Release fixes (#193)

* fixes: jasp-stats/jasp-test-release#2807 * fixes: jasp-stats/jasp-test-release#2806 * fixes: jasp-stats/jasp-test-release#2810 * fixes: jasp-stats/jasp-test-release#2811
jasp-stats · Dec 6, 2024 · 9128378 · 9128378
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Showing 5 changed files with 59 additions and 27 deletions.
diff --git a/R/MixedModelsCommon.R b/R/MixedModelsCommon.R
@@ -159,25 +159,28 @@
 
     if (options$family %in% c("gamma", "inverseGaussian")) {
 
-      if (any(dataset[, options$dependent] <= 0))
+      if (options$dependent.type != "scale" || any(dataset[, options$dependent] <= 0))
         .quitAnalysis(gettextf("%s requires that the dependent variable is positive.",familyText))
 
     } else if (options$family %in% c("negativeBinomial", "poisson")) {
 
-      if (any(dataset[, options$dependent] < 0 | any(!.is.wholenumber(dataset[, options$dependent]))))
+      if (options$dependent.type != "scale" || any(dataset[, options$dependent] < 0 | any(!.is.wholenumber(dataset[, options$dependent]))))
         .quitAnalysis(gettextf("%s requires that the dependent variable is an integer.",familyText))
 
     } else if (options$family == "bernoulli") {
 
-      if (any(!dataset[, options$dependent] %in% c(0, 1)))
+      if (!options$dependent.type %in% c("scale", "nominal") || any(!dataset[, options$dependent] %in% c(0, 1)))
         .quitAnalysis(gettextf("%s requires that the dependent variable contains only 0 and 1.",familyText))
 
     } else if (options$family == "binomial") {
 
-      if (any(dataset[, options$dependentAggregation] < 0) || any(!.is.wholenumber(dataset[, options$dependentAggregation])))
+      if (options$dependentAggregation.type != "scale" || any(dataset[, options$dependentAggregation] < 0) || any(!.is.wholenumber(dataset[, options$dependentAggregation])))
         .quitAnalysis(gettextf("%s requires that the number of trials variable is an integer.",familyText))
 
       # if the user supplies the number of successes, transform them into the corresponding proportion
+      if (options$dependent.type != "scale")
+        .quitAnalysis(gettextf("%s requires that the number or proportion of successes is an integer.",familyText))
+
       if (all(.is.wholenumber(dataset[, options$dependent]))){
         if(any(dataset[, options$dependent] > dataset[, options$dependentAggregation]))
           .quitAnalysis(gettextf("%s requires that the number of successes is lower that the number of trials.",familyText))
@@ -193,9 +196,14 @@
 
     } else if (options$family == "beta") {
 
-      if (any(dataset[, options$dependent] <= 0 | dataset[, options$dependent] >= 1))
+      if (options$dependent.type != "scale" || any(dataset[, options$dependent] <= 0 | dataset[, options$dependent] >= 1))
         .quitAnalysis(gettextf("%s requires that the dependent variable is higher than 0 and lower than 1.",familyText))
 
+    } else if (options$family == "gaussian") {
+
+      if (options$dependent.type != "scale")
+        .quitAnalysis(gettextf("%s requires that the dependent variable is continuous.",familyText))
+
     }
   }
 
@@ -1504,11 +1512,15 @@
     return()
 
   model <- jaspResults[["mmModel"]]$object$model
-  # deal with type II SS
-  if (is.list(model$full_model))
-    model <- model$full_model[[length(model$full_model)]]
-  else
-    model <- model$full_model
+
+  if (type %in% c("LMN", "GLMM")) {
+    # deal with type II SS
+    if (is.list(model$full_model))
+      model <- model$full_model[[length(model$full_model)]]
+    else
+      model <- model$full_model
+  }
+
 
   # deal with continuous predictors
   at <- NULL
@@ -2414,13 +2426,18 @@
     divIterations <- rstan::get_num_divergent(model$stanfit)
     lowBmfi       <- rstan::get_low_bfmi_chains(model$stanfit)
     maxTreedepth  <- rstan::get_num_max_treedepth(model$stanfit)
-    minESS        <- min(rstan::summary(model$stanfit)$summary[, "n_eff"])
 
-    if (any(is.infinite(rstan::summary(model$stanfit)$summary[, "Rhat"])))
-      maxRhat     <- Inf
+    if (any(is.nan(rstan::summary(model$stanfit)$summary[, "n_eff"])))
+      minESS <- NaN
     else
-      maxRhat     <- max(rstan::summary(model$stanfit)$summary[, "Rhat"])
+      minESS <- min(rstan::summary(model$stanfit)$summary[, "n_eff"])
 
+    if (any(is.infinite(rstan::summary(model$stanfit)$summary[, "Rhat"])))
+      maxRhat <- Inf
+    else if (any(is.nan(rstan::summary(model$stanfit)$summary[, "Rhat"])))
+      maxRhat <- NaN
+    else
+      maxRhat <- max(rstan::summary(model$stanfit)$summary[, "Rhat"])
 
     if (divIterations != 0)
       tempTable$addFootnote(.mmMessageDivergentIter(divIterations), symbol = gettext("Warning:"))
@@ -2431,10 +2448,10 @@
     if (maxTreedepth != 0)
       tempTable$addFootnote(.mmMessageMaxTreedepth(maxTreedepth))
 
-    if (maxRhat > 1.01)
+    if (is.nan(maxRhat) || maxRhat > 1.01)
       tempTable$addFootnote(.mmMessageMaxRhat(maxRhat), symbol = gettext("Warning:"))
 
-    if (minESS < 100 * options$mcmcChains || is.nan(minESS))
+    if (is.nan(minESS) || minESS < 100 * options$mcmcChains)
       tempTable$addFootnote(.mmMessageMinESS(minESS, 100 * options$mcmcChains), symbol = gettext("Warning:"))
 
 

diff --git a/R/MixedModelsMessages.R b/R/MixedModelsMessages.R
@@ -177,18 +177,24 @@
 }
 
 .mmMessageMaxRhat       <- function(Rhat) {
-  gettextf(
-    "Inference possibly unreliable -- MCMC chains might not have converged; The largest R-hat is %.3f > 1.01. To lower R-hat please increase 'Iterations', or 'Adapt delta' in the Options section.",
-    Rhat
-  )
+  if (is.nan(Rhat))
+    return(gettext("Inference possibly unreliable -- MCMC chains might not have converged; R-hat cannot be computed for all parameters due too few distinct samples. Please re-scale the variables or increase 'Iterations', or 'Adapt delta' in the Options section."))
+  else
+    return(gettextf(
+      "Inference possibly unreliable -- MCMC chains might not have converged; The largest R-hat is %.3f > 1.01. To lower R-hat please increase 'Iterations', or 'Adapt delta' in the Options section.",
+      Rhat
+    ))
 }
 
 .mmMessageMinESS        <- function(ESS, treshold) {
-  gettextf(
-    "Low estimation accuracy -- The smallest Effective Sample Size (ESS) is %.2f < %1.0f. To increase accuracy please increase 'Iterations', or 'Adapt delta' in the Options section.",
-    ESS,
-    treshold
-  )
+  if (is.nan(ESS))
+    return(gettext("Inference possibly unreliable -- MCMC chains might not have converged; Effective Sample Size (ESS) cannot be computed for all parameters due too few distinct samples. Please re-scale the variables or increase 'Iterations', or 'Adapt delta' in the Options section."))
+  else
+    gettextf(
+      "Low estimation accuracy -- The smallest Effective Sample Size (ESS) is %.2f < %1.0f. To increase accuracy please increase 'Iterations', or 'Adapt delta' in the Options section.",
+      ESS,
+      treshold
+    )
 }
 
 .mmMessageBadWAIC       <- function(n_bad) {

diff --git a/inst/qml/MixedModelsBGLMM.qml b/inst/qml/MixedModelsBGLMM.qml
@@ -209,7 +209,10 @@ Form {
 		}
 	}
 
-	MM.MixedModelsModel {}
+	MM.MixedModelsModel
+	{
+		analysisType: "Bayesian"
+	}
 
 	MM.MixedModelsBOptions {}
 

diff --git a/inst/qml/MixedModelsBLMM.qml b/inst/qml/MixedModelsBLMM.qml
@@ -63,7 +63,10 @@ Form {
 		}
 	}
 
-	MM.MixedModelsModel {}
+	MM.MixedModelsModel
+	{
+		analysisType: "Bayesian"
+	}
 
 	MM.MixedModelsBOptions {}
 

diff --git a/inst/qml/common/MixedModelsModel.qml b/inst/qml/common/MixedModelsModel.qml
@@ -24,6 +24,8 @@ Section
 {
 	title:			qsTr("Model")
 
+	property string analysisType:		"frequentist"
+
 	VariablesForm
 	{
 		preferredHeight: jaspTheme.smallDefaultVariablesFormHeight
@@ -49,6 +51,7 @@ Section
 			label:		qsTr("Include intercept")
 			name:		"includeIntercept"
 			checked:	true
+			visible:	analysisType == "frequentist" // stanova cannot summarize no-intercept models
 		}
 	}