Add RowsSettable interface to IndTest classes

The IndTestConditionalGaussianLrt and IndTestDegenerateGaussianLrt classes have been updated to implement the RowsSettable interface. This change allows users to set which rows are used in the test. Also, redundant spaces were removed from IndTestFisherZ, and parameter changes were made in DegenerateGaussianBic class.
cmu-phil · Jun 12, 2024 · 7cda6c2 · 7cda6c2
1 parent 92b0c22
commit 7cda6c2
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Showing 4 changed files with 93 additions and 6 deletions.
diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/score/DegenerateGaussianBicScore.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/score/DegenerateGaussianBicScore.java
@@ -71,9 +71,9 @@ public DegenerateGaussianBicScore() {
     public Score getScore(DataModel dataSet, Parameters parameters) {
         this.dataSet = dataSet;
         boolean precomputeCovariances = parameters.getBoolean(Params.PRECOMPUTE_COVARIANCES);
-//        DegenerateGaussianScoreOld degenerateGaussianScore = new DegenerateGaussianScoreOld(DataUtils.getMixedDataSet(dataSet));
         DegenerateGaussianScore degenerateGaussianScore = new DegenerateGaussianScore(SimpleDataLoader.getMixedDataSet(dataSet), precomputeCovariances);
-        degenerateGaussianScore.setPenaltyDiscount(parameters.getDouble("penaltyDiscount"));
+        degenerateGaussianScore.setPenaltyDiscount(parameters.getDouble(Params.PENALTY_DISCOUNT));
+        degenerateGaussianScore.setUsePseudoInverse(parameters.getBoolean(Params.USE_PSEUDOINVERSE));
         return degenerateGaussianScore;
     }
 
@@ -102,6 +102,7 @@ public List<String> getParameters() {
         parameters.add(Params.PENALTY_DISCOUNT);
         parameters.add(Params.STRUCTURE_PRIOR);
         parameters.add(Params.PRECOMPUTE_COVARIANCES);
+        parameters.add(Params.USE_PSEUDOINVERSE);
         return parameters;
     }
 

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/test/IndTestConditionalGaussianLrt.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/test/IndTestConditionalGaussianLrt.java
@@ -46,7 +46,7 @@
  * @author josephramsey
  * @version $Id: $Id
  */
-public class IndTestConditionalGaussianLrt implements IndependenceTest {
+public class IndTestConditionalGaussianLrt implements IndependenceTest, RowsSettable {
     /**
      * The data set.
      */
@@ -79,6 +79,10 @@ public class IndTestConditionalGaussianLrt implements IndependenceTest {
      * The minimum sample size per cell for discretization.
      */
     private int minSampleSizePerCell = 4;
+    /**
+     * The rows used in the test.
+     */
+    private List<Integer> rows = new ArrayList<>();
 
     /**
      * Constructor.
@@ -282,6 +286,10 @@ public void setNumCategoriesToDiscretize(int numCategoriesToDiscretize) {
      * @return A list of row indices.
      */
     private List<Integer> getRows(List<Node> allVars, Map<Node, Integer> nodeHash) {
+        if (this.rows != null) {
+            return this.rows;
+        }
+
         List<Integer> rows = new ArrayList<>();
 
         K:
@@ -299,6 +307,42 @@ private List<Integer> getRows(List<Node> allVars, Map<Node, Integer> nodeHash) {
         return rows;
     }
 
+    /**
+     * Returns the rows used in the test.
+     *
+     * @return The rows used in the test.
+     */
+    public List<Integer> getRows() {
+        return rows;
+    }
+
+    /**
+     * Allows the user to set which rows are used in the test. Otherwise, all rows are used, except those with missing
+     * values.
+     */
+    public void setRows(List<Integer> rows) {
+        if (data == null) {
+            return;
+        }
+
+        List<Integer> all = new ArrayList<>();
+        for (int i = 0; i < data.getNumRows(); i++) all.add(i);
+        Collections.shuffle(all);
+
+        List<Integer> _rows = new ArrayList<>();
+        for (int i = 0; i < data.getNumRows() / 2; i++) {
+            _rows.add(all.get(i));
+        }
+
+        for (Integer row : _rows) {
+            if (row < 0 || row >= data.getNumRows()) {
+                throw new IllegalArgumentException("Row index out of bounds.");
+            }
+        }
+
+        this.rows = _rows;
+    }
+
     /**
      * Sets the minimum sample size per cell for the independence test.
      *

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/test/IndTestDegenerateGaussianLrt.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/test/IndTestDegenerateGaussianLrt.java
@@ -50,7 +50,7 @@
  * @author Bryan Andrews
  * @version $Id: $Id
  */
-public class IndTestDegenerateGaussianLrt implements IndependenceTest {
+public class IndTestDegenerateGaussianLrt implements IndependenceTest, RowsSettable {
 
     /**
      * A constant.
@@ -96,6 +96,10 @@ public class IndTestDegenerateGaussianLrt implements IndependenceTest {
      * True if verbose output should be printed.
      */
     private boolean verbose;
+    /**
+     * The rows used in the test.
+     */
+    private List<Integer> rows = new ArrayList<>();
 
     /**
      * Constructs the score using a covariance matrix.
@@ -403,6 +407,10 @@ private Ret getlldof(List<Integer> rows, int i, int... parents) {
      * @return A list of integers representing the row indices that satisfy the conditions.
      */
     private List<Integer> getRows(List<Node> allVars, Map<Node, Integer> nodesHash) {
+        if (this.rows != null) {
+            return this.rows;
+        }
+
         List<Integer> rows = new ArrayList<>();
 
         K:
@@ -459,6 +467,42 @@ private Matrix getCov(List<Integer> rows, int[] cols) {
         return cov;
     }
 
+    /**
+     * Returns the rows used in the test.
+     *
+     * @return The rows used in the test.
+     */
+    public List<Integer> getRows() {
+        return rows;
+    }
+
+    /**
+     * Allows the user to set which rows are used in the test. Otherwise, all rows are used, except those with missing
+     * values.
+     */
+    public void setRows(List<Integer> rows) {
+        if (dataSet == null) {
+            return;
+        }
+
+        List<Integer> all = new ArrayList<>();
+        for (int i = 0; i < dataSet.getNumRows(); i++) all.add(i);
+        Collections.shuffle(all);
+
+        List<Integer> _rows = new ArrayList<>();
+        for (int i = 0; i < dataSet.getNumRows() / 2; i++) {
+            _rows.add(all.get(i));
+        }
+
+        for (Integer row : _rows) {
+            if (row < 0 || row >= dataSet.getNumRows()) {
+                throw new IllegalArgumentException("Row index out of bounds.");
+            }
+        }
+
+        this.rows = _rows;
+    }
+
     /**
      * Stores a return value for a likelihood--i.e., a likelihood value and the degrees of freedom for it.
      */

diff --git a/tetrad-lib/src/main/java/edu/cmu/tetrad/search/test/IndTestFisherZ.java b/tetrad-lib/src/main/java/edu/cmu/tetrad/search/test/IndTestFisherZ.java
@@ -841,8 +841,6 @@ public void setRows(List<Integer> rows) {
             _rows.add(all.get(i));
         }
 
-
-
         for (Integer row : _rows) {
             if (row < 0 || row >= sampleSize()) {
                 throw new IllegalArgumentException("Row index out of bounds.");