/** Find the dataModel model. (If it's a list, take the one that's selected.) */
private DataModel getSelectedDataModel(DataWrapper dataWrapper) {
DataModelList dataModelList = dataWrapper.getDataModelList();
if (dataModelList.size() > 1) {
return dataModelList;
}
DataModel dataModel = dataWrapper.getSelectedDataModel();
if (dataModel instanceof DataSet) {
DataSet dataSet = (DataSet) dataModel;
if (dataSet.isDiscrete()) {
return dataSet;
} else if (dataSet.isContinuous()) {
return dataSet;
} else if (dataSet.isMixed()) {
return dataSet;
}
throw new IllegalArgumentException(
"<html>"
+ "This data set contains a mixture of discrete and continuous "
+ "<br>columns; there are no algorithm in Tetrad currently to "
+ "<br>search over such data sets."
+ "</html>");
} else if (dataModel instanceof ICovarianceMatrix) {
return dataModel;
} else if (dataModel instanceof TimeSeriesData) {
return dataModel;
}
throw new IllegalArgumentException("Unexpected dataModel source: " + dataModel);
}
public FindOneFactorClustersWithCausalIndicators(
DataSet dataSet, TestType testType, double alpha) {
if (dataSet.isContinuous()) {
this.variables = dataSet.getVariables();
this.test = new ContinuousTetradTest(dataSet, testType, alpha);
this.indTest = new IndTestFisherZ(dataSet, alpha);
this.alpha = alpha;
this.testType = testType;
this.dataModel = dataSet;
if (testType == TestType.TETRAD_DELTA) {
deltaTest = new DeltaTetradTest(dataSet);
deltaTest.setCacheFourthMoments(false);
}
this.cov = new CovarianceMatrix(dataSet);
} else if (dataSet.isDiscrete()) {
this.variables = dataSet.getVariables();
this.test = new DiscreteTetradTest(dataSet, alpha);
this.indTest = new IndTestChiSquare(dataSet, alpha);
this.alpha = alpha;
this.testType = testType;
this.dataModel = dataSet;
if (testType == TestType.TETRAD_DELTA) {
deltaTest = new DeltaTetradTest(dataSet);
deltaTest.setCacheFourthMoments(false);
}
}
}
/** Constructs the score using a covariance matrix. */
public BdeuScoreImages(List<DataModel> dataModels) {
if (dataModels == null) {
throw new NullPointerException();
}
List<BDeuScore> scores = new ArrayList<>();
for (DataModel model : dataModels) {
if (model instanceof DataSet) {
DataSet dataSet = (DataSet) model;
if (!dataSet.isDiscrete()) {
throw new IllegalArgumentException("Datasets must be continuous.");
}
scores.add(new BDeuScore(dataSet));
} else {
throw new IllegalArgumentException(
"Only continuous data sets and covariance matrices may be used as input.");
}
}
List<Node> variables = scores.get(0).getVariables();
for (int i = 2; i < scores.size(); i++) {
scores.get(i).setVariables(variables);
}
this.scores = scores;
this.variables = variables;
}
/**
* Factory to return the correct param editor for independence test params. This will go in a
* little box in the search editor.
*/
private JComponent getIndTestParamBox(IndTestParams indTestParams) {
if (indTestParams == null) {
throw new NullPointerException();
}
if (indTestParams instanceof GesIndTestParams) {
if (getAlgorithmRunner() instanceof IGesRunner) {
IGesRunner gesRunner = ((IGesRunner) getAlgorithmRunner());
GesIndTestParams params = (GesIndTestParams) indTestParams;
DataModel dataModel = gesRunner.getDataModel();
boolean discreteData = dataModel instanceof DataSet && ((DataSet) dataModel).isDiscrete();
return new GesIndTestParamsEditor(params, discreteData);
}
if (getAlgorithmRunner() instanceof ImagesRunner) {
ImagesRunner gesRunner = ((ImagesRunner) getAlgorithmRunner());
GesIndTestParams params = (GesIndTestParams) indTestParams;
DataSet dataSet = (DataSet) gesRunner.getDataModel();
boolean discreteData = dataSet.isDiscrete();
return new GesIndTestParamsEditor(params, discreteData);
}
}
return new IndTestParamsEditor(indTestParams);
}
public GesConcurrent(DataSet dataSet) {
setDataSet(dataSet);
if (dataSet.isDiscrete()) {
BDeuScore score = new BDeuScore(dataSet);
score.setSamplePrior(10);
score.setStructurePrior(0.001);
}
setStructurePrior(0.001);
setSamplePrior(10.);
}
private void calcStats() {
// Graph resultGraph = getAlgorithmRunner().getResultGraph();
IGesRunner runner = (IGesRunner) getAlgorithmRunner();
if (runner.getTopGraphs().isEmpty()) {
throw new IllegalArgumentException(
"No patterns were recorded. Please adjust the number of " + "patterns to store.");
}
Graph resultGraph = runner.getTopGraphs().get(runner.getIndex()).getGraph();
if (getAlgorithmRunner().getDataModel() instanceof DataSet) {
// resultGraph may be the output of a PC search.
// Such graphs sometimes contain doubly directed edges.
// /We converte such edges to directed edges here.
// For the time being an orientation is arbitrarily selected.
Set<Edge> allEdges = resultGraph.getEdges();
for (Edge edge : allEdges) {
if (edge.getEndpoint1() == Endpoint.ARROW && edge.getEndpoint2() == Endpoint.ARROW) {
// Option 1 orient it from node1 to node2
resultGraph.setEndpoint(edge.getNode1(), edge.getNode2(), Endpoint.ARROW);
// Option 2 remove such edges:
resultGraph.removeEdge(edge);
}
}
Pattern pattern = new Pattern(resultGraph);
PatternToDag ptd = new PatternToDag(pattern);
Graph dag = ptd.patternToDagMeekRules();
DataSet dataSet = (DataSet) getAlgorithmRunner().getDataModel();
String report;
if (dataSet.isContinuous()) {
report = reportIfContinuous(dag, dataSet);
} else if (dataSet.isDiscrete()) {
report = reportIfDiscrete(dag, dataSet);
} else {
throw new IllegalArgumentException("");
}
JScrollPane dagWorkbenchScroll = dagWorkbenchScroll(dag);
modelStatsText.setLineWrap(true);
modelStatsText.setWrapStyleWord(true);
modelStatsText.setText(report);
removeStatsTabs();
tabbedPane.addTab("DAG in pattern", dagWorkbenchScroll);
tabbedPane.addTab("DAG Model Statistics", modelStatsText);
}
}
private void setDataSet(DataSet dataSet) {
List<String> _varNames = dataSet.getVariableNames();
this.variables = dataSet.getVariables();
this.dataSet = dataSet;
this.discrete = dataSet.isDiscrete();
if (!isDiscrete()) {
this.covariances = new CovarianceMatrix(dataSet);
}
this.sampleSize = dataSet.getNumRows();
}