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Hotfix for RoBMA (vol. II) #197

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merged 3 commits into from
Sep 19, 2023
Merged

Hotfix for RoBMA (vol. II) #197

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c55e45a
fix: plot prior distributions under custom models
FBartos Sep 18, 2023
c57670c
fixing incorrectly disabled prior scale menu on custom
FBartos Sep 18, 2023
75eec32
fix displaying BF instead of marginal likelihood in model summary
FBartos Sep 18, 2023
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20 changes: 16 additions & 4 deletions R/robustbayesianmetaanalysis.R
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Original file line number Diff line number Diff line change
Expand Up @@ -530,11 +530,11 @@ RobustBayesianMetaAnalysis <- function(jaspResults, dataset, options, state = NU

# extract the priors
if (is.null(jaspResults[["model"]]) && options[["modelEnsembleType"]] != "custom")
priors <- RoBMA::check_setup(model_type = options[["modelEnsembleType"]], silent = TRUE)$priors
priors <- .robmaPriorsToOptionsNames(RoBMA::check_setup(model_type = .robmaGetModelTypeOption(options), silent = TRUE)$priors)
else if (is.null(jaspResults[["model"]]))
priors <- jaspResults[["priors"]][["object"]]
else
priors <- jaspResults[["model"]][["object"]][["priors"]]
priors <- .robmaPriorsToOptionsNames(jaspResults[["model"]][["object"]][["priors"]])


# create container for each of the parameters
Expand Down Expand Up @@ -583,7 +583,12 @@ RobustBayesianMetaAnalysis <- function(jaspResults, dataset, options, state = NU
parameterContainer[[type]] <- typeContainer
}

tempPriors <- priors[[paste0(parameter, if (type == "null") "Null")]]
tempPriors <- priors[[paste0(switch(
parameter,
"effect" = "modelsEffect",
"heterogeneity" = "modelsHeterogeneity",
"bias" = "modelsBias"
), if (type == "null") "Null")]]

if (length(tempPriors) == 0)
next
Expand Down Expand Up @@ -1001,7 +1006,7 @@ RobustBayesianMetaAnalysis <- function(jaspResults, dataset, options, state = NU

# compute the BF requested
if (options[["inferenceModelsOverviewBfComparison"]] == "inclusion") {
bf <- fitSummary[["summary"]][, 7]
bf <- fitSummary[["summary"]][, 8]
} else if (options[["inferenceModelsOverviewBfComparison"]] == "best") {
bf <- exp(fitSummary[["summary"]][["marglik"]] - max(fitSummary[["summary"]][["marglik"]]))
} else if (options[["inferenceModelsOverviewBfComparison"]] == "previous") {
Expand Down Expand Up @@ -1770,3 +1775,10 @@ RobustBayesianMetaAnalysis <- function(jaspResults, dataset, options, state = NU
modelSaved[["object"]] <- TRUE

}
.robmaPriorsToOptionsNames <- function(priors) {
priorNames <- names(priors)
substr(priorNames, 1, 1) <- toupper(substr(priorNames, 1, 1))
priorNames <- paste0("models", priorNames)
names(priors) <- priorNames
return(priors)
}
2 changes: 1 addition & 1 deletion inst/qml/RobustBayesianMetaAnalysis.qml
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Original file line number Diff line number Diff line change
Expand Up @@ -230,7 +230,7 @@ Form
id: priorScale
name: "priorScale"
label: qsTr("Prior scale")
enabled: !measuresFitted.checked && !measuresGeneral.checked && !modelType.value == "custom"
enabled: !measuresFitted.checked && !measuresGeneral.checked && modelType.value == "custom"

values: [
{ label: qsTr("Cohen's d"), value: "cohensD"},
Expand Down
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