/**
* Constructs a test using a given data set. If a data set is provided (that is, a tabular data
* set), fourth moment statistics can be calculated (p. 160); otherwise, it must be assumed that
* the data are multivariate Gaussian.
*/
public DeltaSextadTest(DataSet dataSet) {
if (dataSet == null) {
throw new NullPointerException();
}
if (!dataSet.isContinuous()) {
throw new IllegalArgumentException();
}
this.cov = new CovarianceMatrix(dataSet);
List<DataSet> data1 = new ArrayList<DataSet>();
data1.add(dataSet);
List<DataSet> data2 = DataUtils.center(data1);
this.dataSet = data2.get(0);
this.data = this.dataSet.getDoubleData().transpose().toArray();
this.N = dataSet.getNumRows();
this.variables = dataSet.getVariables();
this.numVars = dataSet.getNumColumns();
this.variablesHash = new HashMap<Node, Integer>();
for (int i = 0; i < variables.size(); i++) {
variablesHash.put(variables.get(i), i);
}
this.means = new double[numVars];
for (int i = 0; i < numVars; i++) {
means[i] = mean(data[i], N);
}
}
/**
* Constructs a new Fisher Z independence test with the listed arguments.
*
* @param data A 2D continuous data set with no missing values.
* @param variables A list of variables, a subset of the variables of <code>data</code>.
* @param alpha The significance cutoff level. p values less than alpha will be reported as
* dependent.
*/
public IndTestFisherZShortTriangular(TetradMatrix data, List<Node> variables, double alpha) {
DataSet dataSet = ColtDataSet.makeContinuousData(variables, data);
this.covMatrix = new ShortTriangularMatrix(dataSet.getNumColumns());
this.covMatrix.becomeCorrelationMatrix(dataSet);
this.variables = dataSet.getVariables();
setAlpha(alpha);
this.deterministicTest = new IndTestFisherZGeneralizedInverse(dataSet, alpha);
}
@Test
public void test2() {
RandomUtil.getInstance().setSeed(2999983L);
int sampleSize = 1000;
List<Node> variableNodes = new ArrayList<>();
ContinuousVariable x1 = new ContinuousVariable("X1");
ContinuousVariable x2 = new ContinuousVariable("X2");
ContinuousVariable x3 = new ContinuousVariable("X3");
ContinuousVariable x4 = new ContinuousVariable("X4");
ContinuousVariable x5 = new ContinuousVariable("X5");
variableNodes.add(x1);
variableNodes.add(x2);
variableNodes.add(x3);
variableNodes.add(x4);
variableNodes.add(x5);
Graph _graph = new EdgeListGraph(variableNodes);
SemGraph graph = new SemGraph(_graph);
graph.addDirectedEdge(x1, x3);
graph.addDirectedEdge(x2, x3);
graph.addDirectedEdge(x3, x4);
graph.addDirectedEdge(x2, x4);
graph.addDirectedEdge(x4, x5);
graph.addDirectedEdge(x2, x5);
SemPm semPm = new SemPm(graph);
SemIm semIm = new SemIm(semPm);
DataSet dataSet = semIm.simulateData(sampleSize, false);
print(semPm);
GeneralizedSemPm _semPm = new GeneralizedSemPm(semPm);
GeneralizedSemIm _semIm = new GeneralizedSemIm(_semPm, semIm);
DataSet _dataSet = _semIm.simulateDataMinimizeSurface(sampleSize, false);
print(_semPm);
// System.out.println(_dataSet);
for (int j = 0; j < dataSet.getNumColumns(); j++) {
double[] col = dataSet.getDoubleData().getColumn(j).toArray();
double[] _col = _dataSet.getDoubleData().getColumn(j).toArray();
double mean = StatUtils.mean(col);
double _mean = StatUtils.mean(_col);
double variance = StatUtils.variance(col);
double _variance = StatUtils.variance(_col);
assertEquals(mean, _mean, 0.3);
assertEquals(1.0, variance / _variance, .2);
}
}
/**
* Constructs a new Independence test which checks independence facts based on the correlation
* matrix implied by the given data set (must be continuous). The given significance level is
* used.
*
* @param dataSet A data set containing only continuous columns.
* @param alpha The alpha level of the test.
*/
public IndTestFisherZShortTriangular(DataSet dataSet, double alpha) {
if (!(dataSet.isContinuous())) {
throw new IllegalArgumentException("Data set must be continuous.");
}
this.covMatrix = new ShortTriangularMatrix(dataSet.getNumColumns());
this.covMatrix.becomeCorrelationMatrix(dataSet);
this.variables = dataSet.getVariables();
setAlpha(alpha);
this.deterministicTest = new IndTestFisherZGeneralizedInverse(dataSet, alpha);
this.dataSet = dataSet;
}
/** Creates a cell count table for the given data set. */
public DataSetProbs(DataSet dataSet) {
if (dataSet == null) {
throw new NullPointerException();
}
this.dataSet = dataSet;
dims = new int[dataSet.getNumColumns()];
for (int i = 0; i < dims.length; i++) {
DiscreteVariable variable = (DiscreteVariable) dataSet.getVariable(i);
dims[i] = variable.getNumCategories();
}
numRows = dataSet.getNumRows();
}
public void actionPerformed(ActionEvent e) {
DataSet dataSet = (DataSet) dataEditor.getSelectedDataModel();
if (dataSet == null || dataSet.getNumColumns() == 0) {
JOptionPane.showMessageDialog(
findOwner(), "Cannot display a scatter plot for an empty data set.");
return;
}
JPanel panel = new ScatterPlotView(dataSet);
EditorWindow editorWindow = new EditorWindow(panel, "Scatter Plots", "Save", true, dataEditor);
// JPanel dialog = createScatterPlotDialog(null, null);
// EditorWindow editorWindow = new EditorWindow(dialog, "Scatter Plots", "Save", true,
// dataEditor);
DesktopController.getInstance().addEditorWindow(editorWindow, JLayeredPane.PALETTE_LAYER);
editorWindow.pack();
editorWindow.setVisible(true);
}
/** @return the splitNames selected by the editor. */
public static DataModel createSplits(DataSet dataSet, SplitCasesParams params) {
List<Integer> indices = new ArrayList<Integer>(dataSet.getNumRows());
for (int i = 0; i < dataSet.getNumRows(); i++) {
indices.add(i);
}
if (params.isDataShuffled()) {
Collections.shuffle(indices);
}
SplitCasesSpec spec = params.getSpec();
int numSplits = params.getNumSplits();
int sampleSize = spec.getSampleSize();
int[] breakpoints = spec.getBreakpoints();
List<String> splitNames = spec.getSplitNames();
int[] _breakpoints = new int[breakpoints.length + 2];
_breakpoints[0] = 0;
_breakpoints[_breakpoints.length - 1] = sampleSize;
System.arraycopy(breakpoints, 0, _breakpoints, 1, breakpoints.length);
DataModelList list = new DataModelList();
int ncols = dataSet.getNumColumns();
for (int n = 0; n < numSplits; n++) {
int _sampleSize = _breakpoints[n + 1] - _breakpoints[n];
DataSet _data = new ColtDataSet(_sampleSize, dataSet.getVariables());
_data.setName(splitNames.get(n));
for (int i = 0; i < _sampleSize; i++) {
int oldCase = indices.get(i + _breakpoints[n]);
for (int j = 0; j < ncols; j++) {
_data.setObject(i, j, dataSet.getObject(oldCase, j));
}
}
list.add(_data);
}
return list;
}
private String reportIfDiscrete(Graph dag, DataSet dataSet) {
List vars = dataSet.getVariables();
Map<String, DiscreteVariable> nodesToVars = new HashMap<String, DiscreteVariable>();
for (int i = 0; i < dataSet.getNumColumns(); i++) {
DiscreteVariable var = (DiscreteVariable) vars.get(i);
String name = var.getName();
Node node = new GraphNode(name);
nodesToVars.put(node.getName(), var);
}
BayesPm bayesPm = new BayesPm(new Dag(dag));
List<Node> nodes = bayesPm.getDag().getNodes();
for (Node node : nodes) {
Node var = nodesToVars.get(node.getName());
if (var instanceof DiscreteVariable) {
DiscreteVariable var2 = nodesToVars.get(node.getName());
int numCategories = var2.getNumCategories();
List<String> categories = new ArrayList<String>();
for (int j = 0; j < numCategories; j++) {
categories.add(var2.getCategory(j));
}
bayesPm.setCategories(node, categories);
}
}
BayesProperties properties = new BayesProperties(dataSet, dag);
properties.setGraph(dag);
NumberFormat nf = NumberFormat.getInstance();
nf.setMaximumFractionDigits(4);
StringBuilder buf = new StringBuilder();
buf.append("\nP-value = ").append(properties.getLikelihoodRatioP());
buf.append("\nDf = ").append(properties.getPValueDf());
buf.append("\nChi square = ").append(nf.format(properties.getPValueChisq()));
buf.append("\nBIC score = ").append(nf.format(properties.getBic()));
buf.append("\n\nH0: Completely disconnected graph.");
return buf.toString();
}
public void actionPerformed(ActionEvent e) {
DataSet dataSet = (DataSet) dataEditor.getSelectedDataModel();
if (dataSet == null || dataSet.getNumColumns() == 0) {
JOptionPane.showMessageDialog(
findOwner(), "Cannot run normality tests on an empty data set.");
return;
}
// if there are missing values warn and don't display q-q plot.
// if(DataUtils.containsMissingValue(dataSet)){
// JOptionPane.showMessageDialog(findOwner(), new JLabel("<html>Data has missing
// values, " +
// "remove all missing values before<br>" +
// "running normality tests.</html>"));
// return;
// }
JPanel panel = createNormalityTestDialog(null);
EditorWindow window = new EditorWindow(panel, "Normality Tests", "Close", false, dataEditor);
DesktopController.getInstance().addEditorWindow(window, JLayeredPane.PALETTE_LAYER);
window.setVisible(true);
}
public final DataSet filter(DataSet dataSet) {
// Why does it have to be discrete? Why can't we simply expand
// whatever discrete columns are there and leave the continuous
// ones untouched? jdramsey 7/4/2005
// if (!(dataSet.isDiscrete())) {
// throw new IllegalArgumentException("Data set must be discrete.");
// }
List<Node> variables = new LinkedList<>();
// Add all of the variables to the new data set.
for (int j = 0; j < dataSet.getNumColumns(); j++) {
Node _var = dataSet.getVariable(j);
if (!(_var instanceof DiscreteVariable)) {
variables.add(_var);
continue;
}
DiscreteVariable variable = (DiscreteVariable) _var;
String oldName = variable.getName();
List<String> oldCategories = variable.getCategories();
List<String> newCategories = new LinkedList<>(oldCategories);
String newCategory = "Missing";
int _j = 0;
while (oldCategories.contains(newCategory)) {
newCategory = "Missing" + (++_j);
}
newCategories.add(newCategory);
String newName = oldName + "+";
DiscreteVariable newVariable = new DiscreteVariable(newName, newCategories);
variables.add(newVariable);
}
DataSet newDataSet = new ColtDataSet(dataSet.getNumRows(), variables);
// Copy old values to new data set, replacing missing values with new
// "MissingValue" categories.
for (int j = 0; j < dataSet.getNumColumns(); j++) {
Node _var = dataSet.getVariable(j);
if (_var instanceof ContinuousVariable) {
for (int i = 0; i < dataSet.getNumRows(); i++) {
newDataSet.setDouble(i, j, dataSet.getDouble(i, j));
}
} else if (_var instanceof DiscreteVariable) {
DiscreteVariable variable = (DiscreteVariable) _var;
int numCategories = variable.getNumCategories();
for (int i = 0; i < dataSet.getNumRows(); i++) {
int value = dataSet.getInt(i, j);
if (value == DiscreteVariable.MISSING_VALUE) {
newDataSet.setInt(i, j, numCategories);
} else {
newDataSet.setInt(i, j, value);
}
}
}
}
return newDataSet;
}