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Merged
FBartos merged 1 commit into from
Apr 30, 2025
Merged

add variance-covariance matrix computation #306

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42 changes: 38 additions & 4 deletions R/classicalmetaanalysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,31 @@ ClassicalMetaAnalysis <- function(jaspResults, dataset = NULL, options, ...) {
"permutationTest", "permutationTestIteration", "permutationTestType", "setSeed", "seed",
# multilevel/multivariate specific
"randomEffects", "randomEffectsSpecification",
"computeCovarianceMatrix", "computeCovarianceMatrix"
"computeCovarianceMatrix", "computeCovarianceMatrix",
# multivariate effect size computation
"varianceCovarianceMatrixType",
"varianceCovarianceMatrixFile",
"varianceCovarianceMatrixCorrelationMatrix",
"varianceCovarianceMatrixSubcluster",
"varianceCovarianceMatrixCluster",
"varianceCovarianceMatrixForcePositiveDefiniteness",
"varianceCovarianceMatrixCheckPositiveDefiniteness",
"varianceCovarianceMatrixCorrelationMatrix",
"varianceCovarianceMatrixConstruct",
"varianceCovarianceMatrixConstructType",
"varianceCovarianceMatrixTime1",
"varianceCovarianceMatrixTime2",
"varianceCovarianceMatrixGroup1",
"varianceCovarianceMatrixGroup1",
"varianceCovarianceMatrixGroupSize1",
"varianceCovarianceMatrixGroupSize2",
"varianceCovarianceMatrixConstructCorrelationMatrix",
"varianceCovarianceMatrixConstructCorrelationMatrixValue",
"varianceCovarianceMatrixConstructCorrelationMatrixFilePath",
"varianceCovarianceMatrixConstructTypeCorrelationMatrix",
"varianceCovarianceMatrixConstructTypeCorrelationMatrixValue",
"varianceCovarianceMatrixConstructTypeCorrelationMatrixFilePath",
"varianceCovarianceMatrixTimeLag1Correlation"
)
.maForestPlotDependencies <- c(
# do not forget to add variable carrying options to the .maDataPlottingDependencies
Expand Down Expand Up @@ -183,15 +207,25 @@ ClassicalMetaAnalysis <- function(jaspResults, dataset = NULL, options, ...) {

.hasErrors(
dataset = dataset,
type = c("infinity", "observations", "variance"),
type = c("infinity", "observations"),
all.target = c(
options[["effectSize"]],
options[["effectSizeStandardError"]],
options[["predictors"]][options[["predictors.types"]] == "scale"]
options[["effectSizeStandardError"]]
),
observations.amount = "< 2",
exitAnalysisIfErrors = TRUE)

# do not check effect sizes / standard errors for 0 variance
otherVariable <- options[["predictors"]][options[["predictors.types"]] == "scale"]
if (length(otherVariable) > 0) {
.hasErrors(
dataset = dataset,
type = c("infinity", "observations", "variance"),
all.target = otherVariable,
observations.amount = "< 2",
exitAnalysisIfErrors = TRUE)
}

if (length(options[["effectSizeModelTerms"]]) > 0)
.hasErrors(
dataset = dataset,
Expand Down
49 changes: 39 additions & 10 deletions R/classicalmetaanalysiscommon.R
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,6 @@


# TODO:
# Forest plot
# - allow aggregation of studies by a factor (then show simple REML aggregation within and overlaying shaded estimates)
# AIC/BIC Model-averaging
# Diagnostics
# - model re-run on presence of influential cases
Expand Down Expand Up @@ -97,11 +95,14 @@
if (options[["diagnosticsResidualFunnel"]])
.maResidualFunnelPlot(jaspResults, options)


# additional
if (options[["showMetaforRCode"]])
.maShowMetaforRCode(jaspResults, options)

# export the variance-covariance matrix if requested
if (.maIsMultilevelMultivariate(options) && options[["varianceCovarianceMatrixSaveComputedVarianceCovarianceMatrix"]] != "")
.mammExportVarianceCovarianceMatrix(dataset, options)

return()
}

Expand Down Expand Up @@ -154,10 +155,11 @@
subgroupIndx <- dataset[[options[["subgroup"]]]] == subgroupLevel
subgroupData <- droplevels(dataset[subgroupIndx, ])

# forward NAs information
# forward NAs information and additional attributes
tempNasIds <- attr(dataset, "NasIds")[!attr(dataset, "NasIds")]
attr(subgroupData, "NAs") <- sum(tempNasIds[subgroupIndx])
attr(subgroupData, "NasIds") <- tempNasIds[subgroupIndx]
attr(subgroupData, "NAs") <- sum(tempNasIds[subgroupIndx])
attr(subgroupData, "NasIds") <- tempNasIds[subgroupIndx]
attr(subgroupData, "subgroupIndx") <- subgroupIndx

# fit the model
fitOutput[[paste0("subgroup", subgroupLevel)]] <- .maFitModelFun(subgroupData, options, subgroupName = as.character(subgroupLevel))
Expand All @@ -178,16 +180,17 @@

# specify the effect size and outcome
if (options[["module"]] == "metaAnalysis") {
# specify the univariate input
rmaInput <- list(
yi = as.name(options[["effectSize"]]),
sei = as.name(options[["effectSizeStandardError"]]),
data = dataset
)
} else if (options[["module"]] == "metaAnalysisMultilevelMultivariate") {
# TODO: extend to covariance matrices
# specify the multivariate input
rmaInput <- list(
yi = as.name(options[["effectSize"]]),
V = as.name("samplingVariance"), # precomputed on data load
V = if (.mammVarianceCovarianceMatrixReady(options)) .mammGetVarianceCovarianceMatrix(dataset, options) else as.name("samplingVariance"),
data = dataset
)
}
Expand Down Expand Up @@ -757,6 +760,14 @@
)
}

# add multivariate settings notes
if (.maIsMultilevelMultivariate(options)) {
multivariateReadyNotes <- attr(.mammVarianceCovarianceMatrixReady(options), "messages")
for (i in seq_along(multivariateReadyNotes)) {
testsTable$addFootnote(multivariateReadyNotes[i])
}
}

# bind and clean rows
tests <- .maSafeRbind(tests)
tests <- .maSafeOrderAndSimplify(tests, "test", options)
Expand Down Expand Up @@ -3316,10 +3327,15 @@
data = as.name("dataset")
)
} else if (options[["module"]] == "metaAnalysisMultilevelMultivariate") {
# TODO: extend to covariance matrices

if (.mammVarianceCovarianceMatrixReady(options)) {
vcalcInput <-.mammGetVarianceCovarianceMatrix(NULL, options, returnCall = TRUE)
vcalcInput$data <- as.name("dataset")
}

rmaInput <- list(
yi = as.name(options[["effectSize"]]),
V = paste0(options[["effectSizeStandardError"]], "^2"), # precomputed on data load
V = if (.mammVarianceCovarianceMatrixReady(options)) "effectSizeVarianceCovarianceMatrix" else paste0(options[["effectSizeStandardError"]], "^2"),
data = as.name("dataset")
)
}
Expand Down Expand Up @@ -3401,6 +3417,19 @@
fit <- paste0("fit <- rma(\n\t", paste(names(rmaInput), "=", rmaInput, collapse = ",\n\t"), "\n)\n")
}

if (.maIsMultilevelMultivariate(options) && .mammVarianceCovarianceMatrixReady(options)) {
if (options[["varianceCovarianceMatrixType"]] == "precomputed") {
fit <- paste0(
paste0("effectSizeVarianceCovarianceMatrix <- ", vcalcInput[["file"]], "\n"), "\n",
fit
)
} else {
fit <- paste0(
paste0("effectSizeVarianceCovarianceMatrix <- vcalc(\n\t", paste(names(vcalcInput), "=", vcalcInput, collapse = ",\n\t"), "\n)\n"), "\n",
fit
)
}
}

# add clustering if specified
if (options[["clustering"]] != "") {
Expand Down
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