From 58f01edf16d6daa04bb17a4ffabaa372f4da043a Mon Sep 17 00:00:00 2001
From: vbcwonderland <veritybingchu@cmu.edu>
Date: Thu, 23 May 2024 16:48:25 -0400
Subject: [PATCH] method documentation

---
 .../edu/cmu/tetrad/search/MarkovCheck.java    | 22 +++++++++++++++++++
 .../edu/cmu/tetrad/test/TestCheckMarkov.java  | 14 ------------
 2 files changed, 22 insertions(+), 14 deletions(-)

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/MarkovCheck.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/MarkovCheck.java
index e0f40149a7..11ef450002 100644
--- a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/MarkovCheck.java
+++ b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/MarkovCheck.java
@@ -340,6 +340,17 @@ public List<List<Node>> getAndersonDarlingTestAcceptsRejectsNodesForAllNodes(Ind
         return accepts_rejects;
     }
 
+    /**
+     * Get accepts and rejects nodes for all nodes from Anderson-Darling test and generate the plot data for confusion statistics.
+     *
+     * Confusion statistics were calculated using Adjacency (AdjacencyPrecision, AdjacencyRecall) and Arrowhead (ArrowheadPrecision, ArrowheadRecall)
+     * @param independenceTest
+     * @param estimatedCpdag
+     * @param trueGraph
+     * @param threshold
+     * @param shuffleThreshold
+     * @return
+     */
     public List<List<Node>> getAndersonDarlingTestAcceptsRejectsNodesForAllNodesPlotData(IndependenceTest independenceTest, Graph estimatedCpdag, Graph trueGraph, Double threshold, Double shuffleThreshold) {
         // When calling, default reject null as <=0.05
         List<List<Node>> accepts_rejects = new ArrayList<>();
@@ -479,6 +490,17 @@ public List<List<Node>> getAndersonDarlingTestAcceptsRejectsNodesForAllNodesPlot
         return accepts_rejects;
     }
 
+    /**
+     * Get accepts and rejects nodes for all nodes from Anderson-Darling test and generate the plot data for confusion statistics.
+     *
+     * Confusion statistics were calculated using Local Graph Precision and Recall (LocalGraphPrecision, LocalGraphRecall).
+     * @param independenceTest
+     * @param estimatedCpdag
+     * @param trueGraph
+     * @param threshold
+     * @param shuffleThreshold
+     * @return
+     */
     public List<List<Node>> getAndersonDarlingTestAcceptsRejectsNodesForAllNodesPlotData2(IndependenceTest independenceTest, Graph estimatedCpdag, Graph trueGraph, Double threshold, Double shuffleThreshold) {
         // When calling, default reject null as <=0.05
         List<List<Node>> accepts_rejects = new ArrayList<>();
diff --git a/tetrad-lib/src/test/java/edu/cmu/tetrad/test/TestCheckMarkov.java b/tetrad-lib/src/test/java/edu/cmu/tetrad/test/TestCheckMarkov.java
index 27584cd642..eb896081cf 100644
--- a/tetrad-lib/src/test/java/edu/cmu/tetrad/test/TestCheckMarkov.java
+++ b/tetrad-lib/src/test/java/edu/cmu/tetrad/test/TestCheckMarkov.java
@@ -468,20 +468,6 @@ public void testGaussianDAGPrecisionRecallForLocalOnMarkovBlanket2() {
         List<Node> rejects = accepts_rejects.get(1);
         System.out.println("Accepts size: " + accepts.size());
         System.out.println("Rejects size: " + rejects.size());
-
-//        List<Double> acceptsPrecision = new ArrayList<>();
-//        List<Double> acceptsRecall = new ArrayList<>();
-//        for(Node a: accepts) {
-//            System.out.println("=====================");
-//            markovCheck.getPrecisionAndRecallOnMarkovBlanketGraph2(a, estimatedCpdag, trueGraph);
-//            System.out.println("=====================");
-//
-//        }
-//        for (Node a: rejects) {
-//            System.out.println("=====================");
-//            markovCheck.getPrecisionAndRecallOnMarkovBlanketGraph2(a, estimatedCpdag, trueGraph);
-//            System.out.println("=====================");
-//        }
     }
 
 }