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Add structural invariance and meanstructure identification options #193

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merged 5 commits into from
Nov 5, 2023
Merged

Add structural invariance and meanstructure identification options #193

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fb5a8ba
fix degrees of freedom bug for configural invariance testing
juliuspfadt Jan 20, 2022
50c06ba
add intercepts option and fix grouping bug
juliuspfadt Aug 18, 2023
5ac4d74
add structural invariance
juliuspfadt Nov 3, 2023
e26c90b
add more options to meanstrcuture
juliuspfadt Nov 3, 2023
350ec6c
remove commented code
juliuspfadt Nov 5, 2023
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116 changes: 41 additions & 75 deletions R/confirmatoryfactoranalysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@ gettextf <- function(fmt, ..., domain = NULL) {
confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ...) {
jaspResults$addCitation("Rosseel, Y. (2012). lavaan: An R Package for Structural Equation Modeling. Journal of Statistical Software, 48(2), 1-36. URL http://www.jstatsoft.org/v48/i02/")


# Preprocess options
options <- .cfaPreprocessOptions(options)

Expand Down Expand Up @@ -180,13 +179,14 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..

# define estimator from options
estimator = switch(options[["estimator"]],
"default" = "default",
"maximumLikelihood" = "ML",
"generalizedLeastSquares" = "GLS",
"weightedLeastSquares" = "WLS",
"unweightedLeastSquares" = "ULS",
"diagonallyWeightedLeastSquares" = "DWLS"
)
"default" = "default",
"maximumLikelihood" = "ML",
"generalizedLeastSquares" = "GLS",
"weightedLeastSquares" = "WLS",
"unweightedLeastSquares" = "ULS",
"diagonallyWeightedLeastSquares" = "DWLS"
)


cfaResult[["lav"]] <- try(lavaan::lavaan(
model = mod,
Expand All @@ -198,8 +198,10 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
std.lv = options$modelIdentification == "factorVariance",
auto.fix.first = options$modelIdentification == "markerVariable",
orthogonal = options$factorsUncorrelated,
int.ov.free = TRUE,
int.lv.free = FALSE,
int.ov.free = (options$interceptsFixedToZero == "latent" || options$interceptsFixedToZero == "meanManifest"),
int.lv.free = (options$interceptsFixedToZero == "manifest" || options$interceptsFixedToZero == "meanManifest"),
effect.coding = ifelse(options$modelIdentification == "effectsCoding", TRUE,
ifelse(options$interceptsFixedToZero == "meanManifest", "intercepts", FALSE)),
auto.fix.single = TRUE,
auto.var = TRUE,
auto.cov.lv.x = TRUE,
Expand All @@ -210,7 +212,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
estimator = estimator,
missing = ifelse(options$naAction == "twoStageRobust", "robust.two.stage",
ifelse(options$naAction == "twoStage", "two.stage", options$naAction))
))
))

# are there ordered variables in the data?
cfaResult[["orderedVariables"]] <- any(sapply(dataset, is.ordered))
Expand Down Expand Up @@ -264,7 +266,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
jaspResults[["stateCFAResult"]]$dependOn(c(
"factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification",
"factorsUncorrelated", "packageMimiced", "estimator", "naAction", "seType", "bootstrapSamples",
"group", "invarianceTesting"
"group", "invarianceTesting", "interceptsFixedToZero"

))

Expand Down Expand Up @@ -378,45 +380,8 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
rc <- NULL
}

#' I dont think we need this bit of code, as setting meanstructure to TRUE
#' does already fix the latent means to zero across groups,
#' which is exactly what this piece of code does
if (options$meanStructure && options$group != "") {
lm <- "# Latent means"
lvs <- c(cfaResult[["spec"]]$latents, cfaResult[["spec"]]$soLatents)
for (i in seq_along(lvs)) {
lm <- paste0(lm, '\n', lvs[i], " ~ c(0,",
paste(rep(NA, length(unique(na.omit(dataset[[gv]]))) - 1), collapse = ","),
")*1")
}
} else {
lm <- NULL
}
# lm <- NULL

if (options$modelIdentification == "effectsCoding") {
ef <- "# effects coding restrictions"
for (i in 1:length(labels)) {
if (nchar(options$group) == 0 || options$invarianceTesting !="configural") {
restr <- paste0(labels[[i]][1], " == ",
paste(c(length(labels[[i]]), labels[[i]][-1]),
collapse = " - "))
ef <- paste0(ef, "\n", restr)
} else { # configural invarianceTesting
restr <- ""
for (j in 1:n_levels) {
restr <- paste0(restr, unlist(labels[[i]][1])[j], " == ",
paste(c(length(labels[[i]]), lapply(labels[[i]][-1], function(x) x[j])),
collapse = " - "), "\n")
}
ef <- paste0(ef, "\n", restr)
}
}
} else {
ef <- NULL
}

return(list(model = paste0(c(fo, so, rc, lm, ef), collapse = "\n\n"), simple_model = fo_simp))
return(list(model = paste0(c(fo, so, rc), collapse = "\n\n"), simple_model = fo_simp))
}

.CFAInvariance <- function(options) {
Expand All @@ -425,7 +390,9 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
"configural" = return(""),
"metric" = return("loadings"),
"scalar" = return(c("loadings", "intercepts")),
"strict" = return(c("loadings", "intercepts", "residuals", "residual.covariances"))
"strict" = return(c("loadings", "intercepts", "residuals", "residual.covariances")),
"structural" = return(c("loadings", "intercepts", "residuals", "residual.covariances",
"means", "lv.variances", "lv.covariances"))
)
}

Expand All @@ -436,7 +403,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
jaspResults[["maincontainer"]]$dependOn(c(
"factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification",
"factorsUncorrelated", "packageMimiced", "estimator", "naAction", "seType", "bootstrapSamples",
"group", "invarianceTesting"
"group", "invarianceTesting", "interceptsFixedToZero"
))
}

Expand Down Expand Up @@ -493,7 +460,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..

jaspResults[["maincontainer"]][["kmo"]] <- tabkmo <- createJaspTable(gettext("Kaiser-Meyer-Olkin (KMO) test"))
tabkmo$addColumnInfo(name = "indicator", title = "Indicator", type = "string")
tabkmo$dependOn(c("factors", "naAction", "group", "kaiserMeyerOlkinTest"))
tabkmo$dependOn("kaiserMeyerOlkinTest")
if (is.null(cfaResult)) return()

cov_implied <- lavaan::fitted(cfaResult[["lav"]])
Expand Down Expand Up @@ -523,7 +490,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
if (!options$bartlettTest || !is.null(jaspResults[["maincontainer"]][["bartlett"]])) return()

jaspResults[["maincontainer"]][["bartlett"]] <- tabbartlett <- createJaspTable(gettext("Bartlett's test of sphericity"))
tabbartlett$dependOn(c("factors", "naAction", "group", "bartlettTest"))
tabbartlett$dependOn("bartlettTest")
if (is.null(cfaResult)) return()

cov_implied <- lavaan::fitted(cfaResult[["lav"]])
Expand Down Expand Up @@ -562,8 +529,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
jaspResults[["maincontainer"]][["rSquared"]] <- tabr2 <- createJaspTable(gettext("R-Squared"))
tabr2$addColumnInfo(name = "__var__", title = "", type = "string")
tabr2$setExpectedSize(rows = 1, cols = 1)
tabr2$dependOn(c("factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification", "factorsUncorrelated",
"packageMimiced", "estimator", "naAction", "seType", "bootstrapSamples", "group", "invarianceTesting", "rSquared"))
tabr2$dependOn("rSquared")

if (is.null(cfaResult)) return()

Expand Down Expand Up @@ -596,8 +562,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
.cfaTableFitMeasures <- function(jaspResults, options, cfaResult) {
if (!options$fitMeasures || !is.null(jaspResults[["maincontainer"]][["fits"]])) return()
jaspResults[["maincontainer"]][["fits"]] <- fitms <- createJaspContainer(gettext("Additional fit measures"))
fitms$dependOn(c("factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification", "factorsUncorrelated",
"packageMimiced", "estimator", "naAction", "seType", "bootstrapSamples", "group", "invarianceTesting", "fitMeasures"))
fitms$dependOn("fitMeasures")

# Fit indices
fitms[["indices"]] <- fitin <- createJaspTable(gettext("Fit indices"))
Expand Down Expand Up @@ -685,7 +650,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
jaspResults[["estimates"]] <- ests <- createJaspContainer(gettext("Parameter estimates"), position = 2)
ests$dependOn(c("factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification",
"factorsUncorrelated", "packageMimiced", "estimator", "naAction", "seType", "bootstrapSamples",
"group", "invarianceTesting", "standardized", "ciLevel"))
"group", "invarianceTesting", "standardized", "ciLevel", "interceptsFixedToZero"))


footnote <- NULL
Expand Down Expand Up @@ -915,9 +880,9 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
rc$addColumnInfo(name = "pvalue", title = gettext("p"), type = "number", format = "dp:3;p:.001")

rc$addColumnInfo(name = "ci.lower", title = gettext("Lower"), type = "number", format = "sf:4;dp:3",
overtitle = gettextf("%s%% Confidence Interval", options$ciLevel * 100))
overtitle = gettextf("%s%% Confidence Interval", options$ciLevel * 100))
rc$addColumnInfo(name = "ci.upper", title = gettext("Upper"), type = "number", format = "sf:4;dp:3",
overtitle = gettextf("%s%% Confidence Interval", options$ciLevel * 100))
overtitle = gettextf("%s%% Confidence Interval", options$ciLevel * 100))

if (options$standardized != "none")
rc$addColumnInfo(name = paste0("std.", standardization),
Expand Down Expand Up @@ -950,13 +915,13 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
fi$addColumnInfo(name = "pvalue", title = gettext("p"), type = "number", format = "dp:3;p:.001")

fi$addColumnInfo(name = "ci.lower", title = gettext("Lower"), type = "number", format = "sf:4;dp:3",
overtitle = gettextf("%s%% Confidence Interval", options$ciLevel * 100))
overtitle = gettextf("%s%% Confidence Interval", options$ciLevel * 100))
fi$addColumnInfo(name = "ci.upper", title = gettext("Upper"), type = "number", format = "sf:4;dp:3",
overtitle = gettextf("%s%% Confidence Interval", options$ciLevel * 100))
overtitle = gettextf("%s%% Confidence Interval", options$ciLevel * 100))

if (options$standardized != "none")
fi$addColumnInfo(name = paste0("std.", standardization), title = gettextf("Std. Est. (%s)", standardization),
type = "number", format = "sf:4;dp:3")
type = "number", format = "sf:4;dp:3")

# add data
fidat <- pei[pei$op == "~1" & pei$lhs %in% facNames, colSel[!colSel %in% 'rhs']]
Expand Down Expand Up @@ -986,7 +951,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..

if (options$standardized != "none")
vi$addColumnInfo(name = paste0("std.", standardization), title = gettextf("Std. Est. (%s)", standardization),
type = "number", format = "sf:4;dp:3")
type = "number", format = "sf:4;dp:3")

# add data
vidat <- pei[pei$op == "~1" & !pei$lhs == "SecondOrder" & !pei$lhs %in% facNames,
Expand All @@ -1002,12 +967,12 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..

# Thresholds
if ("|" %in% pei$op) {
.thresholdsTable(jrobject, footnote, options, standardization, pei, colSel, cfaResult)
.cfaThresholdsTable(jrobject, footnote, options, standardization, pei, colSel, cfaResult)
}

}

.thresholdsTable <- function(jrobject, footnote, options, standardization, pei, colSel, cfaResult) {
.cfaThresholdsTable <- function(jrobject, footnote, options, standardization, pei, colSel, cfaResult) {
# Manifest variable intercepts
jrobject[["Thresholds"]] <- th <- createJaspTable(title = gettext("Thresholds"))
if (!is.null(footnote)) th$addFootnote(footnote)
Expand Down Expand Up @@ -1049,8 +1014,8 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
mi <- try(lavaan::modindices(cfaResult[["lav"]]))
jaspResults[["modind"]] <- mic <- createJaspContainer(gettext("Modification Indices"), position = 5)
mic$dependOn(c("factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification", "factorsUncorrelated",
"packageMimiced", "estimator", "naAction", "seType", "bootstrapSamples", "group", "invarianceTesting", "modificationIndices",
"modificationIndicesCutoff"))
"packageMimiced", "estimator", "naAction", "seType", "bootstrapSamples", "group", "invarianceTesting", "modificationIndices",
"modificationIndicesCutoff", "interceptsFixedToZero"))

if (isTryError(mi)) {
mic$setError(.extractErrorMessage(mi))
Expand Down Expand Up @@ -1185,7 +1150,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..

icc$dependOn(c("factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification",
"factorsUncorrelated", "packageMimiced", "estimator", "naAction", "seType", "bootstrapSamples",
"group", "invarianceTesting", "impliedCovarianceMatrix"))
"group", "invarianceTesting", "impliedCovarianceMatrix", "interceptsFixedToZero"))
}

.cfaTableResCov <- function(jaspResults, options, cfaResult) {
Expand Down Expand Up @@ -1219,7 +1184,8 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
}

rcc$dependOn(c("factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification", "factorsUncorrelated",
"packageMimiced", "estimator", "naAction", "seType", "bootstrapSamples", "group", "invarianceTesting", "residualCovarianceMatrix"))
"packageMimiced", "estimator", "naAction", "seType", "bootstrapSamples", "group", "invarianceTesting",
"residualCovarianceMatrix", "interceptsFixedToZero"))
}

.cfaInitPlots <- function(jaspResults, options, cfaResult) {
Expand All @@ -1228,7 +1194,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
jaspResults[["plots"]] <- createJaspContainer(gettext("Plots"), position = 6)
jaspResults[["plots"]]$dependOn(c(
"factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification", "factorsUncorrelated", "packageMimiced",
"estimator", "naAction", "seType", "bootstrapSamples", "group", "invarianceTesting"
"estimator", "naAction", "seType", "bootstrapSamples", "group", "invarianceTesting", "interceptsFixedToZero"
))
}

Expand Down Expand Up @@ -1385,7 +1351,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
aveTable$addColumnInfo(name = "factor", title = gettext("Factor"), type = "string")
aveTable$addColumnInfo(name = "ave", title = gettext("AVE"), type = "number")
aveTable$dependOn(c("factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification", "factorsUncorrelated",
"packageMimiced", "estimator", "naAction", "group", "invarianceTesting", "ave"))
"packageMimiced", "estimator", "naAction", "group", "invarianceTesting", "ave", "interceptsFixedToZero"))

if (options$group != "") {
ave_result <- semTools::AVE(cfaResult[["lav"]])
Expand All @@ -1410,7 +1376,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..

htmtTable <- createJaspTable(gettext("Heterotrait-monotrait ratio"), position = 4.2)
htmtTable$dependOn(c("factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification", "factorsUncorrelated",
"packageMimiced", "estimator", "naAction", "group", "invarianceTesting", "htmt"))
"packageMimiced", "estimator", "naAction", "group", "invarianceTesting", "htmt", "interceptsFixedToZero"))

if (options[["group"]] != "") {
htmtTable$addColumnInfo(name = "group", title = gettext("Group"), type = "string", combine = TRUE)
Expand Down Expand Up @@ -1473,7 +1439,7 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ..
relTable$addColumnInfo(name = "rel", title = gettextf("Coefficient %s", "\u03C9"), type = "number")
relTable$addColumnInfo(name = "alpha", title = gettextf("Coefficient %s", "\u03B1"), type = "number")
relTable$dependOn(c("factors", "secondOrder", "residualsCovarying", "meanStructure", "modelIdentification", "factorsUncorrelated",
"packageMimiced", "estimator", "naAction", "group", "invarianceTesting", "reliability"))
"packageMimiced", "estimator", "naAction", "group", "invarianceTesting", "reliability", "interceptsFixedToZero"))

nfac <- length(cfaResult[["spec"]][["latents"]])

Expand Down
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