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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.tetrad.sem;
import edu.cmu.tetrad.data.*;
import edu.cmu.tetrad.graph.LayoutUtil;
import edu.cmu.tetrad.graph.Node;
import edu.cmu.tetrad.graph.NodeType;
import edu.cmu.tetrad.util.*;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.List;
/**
* Estimates a SemIm given a CovarianceMatrix and a SemPm. (A DataSet may be substituted for the CovarianceMatrix.)
*
* @author Frank Wimberly
* @author Ricardo Silva
* @author Don Crimbchin
* @author josephramsey
*/
public final class SemEstimator implements TetradSerializable {
private static final long serialVersionUID = 23L;
/**
* The SemPm containing the graph and the freeParameters to be estimated.
*
* @serial Cannot be null.
*/
private SemPm semPm;
/**
* The covariance matrix used to estimate the SemIm. Note that the variables names in the covariance matrix must be
* in the same order as the variable names in the semPm.
*
* @serial Cannot be null.
*/
private ICovarianceMatrix covMatrix;
/**
* The algorithm that minimizes the fitting function for the SEM.
*
* @serial
*/
private SemOptimizer semOptimizer;
/**
* The most recently estimated model, or null if no model has been estimated yet.
*
* @serial Can be null.
*/
private SemIm estimatedSem;
/**
* The data set being estimated from (needed to calculate means of variables). May be null in which case means are
* set to zero.
*
* @serial Can be null.
*/
private DataSet dataSet;
private ScoreType scoreType = ScoreType.Fgls;
private int numRestarts = 1;
/**
* Constructs a Sem Estimator that does default estimation.
*
* @param semPm a SemPm specifying the graph and parameterization for the model.
* @param dataSet a DataSet, all of whose variables are contained in the given SemPm. (They are identified by
* name.)
*/
public SemEstimator(DataSet dataSet, SemPm semPm) {
this(dataSet, semPm, null);
}
/**
* Constructs a SEM estimator that does default estimation.
*
* @param semPm a SemPm specifying the graph and parameterization for the model.
* @param covMatrix a CovarianceMatrix, all of whose variables are contained in the given SemPm. (They are
* identified by name.)
*/
public SemEstimator(ICovarianceMatrix covMatrix, SemPm semPm) {
this(covMatrix, semPm, null);
}
/**
* Constructs a new SemEstimator that uses the specified optimizer.
*
* @param semPm a SemPm specifying the graph and parameterization for the model.
* @param dataSet a DataSet, all of whose variables are contained in the given SemPm. (They are identified by
* name.)
* @param semOptimizer the optimizer that optimizes the Sem.
*/
public SemEstimator(DataSet dataSet, SemPm semPm,
SemOptimizer semOptimizer) {
this(new CovarianceMatrix(dataSet), semPm, semOptimizer);
if (DataUtils.containsMissingValue(dataSet)) {
throw new IllegalArgumentException("Expecting a data set with no missing values.");
}
setDataSet(subset(dataSet, semPm));
}
/**
* Constructs a new SemEstimator that uses the specified optimizer.
*
* @param semPm a SemPm specifying the graph and parameterization for the model.
* @param covMatrix a covariance matrix, all of whose variables are contained in the given SemPm. (They are
* identified by name.)
* @param semOptimizer the optimizer that optimizes the Sem.
*/
public SemEstimator(ICovarianceMatrix covMatrix, SemPm semPm,
SemOptimizer semOptimizer) {
if (covMatrix == null) {
throw new NullPointerException(
"CovarianceMatrix must not be null.");
}
if (semPm == null) {
throw new NullPointerException("SemPm must not be null.");
}
if (DataUtils.containsMissingValue(covMatrix.getMatrix())) {
throw new IllegalArgumentException("Expecting a covariance matrix with no missing values.");
}
semPm.getGraph().setShowErrorTerms(false);
setCovMatrix(submatrix(covMatrix, semPm));
setSemPm(semPm);
setSemOptimizer(semOptimizer);
}
/**
* Generates a simple exemplar of this class to test serialization.
*/
public static SemEstimator serializableInstance() {
return new SemEstimator(CovarianceMatrix.serializableInstance(),
SemPm.serializableInstance());
}
private static boolean containsCovarParam(SemPm semPm) {
boolean containsCovarParam = false;
List params = semPm.getParameters();
for (Parameter param : params) {
if (param.getType() == ParamType.COVAR) {
containsCovarParam = true;
break;
}
}
return containsCovarParam;
}
/**
* Runs the estimator on the data and SemPm passed in through the constructor.
*/
public SemIm estimate() {
if (getSemOptimizer() != null) {
getSemOptimizer().setNumRestarts(this.numRestarts);
// TetradLogger.getInstance().log("info", getSemOptimizer().toString());
// TetradLogger.getInstance().log("info", "Score = " + getScoreType());
// TetradLogger.getInstance().log("info", "Num restarts = " + getSemOptimizer().getNumRestarts());
}
//long time = MillisecondTimes.timeMillis();
//System.out.println("Start timer.");
// Forget any previous estimation results. (If the estimation fails,
// the estimatedSem should be null.)
setEstimatedSem(null);
// Create the Sem from the SemPm and CovarianceMatrix.
SemIm semIm = new SemIm(getSemPm(), getCovMatrix());
LayoutUtil.arrangeBySourceGraph(semIm.getSemPm().getGraph(),
getSemPm().getGraph());
// Optimize the Sem.
semIm.setParameterBoundsEnforced(false);
semIm.setScoreType(getScoreType());
SemOptimizer defaultOptimizer = getDefaultOptimization(semIm);
if (this.semOptimizer == null) {
this.semOptimizer = defaultOptimizer;
}
getSemOptimizer().setNumRestarts(this.numRestarts);
getSemOptimizer().optimize(semIm);
semIm.setParameterBoundsEnforced(true);
setMeans(semIm, getDataSet());
// Marks semIm as estimated
semIm.setEstimated(true);
// Set the estimated semIm to this.
setEstimatedSem(semIm);
NumberFormat nf = NumberFormatUtil.getInstance().getNumberFormat();
// TetradLogger.getInstance().log("stats", "Final Score = " + nf.format(semIm.getScore()));
TetradLogger.getInstance().log("stats", "Sample Size = " + semIm.getSampleSize());
TetradLogger.getInstance().log("stats", "Model Chi Square = " + nf.format(semIm.getChiSquare()));
TetradLogger.getInstance().log("stats", "Model DOF = " + nf.format(this.semPm.getDof()));
TetradLogger.getInstance().log("stats", "Model P Value = " + nf.format(semIm.getPValue()));
TetradLogger.getInstance().log("stats", "Model BIC = " + nf.format(semIm.getBicScore()));
System.out.println(this.estimatedSem);
return this.estimatedSem;
}
/**
* @return the estimated SemIm. If the estimate method has not yet been called, null is
* returned.
*/
public SemIm getEstimatedSem() {
return this.estimatedSem;
}
private void setEstimatedSem(SemIm estimatedSem) {
this.estimatedSem = estimatedSem;
}
public DataSet getDataSet() {
return this.dataSet;
}
private void setDataSet(DataSet dataSet) {
List nodes1 = this.semPm.getMeasuredNodes();
List vars = new ArrayList<>();
for (Node node : nodes1) {
Node _node = dataSet.getVariable(node.getName());
vars.add(_node);
}
DataSet _dataSet = new BoxDataSet(new VerticalDoubleDataBox(dataSet.getDoubleData().transpose().toArray()), vars);
_dataSet.setName(dataSet.getName());
this.dataSet = _dataSet;
}
public SemPm getSemPm() {
return this.semPm;
}
private void setSemPm(SemPm semPm) {
this.semPm = semPm;
}
public ICovarianceMatrix getCovMatrix() {
return this.covMatrix;
}
private void setCovMatrix(ICovarianceMatrix covMatrix) {
this.covMatrix = covMatrix;
}
private SemOptimizer getSemOptimizer() {
return this.semOptimizer;
}
public void setSemOptimizer(SemOptimizer semOptimizer) {
this.semOptimizer = semOptimizer;
}
/**
* @return a string representation of the Sem.
*/
public String toString() {
StringBuilder buf = new StringBuilder();
buf.append("\nSemEstimator");
if (this.getEstimatedSem() == null) {
buf.append("\n\t...SemIm has not been estimated yet.");
} else {
SemIm sem = this.getEstimatedSem();
buf.append("\n\n\tfml = ");
buf.append("\n\n\tmeasuredNodes:\n");
buf.append("\t").append(sem.getMeasuredNodes());
buf.append("\n\n\tedgeCoef:\n");
buf.append(MatrixUtils.toString(sem.getEdgeCoef().toArray()));
buf.append("\n\n\terrCovar:\n");
buf.append(MatrixUtils.toString(sem.getErrCovar().toArray()));
}
return buf.toString();
}
private SemOptimizer getDefaultOptimization(SemIm semIm) {
if (semIm == null) throw new NullPointerException();
boolean containsLatent = false;
for (Node node : getSemPm().getGraph().getNodes()) {
if (node.getNodeType() == NodeType.LATENT) {
containsLatent = true;
break;
}
}
SemOptimizer optimizer;
if (containsFixedParam() || getSemPm().getGraph().paths().existsDirectedCycle() ||
SemEstimator.containsCovarParam(getSemPm())) {
optimizer = new SemOptimizerPowell();
} else if (containsLatent) {
optimizer = new SemOptimizerEm();
} else {
optimizer = new SemOptimizerRegression();
}
optimizer.setNumRestarts(this.numRestarts);
return optimizer;
}
private boolean containsFixedParam() {
return new SemIm(getSemPm()).getNumFixedParams() > 0;
}
/**
* @return A submatrix of covMatrix with the order of its variables the same as in semPm.
* @throws IllegalArgumentException if not all of the variables of
* semPm are in covMatrix.
*/
private ICovarianceMatrix submatrix(ICovarianceMatrix covMatrix,
SemPm semPm) {
String[] measuredVarNames = semPm.getMeasuredVarNames();
try {
return covMatrix.getSubmatrix(measuredVarNames);
} catch (IllegalArgumentException e) {
e.printStackTrace();
throw new RuntimeException(
"All of the variables from the SEM parameterized model " +
"must be in the data set.", e);
}
}
private DataSet subset(DataSet dataSet, SemPm semPm) {
String[] measuredVarNames = semPm.getMeasuredVarNames();
int[] varIndices = new int[measuredVarNames.length];
List dataVars = dataSet.getVariables();
for (int i = 0; i < measuredVarNames.length; i++) {
Node variable = dataSet.getVariable(measuredVarNames[i]);
varIndices[i] = dataVars.indexOf(variable);
}
return dataSet.subsetColumns(varIndices);
}
/**
* Sets the means of variables in the SEM IM based on the given data set.
*/
private void setMeans(SemIm semIm, DataSet dataSet) {
if (dataSet != null) {
int numColumns = dataSet.getNumColumns();
for (int j = 0; j < numColumns; j++) {
double[] column = dataSet.getDoubleData().getColumn(j).toArray();
double mean = StatUtils.mean(column);
Node node = dataSet.getVariable(j);
Node variableNode = semIm.getVariableNode(node.getName());
semIm.setMean(variableNode, mean);
double standardDeviation = StatUtils.sd(column);
semIm.setMeanStandardDeviation(variableNode, standardDeviation);
}
} else if (getCovMatrix() != null) {
List variables = getCovMatrix().getVariables();
for (Node node : variables) {
Node variableNode = semIm.getVariableNode(node.getName());
semIm.setMean(variableNode, 0.0);
}
}
}
/**
* Adds semantic checks to the default deserialization method. This method must have the standard signature for a
* readObject method, and the body of the method must begin with "s.defaultReadObject();". Other than that, any
* semantic checks can be specified and do not need to stay the same from version to version. A readObject method of
* this form may be added to any class, even if Tetrad sessions were previously saved out using a version of the
* class that didn't include it. (That's what the "s.defaultReadObject();" is for. See J. Bloch, Effective Java, for
* help.
*/
private void readObject(ObjectInputStream
s)
throws IOException, ClassNotFoundException {
s.defaultReadObject();
if (getCovMatrix() == null) {
throw new NullPointerException();
}
if (getSemPm() == null) {
throw new NullPointerException();
}
}
private ScoreType getScoreType() {
return this.scoreType;
}
public void setScoreType(ScoreType scoreType) {
this.scoreType = scoreType;
}
public void setNumRestarts(int numRestarts) {
this.numRestarts = numRestarts;
}
}
