added fit by group table #145
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| Original file line number | Diff line number | Diff line change |
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@@ -117,7 +117,7 @@ SEMInternal <- function(jaspResults, dataset, options, ...) { | |
| } | ||
| } | ||
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| # Check variance covariance matrix input and its implications: | ||
| if (options[["dataType"]] == "varianceCovariance") { | ||
| if (options[["meanStructure"]]) { | ||
| modelContainer$setError(gettext("Mean structure can not be included when data is variance-covariance matrix")) | ||
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@@ -143,6 +143,15 @@ SEMInternal <- function(jaspResults, dataset, options, ...) { | |
| return() | ||
| } | ||
| } | ||
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| # Check if meanstructure is true but then no checkbox to fix the intercepts to zero is checked | ||
| if (options[["meanStructure"]]) { | ||
| if (!any(c(options[["manifestInterceptFixedToZero"]], options[["latentInterceptFixedToZero"]], | ||
| options[["manifestMeanFixedToZero"]]))) { | ||
| .quitAnalysis(gettext("When mean structure is included, at least one of the checkboxes to fix the intercepts to zero has to be checked")) | ||
| return() | ||
| } | ||
| } | ||
| } | ||
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| checkLavaanModel <- function(model, availableVars) { | ||
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@@ -206,7 +215,7 @@ checkLavaanModel <- function(model, availableVars) { | |
| modelContainer <- createJaspContainer() | ||
| modelContainer$dependOn(c("samplingWeights", "meanStructure", "manifestInterceptFixedToZero", "latentInterceptFixedToZero", "exogenousCovariateFixed", "orthogonal", | ||
| "factorScaling", "residualSingleIndicatorOmitted", "residualVariance", "exogenousLatentCorrelation", | ||
| "dependentCorrelation", "threshold", "scalingParameter", "efaConstrained", "standardizedVariable", "naAction", "estimator", "modelTest", | ||
| "errorCalculationMethod", "informationMatrix", "emulation", "group", "equalLoading", "equalIntercept", | ||
| "equalResidual", "equalResidualCovariance", "equalMean", "equalThreshold", "equalRegression", | ||
| "equalLatentVariance", "equalLatentCovariance", "dataType", "sampleSize", "freeParameters", "manifestMeanFixedToZero")) | ||
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@@ -387,11 +396,11 @@ checkLavaanModel <- function(model, availableVars) { | |
| lavopts[["estimator"]] <- options[["estimator"]] | ||
| lavopts[["se"]] <- ifelse(options[["errorCalculationMethod"]] == "bootstrap", "standard", options[["errorCalculationMethod"]]) | ||
| lavopts[["information"]] <- options[["informationMatrix"]] | ||
| lavopts[["test"]] <- ifelse(options[["modelTest"]] == "satorraBentler", "satorra.bentler", | ||
|
There was a problem hiding this comment. The same here, was this a bug? |
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| ifelse(options[["modelTest"]] == "yuanBentler", "yuan.bentler", | ||
| ifelse(options[["modelTest"]] == "meanAndVarianceAdjusted", "mean.var.adjusted", | ||
| ifelse(options[["modelTest"]] == "scaledAndShifted", "scaled.shifted", | ||
| ifelse(options[["modelTest"]] == "bollenStine", "bollen.stine", | ||
| options[["modelTest"]]))))) | ||
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| # group.equal options | ||
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@@ -633,7 +642,12 @@ checkLavaanModel <- function(model, availableVars) { | |
| fittab$dependOn("models") | ||
| fittab$position <- 0 | ||
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| fittab$addColumnInfo(name = "Model", title = "", type = "string" , combine = TRUE) | ||
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| if (options[["group"]] != "") { | ||
| fittab$addColumnInfo(name = "group", title = gettext("Group"), type = "string" ) | ||
| } | ||
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| fittab$addColumnInfo(name = "AIC", title = gettext("AIC"), type = "number" ) | ||
| fittab$addColumnInfo(name = "BIC", title = gettext("BIC"), type = "number" ) | ||
| fittab$addColumnInfo(name = "N", title = gettext("n"), type = "integer") | ||
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@@ -643,12 +657,15 @@ checkLavaanModel <- function(model, availableVars) { | |
| overtitle = gettext("Baseline test")) | ||
| fittab$addColumnInfo(name = "PrChisq", title = gettext("p"), type = "pvalue", | ||
| overtitle = gettext("Baseline test")) | ||
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| if (length(options[["models"]]) > 1) { | ||
| fittab$addColumnInfo(name = "dchisq", title = "\u0394\u03C7\u00B2", type = "number" , | ||
| overtitle = gettext("Difference test")) | ||
| fittab$addColumnInfo(name = "ddf", title = gettextf("%1$sdf", "\u0394"), type = "integer", | ||
| overtitle = gettext("Difference test")) | ||
| fittab$addColumnInfo(name = "dPrChisq", title = gettext("p"), type = "pvalue" , | ||
| overtitle = gettext("Difference test")) | ||
| } | ||
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| modelContainer[["fittab"]] <- fittab | ||
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@@ -659,54 +676,65 @@ checkLavaanModel <- function(model, availableVars) { | |
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| if (modelContainer$getError()) return() | ||
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| testName <- switch(options[["modelTest"]], | ||
| "satorraBentler" = "satorra.bentler", | ||
| "yuanBentler" = "yuan.bentler", | ||
| "scaledAndShifted" = "scaled.shifted", | ||
| "meanAndVarianceAdjusted" = "mean.var.adjusted", | ||
| "bollenStine" = "bollen.stine", | ||
| options[["modelTest"]]) | ||
| if (testName == "default") | ||
| testName <- "standard" | ||
| if (length(semResults) == 1) { | ||
| lrt <- .withWarnings(lavaan::lavTestLRT(semResults[[1]], type = "Chisq")[-1, ]) | ||
| chiSq <- lavaan::lavInspect(semResults[[1]], what = "test")[[testName]]$stat | ||
| dfs <- lavaan::lavInspect(semResults[[1]], what = "test")[[testName]]$df | ||
| rownames(lrt$value) <- options[["models"]][[1]][["name"]] | ||
| Ns <- lavaan::lavInspect(semResults[[1]], "ntotal") | ||
| } else { | ||
| Ns <- vapply(semResults, lavaan::lavInspect, 0, what = "ntotal") | ||
| lrt_args <- semResults | ||
| names(lrt_args) <- "object" # (the first result is object, the others ...) | ||
| lrt_args[["model.names"]] <- vapply(options[["models"]], getElement, name = "name", "") | ||
| lrt_args[["type"]] <- "Chisq" | ||
| lrt <- .withWarnings(do.call(lavaan::lavTestLRT, lrt_args)) | ||
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| chiSq <- unlist(lapply(semResults, function(x) {lavaan::lavInspect(x, what = "test")[[testName]]$stat})) | ||
| dfs <- unlist(lapply(semResults, function(x) {round(lavaan::lavInspect(x, what = "test")[[testName]]$df, 3)})) | ||
| # because the LRT orders the models according to the df, we need to reorder this as well | ||
| chiSq <- chiSq[order(dfs)] | ||
| dfs <- sort(dfs) | ||
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| } | ||
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| dtFill <- data.frame(matrix(ncol = 0, nrow = length(rownames(lrt$value)))) | ||
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| dtFill[["Model"]] <- rownames(lrt$value) | ||
| dtFill[["AIC"]] <- lrt$value[["AIC"]] | ||
| dtFill[["BIC"]] <- lrt$value[["BIC"]] | ||
| dtFill[["N"]] <- Ns | ||
| dtFill[["Chisq"]] <- chiSq | ||
| dtFill[["Df"]] <- dfs | ||
| dtFill[["PrChisq"]] <- pchisq(q = chiSq, df = dfs, lower.tail = FALSE) | ||
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| if (length(options[["models"]]) > 1) { | ||
| dtFill[["dchisq"]] <- lrt$value[["Chisq diff"]] | ||
| dtFill[["ddf"]] <- lrt$value[["Df diff"]] | ||
| dtFill[["dPrChisq"]] <- lrt$value[["Pr(>Chisq)"]] | ||
| } | ||
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| # add warning footnote | ||
| fnote <- "" | ||
| if (!is.null(lrt$warnings)) { | ||
| fnote <- paste0(fnote, gsub("lavaan WARNING: ", "", lrt$warnings[[1]]$message)) | ||
| } | ||
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| if(options$naAction == "listwise"){ | ||
| nrm <- nrow(dataset) - lavaan::lavInspect(semResults[[1]], "ntotal") | ||
| if (nrm != 0) { | ||
| missingFootnote <- gettextf("A total of %g cases were removed due to missing values. You can avoid this by choosing 'FIML' under 'Missing Data Handling' in the Estimation options.", | ||
| nrm) | ||
| fnote <- paste0(fnote, missingFootnote) | ||
| } | ||
| } | ||
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@@ -729,13 +757,75 @@ checkLavaanModel <- function(model, availableVars) { | |
| "boot", gettext("bootstrap (Bollen-Stine) probability value") | ||
| ) | ||
| testname <- LUT[test == tolower(LUT$option), "name"][[1]] | ||
| if (length(semResults) == 1) | ||
| ftext <- gettextf("Baseline tests based on %s.", testname) | ||
| if (length(semResults) > 1) | ||
| ftext <- gettextf("Baseline tests based on %s. Difference tests based on a function of two standard test-statistics.", testname) | ||
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| fnote <- paste0(fnote, ftext) | ||
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| } | ||
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| if (options$estimator %in% c("dwls", "gls", "wls", "uls")) { | ||
| fnote <- paste0(fnote, gettext("The AIC, BIC and additional information criteria are only available with ML-type estimators")) | ||
| } | ||
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| if (options[["group"]] != "") { | ||
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| groupNames <- semResults[[1]]@[email protected] | ||
| models <- rep(rownames(lrt$value), each = length(groupNames)) | ||
| modelDfs <- unlist(lapply(semResults, function(x) {lavaan::lavInspect(x, what = "test")[[testName]]$df})) | ||
| ord <- match(modelDfs, sort(modelDfs)) | ||
| modelDfs <- modelDfs[ord] | ||
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| chiSq <- sapply(semResults, function(x) {lavaan::lavInspect(x, what = "test")[[testName]]$stat.group}) | ||
| logLGroup <- sapply(semResults, function(x) x@loglik$loglik.group) | ||
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| npar <- sapply(semResults, function(x) x@loglik$npar) | ||
| aics <- -2 * logLGroup + 2 * matrix(npar, nrow(logLGroup), ncol(logLGroup), byrow = TRUE) | ||
| Ns <- sapply(semResults, function(x) x@Data@nobs) | ||
| bics <- -2 * logLGroup + matrix(npar, nrow(logLGroup), ncol(logLGroup), byrow = TRUE) * matrix(sapply(Ns, log), nrow(Ns), ncol(Ns)) | ||
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| aics <- aics[, ord] | ||
| bics <- bics[, ord] | ||
| chiSq <- chiSq[, ord] | ||
| modelDfsRep <- rep(modelDfs, each = length(groupNames)) | ||
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| dtFillGroup <- data.frame(matrix(ncol = 0, nrow = length(models))) | ||
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| dtFillGroup[["Model"]] <- models | ||
| dtFillGroup[["group"]] <- rep(groupNames, length(rownames(lrt$value))) | ||
| dtFillGroup[["AIC"]] <- c(aics) | ||
| dtFillGroup[["BIC"]] <- c(bics) | ||
| dtFillGroup[["N"]] <- c(Ns) | ||
| dtFillGroup[["Chisq"]] <- c(chiSq) | ||
| dtFillGroup[["Df"]] <- c(modelDfsRep) | ||
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| dtFillGroup[["PrChisq"]] <- apply(data.frame(c(chiSq), modelDfsRep), 1, function(x) {pchisq(x[1], x[2], lower.tail = FALSE)}) | ||
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| # we want the LRT for multiple models | ||
| if (length(semResults) > 1) { | ||
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| nGroups <- length(groupNames) | ||
| dchisq <- diff(c(chiSq), lag = nGroups) | ||
| ddf <- diff(c(modelDfsRep), lag = nGroups) | ||
| dprchisq <- apply(data.frame(dchisq, ddf), 1, function(x) {pchisq(x[1], x[2], lower.tail = FALSE)}) | ||
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| dtFillGroup[["dchisq"]] <- c(rep(NA, nGroups), dchisq) | ||
| dtFillGroup[["ddf"]] <- c(rep(NA, nGroups), ddf) | ||
| dtFillGroup[["dPrChisq"]] <- c(rep(NA, nGroups), dprchisq) | ||
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| } | ||
| dtFill[["group"]] <- gettext("all") | ||
| dtFill <- dtFill[, c(1, ncol(dtFill), 2:(ncol(dtFill)-1))] | ||
| dtFill <- rbind(dtFill, dtFillGroup) | ||
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| } | ||
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| fittab$setData(dtFill) | ||
| fittab$addFootnote(message = fnote) | ||
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| } | ||
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| .semParameters <- function(modelContainer, dataset, options, ready) { | ||
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Why do we change it here? Was this a bug?