From 68e3c9d1ffb8d343fc416f68ae25139d4b93316c Mon Sep 17 00:00:00 2001 From: Julius Pfadt Date: Thu, 17 Oct 2024 10:17:35 +0200 Subject: [PATCH 1/4] fix some cov input stuff --- inst/qml/ExploratoryFactorAnalysis.qml | 2 +- inst/qml/PrincipalComponentAnalysis.qml | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/inst/qml/ExploratoryFactorAnalysis.qml b/inst/qml/ExploratoryFactorAnalysis.qml index 272384c..97be6d1 100644 --- a/inst/qml/ExploratoryFactorAnalysis.qml +++ b/inst/qml/ExploratoryFactorAnalysis.qml @@ -284,7 +284,7 @@ Form id: addScores name: "addScores" label: qsTr("Add FA scores to data") - enabled: variables.count > 1 + enabled: variables.count > 1 & dataType.value == "raw" TextField { name: "addedScoresPrefix" diff --git a/inst/qml/PrincipalComponentAnalysis.qml b/inst/qml/PrincipalComponentAnalysis.qml index fadabaa..e1b3e53 100644 --- a/inst/qml/PrincipalComponentAnalysis.qml +++ b/inst/qml/PrincipalComponentAnalysis.qml @@ -40,6 +40,7 @@ Form RadioButtonGroup { name: "dataType" + id: dataType columns: 2 RadioButton { value: "raw"; label: qsTr("Raw"); checked: true } RadioButton @@ -252,7 +253,7 @@ Form id: addScores name: "addScores" label: qsTr("Add PC scores to data") - enabled: variables.count > 1 + enabled: variables.count > 1 & dataType.value == "raw" TextField { name: "addedScoresPrefix" From 3bd2df788fd5587e66dea4a383eae422bad1c0b7 Mon Sep 17 00:00:00 2001 From: Julius Pfadt Date: Thu, 17 Oct 2024 11:12:42 +0200 Subject: [PATCH 2/4] fix cov input options --- R/confirmatoryfactoranalysis.R | 14 +++++++++----- R/exploratoryfactoranalysis.R | 2 +- R/principalcomponentanalysis.R | 12 ++++++++---- inst/qml/ExploratoryFactorAnalysis.qml | 1 + 4 files changed, 19 insertions(+), 10 deletions(-) diff --git a/R/confirmatoryfactoranalysis.R b/R/confirmatoryfactoranalysis.R index eaef458..95e4b31 100644 --- a/R/confirmatoryfactoranalysis.R +++ b/R/confirmatoryfactoranalysis.R @@ -160,20 +160,24 @@ confirmatoryFactorAnalysisInternal <- function(jaspResults, dataset, options, .. .cfaDataCovariance <- function(dataset, options) { + if (options[["dataType"]] == "raw") { return(dataset) } - # possible data matrix? - if ((nrow(dataset) != ncol(dataset)) && !all(dt[lower.tri(dt)] == t(dt)[lower.tri(dt)])) { - .quitAnalysis(gettext("Input data does not seem to be a symmetric matrix! Please check the format of the input data.")) - } - vars <- unlist(lapply(options[["factors"]], `[[`, "indicators"), use.names = FALSE) + # are there any variables specified at all? if (length(vars) == 0) return(data.frame()) + # possible data matrix? + if ((nrow(dataset) != ncol(dataset))) + .quitAnalysis(gettext("Input data does not seem to be a square matrix! Please check the format of the input data.")) + + if (!all(dataset[lower.tri(dataset)] == t(dataset)[lower.tri(dataset)])) + .quitAnalysis(gettext("Input data does not seem to be a symmetric matrix! Please check the format of the input data.")) + duplicateVars <- duplicated(vars) usedvars <- vars[!duplicateVars] var_idx <- match(usedvars, colnames(dataset)) diff --git a/R/exploratoryfactoranalysis.R b/R/exploratoryfactoranalysis.R index c33f255..b21977e 100644 --- a/R/exploratoryfactoranalysis.R +++ b/R/exploratoryfactoranalysis.R @@ -21,7 +21,7 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... # Read dataset dataset <- .pcaAndEfaReadData(dataset, options) ready <- length(options$variables) > 1 - dataset <- .pcaAndEfaDataCovariance(dataset, options) + dataset <- .pcaAndEfaDataCovariance(dataset, options, ready) if (ready) .efaCheckErrors(dataset, options) diff --git a/R/principalcomponentanalysis.R b/R/principalcomponentanalysis.R index a122740..5bf5b1b 100644 --- a/R/principalcomponentanalysis.R +++ b/R/principalcomponentanalysis.R @@ -23,7 +23,7 @@ principalComponentAnalysisInternal <- function(jaspResults, dataset, options, .. dataset <- .pcaAndEfaReadData(dataset, options) ready <- length(options$variables) > 1 - dataset <- .pcaAndEfaDataCovariance(dataset, options) + dataset <- .pcaAndEfaDataCovariance(dataset, options, ready) if (ready) .pcaCheckErrors(dataset, options) @@ -69,16 +69,20 @@ principalComponentAnalysisInternal <- function(jaspResults, dataset, options, .. } -.pcaAndEfaDataCovariance <- function(dataset, options) { +.pcaAndEfaDataCovariance <- function(dataset, options, ready) { + + if (!ready) return() if (options[["dataType"]] == "raw") { return(dataset) } # possible data matrix? - if ((nrow(dataset) != ncol(dataset)) && !all(dt[lower.tri(dt)] == t(dt)[lower.tri(dt)])) { + if ((nrow(dataset) != ncol(dataset))) + .quitAnalysis(gettext("Input data does not seem to be a square matrix! Please check the format of the input data.")) + + if (!all(dataset[lower.tri(dataset)] == t(dataset)[lower.tri(dataset)])) .quitAnalysis(gettext("Input data does not seem to be a symmetric matrix! Please check the format of the input data.")) - } usedvars <- unlist(options[["variables"]]) var_idx <- match(usedvars, colnames(dataset)) diff --git a/inst/qml/ExploratoryFactorAnalysis.qml b/inst/qml/ExploratoryFactorAnalysis.qml index 97be6d1..ae6ec21 100644 --- a/inst/qml/ExploratoryFactorAnalysis.qml +++ b/inst/qml/ExploratoryFactorAnalysis.qml @@ -40,6 +40,7 @@ Form RadioButtonGroup { name: "dataType" + id: dataType columns: 2 RadioButton { value: "raw"; label: qsTr("Raw"); checked: true } RadioButton From 1cd9f000de60c3afacf4e2c275d23ff77a4bd6e8 Mon Sep 17 00:00:00 2001 From: Julius Pfadt Date: Tue, 29 Oct 2024 12:39:55 +0100 Subject: [PATCH 3/4] fix some option things for cov input --- R/exploratoryfactoranalysis.R | 16 ++++++++++------ inst/qml/ExploratoryFactorAnalysis.qml | 3 ++- inst/qml/PrincipalComponentAnalysis.qml | 3 ++- 3 files changed, 14 insertions(+), 8 deletions(-) diff --git a/R/exploratoryfactoranalysis.R b/R/exploratoryfactoranalysis.R index b21977e..aba553d 100644 --- a/R/exploratoryfactoranalysis.R +++ b/R/exploratoryfactoranalysis.R @@ -243,9 +243,11 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... if (options[["analysisBasedOn"]] == "polyTetrachoricCorrelationMatrix") { polyTetraCor <- psych::mixedCor(dataset) kmo <- psych::KMO(polyTetraCor$rho) - } - else{ - kmo <- psych::KMO(dataset) + } else { + if (options[["dataType"]] == "raw") + kmo <- psych::KMO(dataset) + else + kmo <- psych::KMO(cov2cor(as.matrix(dataset))) } kmoTable[["col"]] <- c(gettext("Overall MSA\n"), names(kmo$MSAi)) @@ -269,9 +271,11 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... if (options[["analysisBasedOn"]] == "polyTetrachoricCorrelationMatrix") { polyTetraCor <- psych::mixedCor(dataset) bar <- psych::cortest.bartlett(polyTetraCor$rho, n = nrow(dataset)) - } - else { - bar <- psych::cortest.bartlett(dataset) + } else { + if (options[["dataType"]] == "raw") + bar <- psych::cortest.bartlett(dataset) + else + bar <- psych::cortest.bartlett(cov2cor(as.matrix(dataset))) } bartlettTable[["chisq"]] <- bar[["chisq"]] diff --git a/inst/qml/ExploratoryFactorAnalysis.qml b/inst/qml/ExploratoryFactorAnalysis.qml index ae6ec21..4b77e19 100644 --- a/inst/qml/ExploratoryFactorAnalysis.qml +++ b/inst/qml/ExploratoryFactorAnalysis.qml @@ -190,6 +190,7 @@ Form } RadioButton { + enabled: dataType.value == "raw" value: "polyTetrachoricCorrelationMatrix" label: qsTr("Polychoric/tetrachoric correlation matrix") } @@ -270,7 +271,7 @@ Form title: qsTr("Assumption checks") CheckBox { name: "kaiserMeyerOlkinTest"; label: qsTr("KMO test") } CheckBox { name: "bartlettTest"; label: qsTr("Bartlett's test") } - CheckBox { name: "mardiaTest"; label: qsTr("Mardia's test") } + CheckBox { name: "mardiaTest"; label: qsTr("Mardia's test") ; enabled: dataType.value == "raw" } } RadioButtonGroup { diff --git a/inst/qml/PrincipalComponentAnalysis.qml b/inst/qml/PrincipalComponentAnalysis.qml index e1b3e53..523122d 100644 --- a/inst/qml/PrincipalComponentAnalysis.qml +++ b/inst/qml/PrincipalComponentAnalysis.qml @@ -161,6 +161,7 @@ Form } RadioButton { + enabled: dataType.value == "raw" value: "polyTetrachoricCorrelationMatrix" label: qsTr("Polychoric/tetrachoric correlation matrix") } @@ -237,7 +238,7 @@ Form title: qsTr("Assumption checks") CheckBox { name: "kaiserMeyerOlkinTest"; label: qsTr("KMO test") } CheckBox { name: "bartlettTest"; label: qsTr("Bartlett's test") } - CheckBox { name: "mardiaTest"; label: qsTr("Mardia's test") } + CheckBox { name: "mardiaTest"; label: qsTr("Mardia's test") ; enabled: dataType.value == "raw" } } RadioButtonGroup From 3886b0393872939ed7883d62103ea5c44dc5c58d Mon Sep 17 00:00:00 2001 From: Julius Pfadt Date: Wed, 30 Oct 2024 17:39:03 +0100 Subject: [PATCH 4/4] fix screeplot --- R/exploratoryfactoranalysis.R | 7 +- R/principalcomponentanalysis.R | 6 + renv.lock | 1333 ++++++++++++++++++++++---------- 3 files changed, 953 insertions(+), 393 deletions(-) diff --git a/R/exploratoryfactoranalysis.R b/R/exploratoryfactoranalysis.R index aba553d..e87f9a8 100644 --- a/R/exploratoryfactoranalysis.R +++ b/R/exploratoryfactoranalysis.R @@ -734,9 +734,14 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ... plt <- plt + ggplot2::geom_point(na.rm = TRUE, size = max(0, 3 + log(10) - log(n_col))) } - # theming with special legend thingy + # add axis lines and better breaks plt <- plt + + jaspGraphs::geom_rangeframe() + jaspGraphs::themeJaspRaw() + + ggplot2::scale_x_continuous(breaks = seq(1:n_col)) + + # theming with special legend thingy + plt <- plt + ggplot2::theme( legend.position = c(0.99, 0.95), legend.justification = c(1, 1), diff --git a/R/principalcomponentanalysis.R b/R/principalcomponentanalysis.R index 5bf5b1b..432e1c1 100644 --- a/R/principalcomponentanalysis.R +++ b/R/principalcomponentanalysis.R @@ -532,6 +532,12 @@ principalComponentAnalysisInternal <- function(jaspResults, dataset, options, .. plt <- plt + ggplot2::geom_point(na.rm = TRUE, size = max(0, 3 + log(10) - log(n_col))) } + # add axis lines and better breaks + plt <- plt + + jaspGraphs::geom_rangeframe() + + jaspGraphs::themeJaspRaw() + + ggplot2::scale_x_continuous(breaks = seq(1:n_col)) + # theming with special legend thingy plt <- plt + jaspGraphs::themeJaspRaw() + diff --git a/renv.lock b/renv.lock index 7f41d6a..23b67c9 100644 --- a/renv.lock +++ b/renv.lock @@ -13,316 +13,396 @@ "Package": "BH", "Version": "1.84.0-0", "Source": "Repository", - 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