles with R Markdown

context("apa_print.list()")

test_that(
  "Linear regression"
  , {

    mod1 <- lm(Sepal.Length ~ Sepal.Width, data = iris)
    mod2 <- update(mod1, formula = . ~ . + Petal.Length)
    mod3 <- update(mod2, formula = . ~ . + Petal.Width)

    # No bootstrapped Delta R^2 CI
    model_comp <- apa_print(list(Baseline = mod1, Length = mod2, Both = mod3), boot_samples = 0)

    expect_apa_results(model_comp, allow_row_names = TRUE)

    # stat
    expect_identical(names(model_comp$stat), c("Length", "Both"))
    expect_identical(model_comp$stat$Length, "$F(1, 147) = 853.31$, $p < .001$")
    expect_identical(model_comp$stat$Both, "$F(1, 146) = 19.04$, $p < .001$")

    # est
    expect_identical(names(model_comp$est), c("Length", "Both"))
    expect_identical(model_comp$est$Length, "$\\Delta R^2 = .83$")
    expect_identical(model_comp$est$Both, "$\\Delta R^2 = .02$")

    # full
    expect_identical(names(model_comp$full), c("Length", "Both"))
    expect_identical(model_comp$full$Length, paste(model_comp$est$Length, model_comp$stat$Length, sep = ", "))
    expect_identical(model_comp$full$Both, paste(model_comp$est$Both, model_comp$stat$Both, sep = ", "))

    # table
    correct_table <- structure(
      list(
        Baseline = structure(
          c("6.53 [5.58, 7.47]", "-0.22 [-0.53, 0.08]", "", "", ".01 [0.00, 0.06]", "2.07", "1", "148", ".152", "371.99", "381.02", "", "", "", "", "", "", "")
          , class = c("tiny_labelled", "character")
          , label = "Baseline"
        )
        , Length = structure(
          c("2.25 [1.76, 2.74]",   "0.60 [0.46, 0.73]", "0.47 [0.44, 0.51]", "", ".84 [0.79, 0.87]", "386.39", "2", "147", "< .001", "101.03", "113.07", ".83", "853.31", "1", "147", "< .001", "-270.97", "-267.96")
          , class = c("tiny_labelled", "character")
          , label = "Length"
        )
        , Both = structure(
          c("1.86 [1.36, 2.35]", "0.65 [0.52, 0.78]", "0.71 [0.60, 0.82]", "-0.56 [-0.81, -0.30]", ".86 [0.82, 0.89]", "295.54", "3", "146", "< .001", "84.64", "99.70", ".02", "19.04", "1", "146", "< .001", "-16.38", "-13.37")
          , class = c("tiny_labelled", "character")
          , label = "Both"
        )
      )
      , .Names = c("Baseline", "Length", "Both")
      , row.names = c("Intercept", "Sepal Width", "Petal Length", "Petal Width", "$R^2$ [90\\% CI]", "$F$", "$\\mathit{df}$", "$\\mathit{df}_{\\mathrm{res}}$", "$p$", "$\\mathrm{AIC}$", "$\\mathrm{BIC}$", "$\\Delta R^2$", "$F$ ", "$\\mathit{df}$ ", "$\\mathit{df}_{\\mathrm{res}}$ ", "$p$ ", "$\\Delta \\mathrm{AIC}$", "$\\Delta \\mathrm{BIC}$")
      , class = c("apa_results_table", "data.frame")
    )

    expect_identical(colnames(model_comp$table), c("Baseline", "Length", "Both"))
    expect_identical(model_comp$table$Baseline, correct_table$Baseline)
    expect_identical(model_comp$table$Length, correct_table$Length)
    expect_identical(model_comp$table$Both, correct_table$Both)


    # Test omission of incomplete model names & CI
    incomplete_names <- apa_print(list(mod1, Length = mod2, Both = mod3), boot_samples = 0)
    expect_apa_results(incomplete_names, allow_row_names = TRUE)

    ## stat
    expect_identical(names(incomplete_names$stat), c("model2", "model3"))

    ## est
    expect_identical(names(incomplete_names$est), c("model2", "model3"))

    ## full
    expect_identical(names(incomplete_names$full), c("model2", "model3"))

    ## table
    expect_identical(colnames(incomplete_names$table), paste("Model", 1:3))

    incomplete_names2 <- apa_print(list(mod1, mod2, mod3), boot_samples = 0)
    expect_apa_results(incomplete_names2, allow_row_names = TRUE)
    expect_identical(incomplete_names, incomplete_names2)


    # Bootstrapped Delta R^2 CI
    skip_on_cran() # The bootstrapping is computationally too expensive

    set.seed(1337)
    model_comp_boot <- apa_print(list(Baseline = mod1, Length = mod2, Both = mod3), boot_samples = 1e3)
    expect_apa_results(model_comp_boot, allow_row_names = TRUE)

    expect_identical(model_comp_boot$est$Length, "$\\Delta R^2 = .83$, 90\\% CI $[.76, .86]$")

    expect_identical(model_comp_boot$est$Both, "$\\Delta R^2 = .02$, 90\\% CI $[.01, .04]$")

    model_comp_boot2 <- apa_print(list(Baseline = mod1, Length = mod2), boot_samples = 1e3, conf.int = 0.5)
    expect_apa_results(model_comp_boot2, allow_row_names = TRUE)

    expect_identical(model_comp_boot2$est$Length, "$\\Delta R^2 = .83$, 50\\% CI $[.80, .84]$")

    # Correct df for model comparisons (issue #433)
    comp1 <- apa_print(list(a = mod3, b = mod2, c = mod1), boot_samples = 0)
    expect_identical(
      comp1$statistic$b
      , "$F(1, 146) = 19.04$, $p < .001$"
    )
    expect_identical(
      comp1$statistic$c
      , "$F(1, 146) = 853.31$, $p < .001$"
    )
    comp2 <- apa_print(list(a = mod2, b = mod1, c = mod3), boot_samples = 0)
    expect_identical(
      comp2$statistic$b
      , "$F(1, 147) = 853.31$, $p < .001$"
    )
    expect_identical(
      comp2$statistic$c
      , "$F(2, 146) = 436.17$, $p < .001$"
    )
  }
)

test_that(
  "Deprecated 'ci' argument"
  , {
    mod1 <- lm(yield ~ N, npk)
    mod2 <- lm(yield ~ N * P, npk)

    expect_warning(
      apa_out <- apa_print(list(mod1, mod2), boot_samples = 0L, ci = .96)
      , regexp = "Using argument 'ci' in calls to 'apa_print()' is deprecated. Please use 'conf.int' instead."
      , fixed = TRUE
    )
    expect_identical(
      as.character(apa_out$table$`Model 1`[[1L]], keep_label = FALSE)
      , "52.07 [48.02, 56.11]"
    )
  }
)

test_that(
  "Model comparisons: Many models"
  , {
    models <- list(
      lm(yield ~ N , npk)
      , lm(yield ~ N + P, npk)
      , lm(yield ~ N + P + K, npk)
      , lm(yield ~ N + P + K + N:P, npk)
      , lm(yield ~ N + P + K + N:P + N:K, npk)
      , lm(yield ~ N + P + K + N:P + N:K + P:K, npk)
      , lm(yield ~ N + P + K + N:P + N:K + P:K + N:P:K, npk)
    )

    apa_out <- apa_print(models, boot_samples = 0L)

    expect_apa_results(
      apa_out
      , allow_row_names = TRUE
    )
  }
)

# context("apa_print.anova() - Model comparison")
#
# test_that(
#   "Linear regression"
#   , {
#     baseline <- lm(formula = Fertility ~ ., data = swiss)
#
#     f_test <- drop1(baseline, test = "F")
#     f_test_results <- apa_print(f_test)
#
#
#     lrt_test <- drop1(baseline, test = "Chisq")
#     lrt_test_results <- apa_print(lrt_test)
#   }
# )