Merge pull request #1699 from cmu-phil/joe-work-2023-10-2

Several fixes, updates.
cmu-phil · Oct 31, 2023 · dccf96d · dccf96d
2 parents d81dd7d + 43c260d
commit dccf96d
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Showing 805 changed files with 5,286 additions and 3,600 deletions.
diff --git a/data-reader/pom.xml b/data-reader/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.5.0</version>
+        <version>7.5.1-SNAPSHOT</version>
     </parent>
     <!--    <groupId>io.github.cmu-phil</groupId>-->
     <artifactId>data-reader</artifactId>

diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>io.github.cmu-phil</groupId>
     <artifactId>tetrad</artifactId>
-    <version>7.5.0</version>
+    <version>7.5.1-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <name>Tetrad Project</name>
@@ -116,7 +116,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-javadoc-plugin</artifactId>
-                <version>2.9.1</version>
+                <version>3.6.0</version>
                 <configuration>
                     <javadocExecutable>/usr/bin/javadoc</javadocExecutable>
                 </configuration>

diff --git a/tetrad-gui/pom.xml b/tetrad-gui/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.5.0</version>
+        <version>7.5.1-SNAPSHOT</version>
     </parent>
 
     <artifactId>tetrad-gui</artifactId>

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/CPDAGDisplay.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/CPDAGDisplay.java
@@ -23,8 +23,8 @@
 
 import edu.cmu.tetrad.graph.Graph;
 import edu.cmu.tetrad.graph.GraphNode;
+import edu.cmu.tetrad.graph.GraphTransforms;
 import edu.cmu.tetrad.graph.Node;
-import edu.cmu.tetrad.search.utils.GraphSearchUtils;
 import edu.cmu.tetrad.util.JOptionUtils;
 import edu.cmu.tetrad.util.TetradSerializable;
 import edu.cmu.tetradapp.workbench.DisplayEdge;
@@ -49,7 +49,7 @@ public class CPDAGDisplay extends JPanel implements GraphEditable {
     private GraphWorkbench workbench;
 
     public CPDAGDisplay(Graph graph) {
-        List<Graph> dags = GraphSearchUtils.generateCpdagDags(graph, false);
+        List<Graph> dags = GraphTransforms.generateCpdagDags(graph, false);
 
         if (dags.size() == 0) {
             JOptionPane.showMessageDialog(
@@ -81,7 +81,7 @@ public CPDAGDisplay(Graph graph) {
             String option = (String) box.getSelectedItem();
 
             if ("Orient --- only".equals(option)) {
-                List _dags = GraphSearchUtils.generateCpdagDags(graph, false);
+                List _dags = GraphTransforms.generateCpdagDags(graph, false);
                 dags.clear();
                 dags.addAll(_dags);
                 SpinnerNumberModel model1 =
@@ -97,7 +97,7 @@ public CPDAGDisplay(Graph graph) {
                 totalLabel.setText(" of " + dags.size());
                 CPDAGDisplay.this.workbench.setGraph(dags.get(0));
             } else if ("Orient ---, &lt;->".equals(option)) {
-                List _dags = GraphSearchUtils.generateCpdagDags(graph, true);
+                List _dags = GraphTransforms.generateCpdagDags(graph, true);
                 dags.clear();
                 dags.addAll(_dags);
                 SpinnerNumberModel model1 =

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/DescriptiveStats.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/DescriptiveStats.java
@@ -100,7 +100,7 @@ public static String generateDescriptiveStats(DataSet dataSet, Node variable,
         table.setToken(rowindex, 0, "Skewness:");
         table.setToken(rowindex++, 1, nf.format(StatUtils.skewness(data)));
 
-        table.setToken(rowindex, 0, "Kurtosis:");
+        table.setToken(rowindex, 0, "" + "Kurtosis:");
         table.setToken(rowindex++, 1, nf.format(StatUtils.kurtosis(data)));
 
         if (continuous) {
@@ -120,7 +120,7 @@ public static String generateDescriptiveStats(DataSet dataSet, Node variable,
         }
 
         table.setToken(rowindex, 0, "Constant Columns:");
-        List<Node> constantColumns = DataUtils.getConstantColumns(dataSet);
+        List<Node> constantColumns = DataTransforms.getConstantColumns(dataSet);
         table.setToken(rowindex++, 1, constantColumns.isEmpty() ? "None" : constantColumns.toString());
 
         table.setToken(rowindex, 0, "Example Nonsingular (2 - 3 vars):");

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/DescriptiveStatsAction.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/DescriptiveStatsAction.java
@@ -23,6 +23,7 @@
 
 import edu.cmu.tetrad.data.CovarianceMatrix;
 import edu.cmu.tetrad.data.DataSet;
+import edu.cmu.tetrad.data.DataTransforms;
 import edu.cmu.tetrad.data.DataUtils;
 import edu.cmu.tetrad.graph.Node;
 import edu.cmu.tetradapp.util.DesktopController;
@@ -87,13 +88,16 @@ private Box createDescriptiveStatsDialog() {
 
         String coonstantColumnsString = "Constant Columns: ";
         assert dataSet != null;
-        java.util.List<Node> constantColumns = DataUtils.getConstantColumns(dataSet);
+        java.util.List<Node> constantColumns = DataTransforms.getConstantColumns(dataSet);
         coonstantColumnsString += constantColumns.isEmpty() ? "None" : constantColumns.toString();
+        String nonsingularString = null;
 
-        String nonsingularString = "Example Nonsingular (2 vars): ";
-        CovarianceMatrix covarianceMatrix = new CovarianceMatrix(dataSet);
-        List<Node> exampleNonsingular = DataUtils.getExampleNonsingular(covarianceMatrix, 2);
-        nonsingularString += exampleNonsingular == null ? "None" : exampleNonsingular.toString();
+        if (dataSet.isContinuous()) {
+            nonsingularString = "Example Nonsingular (2 vars): ";
+            CovarianceMatrix covarianceMatrix = new CovarianceMatrix(dataSet);
+            List<Node> exampleNonsingular = DataUtils.getExampleNonsingular(covarianceMatrix, 2);
+            nonsingularString += exampleNonsingular == null ? "None" : exampleNonsingular.toString();
+        }
 
         Box box = Box.createVerticalBox();
 
@@ -128,7 +132,11 @@ private Box createDescriptiveStatsDialog() {
         box.add(b1);
 
         Box b2 = Box.createHorizontalBox();
-        b2.add(new JLabel(nonsingularString));
+        if (nonsingularString != null) {
+            b2.add(new JLabel(nonsingularString));
+        }
+
+//        b2.add(new JLabel(nonsingularString));
         b2.add(Box.createHorizontalGlue());
         box.add(b2);
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/DescriptiveStatsModel.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/DescriptiveStatsModel.java
@@ -108,9 +108,6 @@ public static Ret generateDescriptiveStats(DataSet dataSet, Node variable) {
         names.add("Kurtosis");
         stats.add(StatUtils.kurtosis(data));
 
-        names.add("Skewness");
-        stats.add(StatUtils.skewness(data));
-
 
         if (continuous) {
             double[] median = DescriptiveStats.median(data);

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/FactorAnalysisAction.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/FactorAnalysisAction.java
@@ -160,7 +160,7 @@ private JPanel createDialog(FactorAnalysis analysis) {
             }
         }
 
-        LayoutUtil.circleLayout(graph);
+        LayoutUtil.defaultLayout(graph);
         LayoutUtil.fruchtermanReingoldLayout(graph);
 
         GraphWorkbench workbench = new GraphWorkbench(graph);

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/FactorAnalysisEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/FactorAnalysisEditor.java
@@ -75,7 +75,7 @@ protected void setup(String resultLabel) {
         display.setEditable(false);
         display.setFont(new Font("Monospaced", Font.PLAIN, 12));
 
-        LayoutUtil.circleLayout(graph);
+        LayoutUtil.defaultLayout(graph);
         LayoutUtil.fruchtermanReingoldLayout(graph);
 
         GraphWorkbench workbench = new GraphWorkbench(graph);
@@ -132,7 +132,7 @@ protected void doDefaultArrangement(Graph resultGraph) {
             LayoutUtil.arrangeBySourceGraph(resultGraph,
                     getLatestWorkbenchGraph());
         } else {
-            LayoutUtil.circleLayout(resultGraph);
+            LayoutUtil.defaultLayout(resultGraph);
         }
     }
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GraphAdjacencyIntersectionWrapper.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/GraphAdjacencyIntersectionWrapper.java
@@ -39,7 +39,7 @@
  * @author josephramsey
  */
 public class GraphAdjacencyIntersectionWrapper implements SessionModel, DoNotAddOldModel {
-    static final long serialVersionUID = 23L;
+    private static final long serialVersionUID = 23L;
     private List<Graph> graphs;
     private String name = "";
 

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadBayesImXmlAction.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadBayesImXmlAction.java
@@ -108,7 +108,7 @@ public void actionPerformed(ActionEvent e) {
             }
 
             if (!allSpecified) {
-                LayoutUtil.circleLayout(bayesIm.getBayesPm().getDag());
+                LayoutUtil.defaultLayout(bayesIm.getBayesPm().getDag());
             }
 
             this.bayesImWrapper.setBayesIm(bayesIm);

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadBayesImXsdlXmlAction.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadBayesImXsdlXmlAction.java
@@ -108,7 +108,7 @@ public void actionPerformed(ActionEvent e) {
             }
 
             if (!allSpecified) {
-                LayoutUtil.circleLayout(bayesIm.getBayesPm().getDag());
+                LayoutUtil.defaultLayout(bayesIm.getBayesPm().getDag());
             }
 
             this.bayesImWrapper.setBayesIm(bayesIm);

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraph.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraph.java
@@ -81,7 +81,7 @@ public void actionPerformed(ActionEvent e) {
         Preferences.userRoot().put("fileSaveLocation", file.getParent());
 
         Graph graph = GraphSaveLoadUtils.loadGraph(file);
-        LayoutUtil.circleLayout(graph);
+        LayoutUtil.defaultLayout(graph);
         this.graphEditable.setGraph(graph);
     }
 }

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraphPcalg.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraphPcalg.java
@@ -79,7 +79,7 @@ public void actionPerformed(ActionEvent e) {
         Preferences.userRoot().put("fileSaveLocation", file.getParent());
 
         Graph graph = GraphSaveLoadUtils.loadGraphPcalg(file);
-        LayoutUtil.circleLayout(graph);
+        LayoutUtil.defaultLayout(graph);
         this.graphEditable.setGraph(graph);
     }
 }

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraphTxt.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LoadGraphTxt.java
@@ -81,7 +81,7 @@ public void actionPerformed(ActionEvent e) {
         Preferences.userRoot().put("fileSaveLocation", file.getParent());
 
         Graph graph = GraphSaveLoadUtils.loadGraphTxt(file);
-        LayoutUtil.circleLayout(graph);
+        LayoutUtil.defaultLayout(graph);
         this.graphEditable.setGraph(graph);
     }
 }

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LogisticRegressionEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/LogisticRegressionEditor.java
@@ -135,7 +135,7 @@ public LogisticRegressionEditor(LogisticRegressionRunner regressionRunner) {
             //  modelParameters.setText(regRunner.getReport());
             print(regressionRunner.getResult(), regressionRunner.getAlpha());
             Graph outGraph = regressionRunner.getOutGraph();
-            LayoutUtil.circleLayout(outGraph);
+            LayoutUtil.defaultLayout(outGraph);
             LayoutUtil.fruchtermanReingoldLayout(outGraph);
             workbench.setGraph(outGraph);
             TetradLogger.getInstance().log("result", this.modelParameters.getText());

diff --git a/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/MarkovCheckEditor.java b/tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/MarkovCheckEditor.java
@@ -830,14 +830,15 @@ private Box createHistogramPanel(boolean indep) {
             return Box.createVerticalBox();
         }
 
+
         DataSet dataSet = new BoxDataSet(new VerticalDoubleDataBox(results.size(), 1),
                 Collections.singletonList(new ContinuousVariable("P-Value or Bump")));
 
         for (int i = 0; i < results.size(); i++) {
             dataSet.setDouble(i, 0, results.get(i).getPValue());
         }
 
-        Histogram histogram = new Histogram(dataSet, "P-Value or Bump");
+        Histogram histogram = new Histogram(dataSet, "P-Value or Bump", false);
 //        histogram.setTarget("P-Value or Bump");
         HistogramPanel view = new HistogramPanel(histogram, true);