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fix the add scores option for cov input #240

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merged 4 commits into from
Oct 30, 2024
Merged

fix the add scores option for cov input #240

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68e3c9d
fix some cov input stuff
juliuspfadt Oct 17, 2024
3bd2df7
fix cov input options
juliuspfadt Oct 17, 2024
1cd9f00
fix some option things for cov input
juliuspfadt Oct 29, 2024
3886b03
fix screeplot
juliuspfadt Oct 30, 2024
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14 changes: 9 additions & 5 deletions R/confirmatoryfactoranalysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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))
Expand Down
25 changes: 17 additions & 8 deletions R/exploratoryfactoranalysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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$MSAi))
Expand All @@ -269,9 +271,11 @@ exploratoryFactorAnalysisInternal <- function(jaspResults, dataset, options, ...
if (options[["analysisBasedOn"]] == "polyTetrachoricCorrelationMatrix") {
polyTetraCor <- psych::mixedCor(dataset)
bar <- psych::cortest.bartlett(polyTetraCor$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"]]
Expand Down Expand Up @@ -730,9 +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),
Expand Down
18 changes: 14 additions & 4 deletions R/principalcomponentanalysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
Expand Down Expand Up @@ -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))
Expand Down Expand Up @@ -528,6 +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() +
Expand Down
6 changes: 4 additions & 2 deletions inst/qml/ExploratoryFactorAnalysis.qml
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@ Form
RadioButtonGroup
{
name: "dataType"
id: dataType
columns: 2
RadioButton { value: "raw"; label: qsTr("Raw"); checked: true }
RadioButton
Expand Down Expand Up @@ -189,6 +190,7 @@ Form
}
RadioButton
{
enabled: dataType.value == "raw"
value: "polyTetrachoricCorrelationMatrix"
label: qsTr("Polychoric/tetrachoric correlation matrix")
}
Expand Down Expand Up @@ -269,7 +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
{
Expand All @@ -284,7 +286,7 @@ 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"
Expand Down
6 changes: 4 additions & 2 deletions inst/qml/PrincipalComponentAnalysis.qml
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@ Form
RadioButtonGroup
{
name: "dataType"
id: dataType
columns: 2
RadioButton { value: "raw"; label: qsTr("Raw"); checked: true }
RadioButton
Expand Down Expand Up @@ -160,6 +161,7 @@ Form
}
RadioButton
{
enabled: dataType.value == "raw"
value: "polyTetrachoricCorrelationMatrix"
label: qsTr("Polychoric/tetrachoric correlation matrix")
}
Expand Down Expand Up @@ -236,7 +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
Expand All @@ -252,7 +254,7 @@ 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"
Expand Down
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