Merge pull request #1624 from cmu-phil/development

v7.4.0

README.md

@@ -13,13 +13,13 @@ version of Tetrad and Causal Command.
 
 ## Setting up Java
 
-You will need to set up Java on your machine. For setting up Java, see our Wiki artible, [Setting up Java for Tetrad](https://github.com/cmu-phil/tetrad/wiki/Setting-up-Java-for-Tetrad).
+You will need to set up Java on your machine. For setting up Java, see our Wiki article, [Setting up Java for Tetrad](https://github.com/cmu-phil/tetrad/wiki/Setting-up-Java-for-Tetrad).
 
 ## Tetrad GUI Application
 
 To download the current jar you can use to launch the Tetrad GUI, click this link:
 
-https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.3.3/tetrad-gui-7.3.3-launch.jar.
+https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.3.4/tetrad-gui-7.3.4-launch.jar.
 
 You may be able to launch this jar by double clicking the jar file name, though on a Mac, this presents
 some [security challenges](https://github.com/cmu-phil/tetrad/wiki/Dealing-with-Tetrad-on-a-Mac:--Security-Issues). In
@@ -57,7 +57,7 @@ our [Manual](https://htmlpreview.github.io/?https:///github.com/cmu-phil/tetrad/
 If you like to watch thought-provoking lectures, here are
 some [lectures on the Center for Causal Discovery site](https://www.ccd.pitt.edu/video-tutorials/).
 
-In addition, here are our [Javadocs](https://www.phil.cmu.edu/tetrad-javadocs/7.3.0/lib/).
+In addition, here are our [Javadocs](https://www.phil.cmu.edu/tetrad-javadocs/7.3.4/lib/).
 
 ## Install
 

data-reader/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.3.4</version>
+        <version>7.4.0</version>
     </parent>
     <!--    <groupId>io.github.cmu-phil</groupId>-->
     <artifactId>data-reader</artifactId>

docs/manual/index.html

@@ -5545,6 +5545,74 @@ <h3 class="parameter_description" id="fastIcaA">fastIcaA</h3>
                     id="fastIcaTolerance_value_type">Double</span></li>
         </ul>
 
+        <h3 class="parameter_description"
+            id="thresholdBHat">thresholdBHat</h3>
+        <ul
+                class="parameter_description_list">
+            <li>Short Description: <span
+                    id="thresholdBHat_short_desc">Threshold on the B Hat matrix.
+        </span></li>
+            <li>Long Description: <span
+                    id="thresholdBHat_long_desc">The estimated B matrix
+                    is thresholded by setting small entries less than this threshold
+                    to zero.</span>
+            </li>
+            <li>Default Value: <span
+                    id="thresholdBHat_default_value">0.1</span></li>
+            <li>Lower Bound:
+                <span id="thresholdBHat_lower_bound">0.0</span></li>
+            <li>Upper
+                Bound: <span id="thresholdBHat_upper_bound">Infinity</span></li>
+            <li>Value Type: <span
+                    id="thresholdBHat_value_type">Double</span></li>
+        </ul>
+
+        <h3 class="parameter_description"
+            id="guaranteeAcyclic">guaranteeAcyclic</h3>
+        <ul
+                class="parameter_description_list">
+            <li>Short Description: <span
+                    id="guaranteeAcyclic_short_desc">True if the output should be
+                    guaranteed to be acyclic
+        </span></li>
+            <li>Long Description: <span
+                    id="guaranteeAcyclic_long_desc">The estimated B matrix
+                    is further thresholded by setting small coefficients to zero
+                    until an acyclic model is produced.</span>
+            </li>
+            <li>Default Value: <span
+                    id="guaranteeAcyclic_default_value">true</span></li>
+            <li>Lower Bound:
+                <span id="guaranteeAcyclic_lower_bound"></span></li>
+            <li>Upper
+                Bound: <span id="guaranteeAcyclic_upper_bound"></span></li>
+            <li>Value Type: <span
+                    id="guaranteeAcyclic_value_type">Boolean</span></li>
+        </ul>
+
+        <h3 class="parameter_description"
+            id="thresholdSpine">thresholdSpine</h3>
+        <ul
+                class="parameter_description_list">
+            <li>Short Description: <span
+                    id="thresholdSpine_short_desc">Threshold on the diagonal of the W matrix.
+        </span></li>
+            <li>Long Description: <span
+                    id="thresholdSpine_long_desc">The diagonal of the estimated W matrix
+                    is thresholded by setting small entries less than this threshold
+                    to zero. Should be >= W threshold.</span>
+            </li>
+            <li>Default Value: <span
+                    id="thresholdSpine_default_value">0.8</span></li>
+            <li>Lower Bound:
+                <span id="thresholdSpine_lower_bound">0.0</span></li>
+            <li>Upper
+                Bound: <span id="thresholdSpine_upper_bound">Infinity</span></li>
+            <li>Value Type: <span
+                    id="thresholdSpine_value_type">Double</span></li>
+        </ul>
+
+
         <h3 class="parameter_description"
             id="fisherEpsilon">fisherEpsilon</h3>
         <ul
@@ -9046,6 +9114,7 @@ <h5>Trek</h5>
 
 
 
+
 </script>
 <script async defer
         src="https://www.google-analytics.com/analytics.js"></script>

pom.xml

@@ -4,7 +4,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>io.github.cmu-phil</groupId>
     <artifactId>tetrad</artifactId>
-    <version>7.3.4</version>
+    <version>7.4.0</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>7.3.4</version>
+        <version>7.4.0</version>
     </parent>
 
     <artifactId>tetrad-gui</artifactId>

tetrad-gui/src/main/java/edu/cmu/tetradapp/Tetrad.java

@@ -50,7 +50,7 @@
  * enough to create a copy of this class with a different name and modify
  * it.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 public final class Tetrad implements PropertyChangeListener {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/AboutTetradAction.java

@@ -35,7 +35,7 @@
 /**
  * Closes the frontmost session of the given desktop.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class AboutTetradAction extends AbstractAction {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/CloseSessionAction.java

@@ -32,7 +32,7 @@
 /**
  * Closes the frontmost session of the given desktop.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class CloseSessionAction extends AbstractAction {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/ConstructTemplateAction.java

@@ -40,7 +40,7 @@
  * Adds a new template session subgraph to the frontmost session editor. of one
  * of three types.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class ConstructTemplateAction extends AbstractAction {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/ContributorsAction.java

@@ -30,7 +30,7 @@
 /**
  * Closes the frontmost session of the given desktop.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class ContributorsAction extends AbstractAction {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/CopySubsessionAction.java

@@ -36,7 +36,7 @@
  * Copies a selection of session nodes in the frontmost session editor, to the
  * clipboard.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class CopySubsessionAction extends AbstractAction
         implements ClipboardOwner {

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/CutSubsessionAction.java

@@ -36,7 +36,7 @@
  * Copies a selection of session nodes in the frontmost session editor to the
  * clipboard and deletes them from the session editor.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class CutSubsessionAction extends AbstractAction
         implements ClipboardOwner {

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/DecompressibleInputStream.java

@@ -32,7 +32,7 @@
  * <p>
  * Dec 6, 2017 11:10:24 AM
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  * @author Kevin V. Bui (kvb2@pitt.edu)
  */
 public class DecompressibleInputStream extends ObjectInputStream {

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/DeleteSubsessionAction.java

@@ -32,7 +32,7 @@
 /**
  * Deletes a selection of session nodes from the frontmost session editor.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class DeleteSubsessionAction extends AbstractAction
         implements ClipboardOwner {

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/ExitAction.java

@@ -29,7 +29,7 @@
 /**
  * Exits the Tetrad application.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class ExitAction extends AbstractAction {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/FontSelectionAction.java

@@ -39,7 +39,7 @@
  * Copies a selection of session nodes in the frontmost session editor, to the
  * clipboard.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class FontSelectionAction extends AbstractAction
         implements ClipboardOwner {

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/LaunchFlowchartAction.java

@@ -31,7 +31,7 @@
 /**
  * Closes the frontmost session of the given desktop.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class LaunchFlowchartAction extends AbstractAction {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/LaunchManualAction.java

@@ -31,7 +31,7 @@
 /**
  * Closes the frontmost session of the given desktop.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class LaunchManualAction extends AbstractAction {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/LicenseAction.java

@@ -31,7 +31,7 @@
 /**
  * Closes the frontmost session of the given desktop.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class LicenseAction extends AbstractAction {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/LoadSessionAction.java

@@ -42,7 +42,7 @@
 /**
  * Opens a session from a file.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class LoadSessionAction extends AbstractAction {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/NewSessionAction.java

@@ -29,7 +29,7 @@
 /**
  * Opens a session from a file.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class NewSessionAction extends AbstractAction {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/NoteDisplayComp.java

@@ -29,7 +29,7 @@
 /**
  * Provides a modified appearance for session nodes to be used for notes.
  *
- * @author Joseph Ramsey
+ * @author josephramsey
  */
 public class NoteDisplayComp extends JComponent implements SessionDisplayComp {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/NumberFormatAction.java

@@ -44,7 +44,7 @@
  * Presents a dialog allowing the user to change the number format used to
  * render real numbers throughout Tetrad.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class NumberFormatAction extends AbstractAction
         implements ClipboardOwner {

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/PasteSubsessionAction.java

@@ -39,7 +39,7 @@
  * Copies a parentally closed selection of session nodes in the frontmost
  * session editor to the clipboard.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class PasteSubsessionAction extends AbstractAction
         implements ClipboardOwner {

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/RunSimulationAction.java

@@ -32,7 +32,7 @@
 /**
  * Sets up parameters for logging.
  *
- * @author Joseph Ramsey
+ * @author josephramsey
  */
 class RunSimulationAction extends AbstractAction {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SaveSessionAction.java

@@ -38,7 +38,7 @@
 /**
  * Saves a session from a file.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  * @author Kevin V. Bui (kvb2@pitt.edu)
  */
 final class SaveSessionAction extends AbstractAction {

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SaveSessionAsAction.java

@@ -38,7 +38,7 @@
 /**
  * Saves a session from a file.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class SaveSessionAsAction extends AbstractAction {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SessionDisplayComp.java

@@ -26,7 +26,7 @@
 /**
  * The appearance of a session node.
  *
- * @author Joseph Ramsey
+ * @author josephramsey
  */
 public interface SessionDisplayComp extends DisplayComp {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SessionEditor.java

@@ -39,7 +39,7 @@
 /**
  * Displays a toolbar and workbench for editing Session's.
  *
- * @author Joseph Ramsey
+ * @author josephramsey
  * @see SessionEditorWorkbench
  * @see SessionEditorToolbar
  */

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SessionEditorEdge.java

@@ -29,7 +29,7 @@
 /**
  * Presents an edge in the Tetrad SessionWorkbench.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 final class SessionEditorEdge extends DisplayEdge {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SessionEditorNode.java

@@ -55,7 +55,7 @@
  * parents being added to appropriate SessionNodes underlying. Double clicking
  * these nodes launches corresponding model editors.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  * @see SessionEditorWorkbench
  * @see edu.cmu.tetrad.graph.Edge
  * @see edu.cmu.tetrad.session.SessionNode

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SessionEditorToolbar.java

@@ -38,7 +38,7 @@
  * can take in the session editor workbench, whether it's selecting and moving a
  * node, adding a node of a particular type, or adding an edge.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  * @see SessionEditor
  * @see SessionEditorToolbar
  */

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SessionEditorWorkbench.java

@@ -39,7 +39,7 @@
  * Adds the functionality needed to turn an abstract workbench into a workbench
  * usable for editing sessions.
  *
- * @author Joseph Ramsey jdramsey@andrew.cmu.edu
+ * @author josephramsey
  */
 public final class SessionEditorWorkbench extends AbstractWorkbench {
 

tetrad-gui/src/main/java/edu/cmu/tetradapp/app/SessionUtils.java

@@ -35,7 +35,7 @@
 /**
  * Some utility methods relevant to sessions.
  *
- * @author Joseph Ramsey
+ * @author josephramsey
  */
 final class SessionUtils {