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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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84 changes: 32 additions & 52 deletions R/classicalmetaanalysiscommon.R
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,6 @@
# - vs covariates
# Generic
# - allow different covariates factoring across all settings
# - confidence interval for heterogeneity in multilevel multivariate

ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {

Expand Down Expand Up @@ -856,15 +855,17 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {

# pooled estimates
pooledEstimatesTable <- createJaspTable(gettext("Meta-Analytic Estimates"))
pooledEstimatesTable$showSpecifiedColumnsOnly <- TRUE
pooledEstimatesTable$position <- 4
pooledEstimatesTable$dependOn(c("heterogeneityTau", "heterogeneityTau2", "heterogeneityI2", "heterogeneityH2",
"confidenceIntervals", "confidenceIntervalsLevel", "predictionIntervals", "transformEffectSize",
"includeFullDatasetInSubgroupAnalysis"))
"standardErrors", "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 @@ -1033,13 +1034,13 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
effectSize = 3,
heterogeneity = 4
)
coefficientsTable$dependOn(c("metaregressionCoefficientEstimates", "confidenceIntervals", "confidenceIntervalsLevel", "includeFullDatasetInSubgroupAnalysis"))
coefficientsTable$dependOn(c("metaregressionCoefficientEstimates", "confidenceIntervals", "confidenceIntervalsLevel", "standardErrors", "includeFullDatasetInSubgroupAnalysis"))
metaregressionContainer[[paste0(parameter, "CoefficientTable")]] <- coefficientsTable

coefficientsTable$addColumnInfo(name = "name", type = "string", title = "")
.maAddSubgroupColumn(coefficientsTable, options)
coefficientsTable$addColumnInfo(name = "est", type = "number", title = gettext("Estimate"))
coefficientsTable$addColumnInfo(name = "se", type = "number", title = gettext("Standard Error"))
.maAddSeColumn(coefficientsTable, options, noTransformation = TRUE)
.maAddCiColumn(coefficientsTable, options)
coefficientsTable$addColumnInfo(name = "stat", type = "number", title = if(.maIsMetaregressionFtest(options)) gettext("t") else gettext("z"))
if (.maIsMetaregressionFtest(options))
Expand Down Expand Up @@ -1327,10 +1328,11 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {

estimatedMarginalMeansTable <- createJaspTable(if (selectedVariable == "") gettext("Adjusted Estimate") else gettext("Estimated Marginal Means"))
estimatedMarginalMeansTable$position <- 1
estimatedMarginalMeansTable$showSpecifiedColumnsOnly <- TRUE
estimatedMarginalMeansTable$dependOn(c(switch(
parameter,
effectSize = c("estimatedMarginalMeansEffectSize", "estimatedMarginalMeansEffectSizeSdFactorCovariates", "estimatedMarginalMeansEffectSizeTestAgainst",
"estimatedMarginalMeansEffectSizeTestAgainstValue", "transformEffectSize", "predictionIntervals"),
"estimatedMarginalMeansEffectSizeTestAgainstValue", "transformEffectSize", "predictionIntervals", "standardErrors"),
heterogeneity = c("estimatedMarginalMeansHeterogeneity", "estimatedMarginalMeansHeterogeneityTransformation", "estimatedMarginalMeansHeterogeneitySdFactorCovariates")
)))
variableContainer[["estimatedMarginalMeansTable"]] <- estimatedMarginalMeansTable
Expand All @@ -1340,6 +1342,8 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
estimatedMarginalMeansTable$addColumnInfo(name = "value", type = "string", title = gettext("Level"))
.maAddSubgroupColumn(estimatedMarginalMeansTable, options)
estimatedMarginalMeansTable$addColumnInfo(name = "est", type = "number", title = gettext("Estimate"))
if (parameter == "effectSize")
.maAddSeColumn(estimatedMarginalMeansTable, options)
.maAddCiColumn(estimatedMarginalMeansTable, options)
if (parameter == "effectSize") {
.maAddPiColumn(estimatedMarginalMeansTable, options)
Expand Down Expand Up @@ -1367,15 +1371,6 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
# reorder by estimated marginal means estimate
estimatedMarginalMeans <- .maSafeOrderAndSimplify(estimatedMarginalMeans, "value", options)

# drop non-required columns
estimatedMarginalMeans <- estimatedMarginalMeans[,!colnames(estimatedMarginalMeans) %in% "variable", drop = FALSE]
if (parameter == "effectSize" && !options[["estimatedMarginalMeansEffectSizeTestAgainst"]])
estimatedMarginalMeans <- estimatedMarginalMeans[,!colnames(estimatedMarginalMeans) %in% c("df", "stat", "pval"), drop = FALSE]
if (parameter == "heterogeneity")
estimatedMarginalMeans <- estimatedMarginalMeans[,!colnames(estimatedMarginalMeans) %in% c("lPi", "uPi"), drop = FALSE]
if (selectedVariable == "")
estimatedMarginalMeans <- estimatedMarginalMeans[,!colnames(estimatedMarginalMeans) %in% c("value"), drop = FALSE]

# set data
estimatedMarginalMeansTable$setData(estimatedMarginalMeans)

Expand All @@ -1390,9 +1385,10 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {

contrastsTable <- createJaspTable(gettext("Contrasts"))
contrastsTable$position <- 1
contrastsTable$showSpecifiedColumnsOnly <- TRUE
contrastsTable$dependOn(switch(
parameter,
effectSize = c("contrastsEffectSize", "contrastsEffectSizePValueAdjustment", "predictionIntervals", "transformEffectSize"),
effectSize = c("contrastsEffectSize", "contrastsEffectSizePValueAdjustment", "predictionIntervals", "transformEffectSize", "standardErrors"),
heterogeneity = c("contrastsHeterogeneity", "contrastsHeterogeneityPValueAdjustment", "estimatedMarginalMeansHeterogeneityTransformation")
))
variableContainer[["contrastsTable"]] <- contrastsTable
Expand All @@ -1401,6 +1397,8 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
contrastsTable$addColumnInfo(name = "comparison", type = "string", title = gettext("Comparison"))
.maAddSubgroupColumn(contrastsTable, options)
contrastsTable$addColumnInfo(name = "est", type = "number", title = gettext("Estimate"))
if (parameter == "effectSize")
.maAddSeColumn(contrastsTable, options)
.maAddCiColumn(contrastsTable, options)
if (parameter == "effectSize") {
.maAddPiColumn(contrastsTable, options)
Expand All @@ -1427,10 +1425,6 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
# reorder by estimated marginal means estimate
contrasts <- .maSafeOrderAndSimplify(contrasts, "comparison", options)

# drop non-required columns
if (parameter == "heterogeneity")
contrasts <- contrasts[,!colnames(contrasts) %in% c("lPi", "uPi"), drop = FALSE]

# set data
contrastsTable$setData(contrasts)

Expand Down Expand Up @@ -2283,13 +2277,6 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
.maGetEffectSizeTransformationOptions(options[["transformEffectSize"]]),
list(predictedEffect[,c("est", "lCi", "uCi", "lPi", "uPi")]))

# remove non-requested columns
predictedEffect <- predictedEffect[,c(
"par", "est",
if (options[["confidenceIntervals"]]) c("lCi", "uCi"),
if (options[["predictionIntervals"]]) c("lPi", "uPi")
)]

# return the tau levels
if (.mammHasMultipleHeterogeneities(options, canAddOutput = TRUE) && options[["predictionIntervals"]])
predictedEffect <- cbind(predictedEffect, tauLevels)
Expand Down Expand Up @@ -2416,6 +2403,10 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
colnames(confIntHeterogeneity) <- c("est", "lCi", "uCi")
confIntHeterogeneity$par <- c("\U1D70F", "\U1D70F\U00B2", "I\U00B2", "H\U00B2")

if (options[["standardErrors"]]){
confIntHeterogeneity$se <- c(.maGetSqrtTransformationSeDeltaMethod(fit$tau2 ,fit$se.tau2), fit$se.tau2, NA, NA)
}

# keep only the requested parameters
heterogeneityShow <- c(
if (options[["heterogeneityTau"]]) 1,
Expand Down Expand Up @@ -2937,16 +2928,6 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
)
}


# remove unnecessary columns
computedMarginalMeans <- computedMarginalMeans[,!colnames(computedMarginalMeans) %in% "se", drop = FALSE]

if (!options[["confidenceIntervals"]])
computedMarginalMeans <- computedMarginalMeans[,!colnames(computedMarginalMeans) %in% c("lCi", "uCi"), drop = FALSE]

if (!options[["predictionIntervals"]])
computedMarginalMeans <- computedMarginalMeans[,!colnames(computedMarginalMeans) %in% c("lPi", "uPi"), drop = FALSE]

# return the tau levels
if (.mammHasMultipleHeterogeneities(options, canAddOutput = TRUE) && options[["predictionIntervals"]])
computedMarginalMeans <- cbind(computedMarginalMeans, tauLevels)
Expand Down Expand Up @@ -3106,15 +3087,6 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
# reformat
computedContrasts <- .maExtractAndFormatPrediction(computedContrasts)

# remove unnecessary columns
computedContrasts <- computedContrasts[,!colnames(computedContrasts) %in% "se", drop = FALSE]

if (!options[["confidenceIntervals"]])
computedContrasts <- computedContrasts[,!colnames(computedContrasts) %in% c("lCi", "uCi"), drop = FALSE]

if (!options[["predictionIntervals"]])
computedContrasts <- computedContrasts[,!colnames(computedContrasts) %in% c("lPi", "uPi"), drop = FALSE]

# TODO: ? return the tau levels
# if (.mammHasMultipleHeterogeneities(options, canAddOutput = TRUE) && options[["predictionIntervals"]])
# computedMarginalMeans <- cbind(computedMarginalMeans, tauLevels)
Expand Down Expand Up @@ -4047,6 +4019,7 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
"estimatedMarginalMeansEffectSizeSdFactorCovariates",
"estimatedMarginalMeansEffectSizeAddAdjustedEstimate",

"standardErrors",
"confidenceIntervals",
"confidenceIntervalsLevel",
"predictionIntervals",
Expand Down Expand Up @@ -4466,12 +4439,6 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {
}
row$subgroup <- attr(fit, "subgroup")

row <- row[,c(
"par", "est",
if (options[["confidenceIntervals"]]) c("lCi", "uCi"),
"subgroup"
)]

return(row)
}
.maRowFitMeasures <- function(fit, options) {
Expand Down Expand Up @@ -4715,6 +4682,17 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {

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

if (!options[["standardErrors"]])
return(tempTable)

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

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

if (options[["subgroup"]] != "")
Expand Down Expand Up @@ -5014,7 +4992,9 @@ ClassicalMetaAnalysisCommon <- function(jaspResults, dataset, options, ...) {

return(termsIndicies)
}

.maGetSqrtTransformationSeDeltaMethod <- function(estimate, estimate_se) {
estimate_se / (2 * sqrt(estimate))
}
# messages
.maFixedEffectTextMessage <- function(options) {
return(switch(
Expand Down
11 changes: 11 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 @@ -127,6 +127,16 @@ Section

Group
{

CheckBox
{
text: qsTr("Standard errors")
name: "standardErrors"
checked: true
enabled: transformEffectSizeDropdown.value === "none"
info: qsTr("Include standard errors in the tabular output. Only available when no effect size transformation is applied.")
}

CheckBox
{
name: "confidenceIntervals"
Expand All @@ -152,6 +162,7 @@ Section

DropDown
{//TODO: make shorter or across both rows?
id: transformEffectSizeDropdown
name: "transformEffectSize"
label: qsTr("Transform effect size")
setLabelAbove: true
Expand Down
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