Merging changes for 7.6.1.

INSTALL_APPLICATION.md

@@ -6,7 +6,7 @@ Please use a recent Java JDK. See [Setting up Java for Tetrad](https://github.co
 
 To download the Tetrad jar, please click the following link (which will always be updated to the latest version):
 
-https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.5.0/tetrad-gui-7.5.0-launch.jar
+https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.6.0/tetrad-gui-7.6.0-launch.jar
 
 You may be able to launch this jar by double-clicking the jar file name. However, on a Mac, this presents some security challenges. On all platforms, the jar may be launched at the command line (with a specification of the amount of RAM you will allow it to use) using this command: 
 

README.md

@@ -10,8 +10,6 @@ See out insructions for [Installing the Tetrad Application](https://github.com/c
 
 We have a project, [py-tetrad](https://github.com/cmu-phil/py-tetrad), that allows you to incorporate arbitrary Tetrad code into a Python workflow. It's new, and the installation is still nonstandard, but it had a good response. This requires Python 3.5+. and Java JDK 9+.
 
-Please see our [description](https://sites.google.com/view/tetradcausal/tetrad-in-python
-
 ## Tetrad in R
 
 We also have a project, [rpy-tetrad](https://github.com/cmu-phil/py-tetrad/tree/main/pytetrad/R), that allows you to incorporate _some_ Tetrad functionality in R. It's also new, and the installation for it is also still nonstandard, but has gotten good feedback. This requires Python 3.5+ and Java JDK 9+.

data-reader/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.6.0</version>
+        <version>7.6.1</version>
     </parent>
     <!--    <groupId>io.github.cmu-phil</groupId>-->
     <artifactId>data-reader</artifactId>

pom.xml

@@ -4,7 +4,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>io.github.cmu-phil</groupId>
     <artifactId>tetrad</artifactId>
-    <version>7.6.0</version>
+    <version>7.6.1</version>
     <packaging>pom</packaging>
 
     <name>Tetrad Project</name>

tetrad-gui/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.6.0</version>
+        <version>7.6.1</version>
     </parent>
 
     <artifactId>tetrad-gui</artifactId>

tetrad-gui/src/main/java/edu/cmu/tetradapp/editor/MarkovCheckEditor.java

@@ -27,8 +27,8 @@
 import edu.cmu.tetrad.graph.GraphUtils;
 import edu.cmu.tetrad.graph.IndependenceFact;
 import edu.cmu.tetrad.graph.Node;
+import edu.cmu.tetrad.search.ConditioningSetType;
 import edu.cmu.tetrad.search.IndependenceTest;
-import edu.cmu.tetrad.search.MarkovCheck;
 import edu.cmu.tetrad.search.test.IndependenceResult;
 import edu.cmu.tetrad.search.test.MsepTest;
 import edu.cmu.tetrad.util.NumberFormatUtil;
@@ -99,20 +99,24 @@ public MarkovCheckEditor(MarkovCheckIndTestModel model) {
             throw new NullPointerException("Expecting a model");
         }
 
-        conditioningSetTypeJComboBox.addItem("Parents(X)");
+        conditioningSetTypeJComboBox.addItem("Parents(X) (Local Markov)");
+        conditioningSetTypeJComboBox.addItem("Parents(X) for a Valid Order (Ordered Local Markov)");
         conditioningSetTypeJComboBox.addItem("MarkovBlanket(X)");
-        conditioningSetTypeJComboBox.addItem("All Subsets");
+        conditioningSetTypeJComboBox.addItem("All Subsets (Global Markov)");
 
         conditioningSetTypeJComboBox.addActionListener(e -> {
             switch ((String) Objects.requireNonNull(conditioningSetTypeJComboBox.getSelectedItem())) {
-                case "Parents(X)":
-                    model.getMarkovCheck().setSetType(MarkovCheck.ConditioningSetType.PARENTS);
+                case "Parents(X) (Local Markov)":
+                    model.getMarkovCheck().setSetType(ConditioningSetType.LOCAL_MARKOV);
+                    break;
+                case "Parents(X) for a Valid Order (Ordered Local Markov)":
+                    model.getMarkovCheck().setSetType(ConditioningSetType.ORDERED_LOCAL_MARKOV);
                     break;
                 case "MarkovBlanket(X)":
-                    model.getMarkovCheck().setSetType(MarkovCheck.ConditioningSetType.MARKOV_BLANKET);
+                    model.getMarkovCheck().setSetType(ConditioningSetType.MARKOV_BLANKET);
                     break;
-                case "All Subsets":
-                    model.getMarkovCheck().setSetType(MarkovCheck.ConditioningSetType.ALL_SUBSETS);
+                case "All Subsets (Global Markov)":
+                    model.getMarkovCheck().setSetType(ConditioningSetType.GLOBAL_MARKOV);
                     break;
                 default:
                     throw new IllegalArgumentException("Unknown conditioning set type: " +
@@ -121,7 +125,7 @@ public MarkovCheckEditor(MarkovCheckIndTestModel model) {
 
             class MyWatchedProcess extends WatchedProcess {
                 public void watch() {
-                    if (model.getMarkovCheck().getSetType() == MarkovCheck.ConditioningSetType.ALL_SUBSETS && model.getVars().size() > 12) {
+                    if (model.getMarkovCheck().getSetType() == ConditioningSetType.GLOBAL_MARKOV && model.getVars().size() > 12) {
                         int ret = JOptionPane.showOptionDialog(MarkovCheckEditor.this,
                                 "The all subsets option is exponential and can become extremely slow beyond 12" +
                                         "\nvariables. You may possibly be required to force quit Tetrad. Continue?", "Warning",
@@ -277,7 +281,7 @@ public void watch() {
 
         JTabbedPane pane = new JTabbedPane();
         pane.addTab("Check Markov", indep);
-        pane.addTab("Check Faithfulness", dep);
+        pane.addTab("Check Dependent Distribution", dep);
         pane.addTab("Help", scroll);
         box.add(pane);
 
@@ -310,13 +314,13 @@ public void watch() {
 
     @NotNull
     private static String getHelpMessage() {
-        return "This tool lets you plot statistics for independence tests of a pair of variables given some conditioning calculated for one of those variables, for a given graph and dataset. Two tables are made, one in which the independence facts predicted by the graph using these conditioning sets are tested in the data and the other in which the graph's predicted dependence facts are tested. The first of these sets is a test for \"Markov\" for the relevant conditioning sets; the is a test for \"Faithfulness.”\n" +
+        return "This tool lets you plot statistics for independence tests of a pair of variables given some conditioning calculated for one of those variables, for a given graph and dataset. Two tables are made, one in which the independence facts predicted by the graph using these conditioning sets are tested in the data and the other in which the graph's predicted dependence facts are tested. The first of these sets is a check for \"Markov\" (a check for implied independence facts) for the chosen conditioning sets; the is a check of the \"Dependent Distribution.\" (a check of implied dependence facts)”\n" +
                 "\n" +
                 "Each table gives columns for the independence fact being checked, its test result, and its statistic. This statistic is either a p-value, ranging from 0 to 1, where p-values above the alpha level of the test are judged as independent, or a score bump, where this bump is negative for independent judgments and positive for dependent judgments.\n" +
                 "\n" +
                 "If the independence test yields a p-value, as for instance, for the Fisher Z test (for the linear, Gaussian case) or else the Chi-Square test (for the multinomial case), then under the null hypothesis of independence and for a consistent test, these p-values should be distributed as Uniform(0, 1). That is, it should be just as likely to see p-values in any range of equal width. If the test is inconsistent or the graph is incorrect (i.e., the parents of some or all of the nodes in the graph are incorrect), then this distribution of p-values will not be Uniform. To visualize this, we display the histogram of the p-values with equally sized bins; the bars in this histogram, for this case, should ideally all be of equal height.\n" +
                 "\n" +
-                "If the first bar in this histogram is especially high (for the p-value case), that means that many tests are being judged as dependent. For checking Faithfulness, one hopes that this list is non-empty, then this first bar will be especially high, since high p-values are for examples where the graph is unfaithful to the distribution. These are likely for for cases where paths in the graph cancel unfaithfully. But for checking Markov, one hopes that this first bar will be the same height as all of the other bars.\n" +
+                "If the first bar in this histogram is especially high (for the p-value case), that means that many tests are being judged as dependent. For checking the dependent distribution, one hopes that this list is non-empty, in which case this first bar will be especially high, since high p-values are for examples where the graph is unfaithful to the distribution. These are likely for for cases where paths in the graph cancel unfaithfully. But for checking Markov, one hopes that this first bar will be the same height as all of the other bars.\n" +
                 "\n" +
                 "To make it especially clear, we give two statistics in the interface. The first is the percentage of p-values judged dependent on the test. If an alpha level is used in the test, this number should be very close to the alpha level for the Local Markov check since the distribution of p-values under this condition is Uniform. For the second, we test the Uniformity of the p-values using a Kolmogorov-Smirnov test. The p-value returned by this test should be greater than the user’s preferred alpha level if the distribution of p-values is Uniform and less then this alpha level if the distribution of p-values is non-Uniform.\n" +
                 "\n" +
@@ -492,6 +496,12 @@ public void mouseClicked(MouseEvent e) {
 //        scroll.setPreferredSize(new Dimension(400, 400));
         b1.add(scroll);
 
+        Box b1a = Box.createHorizontalBox();
+        JLabel label = new JLabel("Table contents can be selected and copied in to, e.g., Excel.");
+        b1a.add(label);
+        b1a.add(Box.createHorizontalGlue());
+        b1.add(b1a);
+
         Box b4 = Box.createHorizontalBox();
         b4.add(Box.createGlue());
         b4.add(Box.createHorizontalStrut(10));
@@ -678,6 +688,12 @@ public void mouseClicked(MouseEvent e) {
 //        scroll.setPreferredSize(new Dimension(400, 400));
         b1.add(scroll);
 
+        Box b1a = Box.createHorizontalBox();
+        JLabel label = new JLabel("Table contents can be selected and copied in to, e.g., Excel.");
+        b1a.add(label);
+        b1a.add(Box.createHorizontalGlue());
+        b1.add(b1a);
+
         Box b4 = Box.createHorizontalBox();
         b4.add(Box.createGlue());
         b4.add(Box.createHorizontalStrut(10));

tetrad-gui/src/main/java/edu/cmu/tetradapp/model/MarkovCheckIndTestModel.java

@@ -24,6 +24,7 @@
 import edu.cmu.tetrad.data.DataModel;
 import edu.cmu.tetrad.data.Knowledge;
 import edu.cmu.tetrad.graph.Graph;
+import edu.cmu.tetrad.search.ConditioningSetType;
 import edu.cmu.tetrad.search.IndependenceTest;
 import edu.cmu.tetrad.search.MarkovCheck;
 import edu.cmu.tetrad.search.test.IndependenceResult;
@@ -64,7 +65,7 @@ public static Knowledge serializableInstance() {
     }
 
     public void setIndependenceTest(IndependenceTest test) {
-        this.markovCheck = new MarkovCheck(this.graph, test, this.markovCheck == null ? MarkovCheck.ConditioningSetType.PARENTS : this.markovCheck.getSetType());
+        this.markovCheck = new MarkovCheck(this.graph, test, this.markovCheck == null ? ConditioningSetType.LOCAL_MARKOV : this.markovCheck.getSetType());
 
     }
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/workbench/LayoutUtils.java

@@ -499,7 +499,7 @@ public static void circleLayout(LayoutEditable layoutEditable) {
 
         int m = FastMath.min(r.width, r.height) / 2;
 
-        LayoutUtil.defaultLayout(graph);
+        LayoutUtil.circleLayout(graph);
         layoutEditable.layoutByGraph(graph);
         LayoutUtils.layout = Layout.circle;
     }

tetrad-lib/dependency-reduced-pom.xml

@@ -0,0 +1,62 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <parent>
+    <artifactId>tetrad</artifactId>
+    <groupId>io.github.cmu-phil</groupId>
+    <version>7.6.0-SNAPSHOT</version>
+  </parent>
+  <modelVersion>4.0.0</modelVersion>
+  <artifactId>tetrad-lib</artifactId>
+  <build>
+    <extensions>
+      <extension>
+        <groupId>org.apache.maven.wagon</groupId>
+        <artifactId>wagon-ssh</artifactId>
+        <version>2.10</version>
+      </extension>
+    </extensions>
+    <plugins>
+      <plugin>
+        <artifactId>maven-compiler-plugin</artifactId>
+        <version>3.11.0</version>
+        <configuration>
+          <source>1.8</source>
+          <target>1.8</target>
+        </configuration>
+      </plugin>
+      <plugin>
+        <artifactId>maven-shade-plugin</artifactId>
+        <version>3.1.0</version>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>shade</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+      <plugin>
+        <artifactId>maven-antrun-plugin</artifactId>
+        <version>3.1.0</version>
+        <executions>
+          <execution>
+            <phase>compile</phase>
+            <goals>
+              <goal>run</goal>
+            </goals>
+            <configuration>
+              <target>
+                <copy />
+              </target>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+  <properties>
+    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+  </properties>
+</project>
+

tetrad-lib/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.6.0</version>
+        <version>7.6.1</version>
     </parent>
 
     <artifactId>tetrad-lib</artifactId>
@@ -22,6 +22,35 @@
                     <target>1.8</target>
                 </configuration>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>3.1.0</version>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>shade</goal>
+                        </goals>
+                        <configuration>
+                            <transformers>
+                                <transformer
+                                        implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                    <manifestEntries>
+<!--                                        <Main-Class>edu.cmu.tetradapp.Tetrad</Main-Class>-->
+                                        <Permissions>all-permissions</Permissions>
+                                        <Implementation-Title>${project.name}</Implementation-Title>
+                                        <Implementation-Version>${project.version}</Implementation-Version>
+                                    </manifestEntries>
+                                </transformer>
+                            </transformers>
+                            <shadedArtifactAttached>true</shadedArtifactAttached>
+                            <shadedClassifierName>shaded</shadedClassifierName> <!-- Any name that makes sense -->
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
             <plugin>
                 <artifactId>maven-antrun-plugin</artifactId>
                 <version>3.1.0</version>

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/continuous/dag/DirectLingam.java

@@ -13,6 +13,7 @@
 import edu.cmu.tetrad.graph.EdgeListGraph;
 import edu.cmu.tetrad.graph.Graph;
 import edu.cmu.tetrad.search.score.Score;
+import edu.cmu.tetrad.search.utils.LogUtilsSearch;
 import edu.cmu.tetrad.util.Parameters;
 import edu.cmu.tetrad.util.Params;
 import edu.cmu.tetrad.util.TetradLogger;
@@ -56,6 +57,7 @@ public Graph search(DataModel dataSet, Parameters parameters) {
             Graph graph = search.search();
             TetradLogger.getInstance().forceLogMessage(graph.toString());
 
+            LogUtilsSearch.stampWithBic(graph, dataSet);
             return graph;
         } else {
             DirectLingam algorithm = new DirectLingam();

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/continuous/dag/IcaLingam.java

@@ -11,6 +11,7 @@
 import edu.cmu.tetrad.graph.EdgeListGraph;
 import edu.cmu.tetrad.graph.Graph;
 import edu.cmu.tetrad.search.IcaLingD;
+import edu.cmu.tetrad.search.utils.LogUtilsSearch;
 import edu.cmu.tetrad.util.Matrix;
 import edu.cmu.tetrad.util.Parameters;
 import edu.cmu.tetrad.util.Params;
@@ -56,6 +57,7 @@ public Graph search(DataModel dataSet, Parameters parameters) {
             TetradLogger.getInstance().forceLogMessage(bHat.toString());
             TetradLogger.getInstance().forceLogMessage(graph.toString());
 
+            LogUtilsSearch.stampWithBic(graph, dataSet);
             return graph;
         } else {
             IcaLingam algorithm = new IcaLingam();

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/oracle/cpdag/Boss.java

@@ -15,6 +15,7 @@
 import edu.cmu.tetrad.graph.Graph;
 import edu.cmu.tetrad.search.PermutationSearch;
 import edu.cmu.tetrad.search.score.Score;
+import edu.cmu.tetrad.search.utils.LogUtilsSearch;
 import edu.cmu.tetrad.search.utils.TsUtils;
 import edu.cmu.tetrad.util.Parameters;
 import edu.cmu.tetrad.util.Params;
@@ -51,7 +52,6 @@ public Boss(ScoreWrapper score) {
         this.score = score;
     }
 
-
     @Override
     public Graph search(DataModel dataModel, Parameters parameters) {
         if (parameters.getInt(Params.NUMBER_RESAMPLING) < 1) {
@@ -75,8 +75,9 @@ public Graph search(DataModel dataModel, Parameters parameters) {
             boss.setVerbose(parameters.getBoolean(Params.VERBOSE));
             PermutationSearch permutationSearch = new PermutationSearch(boss);
             permutationSearch.setKnowledge(this.knowledge);
-
-            return permutationSearch.search();
+            Graph graph = permutationSearch.search();
+            LogUtilsSearch.stampWithScores(graph, dataModel, score);
+            return graph;
         } else {
             Boss algorithm = new Boss(this.score);