Test cleanup part 2 (#567)

Co-authored-by: Indrajeet Patil <[email protected]> Co-authored-by: rempsyc <[email protected]>
easystats · Mar 31, 2023 · 7ff3e57 · 7ff3e57
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -102,6 +102,7 @@ Suggests:
     ICS,
     ICSOutlier,
     ISLR,
+    ivreg,
     lavaan,
     lme4,
     lmtest,
@@ -110,6 +111,7 @@ Suggests:
     Matrix,
     mclogit,
     mclust,
+    metadat,
     metafor,
     mgcv,
     mlogit,
@@ -132,7 +134,8 @@ Suggests:
     survival,
     testthat,
     tweedie,
-    VGAM
+    VGAM,
+    withr
 Encoding: UTF-8
 Language: en-US
 RoxygenNote: 7.2.3.9000

diff --git a/tests/testthat.R b/tests/testthat.R
@@ -1,12 +1,4 @@
-if (require("testthat", quietly = TRUE)) {
-  library(performance)
+library(testthat)
+library(performance)
 
-  is_dev_version <- length(strsplit(packageDescription("performance")$Version, "\\.")[[1]]) > 3L
-  if (is_dev_version) {
-    Sys.setenv("RunAllperformanceTests" = "yes")
-  } else {
-    Sys.setenv("RunAllperformanceTests" = "no")
-  }
-
-  test_check("performance")
-}
+test_check("performance")
diff --git a/tests/testthat/_snaps/check_collinearity.md b/tests/testthat/_snaps/check_collinearity.md
@@ -1,7 +1,7 @@
 # check_collinearity, ci = NULL
 
     Code
-      print(out)
+      out
     Output
       # Check for Multicollinearity
       

diff --git a/tests/testthat/_snaps/mclogit.md b/tests/testthat/_snaps/mclogit.md
@@ -0,0 +1,22 @@
+# model_performance
+
+    Code
+      model_performance(mod_mb)
+    Output
+      # Indices of model performance
+      
+      AIC    |    BIC | Nagelkerke's R2 |  RMSE | Sigma
+      -------------------------------------------------
+      38.823 | 47.618 |           0.836 | 0.298 | 1.016
+
+---
+
+    Code
+      model_performance(mod_mc)
+    Output
+      # Indices of model performance
+      
+      AIC    |    BIC | Nagelkerke's R2 |  RMSE | Sigma
+      -------------------------------------------------
+      13.228 | 24.424 |           0.998 | 0.009 | 0.068
+
diff --git a/tests/testthat/_snaps/model_performance.rma.md b/tests/testthat/_snaps/model_performance.rma.md
@@ -1,7 +1,7 @@
 # check_outliers.rma
 
     Code
-      print(out)
+      out
     Output
       2 outliers detected: studies 4 (Hart & Sutherland) and 8 (TPT Madras).
 
diff --git a/tests/testthat/_snaps/pkg-ivreg.md b/tests/testthat/_snaps/pkg-ivreg.md
@@ -0,0 +1,11 @@
+# Issue #530 from the `modelsummary` repo
+
+    Code
+      out
+    Output
+      # Indices of model performance
+      
+      AIC     |     BIC |    R2 | R2 (adj.) |  RMSE | Sigma | Wu & Hausman | p (Wu_Hausman) | Weak instruments | p (weak_instruments)
+      -------------------------------------------------------------------------------------------------------------------------------
+      182.692 | 191.486 | 0.655 |     0.604 | 3.484 | 3.793 |       13.869 |         < .001 |           19.958 |               < .001
+
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
@@ -23,147 +23,155 @@ test_that("check_collinearity, correct order in print", {
 })
 
 
-if (requiet("glmmTMB") && getRversion() >= "4.0.0") {
-  data(Salamanders)
-  m1 <- glmmTMB(count ~ spp + mined + (1 | site),
+test_that("check_collinearity", {
+  skip_if_not_installed("glmmTMB")
+  skip_if_not(getRversion() >= "4.0.0")
+
+  data(Salamanders, package = "glmmTMB")
+
+  m1 <- glmmTMB::glmmTMB(count ~ spp + mined + (1 | site),
     ziformula = ~spp,
     Salamanders,
     family = poisson()
   )
+  expect_equal(
+    suppressWarnings(check_collinearity(m1, component = "conditional", verbose = FALSE)$VIF),
+    c(1.00037354840318, 1.00037354840318),
+    tolerance = 1e-3
+  )
+  expect_equal(
+    suppressWarnings(check_collinearity(m1, component = "all", verbose = FALSE)$VIF),
+    c(1.00037354840318, 1.00037354840318),
+    tolerance = 1e-3
+  )
+  expect_null(check_collinearity(m1, verbose = FALSE, component = "zero_inflated"))
+})
 
-  test_that("check_collinearity", {
-    expect_equal(
-      suppressWarnings(check_collinearity(m1, component = "conditional", verbose = FALSE)$VIF),
-      c(1.00037354840318, 1.00037354840318),
-      tolerance = 1e-3
-    )
-    expect_equal(
-      suppressWarnings(check_collinearity(m1, component = "all", verbose = FALSE)$VIF),
-      c(1.00037354840318, 1.00037354840318),
-      tolerance = 1e-3
-    )
-    expect_null(check_collinearity(m1, verbose = FALSE, component = "zero_inflated"))
-  })
 
-  m2 <- glmmTMB(
+
+test_that("check_collinearity", {
+  skip_if_not_installed("glmmTMB")
+  skip_if_not(getRversion() >= "4.0.0")
+
+  data(Salamanders, package = "glmmTMB")
+
+  m2 <- glmmTMB::glmmTMB(
     count ~ spp + mined + cover + (1 | site),
     ziformula = ~ spp + mined + cover,
-    family = nbinom2,
+    family = glmmTMB::nbinom2,
     data = Salamanders
   )
 
-  test_that("check_collinearity", {
-    expect_equal(
-      suppressWarnings(check_collinearity(m2, component = "conditional", verbose = FALSE)$VIF),
-      c(1.09015, 1.2343, 1.17832),
-      tolerance = 1e-3
+  expect_equal(
+    suppressWarnings(check_collinearity(m2, component = "conditional", verbose = FALSE)$VIF),
+    c(1.09015, 1.2343, 1.17832),
+    tolerance = 1e-3
+  )
+  expect_equal(
+    suppressWarnings(check_collinearity(m2, component = "conditional", verbose = FALSE)$VIF_CI_low),
+    c(1.03392, 1.14674, 1.10105),
+    tolerance = 1e-3
+  )
+  expect_equal(
+    suppressWarnings(check_collinearity(m2, component = "all", verbose = FALSE)$VIF),
+    c(1.09015, 1.2343, 1.17832, 1.26914, 1, 1.26914),
+    tolerance = 1e-3
+  )
+  expect_equal(
+    suppressWarnings(check_collinearity(m2, component = "all", verbose = FALSE)$VIF_CI_low),
+    c(1.03392, 1.14674, 1.10105, 1.17565, 1, 1.17565),
+    tolerance = 1e-3
+  )
+  expect_equal(
+    suppressWarnings(check_collinearity(m2, component = "zero_inflated", verbose = FALSE)$VIF),
+    c(1.26914, 1, 1.26914),
+    tolerance = 1e-3
+  )
+  expect_equal(
+    suppressWarnings(check_collinearity(m2, component = "zero_inflated", verbose = FALSE)$Tolerance_CI_high),
+    c(0.85059, 1, 0.85059),
+    tolerance = 1e-3
+  )
+
+  suppressWarnings(coll <- check_collinearity(m2, component = "all", verbose = FALSE)) # nolint
+  expect_true(all(coll$Tolerance < coll$Tolerance_CI_high))
+  expect_true(all(coll$VIF > coll$VIF_CI_low))
+
+  expect_identical(
+    attributes(coll)$data$Component,
+    c("conditional", "conditional", "conditional", "zero inflated", "zero inflated", "zero inflated")
+  )
+  expect_identical(
+    colnames(attributes(coll)$CI),
+    c("VIF_CI_low", "VIF_CI_high", "Tolerance_CI_low", "Tolerance_CI_high", "Component")
+  )
+})
+
+test_that("check_collinearity | afex", {
+  skip_if_not_installed("afex", minimum_version = "1.0.0")
+
+  data(obk.long, package = "afex")
+
+  obk.long$treatment <- as.character(obk.long$treatment)
+  suppressWarnings(suppressMessages({
+    aM <- afex::aov_car(value ~ treatment * gender + Error(id / (phase * hour)),
+      data = obk.long
     )
-    expect_equal(
-      suppressWarnings(check_collinearity(m2, component = "conditional", verbose = FALSE)$VIF_CI_low),
-      c(1.03392, 1.14674, 1.10105),
-      tolerance = 1e-3
+
+    aW <- afex::aov_car(value ~ Error(id / (phase * hour)),
+      data = obk.long
     )
-    expect_equal(
-      suppressWarnings(check_collinearity(m2, component = "all", verbose = FALSE)$VIF),
-      c(1.09015, 1.2343, 1.17832, 1.26914, 1, 1.26914),
-      tolerance = 1e-3
+
+    aB <- afex::aov_car(value ~ treatment * gender + Error(id),
+      data = obk.long
     )
-    expect_equal(
-      suppressWarnings(check_collinearity(m2, component = "all", verbose = FALSE)$VIF_CI_low),
-      c(1.03392, 1.14674, 1.10105, 1.17565, 1, 1.17565),
-      tolerance = 1e-3
+  }))
+
+  expect_message(ccoM <- check_collinearity(aM)) # nolint
+  expect_warning(expect_message(ccoW <- check_collinearity(aW))) # nolint
+  expect_message(ccoB <- check_collinearity(aB), regexp = NA) # nolint
+
+  expect_identical(nrow(ccoM), 15L)
+  expect_identical(nrow(ccoW), 3L)
+  expect_identical(nrow(ccoB), 3L)
+
+  suppressWarnings(suppressMessages({
+    aM <- afex::aov_car(value ~ treatment * gender + Error(id / (phase * hour)),
+      include_aov = TRUE,
+      data = obk.long
     )
-    expect_equal(
-      suppressWarnings(check_collinearity(m2, component = "zero_inflated", verbose = FALSE)$VIF),
-      c(1.26914, 1, 1.26914),
-      tolerance = 1e-3
+
+    aW <- afex::aov_car(value ~ Error(id / (phase * hour)),
+      include_aov = TRUE,
+      data = obk.long
     )
-    expect_equal(
-      suppressWarnings(check_collinearity(m2, component = "zero_inflated", verbose = FALSE)$Tolerance_CI_high),
-      c(0.85059, 1, 0.85059),
-      tolerance = 1e-3
+
+    aB <- afex::aov_car(value ~ treatment * gender + Error(id),
+      include_aov = TRUE,
+      data = obk.long
     )
+  }))
 
-    suppressWarnings(coll <- check_collinearity(m2, component = "all", verbose = FALSE)) # nolint
-    expect_true(all(coll$Tolerance < coll$Tolerance_CI_high))
-    expect_true(all(coll$VIF > coll$VIF_CI_low))
+  expect_message(ccoM <- check_collinearity(aM)) # nolint
+  expect_warning(expect_message(ccoW <- check_collinearity(aW))) # nolint
+  expect_message(ccoB <- check_collinearity(aB), regexp = NA) # nolint
 
-    expect_identical(
-      attributes(coll)$data$Component,
-      c("conditional", "conditional", "conditional", "zero inflated", "zero inflated", "zero inflated")
-    )
-    expect_identical(
-      colnames(attributes(coll)$CI),
-      c("VIF_CI_low", "VIF_CI_high", "Tolerance_CI_low", "Tolerance_CI_high", "Component")
-    )
-  })
-
-  if (requiet("afex") && utils::packageVersion("afex") >= package_version("1.0.0")) {
-    test_that("check_collinearity | afex", {
-      data(obk.long, package = "afex")
-
-      obk.long$treatment <- as.character(obk.long$treatment)
-      suppressWarnings(suppressMessages({
-        aM <- afex::aov_car(value ~ treatment * gender + Error(id / (phase * hour)),
-          data = obk.long
-        )
-
-        aW <- afex::aov_car(value ~ Error(id / (phase * hour)),
-          data = obk.long
-        )
-
-        aB <- afex::aov_car(value ~ treatment * gender + Error(id),
-          data = obk.long
-        )
-      }))
-
-      expect_message(ccoM <- check_collinearity(aM)) # nolint
-      expect_warning(expect_message(ccoW <- check_collinearity(aW))) # nolint
-      expect_message(ccoB <- check_collinearity(aB), regexp = NA) # nolint
-
-      expect_identical(nrow(ccoM), 15L)
-      expect_identical(nrow(ccoW), 3L)
-      expect_identical(nrow(ccoB), 3L)
-
-      suppressWarnings(suppressMessages({
-        aM <- afex::aov_car(value ~ treatment * gender + Error(id / (phase * hour)),
-          include_aov = TRUE,
-          data = obk.long
-        )
-
-        aW <- afex::aov_car(value ~ Error(id / (phase * hour)),
-          include_aov = TRUE,
-          data = obk.long
-        )
-
-        aB <- afex::aov_car(value ~ treatment * gender + Error(id),
-          include_aov = TRUE,
-          data = obk.long
-        )
-      }))
-
-      expect_message(ccoM <- check_collinearity(aM)) # nolint
-      expect_warning(expect_message(ccoW <- check_collinearity(aW))) # nolint
-      expect_message(ccoB <- check_collinearity(aB), regexp = NA) # nolint
-
-      expect_identical(nrow(ccoM), 15L)
-      expect_identical(nrow(ccoW), 3L)
-      expect_identical(nrow(ccoB), 3L)
-    })
-  }
-
-  test_that("check_collinearity, ci = NULL", { # 518
-    data(npk)
-    m <- lm(yield ~ N + P + K, npk)
-    out <- check_collinearity(m, ci = NULL)
-
-    expect_identical(
-      colnames(out),
-      c(
-        "Term", "VIF", "VIF_CI_low", "VIF_CI_high", "SE_factor", "Tolerance",
-        "Tolerance_CI_low", "Tolerance_CI_high"
-      )
+  expect_identical(nrow(ccoM), 15L)
+  expect_identical(nrow(ccoW), 3L)
+  expect_identical(nrow(ccoB), 3L)
+})
+
+test_that("check_collinearity, ci = NULL", { # 518
+  data(npk)
+  m <- lm(yield ~ N + P + K, npk)
+  out <- check_collinearity(m, ci = NULL)
+
+  expect_identical(
+    colnames(out),
+    c(
+      "Term", "VIF", "VIF_CI_low", "VIF_CI_high", "SE_factor", "Tolerance",
+      "Tolerance_CI_low", "Tolerance_CI_high"
     )
-    expect_snapshot(print(out))
-  })
-}
+  )
+  expect_snapshot(out)
+})