diff --git a/R/classicalmetaanalysiscommon.R b/R/classicalmetaanalysiscommon.R index a0defd92..7102a88c 100644 --- a/R/classicalmetaanalysiscommon.R +++ b/R/classicalmetaanalysiscommon.R @@ -257,7 +257,9 @@ fitPermutation <- try(metafor::permutest( fit, exact = options[["permutationTestType"]] == "exact", - iter = options[["permutationTestIteration"]] + iter = options[["permutationTestIteration"]], + code1 = "jaspBase::startProgressbar(X.iter, label = 'Permutation test')", + code2 = "jaspBase::progressbarTick()", )) fit <- .maFitAddPermutationPValues(fit, fitPermutation, options) } else { @@ -1116,15 +1118,15 @@ if (.maIsMultilevelMultivariate(options)) { # only a subset of diagnostics is available for rma.mv - influenceResultsDfbs <- data.frame(dfbetas(fit)) + influenceResultsDfbs <- data.frame(dfbetas(fit, code1 = "jaspBase::startProgressbar(x$k, label = 'Casewise diagnostics: DFBETAS')", code2 = "jaspBase::progressbarTick()")) influenceResultsInf <- data.frame( - rstudent = rstudent(fit)[["resid"]], - cook.d = cooks.distance(fit), + rstudent = rstudent(fit, code1 = "jaspBase::startProgressbar(x$k, label = 'Casewise diagnostics: Studentized residuals')", code2 = "jaspBase::progressbarTick()")[["resid"]], + cook.d = cooks.distance(fit, code1 = "jaspBase::startProgressbar(x$k, label = 'Casewise diagnostics: Cooks distance')", code2 = "jaspBase::progressbarTick()"), hat = hatvalues(fit) ) } else { # the complete suite of influence diagnostics is only available for rma.uni - influenceResults <- influence(fit) + influenceResults <- influence(fit, code1 = "jaspBase::startProgressbar(x$k, label = 'Casewise diagnostics')", code2 = "jaspBase::progressbarTick()") influenceResultsDfbs <- data.frame(influenceResults$dfbs) influenceResultsInf <- data.frame(influenceResults$inf) influenceResultsInf$tau.del <- sqrt(influenceResultsInf$tau2.del) @@ -1287,13 +1289,32 @@ if (.maIsMultilevelMultivariate(options)) { # use the defaults (too many possible parameter combinations to control) - dfProfile <- try(metafor::profile.rma.mv(fit, plot = FALSE, progbar = FALSE)) + dfProfile <- try(metafor::profile.rma.mv( + fit, + plot = FALSE, + progbar = FALSE, + code1 = "jaspBase::startProgressbar(length(vcs), label = 'Profile likelihood')", + code2 = "jaspBase::progressbarTick()" + )) + + # deal with a single component (not a list) + if (dfProfile[["comps"]] == 1) { + dfProfile <- list(dfProfile) + dfProfile[["comps"]] <- 1 + } jaspResults[["diagnosticsResults"]]$object <- dfProfile } else { # proceed with some nice formatting for rma.uni (too difficult to implement for rma.mv) xTicks <- jaspGraphs::getPrettyAxisBreaks(c(0, max(0.1, 2*fit[["tau2"]]))) - 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