/**
* Calculates the sample likelihood and BIC score for i given its parents in a simple SEM model.
*/
private double localSemScore(int i, int[] parents) {
try {
ICovarianceMatrix cov = getCovMatrix();
double varianceY = cov.getValue(i, i);
double residualVariance = varianceY;
int n = sampleSize();
int p = parents.length;
int k = (p * (p + 1)) / 2 + p;
// int k = (p + 1) * (p + 1);
// int k = p + 1;
TetradMatrix covxx = cov.getSelection(parents, parents);
TetradMatrix covxxInv = covxx.inverse();
TetradVector covxy = cov.getSelection(parents, new int[] {i}).getColumn(0);
TetradVector b = covxxInv.times(covxy);
residualVariance -= covxy.dotProduct(b);
if (residualVariance <= 0 && verbose) {
out.println(
"Nonpositive residual varianceY: resVar / varianceY = "
+ (residualVariance / varianceY));
return Double.NaN;
}
double c = getPenaltyDiscount();
// return -n * log(residualVariance) - 2 * k; //AIC
return -n * Math.log(residualVariance) - c * k * Math.log(n);
// return -n * log(residualVariance) - c * k * (log(n) - log(2 * PI));
} catch (Exception e) {
e.printStackTrace();
throw new RuntimeException(e);
// throwMinimalLinearDependentSet(parents, cov);
}
}
private double score(Node y, List<Node> parents) {
if (score == Score.andersonDarling) {
return andersonDarlingPASquareStar(y, parents);
} else if (score == Score.kurtosis) {
return Math.abs(StatUtils.kurtosis(residual(y, parents)));
} else if (score == Score.skew) {
return Math.abs(StatUtils.skewness(residual(y, parents)));
} else if (score == Score.fifthMoment) {
return Math.abs(StatUtils.standardizedFifthMoment(residual(y, parents)));
} else if (score == Score.absoluteValue) {
return localScoreA(y, parents);
}
throw new IllegalStateException();
}
public static List<Set<Node>> powerSet(List<Node> nodes) {
List<Set<Node>> subsets = new ArrayList<Set<Node>>();
int total = (int) Math.pow(2, nodes.size());
for (int i = 0; i < total; i++) {
Set<Node> newSet = new HashSet<Node>();
String selection = Integer.toBinaryString(i);
for (int j = selection.length() - 1; j >= 0; j--) {
if (selection.charAt(j) == '1') {
newSet.add(nodes.get(selection.length() - j - 1));
}
}
subsets.add(newSet);
}
return subsets;
}
public static boolean existsLocalSepsetWithoutDet(
Node x, Node y, Node z, IndependenceTest test, Graph graph, int depth) {
Set<Node> __nodes = new HashSet<Node>(graph.getAdjacentNodes(x));
__nodes.addAll(graph.getAdjacentNodes(z));
__nodes.remove(x);
__nodes.remove(z);
List<Node> _nodes = new LinkedList<Node>(__nodes);
TetradLogger.getInstance()
.log("adjacencies", "Adjacents for " + x + "--" + y + "--" + z + " = " + _nodes);
int _depth = depth;
if (_depth == -1) {
_depth = 1000;
}
_depth = Math.min(_depth, _nodes.size());
for (int d = 0; d <= _depth; d++) {
if (_nodes.size() >= d) {
ChoiceGenerator cg2 = new ChoiceGenerator(_nodes.size(), d);
int[] choice;
while ((choice = cg2.next()) != null) {
List<Node> condSet = asList(choice, _nodes);
if (condSet.contains(y)) {
continue;
}
if (test.determines(condSet, y)) {
continue;
}
// LogUtils.getInstance().finest("Trying " + condSet);
if (test.isIndependent(x, z, condSet)) {
return true;
}
}
}
}
return false;
}
public static CpcTripleType getCpcTripleType(
Node x, Node y, Node z, IndependenceTest test, int depth, Graph graph) {
// System.out.println("getCpcTripleType 1");
boolean existsSepsetContainingY = false;
boolean existsSepsetNotContainingY = false;
Set<Node> __nodes = new HashSet<Node>(graph.getAdjacentNodes(x));
__nodes.remove(z);
// System.out.println("getCpcTripleType 2");
List<Node> _nodes = new LinkedList<Node>(__nodes);
TetradLogger.getInstance()
.log("adjacencies", "Adjacents for " + x + "--" + y + "--" + z + " = " + _nodes);
// System.out.println("getCpcTripleType 3");
int _depth = depth;
if (_depth == -1) {
_depth = 1000;
}
_depth = Math.min(_depth, _nodes.size());
// System.out.println("getCpcTripleType 4");
for (int d = 0; d <= _depth; d++) {
// System.out.println("getCpcTripleType 5");
ChoiceGenerator cg = new ChoiceGenerator(_nodes.size(), d);
int[] choice;
while ((choice = cg.next()) != null) {
// System.out.println("getCpcTripleType 6");
List<Node> condSet = GraphUtils.asList(choice, _nodes);
// System.out.println("getCpcTripleType 7");
if (test.isIndependent(x, z, condSet)) {
if (condSet.contains(y)) {
existsSepsetContainingY = true;
} else {
existsSepsetNotContainingY = true;
}
}
}
}
// System.out.println("getCpcTripleType 8");
__nodes = new HashSet<Node>(graph.getAdjacentNodes(z));
__nodes.remove(x);
_nodes = new LinkedList<Node>(__nodes);
TetradLogger.getInstance()
.log("adjacencies", "Adjacents for " + x + "--" + y + "--" + z + " = " + _nodes);
// System.out.println("getCpcTripleType 9");
_depth = depth;
if (_depth == -1) {
_depth = 1000;
}
_depth = Math.min(_depth, _nodes.size());
// System.out.println("getCpcTripleType 10");
for (int d = 0; d <= _depth; d++) {
// System.out.println("getCpcTripleType 11");
ChoiceGenerator cg = new ChoiceGenerator(_nodes.size(), d);
int[] choice;
while ((choice = cg.next()) != null) {
List<Node> condSet = GraphUtils.asList(choice, _nodes);
if (test.isIndependent(x, z, condSet)) {
if (condSet.contains(y)) {
existsSepsetContainingY = true;
} else {
existsSepsetNotContainingY = true;
}
}
}
}
// System.out.println("getCpcTripleType 12");
if (existsSepsetContainingY == existsSepsetNotContainingY) {
return CpcTripleType.AMBIGUOUS;
} else if (!existsSepsetNotContainingY) {
return CpcTripleType.NONCOLLIDER;
} else {
return CpcTripleType.COLLIDER;
}
}
private double localScoreB(Node node, List<Node> parents) {
double score = 0.0;
double maxScore = Double.NEGATIVE_INFINITY;
Node _target = node;
List<Node> _regressors = parents;
Node target = getVariable(variables, _target.getName());
List<Node> regressors = new ArrayList<Node>();
for (Node _regressor : _regressors) {
Node variable = getVariable(variables, _regressor.getName());
regressors.add(variable);
}
DATASET:
for (int m = 0; m < dataSets.size(); m++) {
RegressionResult result = regressions.get(m).regress(target, regressors);
TetradVector residualsSingleDataset = result.getResiduals();
DoubleArrayList _residualsSingleDataset =
new DoubleArrayList(residualsSingleDataset.toArray());
for (int h = 0; h < residualsSingleDataset.size(); h++) {
if (Double.isNaN(residualsSingleDataset.get(h))) {
continue DATASET;
}
}
double mean = Descriptive.mean(_residualsSingleDataset);
double std =
Descriptive.standardDeviation(
Descriptive.variance(
_residualsSingleDataset.size(),
Descriptive.sum(_residualsSingleDataset),
Descriptive.sumOfSquares(_residualsSingleDataset)));
for (int i2 = 0; i2 < _residualsSingleDataset.size(); i2++) {
_residualsSingleDataset.set(i2, (_residualsSingleDataset.get(i2) - mean) / std);
}
double[] _f = new double[_residualsSingleDataset.size()];
for (int k = 0; k < _residualsSingleDataset.size(); k++) {
_f[k] = _residualsSingleDataset.get(k);
}
DoubleArrayList f = new DoubleArrayList(_f);
for (int k = 0; k < f.size(); k++) {
f.set(k, Math.abs(f.get(k)));
}
double _mean = Descriptive.mean(f);
double diff = _mean - Math.sqrt(2.0 / Math.PI);
score += diff * diff;
if (score > maxScore) {
maxScore = score;
}
}
double avg = score / dataSets.size();
return avg;
}
/**
* Constructs a new standardized SEM IM from the freeParameters in the given SEM IM.
*
* @param im Stop asking me for these things! The given SEM IM!!!
* @param initialization CALCULATE_FROM_SEM if the initial values will be calculated from the
* given SEM IM; INITIALIZE_FROM_DATA if data will be simulated from the given SEM,
* standardized, and estimated.
*/
public StandardizedSemIm(SemIm im, Initialization initialization) {
this.semPm = new SemPm(im.getSemPm());
this.semGraph = new SemGraph(semPm.getGraph());
semGraph.setShowErrorTerms(true);
if (semGraph.existsDirectedCycle()) {
throw new IllegalArgumentException("The cyclic case is not handled.");
}
if (initialization == Initialization.CALCULATE_FROM_SEM) {
// This code calculates the new coefficients directly from the old ones.
edgeParameters = new HashMap<Edge, Double>();
List<Node> nodes = im.getVariableNodes();
TetradMatrix impliedCovar = im.getImplCovar(true);
for (Parameter parameter : im.getSemPm().getParameters()) {
if (parameter.getType() == ParamType.COEF) {
Node a = parameter.getNodeA();
Node b = parameter.getNodeB();
int aindex = nodes.indexOf(a);
int bindex = nodes.indexOf(b);
double vara = impliedCovar.get(aindex, aindex);
double stda = Math.sqrt(vara);
double varb = impliedCovar.get(bindex, bindex);
double stdb = Math.sqrt(varb);
double oldCoef = im.getEdgeCoef(a, b);
double newCoef = (stda / stdb) * oldCoef;
edgeParameters.put(Edges.directedEdge(a, b), newCoef);
} else if (parameter.getType() == ParamType.COVAR) {
Node a = parameter.getNodeA();
Node b = parameter.getNodeB();
Node exoa = semGraph.getExogenous(a);
Node exob = semGraph.getExogenous(b);
double covar = im.getErrCovar(a, b) / Math.sqrt(im.getErrVar(a) * im.getErrVar(b));
edgeParameters.put(Edges.bidirectedEdge(exoa, exob), covar);
}
}
} else {
// This code estimates the new coefficients from simulated data from the old model.
DataSet dataSet = im.simulateData(1000, false);
TetradMatrix _dataSet = dataSet.getDoubleData();
_dataSet = DataUtils.standardizeData(_dataSet);
DataSet dataSetStandardized = ColtDataSet.makeData(dataSet.getVariables(), _dataSet);
SemEstimator estimator = new SemEstimator(dataSetStandardized, im.getSemPm());
SemIm imStandardized = estimator.estimate();
edgeParameters = new HashMap<Edge, Double>();
for (Parameter parameter : imStandardized.getSemPm().getParameters()) {
if (parameter.getType() == ParamType.COEF) {
Node a = parameter.getNodeA();
Node b = parameter.getNodeB();
double coef = imStandardized.getEdgeCoef(a, b);
edgeParameters.put(Edges.directedEdge(a, b), coef);
} else if (parameter.getType() == ParamType.COVAR) {
Node a = parameter.getNodeA();
Node b = parameter.getNodeB();
Node exoa = semGraph.getExogenous(a);
Node exob = semGraph.getExogenous(b);
double covar = -im.getErrCovar(a, b) / Math.sqrt(im.getErrVar(a) * im.getErrVar(b));
edgeParameters.put(Edges.bidirectedEdge(exoa, exob), covar);
}
}
}
this.measuredNodes = Collections.unmodifiableList(semPm.getMeasuredNodes());
}