/**
* 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);
}
}
/**
* Constructs a test using the given covariance matrix. Fourth moment statistics are not
* caculated; it is assumed that the data are distributed as multivariate Gaussian.
*/
public DeltaSextadTest(ICovarianceMatrix cov) {
if (cov == null) {
throw new NullPointerException();
}
this.cov = cov;
this.N = cov.getSampleSize();
this.numVars = cov.getVariables().size();
this.variables = cov.getVariables();
this.variablesHash = new HashMap<Node, Integer>();
for (int i = 0; i < variables.size(); i++) {
variablesHash.put(variables.get(i), i);
}
}
public FindOneFactorClustersWithCausalIndicators(
ICovarianceMatrix cov, TestType testType, double alpha) {
this.variables = cov.getVariables();
this.test = new ContinuousTetradTest(cov, testType, alpha);
this.indTest = new IndTestFisherZ(cov, alpha);
this.alpha = alpha;
this.testType = testType;
deltaTest = new DeltaTetradTest(cov);
this.dataModel = cov;
this.cov = cov;
}
/**
* If using a covariance matrix or a correlation matrix, just returns the lookups. Otherwise
* calculates the covariance.
*/
private double r(Node _node1, Node _node2) {
int i = variablesHash.get(_node1);
int j = variablesHash.get(_node2);
if (cov != null) {
return cov.getValue(i, j);
} else {
double[] arr1 = data[i];
double[] arr2 = data[j];
return sxy(arr1, arr2, arr1.length);
}
}
// Prints a smallest subset of parents that causes a singular matrix exception.
private void printMinimalLinearlyDependentSet(int[] parents, ICovarianceMatrix cov) {
List<Node> _parents = new ArrayList<>();
for (int p : parents) _parents.add(variables.get(p));
DepthChoiceGenerator gen = new DepthChoiceGenerator(_parents.size(), _parents.size());
int[] choice;
while ((choice = gen.next()) != null) {
int[] sel = new int[choice.length];
List<Node> _sel = new ArrayList<>();
for (int m = 0; m < choice.length; m++) {
sel[m] = parents[m];
_sel.add(variables.get(sel[m]));
}
TetradMatrix m = cov.getSelection(sel, sel);
try {
m.inverse();
} catch (Exception e2) {
out.println("### Linear dependence among variables: " + _sel);
}
}
}
private void setCovMatrix(ICovarianceMatrix covarianceMatrix) {
this.covariances = covarianceMatrix;
this.variables = covarianceMatrix.getVariables();
this.sampleSize = covarianceMatrix.getSampleSize();
}
private TetradVector getSelection2(ICovarianceMatrix cov, int[] rows, int k) {
return cov.getSelection(rows, new int[] {k}).getColumn(0);
}
private TetradMatrix getSelection1(ICovarianceMatrix cov, int[] rows) {
return cov.getSelection(rows, rows);
}