more estimators for cfa, change standardization output

jasp-stats · Oct 14, 2024 · dff0f98 · dff0f98
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: jaspFactor
 Type: Package
 Title: Factor Module for JASP
 Version: 0.19.0
-Date: 2023-04-14
+Date: 2024-08-19
 Author: JASP Team
 Website: jasp-stats.org
 Maintainer: JASP Team <[email protected]>

diff --git a/R/confirmatoryfactoranalysis.R b/R/confirmatoryfactoranalysis.R
diff --git a/inst/help/ConfirmatoryFactorAnalysis.md b/inst/help/ConfirmatoryFactorAnalysis.md
@@ -60,7 +60,7 @@ JASP allows the factors in turn to be indicators of a second-order factor. This
 ### Advanced
 -------
 - Emulation: Emulate results from different software
-- Error calculation: Change how standard errors for the parameters are computed
+- Error calculation: Change how standard errors for the parameters are computed, if bootstrap the CIs are percentile bootstrap type
 - Estimator: change the estimator for the CFA (Auto: ML if only scale variables used, WLS otherwise)
 - Standardization: display standardized parameters for different standardization schemes
 - Missing data handling: change the missing data handling method.

diff --git a/inst/help/forQml/tooltipEstimators.md b/inst/help/forQml/tooltipEstimators.md
@@ -0,0 +1,21 @@
+
+### Help on Estimators
+Some of the estimators come with options that are set in the background:
+
+- Estimators without extra effects (standard errors and model test are standard):
+	- ML, GLS, WLS, ULS, DWLS, DLS
+
+- Extensions of ML-estimators with extra effects: 
+	- MLM: classic robust se (se="robust.sem"), Satorra-Bentler test statistic (test="satorra.bentler")
+	- MLMV: classic robust se, scaled and shifted test statistic (test="scaled.shifted")
+	- MLMVS: classic robust se, mean and var adjusted Satterthwaite style test statistic (test="mean.var.adjusted")
+	- MLF: first-order standard se (information="first.order"), standard test
+	- MLR: Huber-White robust se (se="robust.huber.white"), Yuan-Bentler T2-star test statistic (test="yuan.bentler.mplus")
+
+- Others: 
+	- WLSM: implies DWLS with scaled test and robust se
+	- WLSMV: implies DWLS with mean and var adjusted test and robust se
+	- ULSM: implies ULS with scaled test and robust se
+	- ULSMV: implies ULS with mean-var adjusted test and robust se
+
+- Note: If you specify "Standard errors" instead of leaving it at default the corresponding options set by the estimators in the background will be overwritten
diff --git a/inst/qml/ConfirmatoryFactorAnalysis.qml b/inst/qml/ConfirmatoryFactorAnalysis.qml
@@ -102,8 +102,8 @@ Form
 				label: qsTr("Model identification")
 				name: "modelIdentification"
 				values: [
-					{ label: qsTr("Factor variances"),	value: "factorVariance" },
 					{ label: qsTr("Marker variable"),	value: "markerVariable" },
+					{ label: qsTr("Factor variances"),	value: "factorVariance" },
 					{ label: qsTr("Effects coding"),	value: "effectsCoding"  }
 				]
 			}
@@ -206,64 +206,88 @@ Form
 	Section
 	{
 		title: qsTr("Advanced")
-		RadioButtonGroup
-		{
-			title: qsTr("Mimic package")
-			name: "packageMimiced"
-			RadioButton { label: qsTr("Lavaan"); value: "lavaan"  ; checked: true }
-			RadioButton { label: qsTr("Mplus") ; value: "Mplus" }
-			RadioButton { label: qsTr("EQS")   ; value: "EQS"   }
-		}
 
-		Group
-		{
-			title: qsTr("Error calculation")
-			CIField { text: qsTr("CI level"); name: "ciLevel" }
-			RadioButtonGroup
+		Group {
+			DropDown
 			{
-				title: qsTr("Standard error")
-				name: "seType"
-				RadioButton { label: qsTr("Standard");	value: "standard"; checked: true}
-				RadioButton { label: qsTr("Robust");		value: "robust" }
-				RadioButton {
-					label: qsTr("Bootstrap")
-					value: "bootstrap"
-					IntegerField {
-						label: qsTr("Bootstrap samples")
-						name: "bootstrapSamples"
-						defaultValue: 1000
-						min: 100
-						max: 1000000
-					}
+				name: "packageMimiced"
+				label: qsTr("Mimic")
+				values: [
+					{ label: qsTr("Lavaan"), value: "lavaan" },
+					{ label: qsTr("Mplus"), value: "mplus" },
+					{ label: qsTr("EQS"), value: "eqs" }
+				]
+			}
+			RowLayout 
+			{
+				DropDown
+				{
+					name: "estimator"
+					label: qsTr("Estimator")
+					id: estimator
+					values: [
+						{ label: qsTr("Default"), value: "default" },
+						{ label: qsTr("ML"), value: "ml" },
+						{ label: qsTr("GLS"), value: "gls" },
+						{ label: qsTr("WLS"), value: "wls" },
+						{ label: qsTr("ULS"), value: "uls" },
+						{ label: qsTr("DWLS"), value: "dwls" },
+						{ label: qsTr("DLS"), value: "dls" },
+						{ label: qsTr("PML"), value: "pml" },
+						{ label: qsTr("MLM"), value: "mlm" },
+						{ label: qsTr("MLMV"), value: "mlmv" },
+						{ label: qsTr("MLMVS"), value: "mlmvs" },
+						{ label: qsTr("MLF"), value: "mlf" },
+						{ label: qsTr("MLR"), value: "mlr" },
+						{ label: qsTr("WLSM"), value: "wlsm" },
+						{ label: qsTr("WLSMV"), value: "wlsmv" },
+						{ label: qsTr("ULSM"), value: "ulsm" },
+						{ label: qsTr("ULSMV"), value: "ulsmv" }
+					]
+				}
+				HelpButton
+				{
+					toolTip: 					qsTr("Click for more information")
+					helpPage:					"forQml/tooltipEstimators"
 				}
 			}
-		}
-
-		RadioButtonGroup
-		{
-			title: qsTr("Estimator")
-			name: "estimator"
-			RadioButton { label: qsTr("Auto") ; value: "default"; checked: true }
-			RadioButton { label: qsTr("ML")   ; value: "maximumLikelihood"				}
-			RadioButton { label: qsTr("GLS")  ; value: "generalizedLeastSquares"		}
-			RadioButton { label: qsTr("WLS")  ; value: "weightedLeastSquares"			}
-			RadioButton { label: qsTr("ULS")  ; value: "unweightedLeastSquares"			}
-			RadioButton { label: qsTr("DWLS") ; value: "diagonallyWeightedLeastSquares"	}
-		}
-
-		DropDown
+			DropDown
+			{
+				label: qsTr("Standard errors")
+				name: "seType"
+				id: errorCalc
+				values: [
+					{ label: qsTr("Default"), 				value: "default"						},
+					{ label: qsTr("Standard"),  			value: "standard" 					},
+					{ label: qsTr("Robust"), 				value: "robust" 						},
+					{ label: qsTr("Bootstrap"), 			value: "bootstrap"					}
+				]
+			}
+			IntegerField
+			{
+				visible: errorCalc.value == "bootstrap"
+				name: "bootstrapSamples"
+				label: qsTr("     Bootstrap samples")
+				defaultValue: 1000
+				min: 100
+				max: 1000000
+			}
+			CIField { text: qsTr("     CI level"); name: "ciLevel" }
+
+			DropDown
 			{
 				name: "naAction"
 				label: qsTr("Missing data handling")
 				values:
 				[
-					{ label: qsTr("FIML")				, value: "fiml"				},
 					{ label: qsTr("Listwise deletion")	, value: "listwise"			},
+					{ label: qsTr("FIML")				, value: "fiml"				},
 					{ label: qsTr("Pairwise")			, value: "pairwise"			},
 					{ label: qsTr("Two-stage")			, value: "twoStage"			},
 					{ label: qsTr("Robust two-stage")	, value: "twoStageRobust"	},
 				]
 			}
+		}
 
 		RadioButtonGroup
 		{

diff --git a/tests/testthat/test-confirmatoryfactoranalysis.R b/tests/testthat/test-confirmatoryfactoranalysis.R
@@ -201,48 +201,44 @@ test_that("[CFA Second order] Chi-square test table results match", {
 })
 
 
-test_that("Bootstrapping works", {
-  options <- jaspTools::analysisOptions("confirmatoryFactorAnalysis")
-  options$group <- ""
-  options$invarianceTesting <- "configural"
-  options$packageMimiced <- "lavaan"
-  options$seType <- "bootstrap"
-  options$bootstrapSamples <- 100
-  options$estimator <- "default"
-  options$standardized <- "none"
-  options$factors <- list(
-    list(indicators = list("x1", "x2", "x3"), name = "Factor1", title = "Factor 1", types = rep("scale", 3)),
-    list(indicators = list("x4", "x5", "x6"), name = "Factor2", title = "Factor 2", types = rep("scale", 3)),
-    list(indicators = list("x7", "x8", "x9"), name = "Factor3", title = "Factor 3", types = rep("scale", 3))
-  )
-  options$modelIdentification <- "factorVariance"
-  options$naAction <- "listwise"
-  set.seed(1)
-  results <- jaspTools::runAnalysis("confirmatoryFactorAnalysis", "holzingerswineford.csv", options)
+# factor loadings with bootstrapping are correct
+options <- jaspTools::analysisOptions("confirmatoryFactorAnalysis")
+options$group <- ""
+options$invarianceTesting <- "configural"
+options$packageMimiced <- "lavaan"
+options$seType <- "bootstrap"
+options$bootstrapSamples <- 100
+options$estimator <- "default"
+options$standardized <- "none"
+options$factors <- list(
+  list(indicators = list("x1", "x2", "x3"), name = "Factor1", title = "Factor 1", types = rep("scale", 3)),
+  list(indicators = list("x4", "x5", "x6"), name = "Factor2", title = "Factor 2", types = rep("scale", 3)),
+  list(indicators = list("x7", "x8", "x9"), name = "Factor3", title = "Factor 3", types = rep("scale", 3))
+)
+options$modelIdentification <- "factorVariance"
+options$naAction <- "listwise"
+set.seed(1)
+results <- jaspTools::runAnalysis("confirmatoryFactorAnalysis", "holzingerswineford.csv", options)
 
+test_that("Factor loadings table results match", {
   table <- results[["results"]][["estimates"]][["collection"]][["estimates_fl1"]][["data"]]
   jaspTools::expect_equal_tables(table,
-                                 list(0.712022271311838, 1.11279383173753, 0.899620313867488,
-                                      "Factor 1", 0, "x1", 0.0808465333987386, 11.1275063512065, 0.339182433474584,
-                                      0.693156723678194, 0.49794051110941, "Factor 1",
-                                      1.28623778294923e-10, "x2", 0.0774547818506273, 6.42878979466621,
-                                      0.539990088382033, 0.805660643384033, 0.656156092628451,
-                                      "Factor 1", 0, "x3", 0.0744212256974568, 8.81678696472846, 0.856032790026098,
-                                      1.08543684864592, 0.989693449094392, "Factor 2",
-                                      0, "x4", 0.0566367179185465, 17.4744138690689, 0.954112872546464,
-                                      1.24054019999221, 1.10160465003145, "Factor 2",
-                                      0, "x5", 0.0626757561168699, 17.5762482701815, 0.803928010900409,
-                                      1.03630968014001, 0.916600977759373, "Factor 2",
-                                      0, "x6", 0.0536584940344529, 17.0821226769958, 0.375767927218761,
-                                      0.741040160352204, 0.619475433557926, "Factor 3",
-                                      0, "x7", 0.0695825769015842, 8.90273774186456, 0.506218568773711,
-                                      0.900974372672674, 0.730948802915075, "Factor 3",
-                                      0, "x8", 0.0659093164600047, 11.0902197469857, 0.498364732719689,
-                                      0.860170344673322, 0.669980108781259, "Factor 3",
-                                      0, "x9", 0.0650169734598685, 10.3046954222623))
-
-
-
+                                 list(0.712022271311838, 1.11279383173753, 0.899620313867488, "Factor 1",
+                                      0, "x1", 0.101880932132255, 8.8301146744482, 0.339182433474583,
+                                      0.693156723678194, 0.49794051110941, "Factor 1", 5.03185138001072e-09,
+                                      "x2", 0.0851745954124038, 5.84611536689373, 0.539990088382032,
+                                      0.805660643384033, 0.656156092628451, "Factor 1", 0, "x3", 0.0702283472359389,
+                                      9.34318004699771, 0.856032790026097, 1.08543684864592, 0.989693449094393,
+                                      "Factor 2", 0, "x4", 0.060824826209009, 16.2712088266979, 0.954112872546464,
+                                      1.24054019999221, 1.10160465003145, "Factor 2", 0, "x5", 0.0610564023902934,
+                                      18.042410081577, 0.803928010900409, 1.03630968014001, 0.916600977759372,
+                                      "Factor 2", 0, "x6", 0.0544830064226891, 16.8236123140528, 0.37576792721876,
+                                      0.741040160352204, 0.619475433557926, "Factor 3", 7.69848629289527e-11,
+                                      "x7", 0.0952105063825611, 6.50637683901018, 0.50621856877371,
+                                      0.900974372672673, 0.730948802915075, "Factor 3", 2.32125429988628e-12,
+                                      "x8", 0.104217630469302, 7.0136770489172, 0.498364732719688,
+                                      0.860170344673323, 0.669980108781259, "Factor 3", 5.52868861802835e-12,
+                                      "x9", 0.0972211926575642, 6.8912969535468))
 })