Merge pull request #1587 from cmu-phil/development

v7.3.4

README.md

@@ -19,7 +19,7 @@ You will need to set up Java on your machine. For setting up Java, see our Wiki
 
 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/7.3.0/tetrad-gui-7.3.0-launch.jar.
+https://s01.oss.sonatype.org/content/repositories/releases/io/github/cmu-phil/tetrad-gui/7.3.3/tetrad-gui-7.3.3-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

data-reader/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.3.3</version>
+        <version>7.3.4</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>7.3.3</version>
+    <version>7.3.4</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>7.3.3</version>
+        <version>7.3.4</version>
     </parent>
 
     <artifactId>tetrad-gui</artifactId>

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

@@ -19,8 +19,8 @@
 package edu.cmu.tetradapp.editor;
 
 import edu.cmu.tetrad.algcomparison.algorithm.Algorithm;
-import edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PAG_SAMPLING_RFCI;
-import edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.RFCI_BSC;
+import edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.PagSampleRfci;
+import edu.cmu.tetrad.algcomparison.algorithm.oracle.pag.RfciBsc;
 import edu.cmu.tetrad.algcomparison.utils.TakesIndependenceWrapper;
 import edu.cmu.tetrad.algcomparison.utils.UsesScoreWrapper;
 import edu.cmu.tetrad.annotation.Score;
@@ -74,7 +74,7 @@ public void addToPanel(GeneralAlgorithmRunner algorithmRunner) {
         Parameters parameters = algorithmRunner.getParameters();
 
         // Hard-coded parameter groups for Rfci-Bsc
-        if (algorithm instanceof RFCI_BSC) {
+        if (algorithm instanceof RfciBsc) {
             // Phase one: PAG and constraints candidates Searching
             String title = algorithm
                     .getClass().getAnnotation(edu.cmu.tetrad.annotation.Algorithm.class).name();
@@ -107,7 +107,7 @@ public void addToPanel(GeneralAlgorithmRunner algorithmRunner) {
             this.mainPanel.add(createSubPanel(title, params, parameters));
             this.mainPanel.add(Box.createVerticalStrut(10));
 
-        } else if (algorithm instanceof PAG_SAMPLING_RFCI) {
+        } else if (algorithm instanceof PagSampleRfci) {
             String title = algorithm.getClass().getAnnotation(edu.cmu.tetrad.annotation.Algorithm.class).name();
 
             Set<String> params = new LinkedHashSet<>();
@@ -118,13 +118,13 @@ public void addToPanel(GeneralAlgorithmRunner algorithmRunner) {
 
             title = "RFCI Parameters";
             params.clear();
-            params.addAll(PAG_SAMPLING_RFCI.RFCI_PARAMETERS);
+            params.addAll(PagSampleRfci.RFCI_PARAMETERS);
             this.mainPanel.add(createSubPanel(title, params, parameters));
             this.mainPanel.add(Box.createVerticalStrut(10));
 
             title = "Probabilistic Test Parameters";
             params.clear();
-            params.addAll(PAG_SAMPLING_RFCI.PROBABILISTIC_TEST_PARAMETERS);
+            params.addAll(PagSampleRfci.PROBABILISTIC_TEST_PARAMETERS);
             this.mainPanel.add(createSubPanel(title, params, parameters));
             this.mainPanel.add(Box.createVerticalStrut(10));
         } else {

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

@@ -129,15 +129,15 @@ private List<Statistic> statistics() {
         statistics.add(new ArrowheadRecall());
         statistics.add(new ArrowheadPrecisionCommonEdges());
         statistics.add(new ArrowheadRecallCommonEdges());
-        statistics.add(new AdjacencyTN());
-        statistics.add(new AdjacencyTP());
-        statistics.add(new AdjacencyTPR());
-        statistics.add(new AdjacencyFPR());
-        statistics.add(new AdjacencyFN());
-        statistics.add(new AdjacencyFP());
-        statistics.add(new AdjacencyFN());
-        statistics.add(new ArrowheadTN());
-        statistics.add(new ArrowheadTP());
+        statistics.add(new AdjacencyTn());
+        statistics.add(new AdjacencyTp());
+        statistics.add(new AdjacencyTpr());
+        statistics.add(new AdjacencyFpr());
+        statistics.add(new AdjacencyFn());
+        statistics.add(new AdjacencyFp());
+        statistics.add(new AdjacencyFn());
+        statistics.add(new ArrowheadTn());
+        statistics.add(new ArrowheadTp());
         statistics.add(new F1Adj());
         statistics.add(new F1All());
         statistics.add(new F1Arrow());

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

@@ -20,7 +20,7 @@
 
 import edu.cmu.tetrad.algcomparison.algorithm.Algorithm;
 import edu.cmu.tetrad.algcomparison.algorithm.AlgorithmFactory;
-import edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SINGLE_GRAPH_ALG;
+import edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg;
 import edu.cmu.tetrad.algcomparison.utils.HasKnowledge;
 import edu.cmu.tetrad.algcomparison.utils.TakesExternalGraph;
 import edu.cmu.tetrad.annotation.*;
@@ -391,7 +391,7 @@ public Algorithm getAlgorithmFromInterface(AlgorithmModel algoModel, Independenc
 
         // Those pairwise algos (R3, RShew, Skew..) require source graph to initialize - Zhou
         if (algorithm != null && algorithm instanceof TakesExternalGraph && this.algorithmRunner.getSourceGraph() != null && !this.algorithmRunner.getDataModelList().isEmpty()) {
-            Algorithm externalGraph = new SINGLE_GRAPH_ALG(this.algorithmRunner.getSourceGraph());
+            Algorithm externalGraph = new SingleGraphAlg(this.algorithmRunner.getSourceGraph());
             ((TakesExternalGraph) algorithm).setExternalGraph(externalGraph);
         }
 

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

@@ -138,7 +138,7 @@ public void execute() {
                 } else if (dataSet.isDiscrete()) {
                     double samplePrior = getParams().getDouble("samplePrior", 1);
                     double structurePrior = getParams().getDouble("structurePrior", 1);
-                    BDeuScore score = new BDeuScore(dataSet);
+                    BdeuScore score = new BdeuScore(dataSet);
                     score.setSamplePrior(samplePrior);
                     score.setStructurePrior(structurePrior);
                     this.fges = new Fges(score);

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

@@ -22,7 +22,7 @@
 
 import edu.cmu.tetrad.algcomparison.algorithm.Algorithm;
 import edu.cmu.tetrad.algcomparison.algorithm.MultiDataSetAlgorithm;
-import edu.cmu.tetrad.algcomparison.algorithm.cluster.CLUSTER_ALGORITHM;
+import edu.cmu.tetrad.algcomparison.algorithm.cluster.ClusterAlgorithm;
 import edu.cmu.tetrad.algcomparison.independence.DSeparationTest;
 import edu.cmu.tetrad.algcomparison.independence.IndependenceWrapper;
 import edu.cmu.tetrad.algcomparison.independence.TakesGraph;
@@ -316,7 +316,7 @@ public void execute() {
 
                     graphList.add(((MultiDataSetAlgorithm) algo).search(sub, this.parameters));
                 }
-            } else if (getAlgorithm() instanceof CLUSTER_ALGORITHM) {
+            } else if (getAlgorithm() instanceof ClusterAlgorithm) {
                 for (int k = 0; k < this.parameters.getInt("numRuns"); k++) {
                     getDataModelList().forEach(dataModel -> {
                         if (dataModel instanceof ICovarianceMatrix) {

tetrad-gui/src/test/java/edu/cmu/tetradapp/test/FgsApiExample.java

@@ -2,7 +2,7 @@
 
 import edu.cmu.tetrad.algcomparison.algorithm.Algorithm;
 import edu.cmu.tetrad.algcomparison.algorithm.AlgorithmFactory;
-import edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.FGES;
+import edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.Fges;
 import edu.cmu.tetrad.algcomparison.score.ConditionalGaussianBicScore;
 import edu.cmu.tetrad.data.DataModel;
 import edu.cmu.tetrad.graph.Graph;
@@ -71,7 +71,7 @@ public static void main(String[] args) throws Exception {
         //Algorithm fges = AlgorithmFactory.create(Fges.class, null, BdeuScore.class);
 
         // for mixed data can use Conditional Gaussian
-        Algorithm fges = AlgorithmFactory.create(FGES.class, null, ConditionalGaussianBicScore.class);
+        Algorithm fges = AlgorithmFactory.create(Fges.class, null, ConditionalGaussianBicScore.class);
 
 
         // Set algorithm parameters

tetrad-lib/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>io.github.cmu-phil</groupId>
         <artifactId>tetrad</artifactId>
-        <version>7.3.3</version>
+        <version>7.3.4</version>
     </parent>
 
     <artifactId>tetrad-lib</artifactId>

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/AlgorithmFactory.java

@@ -18,7 +18,7 @@
  */
 package edu.cmu.tetrad.algcomparison.algorithm;
 
-import edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SINGLE_GRAPH_ALG;
+import edu.cmu.tetrad.algcomparison.algorithm.oracle.cpdag.SingleGraphAlg;
 import edu.cmu.tetrad.algcomparison.independence.IndependenceWrapper;
 import edu.cmu.tetrad.algcomparison.score.ScoreWrapper;
 import edu.cmu.tetrad.algcomparison.utils.TakesExternalGraph;
@@ -69,7 +69,7 @@ public static Algorithm create(Class<? extends Algorithm> algoClass, Independenc
             throws IllegalAccessException, InstantiationException {
         Algorithm algorithm = AlgorithmFactory.create(algoClass, test, score);
         if (externalGraph != null && algorithm instanceof TakesExternalGraph) {
-            ((TakesExternalGraph) algorithm).setExternalGraph(new SINGLE_GRAPH_ALG(externalGraph));
+            ((TakesExternalGraph) algorithm).setExternalGraph(new SingleGraphAlg(externalGraph));
         }
 
         return algorithm;
@@ -91,7 +91,7 @@ public static Algorithm create(Class<? extends Algorithm> algoClass, Class<? ext
             throws IllegalAccessException, InstantiationException {
         Algorithm algorithm = AlgorithmFactory.create(algoClass, indTestClass, scoreClass);
         if (externalGraph != null && algorithm instanceof TakesExternalGraph) {
-            ((TakesExternalGraph) algorithm).setExternalGraph(new SINGLE_GRAPH_ALG(externalGraph));
+            ((TakesExternalGraph) algorithm).setExternalGraph(new SingleGraphAlg(externalGraph));
         }
 
         return algorithm;

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/cluster/BPC.java → tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/cluster/Bpc.java

@@ -29,12 +29,12 @@
         algoType = AlgType.search_for_structure_over_latents
 )
 @Bootstrapping
-public class BPC implements Algorithm, HasKnowledge, CLUSTER_ALGORITHM {
+public class Bpc implements Algorithm, HasKnowledge, ClusterAlgorithm {
 
     static final long serialVersionUID = 23L;
     private Knowledge knowledge = new Knowledge();
 
-    public BPC() {
+    public Bpc() {
     }
 
     @Override
@@ -105,7 +105,7 @@ public Graph search(DataModel dataSet, Parameters parameters) {
                 return fullGraph;
             }
         } else {
-            BPC algorithm = new BPC();
+            Bpc algorithm = new Bpc();
 
             DataSet data = (DataSet) dataSet;
             GeneralResamplingTest search = new GeneralResamplingTest(data, algorithm,

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/cluster/CLUSTER_ALGORITHM.java → tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/cluster/ClusterAlgorithm.java

@@ -5,5 +5,5 @@
  *
  * @author jdramsey
  */
-public interface CLUSTER_ALGORITHM {
+public interface ClusterAlgorithm {
 }

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/cluster/FOFC.java → tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/cluster/Fofc.java

@@ -28,12 +28,12 @@
         algoType = AlgType.search_for_structure_over_latents
 )
 @Bootstrapping
-public class FOFC implements Algorithm, HasKnowledge, CLUSTER_ALGORITHM {
+public class Fofc implements Algorithm, HasKnowledge, ClusterAlgorithm {
 
     static final long serialVersionUID = 23L;
     private Knowledge knowledge = new Knowledge();
 
-    public FOFC() {
+    public Fofc() {
     }
 
     @Override
@@ -116,7 +116,7 @@ public Graph search(DataModel dataSet, Parameters parameters) {
                 return fullGraph;
             }
         } else {
-            FOFC algorithm = new FOFC();
+            Fofc algorithm = new Fofc();
 
             DataSet data = (DataSet) dataSet;
             GeneralResamplingTest search = new GeneralResamplingTest(data, algorithm, parameters.getInt(Params.NUMBER_RESAMPLING), parameters.getDouble(Params.PERCENT_RESAMPLE_SIZE), parameters.getBoolean(Params.RESAMPLING_WITH_REPLACEMENT), parameters.getInt(Params.RESAMPLING_ENSEMBLE), parameters.getBoolean(Params.ADD_ORIGINAL_DATASET));

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/cluster/FTFC.java → tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/cluster/Ftfc.java

@@ -27,12 +27,12 @@
         algoType = AlgType.search_for_structure_over_latents
 )
 @Bootstrapping
-public class FTFC implements Algorithm, HasKnowledge, CLUSTER_ALGORITHM {
+public class Ftfc implements Algorithm, HasKnowledge, ClusterAlgorithm {
 
     static final long serialVersionUID = 23L;
     private Knowledge knowledge = new Knowledge();
 
-    public FTFC() {
+    public Ftfc() {
     }
 
     @Override
@@ -65,7 +65,7 @@ public Graph search(DataModel dataSet, Parameters parameters) {
 
             return search.search();
         } else {
-            FTFC algorithm = new FTFC();
+            Ftfc algorithm = new Ftfc();
 
             DataSet data = (DataSet) dataSet;
             GeneralResamplingTest search = new GeneralResamplingTest(data, algorithm, parameters.getInt(Params.NUMBER_RESAMPLING), parameters.getDouble(Params.PERCENT_RESAMPLE_SIZE), parameters.getBoolean(Params.RESAMPLING_WITH_REPLACEMENT), parameters.getInt(Params.RESAMPLING_ENSEMBLE), parameters.getBoolean(Params.ADD_ORIGINAL_DATASET));

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/continuous/dag/LING.java → tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/continuous/dag/Ling.java

@@ -30,7 +30,7 @@
 )
 @Bootstrapping
 @Experimental
-public class LING implements Algorithm {
+public class Ling implements Algorithm {
 
     static final long serialVersionUID = 23L;
 
@@ -47,7 +47,7 @@ public Graph search(DataModel dataSet, Parameters parameters) {
                 return new EdgeListGraph();
             }
         } else {
-            LING algorithm = new LING();
+            Ling algorithm = new Ling();
 
             DataSet data = (DataSet) dataSet;
             GeneralResamplingTest search = new GeneralResamplingTest(data, algorithm, parameters.getInt(Params.NUMBER_RESAMPLING), parameters.getDouble(Params.PERCENT_RESAMPLE_SIZE), parameters.getBoolean(Params.RESAMPLING_WITH_REPLACEMENT), parameters.getInt(Params.RESAMPLING_ENSEMBLE), parameters.getBoolean(Params.ADD_ORIGINAL_DATASET));

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/continuous/dag/LINGAM.java → tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/continuous/dag/Lingam.java

@@ -29,7 +29,7 @@
 )
 @Bootstrapping
 //@Experimental
-public class LINGAM implements Algorithm {
+public class Lingam implements Algorithm {
 
     static final long serialVersionUID = 23L;
 
@@ -42,7 +42,7 @@ public Graph search(DataModel dataSet, Parameters parameters) {
             lingam.setFastIcaTolerance(parameters.getDouble(Params.FAST_ICA_TOLERANCE));
             return lingam.search(SimpleDataLoader.getContinuousDataSet(dataSet));
         } else {
-            LINGAM algorithm = new LINGAM();
+            Lingam algorithm = new Lingam();
 
             DataSet data = (DataSet) dataSet;
             GeneralResamplingTest search = new GeneralResamplingTest(data, algorithm, parameters.getInt(Params.NUMBER_RESAMPLING), parameters.getDouble(Params.PERCENT_RESAMPLE_SIZE), parameters.getBoolean(Params.RESAMPLING_WITH_REPLACEMENT), parameters.getInt(Params.RESAMPLING_ENSEMBLE), parameters.getBoolean(Params.ADD_ORIGINAL_DATASET));

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/mixed/MGM.java → tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/mixed/Mgm.java

@@ -23,11 +23,11 @@
         algoType = AlgType.produce_undirected_graphs
 )
 @Bootstrapping
-public class MGM implements Algorithm {
+public class Mgm implements Algorithm {
 
     static final long serialVersionUID = 23L;
 
-    public MGM() {
+    public Mgm() {
     }
 
     @Override
@@ -84,11 +84,11 @@ public Graph search(DataModel ds, Parameters parameters) {
                     mgmParam3
             };
 
-            edu.pitt.csb.mgm.MGM m = new edu.pitt.csb.mgm.MGM(_ds, lambda);
+            edu.pitt.csb.mgm.Mgm m = new edu.pitt.csb.mgm.Mgm(_ds, lambda);
 
             return m.search();
         } else {
-            MGM algorithm = new MGM();
+            Mgm algorithm = new Mgm();
 
             DataSet data = (DataSet) ds;
             GeneralResamplingTest search = new GeneralResamplingTest(data, algorithm, parameters.getInt(Params.NUMBER_RESAMPLING), parameters.getDouble(Params.PERCENT_RESAMPLE_SIZE), parameters.getBoolean(Params.RESAMPLING_WITH_REPLACEMENT), parameters.getInt(Params.RESAMPLING_ENSEMBLE), parameters.getBoolean(Params.ADD_ORIGINAL_DATASET));

tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/multi/CCD_MAX_CONCATENATED.java → tetrad-lib/src/main/java/edu/cmu/tetrad/algcomparison/algorithm/multi/CcdMaxConcatenated.java

@@ -25,12 +25,12 @@
  * @author jdramsey
  */
 @Bootstrapping
-public class CCD_MAX_CONCATENATED implements MultiDataSetAlgorithm, HasKnowledge {
+public class CcdMaxConcatenated implements MultiDataSetAlgorithm, HasKnowledge {
     static final long serialVersionUID = 23L;
     private Knowledge knowledge = new Knowledge();
     private final IndependenceWrapper test;
 
-    public CCD_MAX_CONCATENATED(IndependenceWrapper test) {
+    public CcdMaxConcatenated(IndependenceWrapper test) {
         this.test = test;
     }
 
@@ -56,7 +56,7 @@ public Graph search(List<DataModel> dataModels, Parameters parameters) {
             search.setUseOrientTowardDConnections(parameters.getBoolean(Params.ORIENT_TOWARD_DCONNECTIONS));
             return search.search();
         } else {
-            CCD_MAX_CONCATENATED algorithm = new CCD_MAX_CONCATENATED(this.test);
+            CcdMaxConcatenated algorithm = new CcdMaxConcatenated(this.test);
 
             List<DataSet> dataSets = new ArrayList<>();
 
@@ -88,7 +88,7 @@ public Graph search(DataModel dataSet, Parameters parameters) {
         if (parameters.getInt(Params.NUMBER_RESAMPLING) < 1) {
             return search(Collections.singletonList(SimpleDataLoader.getContinuousDataSet(dataSet)), parameters);
         } else {
-            CCD_MAX_CONCATENATED algorithm = new CCD_MAX_CONCATENATED(this.test);
+            CcdMaxConcatenated algorithm = new CcdMaxConcatenated(this.test);
 
             List<DataSet> dataSets = Collections.singletonList(SimpleDataLoader.getContinuousDataSet(dataSet));
             GeneralResamplingTest search = new GeneralResamplingTest(dataSets,