From 21d74f50e6f3b4ecac214dc4bd791a05d16e4c49 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 10 Sep 2025 11:37:31 +0000
Subject: [PATCH 1/7] Initial plan


From 5f5b6bbe3b43823472bd6dc1a619cf0fb4dabdcf Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 10 Sep 2025 11:46:26 +0000
Subject: [PATCH 2/7] Add optimizer control settings for classical LMM and GLMM

Co-authored-by: FBartos <38475991+FBartos@users.noreply.github.com>
---
 R/MixedModelsCommon.R                  | 90 +++++++++++++++++++++++---
 R/MixedModelsMessages.R                |  2 +-
 inst/qml/common/MixedModelsOptions.qml | 69 ++++++++++++++++++++
 3 files changed, 152 insertions(+), 9 deletions(-)

diff --git a/R/MixedModelsCommon.R b/R/MixedModelsCommon.R
index c8bc4f77..24f0e3e2 100644
--- a/R/MixedModelsCommon.R
+++ b/R/MixedModelsCommon.R
@@ -411,20 +411,89 @@
 
   return(dataset)
 }
-.mixedInterceptML   <- function(formula, dataset, type, family = NULL) {
+.mmCreateOptimizerControl <- function(type, options) {
+  # Create optimizer control objects based on user settings
+  # Returns default controls if options is NULL or optimizer settings not specified
+  
+  if (is.null(options) || is.null(options$optimizerMethod) || options$optimizerMethod == "default") {
+    # Return default controls
+    if (type == "LMM") {
+      return(lmerTest::lmerControl())
+    } else if (type == "GLMM") {
+      return(lme4::glmerControl())
+    }
+  }
+  
+  # Build control arguments from user options
+  control_args <- list()
+  
+  # Set optimizer method
+  if (!is.null(options$optimizerMethod) && options$optimizerMethod != "default") {
+    control_args$optimizer <- options$optimizerMethod
+  }
+  
+  # Set convergence checking
+  if (!is.null(options$optimizerCheckConv)) {
+    control_args$check.conv.singular <- options$optimizerCheckConv
+    control_args$check.conv.grad <- options$optimizerCheckConv
+    control_args$check.conv.hess <- options$optimizerCheckConv
+  }
+  
+  # Build optimizer control list
+  optCtrl <- list()
+  
+  if (!is.null(options$optimizerMaxIter)) {
+    optCtrl$maxfun <- options$optimizerMaxIter
+    optCtrl$maxit <- options$optimizerMaxIter
+  }
+  
+  if (!is.null(options$optimizerMaxFunEvals)) {
+    optCtrl$maxfun <- options$optimizerMaxFunEvals
+  }
+  
+  if (!is.null(options$optimizerTolerance)) {
+    optCtrl$ftol_abs <- options$optimizerTolerance
+    optCtrl$xtol_abs <- options$optimizerTolerance
+    optCtrl$reltol <- options$optimizerTolerance
+  }
+  
+  if (length(optCtrl) > 0) {
+    control_args$optCtrl <- optCtrl
+  }
+  
+  # Create appropriate control object
+  if (type == "LMM") {
+    return(do.call(lmerTest::lmerControl, control_args))
+  } else if (type == "GLMM") {
+    return(do.call(lme4::glmerControl, control_args))
+  }
+  
+  # Fallback to default
+  if (type == "LMM") {
+    return(lmerTest::lmerControl())
+  } else {
+    return(lme4::glmerControl())
+  }
+}
+
+.mixedInterceptML   <- function(formula, dataset, type, family = NULL, options = NULL) {
   # this is a simple function to fit a mixed-effects model with a fixed intercept only
   # because afex does not allow those models for GLMMs (or LMMs with LRT/PB)
   if (type == "LMM") {
+    control <- .mmCreateOptimizerControl(type, options)
     fit <- lmerTest::lmer(
       formula         = formula,
       data            = dataset,
-      REML            = FALSE
+      REML            = FALSE,
+      control         = control
     )
   } else if (type == "GLMM") {
+    control <- .mmCreateOptimizerControl(type, options)
     fit <- lme4::glmer(
       formula         = formula,
       data            = dataset,
-      family          = family
+      family          = family,
+      control         = control
     )
   }
 
@@ -504,7 +573,8 @@
         .mixedInterceptML(
           formula         = as.formula(modelFormula$modelFormula),
           data            = dataset,
-          type            = "LMM"
+          type            = "LMM",
+          options         = options
         ))
     else
       model <- try(
@@ -515,7 +585,8 @@
           method          = .mmGetTestMethod(options),
           test_intercept  = .mmGetTestIntercept(options),
           args_test       = list(nsim = options$bootstrapSamples),
-          check_contrasts = FALSE
+          check_contrasts = FALSE,
+          control         = .mmCreateOptimizerControl("LMM", options)
         ))
   } else if (type == "GLMM") {
     # needs to be evaluated in the global environment
@@ -540,7 +611,8 @@
           args_test       = list(nsim = options$bootstrapSamples),
           check_contrasts = FALSE,
           family          = glmmFamily,
-          weights         = glmmWeight
+          weights         = glmmWeight,
+          control         = .mmCreateOptimizerControl("GLMM", options)
         ))
     } else {
       if (.isInterceptML(options))
@@ -549,7 +621,8 @@
             formula         = as.formula(modelFormula$modelFormula),
             data            = dataset,
             family          = glmmFamily,
-            type            = "GLMM"
+            type            = "GLMM",
+            options         = options
           ))
       else
         model <- try(
@@ -562,7 +635,8 @@
             args_test       = list(nsim = options$bootstrapSamples),
             check_contrasts = FALSE,
             #start           = start,
-            family          = glmmFamily
+            family          = glmmFamily,
+            control         = .mmCreateOptimizerControl("GLMM", options)
         ))
     }
   }
diff --git a/R/MixedModelsMessages.R b/R/MixedModelsMessages.R
index 721809fb..8b7d5f8a 100644
--- a/R/MixedModelsMessages.R
+++ b/R/MixedModelsMessages.R
@@ -237,7 +237,7 @@
   else if (grepl("Downdated VtV is not positive definite", error))
     return(gettext("The optimizer failed to find a solution. Probably due to scaling issues quasi-separation in the data. Try rescaling or removing some of the predictors."))
   else if (grepl("did not converge in (maxit) iterations", error))
-    return(gettext("The optimizer failed to find a solution in the specified number of iterations. (JASP currently does not support modifying the optimizer settings.)"))
+    return(gettext("The optimizer failed to find a solution in the specified number of iterations. Try adjusting the optimizer settings in the Advanced Options section."))
   else if (grepl("unexpected symbol", error)) # triggered by right hand side formula larger than 500 characters -- the maximum length
     return(gettext("The model formula is probably too long. Try shortening variable names."))
   else
diff --git a/inst/qml/common/MixedModelsOptions.qml b/inst/qml/common/MixedModelsOptions.qml
index 3edeeb97..d937e932 100644
--- a/inst/qml/common/MixedModelsOptions.qml
+++ b/inst/qml/common/MixedModelsOptions.qml
@@ -121,4 +121,73 @@ Section
 		label:	qsTr("Vovk-Sellke maximum p-ratio")
 	}
 
+	Section
+	{
+		title:		qsTr("Advanced Options")
+		expanded:	false
+		visible:	allMethodOptions  // Only show for classical models (LMM/GLMM)
+
+		Group
+		{
+			title: qsTr("Optimizer Settings")
+
+			DropDown
+			{
+				name:	"optimizerMethod"
+				label:	qsTr("Optimizer")
+				info:	qsTr("Optimization algorithm used for parameter estimation")
+				values:
+				[
+					{ label: qsTr("Default"),		value: "default"},
+					{ label: "nlminb",				value: "nlminb"},
+					{ label: "BFGS",				value: "BFGS"},
+					{ label: "Nelder-Mead",			value: "Nelder_Mead"},
+					{ label: "bobyqa",				value: "bobyqa"}
+				]
+			}
+
+			IntegerField
+			{
+				name:			"optimizerMaxIter"
+				label:			qsTr("Maximum iterations")
+				info:			qsTr("Maximum number of iterations for the optimizer")
+				defaultValue:	10000
+				min:			100
+				max:			1000000
+				fieldWidth:		80 * jaspTheme.uiScale
+			}
+
+			IntegerField
+			{
+				name:			"optimizerMaxFunEvals"
+				label:			qsTr("Maximum function evaluations")
+				info:			qsTr("Maximum number of function evaluations")
+				defaultValue:	100000
+				min:			1000
+				max:			10000000
+				fieldWidth:		80 * jaspTheme.uiScale
+			}
+
+			DoubleField
+			{
+				name:			"optimizerTolerance"
+				label:			qsTr("Convergence tolerance")
+				info:			qsTr("Convergence tolerance for parameter estimates")
+				defaultValue:	1e-6
+				min:			1e-12
+				max:			1e-3
+				decimals:		12
+				fieldWidth:		100 * jaspTheme.uiScale
+			}
+
+			CheckBox
+			{
+				name:	"optimizerCheckConv"
+				label:	qsTr("Check convergence")
+				info:	qsTr("Check for convergence warnings and errors")
+				checked: true
+			}
+		}
+	}
+
 }

From 45ed33dca29726166cadcf1105e1f7888321f310 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 10 Sep 2025 11:51:59 +0000
Subject: [PATCH 3/7] Add tests for optimizer settings and finalize
 implementation

Co-authored-by: FBartos <38475991+FBartos@users.noreply.github.com>
---
 R/MixedModelsCommon.R                  |  6 ++---
 inst/qml/common/MixedModelsOptions.qml |  2 +-
 tests/testthat/test-mixedmodelsglmm.R  | 35 ++++++++++++++++++++++++++
 tests/testthat/test-mixedmodelslmm.R   | 32 +++++++++++++++++++++++
 4 files changed, 71 insertions(+), 4 deletions(-)

diff --git a/R/MixedModelsCommon.R b/R/MixedModelsCommon.R
index 24f0e3e2..25b40aa1 100644
--- a/R/MixedModelsCommon.R
+++ b/R/MixedModelsCommon.R
@@ -418,7 +418,7 @@
   if (is.null(options) || is.null(options$optimizerMethod) || options$optimizerMethod == "default") {
     # Return default controls
     if (type == "LMM") {
-      return(lmerTest::lmerControl())
+      return(lme4::lmerControl())
     } else if (type == "GLMM") {
       return(lme4::glmerControl())
     }
@@ -463,14 +463,14 @@
   
   # Create appropriate control object
   if (type == "LMM") {
-    return(do.call(lmerTest::lmerControl, control_args))
+    return(do.call(lme4::lmerControl, control_args))
   } else if (type == "GLMM") {
     return(do.call(lme4::glmerControl, control_args))
   }
   
   # Fallback to default
   if (type == "LMM") {
-    return(lmerTest::lmerControl())
+    return(lme4::lmerControl())
   } else {
     return(lme4::glmerControl())
   }
diff --git a/inst/qml/common/MixedModelsOptions.qml b/inst/qml/common/MixedModelsOptions.qml
index d937e932..8864fae2 100644
--- a/inst/qml/common/MixedModelsOptions.qml
+++ b/inst/qml/common/MixedModelsOptions.qml
@@ -125,7 +125,7 @@ Section
 	{
 		title:		qsTr("Advanced Options")
 		expanded:	false
-		visible:	allMethodOptions  // Only show for classical models (LMM/GLMM)
+		// Show optimizer settings for all classical models (LMM and GLMM)
 
 		Group
 		{
diff --git a/tests/testthat/test-mixedmodelsglmm.R b/tests/testthat/test-mixedmodelsglmm.R
index cc160fdb..e2e2109d 100644
--- a/tests/testthat/test-mixedmodelsglmm.R
+++ b/tests/testthat/test-mixedmodelsglmm.R
@@ -973,3 +973,38 @@ context("Generalized Linear Mixed Models")
     jaspTools::expect_equal_plots(testPlot, "plot-glmm-5")
   })
 }
+
+### Test optimizer options for GLMM
+{
+  test_that("GLMM optimizer options can be set without errors", {
+    options <- jaspTools::analysisOptions("MixedModelsGLMM")
+    options$dependent <- "dependent"
+    options$fixedEffects <- list(list(components = "factor1"))
+    options$randomEffects <- list(list(
+      randomComponents = list(list(randomSlopes = FALSE, value = "grouping"))
+    ))
+    options$family <- "binomial"
+    options$link <- "logit"
+    
+    # Test custom optimizer settings
+    options$optimizerMethod <- "bobyqa"
+    options$optimizerMaxIter <- 5000
+    options$optimizerMaxFunEvals <- 50000
+    options$optimizerTolerance <- 1e-8
+    options$optimizerCheckConv <- TRUE
+    
+    # Create simple test dataset for binomial GLMM
+    dataset <- data.frame(
+      dependent = rbinom(40, 1, 0.5),
+      factor1 = factor(rep(c("A", "B"), each = 20)),
+      grouping = factor(rep(1:4, each = 10))
+    )
+    
+    # Should not error during options processing
+    results <- jaspTools::runAnalysis("MixedModelsGLMM", dataset = dataset, options)
+    
+    # Basic check that analysis ran and produced some output
+    expect_true(!is.null(results))
+    expect_true(length(results$results) > 0)
+  })
+}
diff --git a/tests/testthat/test-mixedmodelslmm.R b/tests/testthat/test-mixedmodelslmm.R
index 81edf48d..9975ff13 100644
--- a/tests/testthat/test-mixedmodelslmm.R
+++ b/tests/testthat/test-mixedmodelslmm.R
@@ -1067,3 +1067,35 @@ context("Linear Mixed Models")
   })
 }
 
+### Test optimizer options
+{
+  test_that("Optimizer options can be set without errors", {
+    options <- jaspTools::analysisOptions("MixedModelsLMM")
+    options$dependent <- "Variable4"
+    options$fixedEffects <- list(list(components = "Variable1"))
+    options$randomEffects <- list(list(
+      randomComponents = list(list(randomSlopes = FALSE, value = "Variable2"))
+    ))
+    
+    # Test custom optimizer settings
+    options$optimizerMethod <- "nlminb"
+    options$optimizerMaxIter <- 5000
+    options$optimizerMaxFunEvals <- 50000
+    options$optimizerTolerance <- 1e-8
+    options$optimizerCheckConv <- TRUE
+    
+    dataset <- data.frame(
+      Variable1 = factor(rep(c("A", "B"), each = 20)),
+      Variable2 = factor(rep(1:4, each = 10)),
+      Variable4 = rnorm(40)
+    )
+    
+    # Should not error during options processing
+    results <- jaspTools::runAnalysis("MixedModelsLMM", dataset = dataset, options)
+    
+    # Basic check that analysis ran and produced some output
+    expect_true(!is.null(results))
+    expect_true(length(results$results) > 0)
+  })
+}
+

From 72562215c4eef62da2c7acd22890269d212fa9e4 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 10 Sep 2025 12:03:09 +0000
Subject: [PATCH 4/7] Refactor optimizer settings into separate Advanced.qml
 component

Co-authored-by: FBartos <38475991+FBartos@users.noreply.github.com>
---
 inst/qml/MixedModelsGLMM.qml           |  2 +
 inst/qml/MixedModelsLMM.qml            |  2 +
 inst/qml/common/Advanced.qml           | 89 ++++++++++++++++++++++++++
 inst/qml/common/MixedModelsOptions.qml | 69 --------------------
 4 files changed, 93 insertions(+), 69 deletions(-)
 create mode 100644 inst/qml/common/Advanced.qml

diff --git a/inst/qml/MixedModelsGLMM.qml b/inst/qml/MixedModelsGLMM.qml
index 98de4c3e..a3c8412c 100644
--- a/inst/qml/MixedModelsGLMM.qml
+++ b/inst/qml/MixedModelsGLMM.qml
@@ -419,4 +419,6 @@ Form {
 		}
 	}
 
+	MM.Advanced {}
+
 }
diff --git a/inst/qml/MixedModelsLMM.qml b/inst/qml/MixedModelsLMM.qml
index f081e783..098e623f 100755
--- a/inst/qml/MixedModelsLMM.qml
+++ b/inst/qml/MixedModelsLMM.qml
@@ -317,4 +317,6 @@ Form {
 		}
 	}
 
+	MM.Advanced {}
+
 }
diff --git a/inst/qml/common/Advanced.qml b/inst/qml/common/Advanced.qml
new file mode 100644
index 00000000..2ef8fa2e
--- /dev/null
+++ b/inst/qml/common/Advanced.qml
@@ -0,0 +1,89 @@
+//
+// Copyright (C) 2013-2020 University of Amsterdam
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Affero General Public License as
+// published by the Free Software Foundation, either version 3 of the
+// License, or (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Affero General Public License for more details.
+//
+// You should have received a copy of the GNU Affero General Public
+// License along with this program.  If not, see
+// <http://www.gnu.org/licenses/>.
+//
+import QtQuick
+import QtQuick.Layouts
+import JASP
+import JASP.Controls
+
+Section
+{
+	title:		qsTr("Advanced Options")
+	expanded:	false
+
+	Group
+	{
+		title: qsTr("Optimizer Settings")
+
+		DropDown
+		{
+			name:	"optimizerMethod"
+			label:	qsTr("Optimizer")
+			info:	qsTr("Optimization algorithm used for parameter estimation")
+			values:
+			[
+				{ label: qsTr("Default"),		value: "default"},
+				{ label: "nlminb",				value: "nlminb"},
+				{ label: "BFGS",				value: "BFGS"},
+				{ label: "Nelder-Mead",			value: "Nelder_Mead"},
+				{ label: "bobyqa",				value: "bobyqa"}
+			]
+		}
+
+		IntegerField
+		{
+			name:			"optimizerMaxIter"
+			label:			qsTr("Maximum iterations")
+			info:			qsTr("Maximum number of iterations for the optimizer")
+			defaultValue:	10000
+			min:			100
+			max:			1000000
+			fieldWidth:		80 * jaspTheme.uiScale
+		}
+
+		IntegerField
+		{
+			name:			"optimizerMaxFunEvals"
+			label:			qsTr("Maximum function evaluations")
+			info:			qsTr("Maximum number of function evaluations")
+			defaultValue:	100000
+			min:			1000
+			max:			10000000
+			fieldWidth:		80 * jaspTheme.uiScale
+		}
+
+		DoubleField
+		{
+			name:			"optimizerTolerance"
+			label:			qsTr("Convergence tolerance")
+			info:			qsTr("Convergence tolerance for parameter estimates")
+			defaultValue:	1e-6
+			min:			1e-12
+			max:			1e-3
+			decimals:		12
+			fieldWidth:		100 * jaspTheme.uiScale
+		}
+
+		CheckBox
+		{
+			name:	"optimizerCheckConv"
+			label:	qsTr("Check convergence")
+			info:	qsTr("Check for convergence warnings and errors")
+			checked: true
+		}
+	}
+}
\ No newline at end of file
diff --git a/inst/qml/common/MixedModelsOptions.qml b/inst/qml/common/MixedModelsOptions.qml
index 8864fae2..3edeeb97 100644
--- a/inst/qml/common/MixedModelsOptions.qml
+++ b/inst/qml/common/MixedModelsOptions.qml
@@ -121,73 +121,4 @@ Section
 		label:	qsTr("Vovk-Sellke maximum p-ratio")
 	}
 
-	Section
-	{
-		title:		qsTr("Advanced Options")
-		expanded:	false
-		// Show optimizer settings for all classical models (LMM and GLMM)
-
-		Group
-		{
-			title: qsTr("Optimizer Settings")
-
-			DropDown
-			{
-				name:	"optimizerMethod"
-				label:	qsTr("Optimizer")
-				info:	qsTr("Optimization algorithm used for parameter estimation")
-				values:
-				[
-					{ label: qsTr("Default"),		value: "default"},
-					{ label: "nlminb",				value: "nlminb"},
-					{ label: "BFGS",				value: "BFGS"},
-					{ label: "Nelder-Mead",			value: "Nelder_Mead"},
-					{ label: "bobyqa",				value: "bobyqa"}
-				]
-			}
-
-			IntegerField
-			{
-				name:			"optimizerMaxIter"
-				label:			qsTr("Maximum iterations")
-				info:			qsTr("Maximum number of iterations for the optimizer")
-				defaultValue:	10000
-				min:			100
-				max:			1000000
-				fieldWidth:		80 * jaspTheme.uiScale
-			}
-
-			IntegerField
-			{
-				name:			"optimizerMaxFunEvals"
-				label:			qsTr("Maximum function evaluations")
-				info:			qsTr("Maximum number of function evaluations")
-				defaultValue:	100000
-				min:			1000
-				max:			10000000
-				fieldWidth:		80 * jaspTheme.uiScale
-			}
-
-			DoubleField
-			{
-				name:			"optimizerTolerance"
-				label:			qsTr("Convergence tolerance")
-				info:			qsTr("Convergence tolerance for parameter estimates")
-				defaultValue:	1e-6
-				min:			1e-12
-				max:			1e-3
-				decimals:		12
-				fieldWidth:		100 * jaspTheme.uiScale
-			}
-
-			CheckBox
-			{
-				name:	"optimizerCheckConv"
-				label:	qsTr("Check convergence")
-				info:	qsTr("Check for convergence warnings and errors")
-				checked: true
-			}
-		}
-	}
-
 }

From 736148fe4de76c0737fc4d1aa8a595ab9891bc93 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Franti=C5=A1ek=20Barto=C5=A1?= <f.bartos96@gmail.com>
Date: Wed, 10 Sep 2025 15:35:17 +0200
Subject: [PATCH 5/7] fix basic issues

---
 R/MixedModelsCommon.R | 56 ++++++++++++++++++-------------------------
 1 file changed, 23 insertions(+), 33 deletions(-)

diff --git a/R/MixedModelsCommon.R b/R/MixedModelsCommon.R
index 25b40aa1..db020bc2 100644
--- a/R/MixedModelsCommon.R
+++ b/R/MixedModelsCommon.R
@@ -413,67 +413,50 @@
 }
 .mmCreateOptimizerControl <- function(type, options) {
   # Create optimizer control objects based on user settings
-  # Returns default controls if options is NULL or optimizer settings not specified
-  
-  if (is.null(options) || is.null(options$optimizerMethod) || options$optimizerMethod == "default") {
-    # Return default controls
-    if (type == "LMM") {
-      return(lme4::lmerControl())
-    } else if (type == "GLMM") {
-      return(lme4::glmerControl())
-    }
-  }
-  
+
   # Build control arguments from user options
   control_args <- list()
-  
+
   # Set optimizer method
-  if (!is.null(options$optimizerMethod) && options$optimizerMethod != "default") {
+  if (options$optimizerMethod != "default") {
     control_args$optimizer <- options$optimizerMethod
   }
-  
+
   # Set convergence checking
   if (!is.null(options$optimizerCheckConv)) {
     control_args$check.conv.singular <- options$optimizerCheckConv
     control_args$check.conv.grad <- options$optimizerCheckConv
     control_args$check.conv.hess <- options$optimizerCheckConv
   }
-  
+
   # Build optimizer control list
   optCtrl <- list()
-  
+
   if (!is.null(options$optimizerMaxIter)) {
     optCtrl$maxfun <- options$optimizerMaxIter
     optCtrl$maxit <- options$optimizerMaxIter
   }
-  
+
   if (!is.null(options$optimizerMaxFunEvals)) {
     optCtrl$maxfun <- options$optimizerMaxFunEvals
   }
-  
+
   if (!is.null(options$optimizerTolerance)) {
     optCtrl$ftol_abs <- options$optimizerTolerance
     optCtrl$xtol_abs <- options$optimizerTolerance
     optCtrl$reltol <- options$optimizerTolerance
   }
-  
+
   if (length(optCtrl) > 0) {
     control_args$optCtrl <- optCtrl
   }
-  
+
   # Create appropriate control object
   if (type == "LMM") {
     return(do.call(lme4::lmerControl, control_args))
   } else if (type == "GLMM") {
     return(do.call(lme4::glmerControl, control_args))
   }
-  
-  # Fallback to default
-  if (type == "LMM") {
-    return(lme4::lmerControl())
-  } else {
-    return(lme4::glmerControl())
-  }
 }
 
 .mixedInterceptML   <- function(formula, dataset, type, family = NULL, options = NULL) {
@@ -543,7 +526,8 @@
   return(added)
 }
 .mmFitModel      <- function(jaspResults, dataset, options, type = "LMM") {
-
+saveRDS(options, file = "C:/JASP-Packages/options.RDS")
+saveRDS(dataset, file = "C:/JASP-Packages/dataset.RDS")
   if (!is.null(jaspResults[["mmModel"]]))
     return()
 
@@ -567,6 +551,10 @@
   # specify contrasts
   dataset <- .mmSetContrasts(dataset, options)
 
+  # the control arguments needs to be assigned outside of the call because
+  # forwarding the call crashes afex
+  lmControl <- .mmCreateOptimizerControl(type, options)
+
   if (type == "LMM") {
     if (.isInterceptML(options))
       model <- try(
@@ -574,7 +562,8 @@
           formula         = as.formula(modelFormula$modelFormula),
           data            = dataset,
           type            = "LMM",
-          options         = options
+          options         = options,
+          control         = lmControl
         ))
     else
       model <- try(
@@ -586,7 +575,7 @@
           test_intercept  = .mmGetTestIntercept(options),
           args_test       = list(nsim = options$bootstrapSamples),
           check_contrasts = FALSE,
-          control         = .mmCreateOptimizerControl("LMM", options)
+          control         = lmControl
         ))
   } else if (type == "GLMM") {
     # needs to be evaluated in the global environment
@@ -612,7 +601,7 @@
           check_contrasts = FALSE,
           family          = glmmFamily,
           weights         = glmmWeight,
-          control         = .mmCreateOptimizerControl("GLMM", options)
+          control         = lmControl
         ))
     } else {
       if (.isInterceptML(options))
@@ -622,7 +611,8 @@
             data            = dataset,
             family          = glmmFamily,
             type            = "GLMM",
-            options         = options
+            options         = options,
+            control         = lmControl
           ))
       else
         model <- try(
@@ -636,7 +626,7 @@
             check_contrasts = FALSE,
             #start           = start,
             family          = glmmFamily,
-            control         = .mmCreateOptimizerControl("GLMM", options)
+            control         = lmControl
         ))
     }
   }

From f347a0d04c14c1c22959c5a2af4308729e6f20b3 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 10 Sep 2025 13:54:16 +0000
Subject: [PATCH 6/7] Implement optimizer-specific settings and fix title

Co-authored-by: FBartos <38475991+FBartos@users.noreply.github.com>
---
 R/MixedModelsCommon.R        |  64 +++++++++++----
 inst/qml/common/Advanced.qml | 153 ++++++++++++++++++++++++++++++++---
 2 files changed, 192 insertions(+), 25 deletions(-)

diff --git a/R/MixedModelsCommon.R b/R/MixedModelsCommon.R
index db020bc2..8c9354e7 100644
--- a/R/MixedModelsCommon.R
+++ b/R/MixedModelsCommon.R
@@ -429,22 +429,56 @@
     control_args$check.conv.hess <- options$optimizerCheckConv
   }
 
-  # Build optimizer control list
+  # Build optimizer-specific control list
   optCtrl <- list()
 
-  if (!is.null(options$optimizerMaxIter)) {
-    optCtrl$maxfun <- options$optimizerMaxIter
-    optCtrl$maxit <- options$optimizerMaxIter
-  }
-
-  if (!is.null(options$optimizerMaxFunEvals)) {
-    optCtrl$maxfun <- options$optimizerMaxFunEvals
-  }
-
-  if (!is.null(options$optimizerTolerance)) {
-    optCtrl$ftol_abs <- options$optimizerTolerance
-    optCtrl$xtol_abs <- options$optimizerTolerance
-    optCtrl$reltol <- options$optimizerTolerance
+  if (options$optimizerMethod == "Nelder_Mead") {
+    # Nelder-Mead specific options
+    if (!is.null(options$nelderMeadMaxfun) && options$nelderMeadMaxfun > 0) {
+      optCtrl$maxfun <- options$nelderMeadMaxfun
+    }
+    if (!is.null(options$nelderMeadFtolAbs) && options$nelderMeadFtolAbs > 0) {
+      optCtrl$FtolAbs <- options$nelderMeadFtolAbs
+    }
+    if (!is.null(options$nelderMeadFtolRel) && options$nelderMeadFtolRel > 0) {
+      optCtrl$FtolRel <- options$nelderMeadFtolRel
+    }
+    if (!is.null(options$nelderMeadXtolRel) && options$nelderMeadXtolRel > 0) {
+      optCtrl$XtolRel <- options$nelderMeadXtolRel
+    }
+  } else if (options$optimizerMethod == "bobyqa") {
+    # bobyqa specific options
+    if (!is.null(options$bobyqaNpt) && options$bobyqaNpt > 0) {
+      optCtrl$npt <- options$bobyqaNpt
+    }
+    if (!is.null(options$bobyqaRhobeg) && options$bobyqaRhobeg > 0) {
+      optCtrl$rhobeg <- options$bobyqaRhobeg
+    }
+    if (!is.null(options$bobyqaRhoend) && options$bobyqaRhoend > 0) {
+      optCtrl$rhoend <- options$bobyqaRhoend
+    }
+    if (!is.null(options$bobyqaMaxfun) && options$bobyqaMaxfun > 0) {
+      optCtrl$maxfun <- options$bobyqaMaxfun
+    }
+  } else if (options$optimizerMethod == "nlminb") {
+    # nlminb specific options
+    if (!is.null(options$nlminbTol) && options$nlminbTol > 0) {
+      optCtrl$tol <- options$nlminbTol
+    }
+    if (!is.null(options$nlminbRelTol) && options$nlminbRelTol > 0) {
+      optCtrl$relTol <- options$nlminbRelTol
+    }
+    if (!is.null(options$nlminbMaxit) && options$nlminbMaxit > 0) {
+      optCtrl$maxit <- options$nlminbMaxit
+    }
+  } else {
+    # Default and BFGS: use generic options
+    if (!is.null(options$optimizerMaxIter) && options$optimizerMaxIter > 0) {
+      optCtrl$maxit <- options$optimizerMaxIter
+    }
+    if (!is.null(options$optimizerTolerance) && options$optimizerTolerance > 0) {
+      optCtrl$reltol <- options$optimizerTolerance
+    }
   }
 
   if (length(optCtrl) > 0) {
@@ -526,8 +560,6 @@
   return(added)
 }
 .mmFitModel      <- function(jaspResults, dataset, options, type = "LMM") {
-saveRDS(options, file = "C:/JASP-Packages/options.RDS")
-saveRDS(dataset, file = "C:/JASP-Packages/dataset.RDS")
   if (!is.null(jaspResults[["mmModel"]]))
     return()
 
diff --git a/inst/qml/common/Advanced.qml b/inst/qml/common/Advanced.qml
index 2ef8fa2e..e1a40a01 100644
--- a/inst/qml/common/Advanced.qml
+++ b/inst/qml/common/Advanced.qml
@@ -22,7 +22,7 @@ import JASP.Controls
 
 Section
 {
-	title:		qsTr("Advanced Options")
+	title:		qsTr("Advanced")
 	expanded:	false
 
 	Group
@@ -31,6 +31,7 @@ Section
 
 		DropDown
 		{
+			id:		optimizerDropdown
 			name:	"optimizerMethod"
 			label:	qsTr("Optimizer")
 			info:	qsTr("Optimization algorithm used for parameter estimation")
@@ -44,26 +45,159 @@ Section
 			]
 		}
 
+		// Nelder-Mead specific options
 		IntegerField
 		{
-			name:			"optimizerMaxIter"
-			label:			qsTr("Maximum iterations")
-			info:			qsTr("Maximum number of iterations for the optimizer")
+			name:			"nelderMeadMaxfun"
+			label:			qsTr("Maximum function evaluations")
+			info:			qsTr("Maximum number of function evaluations allowed")
 			defaultValue:	10000
 			min:			100
 			max:			1000000
 			fieldWidth:		80 * jaspTheme.uiScale
+			visible:		optimizerDropdown.currentValue === "Nelder_Mead"
+		}
+
+		DoubleField
+		{
+			name:			"nelderMeadFtolAbs"
+			label:			qsTr("Absolute function tolerance")
+			info:			qsTr("Absolute tolerance on change in function values")
+			defaultValue:	1e-5
+			min:			1e-12
+			max:			1e-1
+			decimals:		12
+			fieldWidth:		100 * jaspTheme.uiScale
+			visible:		optimizerDropdown.currentValue === "Nelder_Mead"
+		}
+
+		DoubleField
+		{
+			name:			"nelderMeadFtolRel"
+			label:			qsTr("Relative function tolerance")
+			info:			qsTr("Relative tolerance on change in function values")
+			defaultValue:	1e-15
+			min:			1e-20
+			max:			1e-5
+			decimals:		20
+			fieldWidth:		100 * jaspTheme.uiScale
+			visible:		optimizerDropdown.currentValue === "Nelder_Mead"
+		}
+
+		DoubleField
+		{
+			name:			"nelderMeadXtolRel"
+			label:			qsTr("Relative parameter tolerance")
+			info:			qsTr("Relative tolerance on change in parameter values")
+			defaultValue:	1e-7
+			min:			1e-15
+			max:			1e-3
+			decimals:		15
+			fieldWidth:		100 * jaspTheme.uiScale
+			visible:		optimizerDropdown.currentValue === "Nelder_Mead"
+		}
+
+		// bobyqa specific options
+		IntegerField
+		{
+			name:			"bobyqaNpt"
+			label:			qsTr("Number of interpolation points")
+			info:			qsTr("Number of points used to approximate the objective function")
+			defaultValue:	0
+			min:			0
+			max:			100
+			fieldWidth:		80 * jaspTheme.uiScale
+			visible:		optimizerDropdown.currentValue === "bobyqa"
+		}
+
+		DoubleField
+		{
+			name:			"bobyqaRhobeg"
+			label:			qsTr("Initial trust region radius")
+			info:			qsTr("Initial value of the trust region radius")
+			defaultValue:	0
+			min:			0
+			max:			10
+			decimals:		6
+			fieldWidth:		100 * jaspTheme.uiScale
+			visible:		optimizerDropdown.currentValue === "bobyqa"
+		}
+
+		DoubleField
+		{
+			name:			"bobyqaRhoend"
+			label:			qsTr("Final trust region radius")
+			info:			qsTr("Final value of the trust region radius")
+			defaultValue:	0
+			min:			0
+			max:			1
+			decimals:		10
+			fieldWidth:		100 * jaspTheme.uiScale
+			visible:		optimizerDropdown.currentValue === "bobyqa"
 		}
 
 		IntegerField
 		{
-			name:			"optimizerMaxFunEvals"
+			name:			"bobyqaMaxfun"
 			label:			qsTr("Maximum function evaluations")
-			info:			qsTr("Maximum number of function evaluations")
-			defaultValue:	100000
-			min:			1000
-			max:			10000000
+			info:			qsTr("Maximum number of function evaluations allowed")
+			defaultValue:	10000
+			min:			100
+			max:			1000000
+			fieldWidth:		80 * jaspTheme.uiScale
+			visible:		optimizerDropdown.currentValue === "bobyqa"
+		}
+
+		// nlminb specific options
+		DoubleField
+		{
+			name:			"nlminbTol"
+			label:			qsTr("Tolerance")
+			info:			qsTr("Convergence tolerance")
+			defaultValue:	1e-6
+			min:			1e-12
+			max:			1e-3
+			decimals:		12
+			fieldWidth:		100 * jaspTheme.uiScale
+			visible:		optimizerDropdown.currentValue === "nlminb"
+		}
+
+		DoubleField
+		{
+			name:			"nlminbRelTol"
+			label:			qsTr("Relative tolerance")
+			info:			qsTr("Relative convergence tolerance")
+			defaultValue:	1e-10
+			min:			1e-20
+			max:			1e-5
+			decimals:		20
+			fieldWidth:		100 * jaspTheme.uiScale
+			visible:		optimizerDropdown.currentValue === "nlminb"
+		}
+
+		IntegerField
+		{
+			name:			"nlminbMaxit"
+			label:			qsTr("Maximum iterations")
+			info:			qsTr("Maximum number of iterations")
+			defaultValue:	10000
+			min:			100
+			max:			1000000
+			fieldWidth:		80 * jaspTheme.uiScale
+			visible:		optimizerDropdown.currentValue === "nlminb"
+		}
+
+		// Default and BFGS options (generic fallback)
+		IntegerField
+		{
+			name:			"optimizerMaxIter"
+			label:			qsTr("Maximum iterations")
+			info:			qsTr("Maximum number of iterations for the optimizer")
+			defaultValue:	10000
+			min:			100
+			max:			1000000
 			fieldWidth:		80 * jaspTheme.uiScale
+			visible:		optimizerDropdown.currentValue === "default" || optimizerDropdown.currentValue === "BFGS"
 		}
 
 		DoubleField
@@ -76,6 +210,7 @@ Section
 			max:			1e-3
 			decimals:		12
 			fieldWidth:		100 * jaspTheme.uiScale
+			visible:		optimizerDropdown.currentValue === "default" || optimizerDropdown.currentValue === "BFGS"
 		}
 
 		CheckBox

From ca0a2f8a5103835db3214d8a061fa2c32265716b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Franti=C5=A1ek=20Barto=C5=A1?= <f.bartos96@gmail.com>
Date: Wed, 10 Sep 2025 16:31:03 +0200
Subject: [PATCH 7/7] additional fixes

---
 R/MixedModelsCommon.R                         | 18 ++++----------
 inst/qml/MixedModelsGLMM.qml                  |  2 +-
 inst/qml/MixedModelsLMM.qml                   |  2 +-
 .../{Advanced.qml => MixedModelsAdvanced.qml} | 24 +++++++------------
 4 files changed, 15 insertions(+), 31 deletions(-)
 rename inst/qml/common/{Advanced.qml => MixedModelsAdvanced.qml} (91%)

diff --git a/R/MixedModelsCommon.R b/R/MixedModelsCommon.R
index 8c9354e7..aac3df89 100644
--- a/R/MixedModelsCommon.R
+++ b/R/MixedModelsCommon.R
@@ -422,13 +422,6 @@
     control_args$optimizer <- options$optimizerMethod
   }
 
-  # Set convergence checking
-  if (!is.null(options$optimizerCheckConv)) {
-    control_args$check.conv.singular <- options$optimizerCheckConv
-    control_args$check.conv.grad <- options$optimizerCheckConv
-    control_args$check.conv.hess <- options$optimizerCheckConv
-  }
-
   # Build optimizer-specific control list
   optCtrl <- list()
 
@@ -496,21 +489,20 @@
 .mixedInterceptML   <- function(formula, dataset, type, family = NULL, options = NULL) {
   # this is a simple function to fit a mixed-effects model with a fixed intercept only
   # because afex does not allow those models for GLMMs (or LMMs with LRT/PB)
+  lmControl <<- .mmCreateOptimizerControl(type, options)
+
   if (type == "LMM") {
-    control <- .mmCreateOptimizerControl(type, options)
     fit <- lmerTest::lmer(
       formula         = formula,
       data            = dataset,
       REML            = FALSE,
-      control         = control
+      control         = lmControl
     )
   } else if (type == "GLMM") {
-    control <- .mmCreateOptimizerControl(type, options)
     fit <- lme4::glmer(
       formula         = formula,
       data            = dataset,
-      family          = family,
-      control         = control
+      family          = family
     )
   }
 
@@ -585,7 +577,7 @@
 
   # the control arguments needs to be assigned outside of the call because
   # forwarding the call crashes afex
-  lmControl <- .mmCreateOptimizerControl(type, options)
+  lmControl <<- .mmCreateOptimizerControl(type, options)
 
   if (type == "LMM") {
     if (.isInterceptML(options))
diff --git a/inst/qml/MixedModelsGLMM.qml b/inst/qml/MixedModelsGLMM.qml
index a3c8412c..012bde9d 100644
--- a/inst/qml/MixedModelsGLMM.qml
+++ b/inst/qml/MixedModelsGLMM.qml
@@ -419,6 +419,6 @@ Form {
 		}
 	}
 
-	MM.Advanced {}
+	MM.MixedModelsAdvanced {}
 
 }
diff --git a/inst/qml/MixedModelsLMM.qml b/inst/qml/MixedModelsLMM.qml
index 098e623f..74ddcd1b 100755
--- a/inst/qml/MixedModelsLMM.qml
+++ b/inst/qml/MixedModelsLMM.qml
@@ -317,6 +317,6 @@ Form {
 		}
 	}
 
-	MM.Advanced {}
+	MM.MixedModelsAdvanced {}
 
 }
diff --git a/inst/qml/common/Advanced.qml b/inst/qml/common/MixedModelsAdvanced.qml
similarity index 91%
rename from inst/qml/common/Advanced.qml
rename to inst/qml/common/MixedModelsAdvanced.qml
index e1a40a01..bb34f646 100644
--- a/inst/qml/common/Advanced.qml
+++ b/inst/qml/common/MixedModelsAdvanced.qml
@@ -67,7 +67,7 @@ Section
 			min:			1e-12
 			max:			1e-1
 			decimals:		12
-			fieldWidth:		100 * jaspTheme.uiScale
+			fieldWidth:		80 * jaspTheme.uiScale
 			visible:		optimizerDropdown.currentValue === "Nelder_Mead"
 		}
 
@@ -80,7 +80,7 @@ Section
 			min:			1e-20
 			max:			1e-5
 			decimals:		20
-			fieldWidth:		100 * jaspTheme.uiScale
+			fieldWidth:		80 * jaspTheme.uiScale
 			visible:		optimizerDropdown.currentValue === "Nelder_Mead"
 		}
 
@@ -93,7 +93,7 @@ Section
 			min:			1e-15
 			max:			1e-3
 			decimals:		15
-			fieldWidth:		100 * jaspTheme.uiScale
+			fieldWidth:		80 * jaspTheme.uiScale
 			visible:		optimizerDropdown.currentValue === "Nelder_Mead"
 		}
 
@@ -119,7 +119,7 @@ Section
 			min:			0
 			max:			10
 			decimals:		6
-			fieldWidth:		100 * jaspTheme.uiScale
+			fieldWidth:		80 * jaspTheme.uiScale
 			visible:		optimizerDropdown.currentValue === "bobyqa"
 		}
 
@@ -132,7 +132,7 @@ Section
 			min:			0
 			max:			1
 			decimals:		10
-			fieldWidth:		100 * jaspTheme.uiScale
+			fieldWidth:		80 * jaspTheme.uiScale
 			visible:		optimizerDropdown.currentValue === "bobyqa"
 		}
 
@@ -158,7 +158,7 @@ Section
 			min:			1e-12
 			max:			1e-3
 			decimals:		12
-			fieldWidth:		100 * jaspTheme.uiScale
+			fieldWidth:		80 * jaspTheme.uiScale
 			visible:		optimizerDropdown.currentValue === "nlminb"
 		}
 
@@ -171,7 +171,7 @@ Section
 			min:			1e-20
 			max:			1e-5
 			decimals:		20
-			fieldWidth:		100 * jaspTheme.uiScale
+			fieldWidth:		80 * jaspTheme.uiScale
 			visible:		optimizerDropdown.currentValue === "nlminb"
 		}
 
@@ -209,16 +209,8 @@ Section
 			min:			1e-12
 			max:			1e-3
 			decimals:		12
-			fieldWidth:		100 * jaspTheme.uiScale
+			fieldWidth:		80 * jaspTheme.uiScale
 			visible:		optimizerDropdown.currentValue === "default" || optimizerDropdown.currentValue === "BFGS"
 		}
-
-		CheckBox
-		{
-			name:	"optimizerCheckConv"
-			label:	qsTr("Check convergence")
-			info:	qsTr("Check for convergence warnings and errors")
-			checked: true
-		}
 	}
 }
\ No newline at end of file