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Add standard errors to classical meta-analysis tabular output with user control #363

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Add standard errors to classical meta-analysis tabular output with user control #363

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2357b26
Initial plan
Copilot Sep 9, 2025
8430d6a
Add SE column helper function and integrate SE columns into main tables
Copilot Sep 9, 2025
624b842
Change SE column title to "Standard Error" with proper translation
Copilot Sep 9, 2025
3ae2100
Add standardError checkbox and update dependencies
Copilot Sep 9, 2025
1f57ce1
Enable standardError checkbox only when transformation is not specified
Copilot Sep 9, 2025
cf8dab8
styling fixes
FBartos Sep 9, 2025
71586d1
clean up column removal
FBartos Sep 10, 2025
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24 changes: 19 additions & 5 deletions R/classicalmetaanalysiscommon.R
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Original file line number Diff line number Diff line change
Expand Up @@ -859,12 +859,13 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
pooledEstimatesTable$position <- 4
pooledEstimatesTable$dependOn(c("heterogeneityTau", "heterogeneityTau2", "heterogeneityI2", "heterogeneityH2",
"confidenceIntervals", "confidenceIntervalsLevel", "predictionIntervals", "transformEffectSize",
"includeFullDatasetInSubgroupAnalysis"))
"standardError", "includeFullDatasetInSubgroupAnalysis"))
modelSummaryContainer[["pooledEstimatesTable"]] <- pooledEstimatesTable

pooledEstimatesTable$addColumnInfo(name = "par", type = "string", title = "")
.maAddSubgroupColumn(pooledEstimatesTable, options)
pooledEstimatesTable$addColumnInfo(name = "est", type = "number", title = gettext("Estimate"))
.maAddSeColumn(pooledEstimatesTable, options)
.maAddCiColumn(pooledEstimatesTable, options)
.maAddPiColumn(pooledEstimatesTable, options)
if (options[["predictionIntervals"]] && .mammHasMultipleHeterogeneities(options, canAddOutput = TRUE)) {
Expand Down Expand Up @@ -1330,7 +1331,7 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
estimatedMarginalMeansTable$dependOn(c(switch(
parameter,
effectSize = c("estimatedMarginalMeansEffectSize", "estimatedMarginalMeansEffectSizeSdFactorCovariates", "estimatedMarginalMeansEffectSizeTestAgainst",
"estimatedMarginalMeansEffectSizeTestAgainstValue", "transformEffectSize", "predictionIntervals"),
"estimatedMarginalMeansEffectSizeTestAgainstValue", "transformEffectSize", "predictionIntervals", "standardError"),
heterogeneity = c("estimatedMarginalMeansHeterogeneity", "estimatedMarginalMeansHeterogeneityTransformation", "estimatedMarginalMeansHeterogeneitySdFactorCovariates")
)))
variableContainer[["estimatedMarginalMeansTable"]] <- estimatedMarginalMeansTable
Expand All @@ -1340,6 +1341,7 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
estimatedMarginalMeansTable$addColumnInfo(name = "value", type = "string", title = gettext("Level"))
.maAddSubgroupColumn(estimatedMarginalMeansTable, options)
estimatedMarginalMeansTable$addColumnInfo(name = "est", type = "number", title = gettext("Estimate"))
.maAddSeColumn(estimatedMarginalMeansTable, options)
.maAddCiColumn(estimatedMarginalMeansTable, options)
if (parameter == "effectSize") {
.maAddPiColumn(estimatedMarginalMeansTable, options)
Expand Down Expand Up @@ -1392,7 +1394,7 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
contrastsTable$position <- 1
contrastsTable$dependOn(switch(
parameter,
effectSize = c("contrastsEffectSize", "contrastsEffectSizePValueAdjustment", "predictionIntervals", "transformEffectSize"),
effectSize = c("contrastsEffectSize", "contrastsEffectSizePValueAdjustment", "predictionIntervals", "transformEffectSize", "standardError"),
heterogeneity = c("contrastsHeterogeneity", "contrastsHeterogeneityPValueAdjustment", "estimatedMarginalMeansHeterogeneityTransformation")
))
variableContainer[["contrastsTable"]] <- contrastsTable
Expand All @@ -1401,6 +1403,7 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
contrastsTable$addColumnInfo(name = "comparison", type = "string", title = gettext("Comparison"))
.maAddSubgroupColumn(contrastsTable, options)
contrastsTable$addColumnInfo(name = "est", type = "number", title = gettext("Estimate"))
.maAddSeColumn(contrastsTable, options)
.maAddCiColumn(contrastsTable, options)
if (parameter == "effectSize") {
.maAddPiColumn(contrastsTable, options)
Expand Down Expand Up @@ -2286,6 +2289,7 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
# remove non-requested columns
predictedEffect <- predictedEffect[,c(
"par", "est",
if (options[["transformEffectSize"]] == "none") "se",
if (options[["confidenceIntervals"]]) c("lCi", "uCi"),
if (options[["predictionIntervals"]]) c("lPi", "uPi")
)]
Expand Down Expand Up @@ -2939,7 +2943,8 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {


# remove unnecessary columns
computedMarginalMeans <- computedMarginalMeans[,!colnames(computedMarginalMeans) %in% "se", drop = FALSE]
seColumnsToRemove <- if (options[["transformEffectSize"]] == "none") character(0) else "se"
computedMarginalMeans <- computedMarginalMeans[,!colnames(computedMarginalMeans) %in% seColumnsToRemove, drop = FALSE]

if (!options[["confidenceIntervals"]])
computedMarginalMeans <- computedMarginalMeans[,!colnames(computedMarginalMeans) %in% c("lCi", "uCi"), drop = FALSE]
Expand Down Expand Up @@ -3107,7 +3112,8 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
computedContrasts <- .maExtractAndFormatPrediction(computedContrasts)

# remove unnecessary columns
computedContrasts <- computedContrasts[,!colnames(computedContrasts) %in% "se", drop = FALSE]
seColumnsToRemove <- if (options[["transformEffectSize"]] == "none") character(0) else "se"
computedContrasts <- computedContrasts[,!colnames(computedContrasts) %in% seColumnsToRemove, drop = FALSE]

if (!options[["confidenceIntervals"]])
computedContrasts <- computedContrasts[,!colnames(computedContrasts) %in% c("lCi", "uCi"), drop = FALSE]
Expand Down Expand Up @@ -4715,6 +4721,14 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {

return(tempTable)
}
.maAddSeColumn <- function(tempTable, options) {

if (options[["standardError"]] && options[["transformEffectSize"]] == "none") {
tempTable$addColumnInfo(name = "se", title = gettext("Standard Error"), type = "number")
}

return(tempTable)
}
.maAddSubgroupColumn <- function(tempTable, options) {

if (options[["subgroup"]] != "")
Expand Down
8 changes: 8 additions & 0 deletions inst/qml/qml_components/ClassicalMetaAnalysisStatistics.qml
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Original file line number Diff line number Diff line change
Expand Up @@ -141,6 +141,14 @@ Section
}
}

CheckBox
{
text: qsTr("Standard errors")
name: "standardError"
checked: true
info: qsTr("Include standard errors in the tabular output. Only available when no effect size transformation is applied.")
}

CheckBox
{
text: qsTr("Prediction intervals")
Expand Down