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Merge pull request #96 from bd2kccd/v1.2.1
Update Tetrad lib jar to version 6.8.0
2 parents 8fa4b5f + 90a650a commit 1c1745f

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‎DESCRIPTION

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Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
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Package: rcausal
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Version: 1.2.0
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Date: 2019-8-8
2+
Version: 1.2.1
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Date: 2019-12-25
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Title: R-Causal Library
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Author: Chirayu Wongchokprasitti
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Maintainer: Chirayu Wongchokprasitti <[email protected]>
@@ -12,4 +12,4 @@ SystemRequirements: Java (>= 1.8), JRI
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License: LGPL (>= 2.1)
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biocViews: Bayesian, GraphAndNetwork
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NeedsCompilation: no
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Packaged: 2019-3-14 EDT
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Packaged: 2019-12-25 EDT

‎inst/java/causal-cmd-1.2.0-SNAPSHOT-jar-with-dependencies.jar

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‎java/edu/cmu/tetrad/algcomparison/Comparison.java

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‎java/edu/cmu/tetrad/algcomparison/TimeoutComparison.java

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@@ -26,7 +26,7 @@
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import edu.cmu.tetrad.algcomparison.independence.IndependenceWrapper;
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import edu.cmu.tetrad.algcomparison.score.BdeuScore;
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import edu.cmu.tetrad.algcomparison.score.ScoreWrapper;
29-
import edu.cmu.tetrad.algcomparison.simulation.LoadDataAndGraphs;
29+
import edu.cmu.tetrad.data.simulation.LoadDataAndGraphs;
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import edu.cmu.tetrad.algcomparison.simulation.Simulation;
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import edu.cmu.tetrad.algcomparison.simulation.Simulations;
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import edu.cmu.tetrad.algcomparison.statistic.ElapsedTime;
@@ -37,55 +37,21 @@
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import edu.cmu.tetrad.algcomparison.utils.HasParameterValues;
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import edu.cmu.tetrad.algcomparison.utils.HasParameters;
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import edu.cmu.tetrad.algcomparison.utils.TakesInitialGraph;
40-
import edu.cmu.tetrad.data.ContinuousVariable;
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import edu.cmu.tetrad.data.DataModel;
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import edu.cmu.tetrad.data.DataSet;
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import edu.cmu.tetrad.data.DataType;
44-
import edu.cmu.tetrad.data.DataWriter;
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import edu.cmu.tetrad.data.DiscreteVariable;
46-
import edu.cmu.tetrad.graph.Edge;
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import edu.cmu.tetrad.graph.EdgeListGraph;
48-
import edu.cmu.tetrad.graph.Graph;
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import edu.cmu.tetrad.graph.GraphUtils;
50-
import edu.cmu.tetrad.graph.Node;
51-
import edu.cmu.tetrad.search.DagToPag;
40+
import edu.cmu.tetrad.data.*;
41+
import edu.cmu.tetrad.graph.*;
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import edu.cmu.tetrad.search.DagToPag2;
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import edu.cmu.tetrad.search.SearchGraphUtils;
54-
import edu.cmu.tetrad.util.CombinationGenerator;
55-
import edu.cmu.tetrad.util.Experimental;
56-
import edu.cmu.tetrad.util.ParamDescription;
57-
import edu.cmu.tetrad.util.ParamDescriptions;
58-
import edu.cmu.tetrad.util.Parameters;
59-
import edu.cmu.tetrad.util.StatUtils;
60-
import edu.cmu.tetrad.util.TextTable;
61-
import java.io.File;
62-
import java.io.FileNotFoundException;
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import java.io.FileOutputStream;
64-
import java.io.FileWriter;
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import java.io.IOException;
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import java.io.PrintStream;
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import java.io.Writer;
44+
import edu.cmu.tetrad.util.*;
45+
import org.reflections.Reflections;
46+
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import java.io.*;
6848
import java.lang.reflect.Constructor;
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import java.text.DateFormat;
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import java.text.DecimalFormat;
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import java.text.NumberFormat;
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import java.text.SimpleDateFormat;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.Date;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Set;
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import java.util.concurrent.Callable;
82-
import java.util.concurrent.ExecutionException;
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import java.util.concurrent.ExecutorService;
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import java.util.concurrent.Executors;
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import java.util.concurrent.Future;
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import java.util.concurrent.TimeUnit;
87-
import java.util.concurrent.TimeoutException;
88-
import org.reflections.Reflections;
53+
import java.util.*;
54+
import java.util.concurrent.*;
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/**
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*
@@ -1113,14 +1079,14 @@ private void printParameters(List<String> names, Parameters parameters, PrintStr
11131079
Object value = parameters.get(name);
11141080

11151081
if (value instanceof Double) {
1116-
out.println(description.getDescription() + " = " + value.toString());
1082+
out.println(description.getShortDescription() + " = " + value.toString());
11171083
} else if (value instanceof Integer) {
1118-
out.println(description.getDescription() + " = " + value.toString());
1084+
out.println(description.getShortDescription() + " = " + value.toString());
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} else if (value instanceof Boolean) {
11201086
boolean b = (Boolean) value;
1121-
out.println(description.getDescription() + " = " + (b ? "Yes" : "No"));
1087+
out.println(description.getShortDescription() + " = " + (b ? "Yes" : "No"));
11221088
} else if (value instanceof String) {
1123-
out.println(description.getDescription() + " = " + value);
1089+
out.println(description.getShortDescription() + " = " + value);
11241090
}
11251091
}
11261092
}
@@ -1242,7 +1208,7 @@ private void doRun(List<AlgorithmSimulationWrapper> algorithmSimulationWrappers,
12421208
} else if (this.comparisonGraph == ComparisonGraph.Pattern_of_the_true_DAG) {
12431209
comparisonGraph = SearchGraphUtils.patternForDag(new EdgeListGraph(trueGraph));
12441210
} else if (this.comparisonGraph == ComparisonGraph.PAG_of_the_true_DAG) {
1245-
comparisonGraph = new DagToPag(new EdgeListGraph(trueGraph)).convert();
1211+
comparisonGraph = new DagToPag2(new EdgeListGraph(trueGraph)).convert();
12461212
} else {
12471213
throw new IllegalArgumentException("Unrecognized graph type.");
12481214
}
@@ -1291,7 +1257,7 @@ private void doRun(List<AlgorithmSimulationWrapper> algorithmSimulationWrappers,
12911257
if (_stat instanceof ElapsedTime) {
12921258
stat = elapsed / 1000.0;
12931259
} else {
1294-
stat = _stat.getValue(truth[u], est[u]);
1260+
stat = _stat.getValue(truth[u], est[u], null);
12951261
}
12961262

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allStats[u][run.getAlgSimIndex()][statIndex][run.getRunIndex()] = stat;

‎java/edu/cmu/tetrad/algcomparison/algorithm/MIMBuild.java

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‎java/edu/cmu/tetrad/algcomparison/algorithm/cluster/Bpc.java

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@@ -3,30 +3,31 @@
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import edu.cmu.tetrad.algcomparison.algorithm.Algorithm;
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import edu.cmu.tetrad.algcomparison.utils.HasKnowledge;
55
import edu.cmu.tetrad.algcomparison.utils.TakesInitialGraph;
6-
import edu.cmu.tetrad.annotation.AlgType;
6+
import edu.cmu.tetrad.annotation.Bootstrapping;
77
import edu.cmu.tetrad.data.*;
88
import edu.cmu.tetrad.graph.EdgeListGraph;
99
import edu.cmu.tetrad.graph.Graph;
1010
import edu.cmu.tetrad.search.BuildPureClusters;
1111
import edu.cmu.tetrad.search.SearchGraphUtils;
1212
import edu.cmu.tetrad.search.TestType;
1313
import edu.cmu.tetrad.util.Parameters;
14+
import edu.cmu.tetrad.util.Params;
1415
import edu.pitt.dbmi.algo.resampling.GeneralResamplingTest;
1516
import edu.pitt.dbmi.algo.resampling.ResamplingEdgeEnsemble;
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1717
import java.util.ArrayList;
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import java.util.List;
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2020
/**
21-
* BPC.
21+
* BPC. Disabled on 4/2/2019
2222
*
2323
* @author jdramsey
2424
*/
25-
@edu.cmu.tetrad.annotation.Algorithm(
26-
name = "BPC",
27-
command = "bpc",
28-
algoType = AlgType.search_for_structure_over_latents
29-
)
25+
//@edu.cmu.tetrad.annotation.Algorithm(
26+
// name = "BPC",
27+
// command = "bpc",
28+
// algoType = AlgType.search_for_structure_over_latents
29+
//)
30+
@Bootstrapping
3031
public class Bpc implements Algorithm, TakesInitialGraph, HasKnowledge, ClusterAlgorithm {
3132

3233
static final long serialVersionUID = 23L;
@@ -39,11 +40,11 @@ public Bpc() {
3940

4041
@Override
4142
public Graph search(DataModel dataSet, Parameters parameters) {
42-
if (parameters.getInt("numberResampling") < 1) {
43+
if (parameters.getInt(Params.NUMBER_RESAMPLING) < 1) {
4344
ICovarianceMatrix cov = DataUtils.getCovMatrix(dataSet);
44-
double alpha = parameters.getDouble("alpha");
45+
double alpha = parameters.getDouble(Params.ALPHA);
4546

46-
boolean wishart = parameters.getBoolean("useWishart", true);
47+
boolean wishart = parameters.getBoolean(Params.USE_WISHART, true);
4748
TestType testType;
4849

4950
if (wishart) {
@@ -55,7 +56,7 @@ public Graph search(DataModel dataSet, Parameters parameters) {
5556
TestType purifyType = TestType.TETRAD_BASED;
5657

5758
BuildPureClusters bpc = new BuildPureClusters(cov, alpha, testType, purifyType);
58-
bpc.setVerbose(parameters.getBoolean("verbose"));
59+
bpc.setVerbose(parameters.getBoolean(Params.VERBOSE));
5960

6061
return bpc.search();
6162
} else {
@@ -67,14 +68,14 @@ public Graph search(DataModel dataSet, Parameters parameters) {
6768
// }
6869

6970
DataSet data = (DataSet) dataSet;
70-
GeneralResamplingTest search = new GeneralResamplingTest(data, algorithm, parameters.getInt("numberResampling"));
71+
GeneralResamplingTest search = new GeneralResamplingTest(data, algorithm, parameters.getInt(Params.NUMBER_RESAMPLING));
7172
search.setKnowledge(knowledge);
7273

73-
search.setPercentResampleSize(parameters.getDouble("percentResampleSize"));
74-
search.setResamplingWithReplacement(parameters.getBoolean("resamplingWithReplacement"));
74+
search.setPercentResampleSize(parameters.getDouble(Params.PERCENT_RESAMPLE_SIZE));
75+
search.setResamplingWithReplacement(parameters.getBoolean(Params.RESAMPLING_WITH_REPLACEMENT));
7576

7677
ResamplingEdgeEnsemble edgeEnsemble = ResamplingEdgeEnsemble.Highest;
77-
switch (parameters.getInt("resamplingEnsemble", 1)) {
78+
switch (parameters.getInt(Params.RESAMPLING_ENSEMBLE, 1)) {
7879
case 0:
7980
edgeEnsemble = ResamplingEdgeEnsemble.Preserved;
8081
break;
@@ -85,10 +86,10 @@ public Graph search(DataModel dataSet, Parameters parameters) {
8586
edgeEnsemble = ResamplingEdgeEnsemble.Majority;
8687
}
8788
search.setEdgeEnsemble(edgeEnsemble);
88-
search.setAddOriginalDataset(parameters.getBoolean("addOriginalDataset"));
89+
search.setAddOriginalDataset(parameters.getBoolean(Params.ADD_ORIGINAL_DATASET));
8990

9091
search.setParameters(parameters);
91-
search.setVerbose(parameters.getBoolean("verbose"));
92+
search.setVerbose(parameters.getBoolean(Params.VERBOSE));
9293
return search.search();
9394
}
9495
}
@@ -111,15 +112,10 @@ public DataType getDataType() {
111112
@Override
112113
public List<String> getParameters() {
113114
List<String> parameters = new ArrayList<>();
114-
parameters.add("alpha");
115-
parameters.add("useWishart");
116-
parameters.add("verbose");
117-
// Resampling
118-
parameters.add("numberResampling");
119-
parameters.add("percentResampleSize");
120-
parameters.add("resamplingWithReplacement");
121-
parameters.add("resamplingEnsemble");
122-
parameters.add("addOriginalDataset");
115+
parameters.add(Params.ALPHA);
116+
parameters.add(Params.USE_WISHART);
117+
parameters.add(Params.VERBOSE);
118+
123119
return parameters;
124120
}
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