add mean structure option fixing mean intercepts to zero (#186)

jasp-stats · Nov 5, 2023 · 6797d29 · 6797d29
1 parent 9a4d9b8
commit 6797d29
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Showing 3 changed files with 47 additions and 5 deletions.
diff --git a/R/sem.R b/R/sem.R
@@ -207,7 +207,7 @@ checkLavaanModel <- function(model, availableVars) {
                               "dependentCorrelation", "threshold", "scalingParameter", "efaConstrained", "standardizedVariable", "naAction", "estimator", "test",
                               "errorCalculationMethod", "informationMatrix", "emulation", "group", "equalLoading", "equalIntercept",
                               "equalResidual", "equalResidualCovariance", "equalMean", "equalThreshold", "equalRegression",
-                              "equalVariance", "equalLatentCovariance", "dataType", "sampleSize", "freeParameters"))
+                              "equalVariance", "equalLatentCovariance", "dataType", "sampleSize", "freeParameters", "manifestMeanFixedToZero"))
     jaspResults[["modelContainer"]] <- modelContainer
   }
 
@@ -331,15 +331,15 @@ checkLavaanModel <- function(model, availableVars) {
 
   lavopts[["mimic"]] <- options[["emulation"]]
 
-
   # model features
   lavopts[["meanstructure"]]   <- options[["meanStructure"]]
   lavopts[["int.ov.free"]]     <- !options[["manifestInterceptFixedToZero"]]
   lavopts[["int.lv.free"]]     <- !options[["latentInterceptFixedToZero"]]
   lavopts[["fixed.x"]]         <- options[["exogenousCovariateFixed"]]
   lavopts[["orthogonal"]]      <- options[["orthogonal"]]
   lavopts[["std.lv"]]          <- options[["factorScaling"]] == "factorVariance"
-  lavopts[["effect.coding"]]   <- options[["factorScaling"]] == "effectCoding"
+  lavopts[["effect.coding"]]   <- ifelse(options[["factorScaling"]] == "effectCoding", TRUE,
+                                         ifelse(options[["manifestMeanFixedToZero"]], "intercepts", FALSE))
   lavopts[["auto.fix.first"]]  <- options[["factorScaling"]] == "factorLoading"
   lavopts[["auto.fix.single"]] <- options[["residualSingleIndicatorOmitted"]]
   lavopts[["auto.var"]]        <- options[["residualVariance"]]
@@ -751,7 +751,7 @@ checkLavaanModel <- function(model, availableVars) {
 
   # Means
   if (options[["meanStructure"]]) {
-    mutab <- createJaspTable(title = gettext("Means"))
+    mutab <- createJaspTable(title = gettext("Intercepts"))
 
     if (options[["group"]] != "")
       mutab$addColumnInfo(name = "group",  title = gettext("Group"),      type = "string", combine = TRUE)

diff --git a/inst/qml/SEM.qml b/inst/qml/SEM.qml
@@ -154,8 +154,9 @@ Form
 				]
 			}
 			CheckBox { name: "meanStructure";					label: qsTr("Include mean structure")							}
-			CheckBox { name: "manifestInterceptFixedToZero";	label: qsTr("Fix manifest intercepts to zero")					}
 			CheckBox { name: "latentInterceptFixedToZero";		label: qsTr("Fix latent intercepts to zero");	checked: true	}
+			CheckBox { name: "manifestInterceptFixedToZero";	label: qsTr("Fix manifest intercepts to zero")					}
+			CheckBox { name: "manifestMeanFixedToZero";		label: qsTr("Fix mean of manifest intercepts to zero")}
 			CheckBox { name: "orthogonal";						label: qsTr("Assume factors uncorrelated")						}
 		}
 

diff --git a/tests/testthat/test-sem.R b/tests/testthat/test-sem.R
@@ -652,3 +652,44 @@ test_that("Variance-covariance input works", {
                                       "", "", 1095.63355300897, 1109.53848169019, 0, 0, "Model2", 75,
                                       1, "", 0, 0))
 })
+
+
+test_that("Fixing mean manifest intercepts works", {
+  options <- jaspTools::analysisOptions("SEM")
+  options$models <- list(list(name = "Model1", syntax = list(model = "factor =~ x2 + x3 + y1 + x1", columns = c("x1", "x2", "x3", "y1"))))
+  options$emulation         <- "lavaan"
+  options$estimator         <- "default"
+  options$meanStructure     <- TRUE
+  options$manifestMeanFixedToZero <- TRUE
+  options$group             <- "group"
+  options$samplingWeights   <- ""
+  options$informationMatrix <- "expected"
+  options$naAction          <- "fiml"
+  options$modelTest         <- "standard"
+
+  set.seed(1)
+
+  results <- jaspTools::runAnalysis("SEM", "poldem_grouped.csv", options)
+  table <- results[["results"]][["modelContainer"]][["collection"]][["modelContainer_params"]][["collection"]][["modelContainer_params_mu"]][["data"]]
+  jaspTools::expect_equal_tables(table,
+                                 list(-3.0031653252094, -0.238164753555845, -1.62066503938262, 1, "",
+                                      "x2", 0.0215840525894235, 0.705370250031003, -2.29760900649183,
+                                      -2.90748296601922, -0.257527727837225, -1.58250534692822, 1,
+                                      "", "x3", 0.0192367987813871, 0.676021411384215, -2.34091009586205,
+                                      -2.02601609127232, 3.81817181538369, 0.896077862055687, 1, "",
+                                      "y1", 0.547816766514775, 1.49089165738611, 0.601034862336494,
+                                      1.63165251250819, 2.98253253600213, 2.30709252425516, 1, "",
+                                      "x1", 2.16224815829946e-11, 0.344618583338652, 6.6946259888371,
+                                      5.33697746290641, 8.26080927533766, 6.79889336912203, 1, "",
+                                      "factor", 0, 0.745889168243412, 9.11515230222956, -4.07239223241945,
+                                      -0.696581025547053, -2.38448662898325, 2, "", "x2", 0.00562595928754916,
+                                      0.861192152891677, -2.76882066444372, -3.8707672830057, -0.886230339808109,
+                                      -2.37849881140691, 2, "", "x3", 0.00178440810521097, 0.761375455554092,
+                                      -3.12394994356096, -0.553574385842091, 6.22823829704087, 2.83733195559939,
+                                      2, "", "y1", 0.101006267898262, 1.73008604657459, 1.63999470501311,
+                                      1.12212007800144, 2.7291868915801, 1.92565348479077, 2, "",
+                                      "x1", 2.63986228365987e-06, 0.409973557232427, 4.69701874869713,
+                                      5.05992393096499, 8.54168933431517, 6.80080663264008, 2, "",
+                                      "factor", 1.90958360235527e-14, 0.88822178132198, 7.65665374983052
+                                 ))
+})