From 9f7194f62b73d6371ca31180768e66d59ca57f42 Mon Sep 17 00:00:00 2001
From: Koen Derks <koen-derks@hotmail.com>
Date: Sun, 19 Jan 2025 12:50:51 -0500
Subject: [PATCH] Add mcmc options

---
 R/auditBayesianEvaluation.R            |  5 +++
 R/auditCommonFunctions.R               |  2 +-
 inst/qml/common/planning/Algorithm.qml | 61 ++++++++++++++++++++++++++
 3 files changed, 67 insertions(+), 1 deletion(-)

diff --git a/R/auditBayesianEvaluation.R b/R/auditBayesianEvaluation.R
index 815bbaa1..e3098227 100644
--- a/R/auditBayesianEvaluation.R
+++ b/R/auditBayesianEvaluation.R
@@ -19,6 +19,11 @@
 # reviewer in the pull Request.
 
 auditBayesianEvaluation <- function(jaspResults, dataset, options, ...) {
+  set.seed(options[["mcmc.seed"]])
+  options(mc.iterations = options[["iter"]],
+          mc.warmup = options[["warmup"]],
+          mc.chains = options[["chains"]],
+          jfa.iterations = options[["iter"]])
   # For the evaluation constituents, see auditCommonFunctions.R
   .jfaEvaluationStage(options, jaspResults, workflow = FALSE)
   .jfaCreatedByText(jaspResults)
diff --git a/R/auditCommonFunctions.R b/R/auditCommonFunctions.R
index 451a6554..a3ce53e3 100644
--- a/R/auditCommonFunctions.R
+++ b/R/auditCommonFunctions.R
@@ -742,7 +742,7 @@
       "min_precision_test", "min_precision_rel_val",
       "by", "prior_method", "prior_n", "prior_x", "alpha", "beta",
       "critical_items", "critical_negative", "critical_action",
-      "stratum", "pooling", "hurdle"
+      "stratum", "pooling", "hurdle", "mcmc.seed", "iter", "warmup", "chains"
     ))
 
     jaspResults[["evaluationContainer"]] <- container
diff --git a/inst/qml/common/planning/Algorithm.qml b/inst/qml/common/planning/Algorithm.qml
index 1c93e031..b80ca436 100644
--- a/inst/qml/common/planning/Algorithm.qml
+++ b/inst/qml/common/planning/Algorithm.qml
@@ -100,4 +100,65 @@ Group
 			helpPage:	"Audit/hurdle"
 		}
 	}
+
+	Section
+	{
+		title:						qsTr("MCMC Options")
+		enabled:					hurdle.checked || enable_pooling
+		info:						qsTr("Options to customize the MCMC sampling process.")
+		visible:					!(hide_hurdle && hide_pooling)
+
+		Group
+		{
+			IntegerField
+			{
+				id:					warmup
+				name:				"warmup"
+				text:				qsTr("Warmup")
+				defaultValue:		1000
+				min:				100
+				max:				iter.value
+				fieldWidth:			60 * preferencesModel.uiScale
+				Layout.leftMargin:	15 * preferencesModel.uiScale
+				info:				qsTr("Sets the number of warmup MCMC iterations.")
+			}
+
+			IntegerField
+			{
+				id:					iter
+				name:				"iter"
+				text:				qsTr("Iterations")
+				defaultValue:		2000
+				min:				warmup.value
+				max:				10000
+				fieldWidth:			60 * preferencesModel.uiScale
+				Layout.leftMargin:	15 * preferencesModel.uiScale
+				info:				qsTr("Sets the total number of MCMC iterations.")
+			}
+
+			IntegerField
+			{
+				name:				"chains"
+				text:				qsTr("Chains")
+				defaultValue:		4
+				min:				1
+				max:				10
+				fieldWidth:			60 * preferencesModel.uiScale
+				Layout.leftMargin:	15 * preferencesModel.uiScale
+				info:				qsTr("Sets the number of MCMC chains.")
+			}
+
+			IntegerField
+			{
+				name:				"mcmc.seed"
+				text:				qsTr("Seed")
+				defaultValue:		Math.floor(Math.random() * 1000) // Init with random integer in [1,...,999]
+				min:				-999
+				max:				999
+				fieldWidth:			60 * preferencesModel.uiScale
+				Layout.leftMargin:	15 * preferencesModel.uiScale
+				info:				qsTr("Selects the seed for the random number generator in order to reproduce results.")
+			}
+		}
+	}
 }