Example 6 with DataSet
use of edu.cmu.tetrad.data.DataSet in project tetrad by cmu-phil.
the class ScatterPlot method getCorrelationCoeff.
public double getCorrelationCoeff() {
DataSet dataSet = getDataSet();
TetradMatrix data = dataSet.getDoubleData();
int _x = dataSet.getColumn(dataSet.getVariable(x));
int _y = dataSet.getColumn(dataSet.getVariable(y));
double[] xdata = data.getColumn(_x).toArray();
double[] ydata = data.getColumn(_y).toArray();
double correlation = StatUtils.correlation(xdata, ydata);
if (correlation > 1)
correlation = 1;
else if (correlation < -1)
correlation = -1;
return correlation;
}
Also used :
DataSet(edu.cmu.tetrad.data.DataSet)
TetradMatrix(edu.cmu.tetrad.util.TetradMatrix)
Example 7 with DataSet
use of edu.cmu.tetrad.data.DataSet in project tetrad by cmu-phil.
the class PurifyParamsEditor method setVarNames.
private boolean setVarNames(Object[] parentModels, Parameters params) {
DataModel dataModel = null;
for (Object parentModel : parentModels) {
if (parentModel instanceof DataWrapper) {
DataWrapper dataWrapper = (DataWrapper) parentModel;
dataModel = dataWrapper.getSelectedDataModel();
}
}
boolean discreteModel;
if (dataModel instanceof ICovarianceMatrix) {
discreteModel = false;
} else {
DataSet dataSet = (DataSet) dataModel;
assert dataSet != null;
discreteModel = dataSet.isDiscrete();
// try {
// new DataSet((DataSet) dataModel);
// discreteModel = true;
// }
// catch (IllegalArgumentException e) {
// discreteModel = false;
// }
}
getParams().set("varNames", params.get("varNames", null));
return discreteModel;
}
Also used :
DataWrapper(edu.cmu.tetradapp.model.DataWrapper)
DataSet(edu.cmu.tetrad.data.DataSet)
DataModel(edu.cmu.tetrad.data.DataModel)
ICovarianceMatrix(edu.cmu.tetrad.data.ICovarianceMatrix)
Example 8 with DataSet
use of edu.cmu.tetrad.data.DataSet in project tetrad by cmu-phil.
the class QQPlotAction method createQQPlotDialog.
/**
* Creates a dialog that is showing the histogram for the given node (if null
* one is selected for you)
*/
private JPanel createQQPlotDialog(Node selected) {
String dialogTitle = "Q-Q Plots";
// new JPanel(findOwner(), dialogTitle, false);
JPanel panel = new JPanel();
panel.setLayout(new BorderLayout());
// dialog.setResizable(false);
// dialog.getContentPane().setLayout(new BorderLayout());
DataSet dataSet = (DataSet) dataEditor.getSelectedDataModel();
QQPlot qqPlot = new QQPlot(dataSet, selected);
QQPlotEditorPanel editorPanel = new QQPlotEditorPanel(qqPlot, dataSet);
QQPlotDisplayPanel display = new QQPlotDisplayPanel(qqPlot);
editorPanel.addPropertyChangeListener(new QQPlotListener(display));
JMenuBar bar = new JMenuBar();
JMenu menu = new JMenu("File");
menu.add(new JMenuItem(new SaveComponentImage(display, "Save Q-Q Plot")));
bar.add(menu);
Box box = Box.createHorizontalBox();
box.add(display);
box.add(Box.createHorizontalStrut(3));
box.add(editorPanel);
box.add(Box.createHorizontalStrut(5));
box.add(Box.createHorizontalGlue());
Box vBox = Box.createVerticalBox();
vBox.add(Box.createVerticalStrut(15));
vBox.add(box);
vBox.add(Box.createVerticalStrut(5));
panel.add(bar, BorderLayout.NORTH);
panel.add(vBox, BorderLayout.CENTER);
// return dialog;
return panel;
}
Also used :
DataSet(edu.cmu.tetrad.data.DataSet)
Example 9 with DataSet
use of edu.cmu.tetrad.data.DataSet in project tetrad by cmu-phil.
the class QQPlotAction method actionPerformed.
public void actionPerformed(ActionEvent e) {
DataSet dataSet = (DataSet) dataEditor.getSelectedDataModel();
if (dataSet == null || dataSet.getNumColumns() == 0) {
JOptionPane.showMessageDialog(findOwner(), "Cannot display a Q-Q plot for 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>" +
// "displaying data in a Q-Q plot.</html>"));
// return;
// }
int[] selected = dataSet.getSelectedIndices();
// if more then one column is selected then open up more than one histogram
if (selected != null && 0 < selected.length) {
// warn user if they selected more than 10
if (10 < selected.length) {
int option = JOptionPane.showConfirmDialog(findOwner(), "You are about to open " + selected.length + " Q-Q plots, are you sure you want to proceed?", "Q-Q Plot Warning", JOptionPane.YES_NO_OPTION);
// if selected no, return
if (option == JOptionPane.NO_OPTION) {
return;
}
}
for (int index : selected) {
JPanel dialog = createQQPlotDialog(dataSet.getVariable(index));
EditorWindow editorWindow = new EditorWindow(dialog, "QQPlot", "Save", true, dataEditor);
DesktopController.getInstance().addEditorWindow(editorWindow, JLayeredPane.PALETTE_LAYER);
editorWindow.pack();
editorWindow.setVisible(true);
// dialog.pack();
// setLocation(dialog, index);
// dialog.setVisible(true);
}
} else {
JPanel dialog = createQQPlotDialog(null);
EditorWindow editorWindow = new EditorWindow(dialog, "QQPlot", "Save", true, dataEditor);
DesktopController.getInstance().addEditorWindow(editorWindow, JLayeredPane.PALETTE_LAYER);
editorWindow.pack();
editorWindow.setVisible(true);
// JDialog dialog = createQQPlotDialog(null);
// dialog.pack();
// dialog.setLocationRelativeTo(dialog.getOwner());
// dialog.setVisible(true);
}
}
Also used :
DataSet(edu.cmu.tetrad.data.DataSet)
Example 10 with DataSet
use of edu.cmu.tetrad.data.DataSet in project tetrad by cmu-phil.
the class MimSearchEditor2 method getIndTestParamBox.
/**
* 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(Parameters params) {
if (params == null) {
throw new NullPointerException();
}
if (params instanceof Parameters) {
MimRunner runner = getMimRunner();
params.set("varNames", runner.getParams().get("varNames", null));
DataModel dataModel = runner.getData();
if (dataModel instanceof DataSet) {
DataSet data = (DataSet) runner.getData();
boolean discrete = data.isDiscrete();
return new BuildPureClustersIndTestParamsEditor2(params, discrete);
} else if (dataModel instanceof ICovarianceMatrix) {
return new BuildPureClustersIndTestParamsEditor2(params, false);
}
}
if (params instanceof Parameters) {
MimRunner runner = getMimRunner();
params.set("varNames", runner.getParams().get("varNames", null));
boolean discreteData = false;
if (runner.getData() instanceof DataSet) {
discreteData = ((DataSet) runner.getData()).isDiscrete();
}
return new PurifyIndTestParamsEditor(params, discreteData);
}
if (params instanceof Parameters) {
MimRunner runner = getMimRunner();
params.set("varNames", runner.getParams().get("varNames", null));
return new MimBuildIndTestParamsEditor(params);
}
throw new IllegalArgumentException("Unrecognized Parameters: " + params.getClass());
}
Also used :
Parameters(edu.cmu.tetrad.util.Parameters)
DataSet(edu.cmu.tetrad.data.DataSet)
DataModel(edu.cmu.tetrad.data.DataModel)
ICovarianceMatrix(edu.cmu.tetrad.data.ICovarianceMatrix)
MimRunner(edu.cmu.tetradapp.model.MimRunner)
Aggregations
DataSet (edu.cmu.tetrad.data.DataSet)216
Test (org.junit.Test)65
Graph (edu.cmu.tetrad.graph.Graph)64
Node (edu.cmu.tetrad.graph.Node)60
ContinuousVariable (edu.cmu.tetrad.data.ContinuousVariable)48
ArrayList (java.util.ArrayList)45
ColtDataSet (edu.cmu.tetrad.data.ColtDataSet)36
GeneralBootstrapTest (edu.pitt.dbmi.algo.bootstrap.GeneralBootstrapTest)32
EdgeListGraph (edu.cmu.tetrad.graph.EdgeListGraph)29
SemIm (edu.cmu.tetrad.sem.SemIm)28
SemPm (edu.cmu.tetrad.sem.SemPm)28
BootstrapEdgeEnsemble (edu.pitt.dbmi.algo.bootstrap.BootstrapEdgeEnsemble)26
DataModel (edu.cmu.tetrad.data.DataModel)22
Parameters (edu.cmu.tetrad.util.Parameters)22
DiscreteVariable (edu.cmu.tetrad.data.DiscreteVariable)20
File (java.io.File)16
ParseException (java.text.ParseException)16
LinkedList (java.util.LinkedList)14
ICovarianceMatrix (edu.cmu.tetrad.data.ICovarianceMatrix)13
DMSearch (edu.cmu.tetrad.search.DMSearch)10
