fix metaBMA unit tests (MCMC changes due to Stan?)

jasp-stats · Sep 19, 2023 · 0398e17 · 0398e17
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commit 0398e17
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diff --git a/tests/testthat/_snaps/bayesianmetaanalysis/effect-size-subplot-3.svg b/tests/testthat/_snaps/bayesianmetaanalysis/effect-size-subplot-3.svg
diff --git a/tests/testthat/_snaps/bayesianmetaanalysis/effect-size-subplot-4.svg b/tests/testthat/_snaps/bayesianmetaanalysis/effect-size-subplot-4.svg
diff --git a/tests/testthat/_snaps/bayesianmetaanalysis/heterogeneity-subplot-3.svg b/tests/testthat/_snaps/bayesianmetaanalysis/heterogeneity-subplot-3.svg
diff --git a/tests/testthat/_snaps/bayesianmetaanalysis/heterogeneity-subplot-4.svg b/tests/testthat/_snaps/bayesianmetaanalysis/heterogeneity-subplot-4.svg
diff --git a/tests/testthat/_snaps/bayesianmetaanalysis/observed-study-effects.svg b/tests/testthat/_snaps/bayesianmetaanalysis/observed-study-effects.svg
diff --git a/tests/testthat/test-bayesianmetaanalysis.R b/tests/testthat/test-bayesianmetaanalysis.R
@@ -34,9 +34,9 @@ options$inverseGammaShape                       <- 1
 options$inverseGammaScale                       <- 0.15
 options$chains                                  <- 4
 options$seed                                    <- 1
-options$.meta <- list(effectSizeCi = list(containsColumn = TRUE), 
-                      effectSize = list(containsColumn = TRUE), 
-                      effectSizeSe = list(containsColumn = TRUE), 
+options$.meta <- list(effectSizeCi = list(containsColumn = TRUE),
+                      effectSize = list(containsColumn = TRUE),
+                      effectSizeSe = list(containsColumn = TRUE),
                       studyLabel = list(containsColumn = TRUE))
 options$effectSizeCi <- list()
 set.seed(1)
@@ -49,40 +49,38 @@ results <- jaspTools::runAnalysis("BayesianMetaAnalysis", "BCG Vaccine.csv", opt
 ##############################################################
 
 test_that("Posterior Estimates per Model table results match", {
-  testthat::skip_on_os(c("mac", "linux", "solaris"))
   table <- results[["results"]][["bmaTable"]][["data"]]
   jaspTools::expect_equal_tables(table,
-                                list("TRUE", 4.70377989938849e+21, -0.434254495375077, 0.0413386758998794,
-                                      -0.51661689869485, "Fixed effects", "<unicode><unicode>", -0.354044245070268,
-                                      "TRUE", 46.1842149375581, -0.700934189539198, 0.191389586956929,
-                                      -1.09512063075207, "Random effects", "<unicode><unicode>", -0.313314935687268,
-                                      1, "FALSE", 8.63965964148833e+26, 0.587415453102927, 0.174455537927642,
-                                      0.341965384464118, "Random effects", "<unicode><unicode>", 0.977068560913425,
-                                      2, "TRUE", 46.184214937558, -0.70093422222471, 0.192829673436622,
-                                      -1.10318957647626, "Averaged", "<unicode><unicode>", -0.322201994073094,
-                                      3, "FALSE", 8.82672917711143e+26, "", "", "", "Averaged", "<unicode><unicode>",
+                                 list("TRUE", 4.70377989938849e+21, -0.434254495375077, 0.0413386758998794,
+                                      -0.516616898694849, "Fixed effects", "<unicode>", -0.35404424507026,
+                                      "TRUE", 46.1842149375581, -0.691684127331745, 0.194674438261359,
+                                      -1.05371165363577, "Random effects", "<unicode>", -0.29988113833234,
+                                      1, "FALSE", 8.63965964148833e+26, 0.585325517009774, 0.167159875616352,
+                                      0.343234248728213, "Random effects", "<unicode>", 0.993677396740531,
+                                      2, "TRUE", 46.184214937558, -0.691684144187806, 0.195426184793392,
+                                      -1.05915644399236, "Averaged", "<unicode>", -0.277506371377729,
+                                      3, "FALSE", 8.82672917711143e+26, "", "", "", "Averaged", "<unicode>",
                                       ""))
 })
 
 test_that("Effect Sizes per Study table results match", {
-  testthat::skip_on_os(c("mac", "linux", "solaris"))
   table <- results[["results"]][["effectSizePerStudy"]][["data"]]
   jaspTools::expect_equal_tables(table,
-                                list(-0.810675161337492, -1.68394255502823, 0.00390957421349684, -0.9387,
-                                      "Study 1", -1.28269463814809, -2.02557257455892, -0.578076727966483,
-                                      -1.6662, "Study 2", -0.996207535379598, -1.91697987764739, -0.137535263863821,
-                                      -1.3863, "Study 3", -1.40296899560657, -1.68366211044064, -1.12263629534387,
-                                      -1.4564, "Study 4", -0.291114685435556, -0.70248689247515, 0.129769093323344,
-                                      -0.2191, "Study 5", -0.948970505192553, -1.14550800371907, -0.75676856452674,
-                                      -0.9581, "Study 6", -1.23621664010226, -2.02727979088307, -0.506882158451203,
-                                      -1.6338, "Study 7", 0.00212364835628054, -0.121206326357141,
-                                      0.126228703001128, 0.012, "Study 8", -0.50606742399599, -0.934996647644956,
-                                      -0.0771038611477936, -0.4717, "Study 9", -1.25397766949404,
-                                      -1.74487198539962, -0.762447203053708, -1.4012, "Study 10",
-                                      -0.355110794879739, -0.573286768149591, -0.141056308764899,
-                                      -0.3408, "Study 11", -0.266903956259088, -1.19606414841548,
-                                      0.753566949784523, 0.4466, "Study 12", -0.148194690282786, -0.628570090461296,
-                                      0.345693436706941, -0.0173, "Study 13"))
+                                 list(-0.809128072433214, -1.65195861984318, 0.0291494666483802, -0.9387,
+                                      "Study 1", -1.27392183924008, -2.04585172754217, -0.550502001072192,
+                                      -1.6662, "Study 2", -0.987605843372775, -1.89764125756983, -0.131147744375098,
+                                      -1.3863, "Study 3", -1.4025680591068, -1.67918997790265, -1.13439697200656,
+                                      -1.4564, "Study 4", -0.292551414527035, -0.713785940836336,
+                                      0.150204176975293, -0.2191, "Study 5", -0.948574718058429, -1.14002067256022,
+                                      -0.754825669673909, -0.9581, "Study 6", -1.23879932796539, -2.02118617092247,
+                                      -0.514836725420342, -1.6338, "Study 7", 0.00199996360424655,
+                                      -0.11868785432434, 0.121531187105811, 0.012, "Study 8", -0.511556112765042,
+                                      -0.939053440577442, -0.0814585678966693, -0.4717, "Study 9",
+                                      -1.25406731815491, -1.76606641390657, -0.751053323311322, -1.4012,
+                                      "Study 10", -0.354049282748894, -0.568645513271642, -0.143878543957096,
+                                      -0.3408, "Study 11", -0.264061608492473, -1.16024809868433,
+                                      0.690555229532794, 0.4466, "Study 12", -0.147144689281277, -0.643591471297769,
+                                      0.355581782256767, -0.0173, "Study 13"))
 })
 
 test_that("Observed study effects plot matches", {
@@ -110,13 +108,11 @@ test_that("Model Probabilities table results match", {
   if (Sys.info()["sysname"] == "Darwin")
     testthat::skip("this test doesn't work on macOS + maybe a reason for future us to look at")
 
-  table <- results[["results"]][["modelProbability"]][["data"]]
-  jaspTools::expect_equal_tables(table,
-                                 list("Fixed H<unicode><unicode><unicode>", 2.40853635687008e-49, 0.25,
-                                      "Fixed H<unicode><unicode><unicode>", 1.13292249023919e-27,
-                                      0.25, "Random H<unicode><unicode><unicode>", 0.0211935284146057,
-                                      0.25, "Random H<unicode><unicode><unicode>", 0.978806471585394,
-                                      0.25))
+    table <- results[["results"]][["modelProbability"]][["data"]]
+    jaspTools::expect_equal_tables(table,
+                                   list("Fixed H<unicode>", 2.40853635687009e-49, 0.25, "Fixed H<unicode>",
+                                        1.13292249023919e-27, 0.25, "Random H<unicode>", 0.0211935284146057,
+                                        0.25, "Random H<unicode>", 0.978806471585394, 0.25))
 })
 
 test_that("Effect Size plot matches", {
@@ -131,4 +127,4 @@ test_that("Heterogeneity plot matches", {
   plotName <- results[["results"]][["priorContainer"]][["collection"]][["priorContainer_SE"]][["data"]]
   testPlot <- results[["state"]][["figures"]][[plotName]][["obj"]]
   jaspTools::expect_equal_plots(testPlot, "heterogeneity-2")
-})
+})