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///////////////////////////////////////////////////////////////////////////////
// For information as to what this class does, see the Javadoc, below. //
// Copyright (C) 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005, 2006, //
// 2007, 2008, 2009, 2010, 2014, 2015, 2022 by Peter Spirtes, Richard //
// Scheines, Joseph Ramsey, and Clark Glymour. //
// //
// This program is free software; you can redistribute it and/or modify //
// it under the terms of the GNU General Public License as published by //
// the Free Software Foundation; either version 2 of the License, or //
// (at your option) any later version. //
// //
// This program is distributed in the hope that it will be useful, //
// but WITHOUT ANY WARRANTY; without even the implied warranty of //
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the //
// GNU General Public License for more details. //
// //
// You should have received a copy of the GNU General Public License //
// along with this program; if not, write to the Free Software //
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA //
///////////////////////////////////////////////////////////////////////////////
package edu.cmu.tetradapp.model;
import edu.cmu.tetrad.data.*;
import edu.cmu.tetrad.graph.EdgeListGraph;
import edu.cmu.tetrad.graph.Graph;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.graph.Triple;
import edu.cmu.tetrad.regression.LogisticRegression;
import edu.cmu.tetrad.search.utils.MeekRules;
import edu.cmu.tetrad.util.Parameters;
import edu.cmu.tetrad.util.TetradLogger;
import edu.cmu.tetrad.util.TetradSerializableUtils;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serial;
import java.util.*;
/**
* Extends AbstractAlgorithmRunner to produce a wrapper for the Regression algorithm.
*
* @author Frank Wimberly after Joe Ramsey's PcRunner
* @version $Id: $Id
*/
public class LogisticRegressionRunner implements AlgorithmRunner, RegressionModel {
@Serial
private static final long serialVersionUID = 23L;
/**
* The parameters for the algorithm.
*/
private final Parameters params;
/**
* The names of the variables.
*/
private final List variableNames;
/**
* The name of the response variable.
*/
private String name;
/**
* The name of the response variable.
*/
private String targetName;
/**
* The names of the predictor variables.
*/
private List regressorNames;
/**
* The data model to run the algorithm on.
*/
private List dataSets;
/**
* The report produced by the algorithm.
*/
private String report;
/**
* The graph produced by the algorithm.
*/
private Graph outGraph;
/**
* The result produced by the algorithm.
*/
private LogisticRegression.Result result;
/**
* The alpha parameter for the algorithm.
*/
private double alpha = 0.001;
/**
* The number of models.
*/
private int numModels = 1;
/**
* The index of the model.
*/
private int modelIndex;
/**
* The name of the model source.
*/
private String modelSourceName;
//=========================CONSTRUCTORS===============================//
/**
* Constructs a wrapper for the given DataWrapper. The DataWrapper must contain a DataSet that is either a DataSet
* or a DataSet or a DataList containing either a DataSet or a DataSet as its selected model.
*
* @param dataWrapper a {@link edu.cmu.tetradapp.model.DataWrapper} object
* @param params a {@link edu.cmu.tetrad.util.Parameters} object
*/
public LogisticRegressionRunner(DataWrapper dataWrapper, Parameters params) {
if (dataWrapper == null) {
throw new NullPointerException();
}
if (params == null) {
throw new NullPointerException();
}
if (dataWrapper instanceof Simulation simulation) {
DataModelList dataModelList = dataWrapper.getDataModelList();
dataSets = new ArrayList<>();
for (DataModel dataModel : dataModelList) {
dataSets.add((DataSet) dataModel);
}
numModels = dataModelList.size();
modelIndex = 0;
modelSourceName = simulation.getName();
} else {
DataModel dataModel = dataWrapper.getSelectedDataModel();
if (!(dataModel instanceof DataSet)) {
throw new IllegalArgumentException("Data set must be tabular.");
}
this.setDataSet((DataSet) dataModel);
}
this.params = params;
variableNames = this.getDataModel().getVariableNames();
targetName = null;
regressorNames = new ArrayList<>();
TetradLogger.getInstance().log("Linear Regression");
if (result == null) {
TetradLogger.getInstance().log("Please double click this regression node to run the regession.");
} else {
TetradLogger.getInstance().log(report);
}
}
/**
* Generates a simple exemplar of this class to test serialization.
*
* @return a {@link edu.cmu.tetradapp.model.LogisticRegressionRunner} object
* @see TetradSerializableUtils
*/
public static LogisticRegressionRunner serializableInstance() {
List variables = new LinkedList<>();
ContinuousVariable var1 = new ContinuousVariable("X");
ContinuousVariable var2 = new ContinuousVariable("Y");
variables.add(var1);
variables.add(var2);
DataSet dataSet = new BoxDataSet(new VerticalDoubleDataBox(3, variables.size()), variables);
double[] col1data = {0.0, 1.0, 2.0};
double[] col2data = {2.3, 4.3, 2.5};
for (int i = 0; i < 3; i++) {
dataSet.setDouble(i, 0, col1data[i]);
dataSet.setDouble(i, 1, col2data[i]);
}
DataWrapper dataWrapper = new DataWrapper(dataSet);
return new LogisticRegressionRunner(dataWrapper, new Parameters());
}
//===========================PUBLIC METHODS============================//
/**
* getDataModel.
*
* @return a {@link edu.cmu.tetrad.data.DataModel} object
*/
public DataModel getDataModel() {
return dataSets.get(this.getModelIndex());
}
/**
* Getter for the field alpha.
*
* @return the alpha or -1.0 if the params aren't set.
*/
public double getAlpha() {
return alpha;//this.params.getDouble("alpha", 0.001);
}
/**
* Setter for the field alpha.
*
* @param alpha a double
*/
public void setAlpha(double alpha) {
this.alpha = alpha;
}
/**
* Getter for the field result.
*
* @return a {@link edu.cmu.tetrad.regression.LogisticRegression.Result} object
*/
public LogisticRegression.Result getResult() {
return this.result;
}
/**
* Getter for the field params.
*
* @return a {@link edu.cmu.tetrad.util.Parameters} object
*/
public Parameters getParams() {
return this.params;
}
/**
* getResultGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getResultGraph() {
return this.outGraph;
}
/**
* setResultGraph.
*
* @param graph a {@link edu.cmu.tetrad.graph.Graph} object
*/
public void setResultGraph(Graph graph) {
this.outGraph = graph;
}
/**
* getSourceGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getSourceGraph() {
return null;
}
//=================PUBLIC METHODS OVERRIDING ABSTRACT=================//
/**
* Executes the algorithm, producing (at least) a result workbench. Must be implemented in the extending class.
*/
public void execute() {
this.outGraph = new EdgeListGraph();
if (this.regressorNames == null || this.regressorNames.isEmpty() || this.targetName == null) {
this.report = "Response and predictor variables not set.";
return;
}
if (this.regressorNames.contains(this.targetName)) {
this.report = "Response must not be a predictor.";
return;
}
DataSet regressorsDataSet = this.dataSets.get(getModelIndex()).copy();
Node target = regressorsDataSet.getVariable(this.targetName);
regressorsDataSet.removeColumn(target);
List names = regressorsDataSet.getVariableNames();
//Get the list of regressors selected by the user
List regressorNodes = new ArrayList<>();
for (String s : this.regressorNames) {
regressorNodes.add(this.dataSets.get(getModelIndex()).getVariable(s));
}
//If the user selected none, use them all
if (this.regressorNames.size() > 0) {
for (String name1 : names) {
Node regressorVar = regressorsDataSet.getVariable(name1);
if (!this.regressorNames.contains(regressorVar.getName())) {
regressorsDataSet.removeColumn(regressorVar);
}
}
}
int ncases = regressorsDataSet.getNumRows();
int nvars = regressorsDataSet.getNumColumns();
double[][] regressors = new double[nvars][ncases];
for (int i = 0; i < nvars; i++) {
for (int j = 0; j < ncases; j++) {
regressors[i][j] = regressorsDataSet.getDouble(j, i);
}
}
LogisticRegression logRegression = new LogisticRegression(this.dataSets.get(getModelIndex()));
logRegression.setAlpha(this.alpha);
this.result = logRegression.regress((DiscreteVariable) target, regressorNodes);
}
/**
* supportsKnowledge.
*
* @return a boolean
*/
public boolean supportsKnowledge() {
return false;
}
/**
* getMeekRules.
*
* @return a {@link edu.cmu.tetrad.search.utils.MeekRules} object
*/
public MeekRules getMeekRules() {
throw new UnsupportedOperationException();
}
/**
* getExternalGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getExternalGraph() {
return null;
}
/**
* {@inheritDoc}
*/
public void setExternalGraph(Graph graph) {
}
/**
* {@inheritDoc}
*/
@Override
public String getAlgorithmName() {
return "Logistic-Regression";
}
/**
* Getter for the field outGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getOutGraph() {
return this.outGraph;
}
/**
* {@inheritDoc}
*/
@Override
public List getVariableNames() {
return this.variableNames;
}
/**
* {@inheritDoc}
*/
@Override
public List getRegressorNames() {
return new ArrayList<>();
}
/**
* {@inheritDoc}
*/
@Override
public void setRegressorName(List predictors) {
this.regressorNames = predictors;
}
/**
* Getter for the field targetName.
*
* @return a {@link java.lang.String} object
*/
public String getTargetName() {
return this.targetName;
}
/**
* {@inheritDoc}
*/
@Override
public void setTargetName(String target) {
this.targetName = target;
}
/**
* Writes the object to the specified ObjectOutputStream.
*
* @param out The ObjectOutputStream to write the object to.
* @throws IOException If an I/O error occurs.
*/
@Serial
private void writeObject(ObjectOutputStream out) throws IOException {
try {
out.defaultWriteObject();
} catch (IOException e) {
TetradLogger.getInstance().log("Failed to serialize object: " + getClass().getCanonicalName()
+ ", " + e.getMessage());
throw e;
}
}
/**
* Reads the object from the specified ObjectInputStream. This method is used during deserialization
* to restore the state of the object.
*
* @param in The ObjectInputStream to read the object from.
* @throws IOException If an I/O error occurs.
* @throws ClassNotFoundException If the class of the serialized object cannot be found.
*/
@Serial
private void readObject(ObjectInputStream in) throws IOException, ClassNotFoundException {
try {
in.defaultReadObject();
} catch (IOException e) {
TetradLogger.getInstance().log("Failed to deserialize object: " + getClass().getCanonicalName()
+ ", " + e.getMessage());
throw e;
}
}
/**
* Getter for the field name.
*
* @return a {@link java.lang.String} object
*/
public String getName() {
return this.name;
}
/**
* {@inheritDoc}
*/
public void setName(String name) {
this.name = name;
}
/**
* getGraph.
*
* @return a {@link edu.cmu.tetrad.graph.Graph} object
*/
public Graph getGraph() {
return this.outGraph;
}
/**
* getTriplesClassificationTypes.
*
* @return the names of the triple classifications. Coordinates with
*/
public List getTriplesClassificationTypes() {
return new LinkedList<>();
}
/**
* {@inheritDoc}
*/
public List> getTriplesLists(Node node) {
return new LinkedList<>();
}
/**
* {@inheritDoc}
*/
@Override
public Map getParamSettings() {
Map paramSettings = new HashMap<>();
paramSettings.put("Algorithm", "Regression");
return paramSettings;
}
/**
* {@inheritDoc}
*/
@Override
public Map getAllParamSettings() {
return null;
}
/**
* {@inheritDoc}
*/
@Override
public void setAllParamSettings(Map paramSettings) {
// Map allParamsSettings = paramSettings;
}
/**
* Getter for the field numModels.
*
* @return a int
*/
public int getNumModels() {
return this.numModels;
}
/**
* Getter for the field modelIndex.
*
* @return a int
*/
public int getModelIndex() {
return this.modelIndex;
}
/**
* Setter for the field modelIndex.
*
* @param modelIndex a int
*/
public void setModelIndex(int modelIndex) {
this.modelIndex = modelIndex;
}
/**
* Getter for the field modelSourceName.
*
* @return a {@link java.lang.String} object
*/
public String getModelSourceName() {
return this.modelSourceName;
}
/**
* setDataSet.
*
* @param dataSet a {@link edu.cmu.tetrad.data.DataSet} object
*/
public void setDataSet(DataSet dataSet) {
this.dataSets = new ArrayList<>();
this.dataSets.add(dataSet);
}
/**
* {@inheritDoc}
*/
@Override
public List getGraphs() {
return null;
}
}
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