Examples with SemGraph edu.cmu.tetrad.graph.SemGraph used on opensource projects

Example 6 with SemGraph

use of edu.cmu.tetrad.graph.SemGraph in project tetrad by cmu-phil.

the class DiscreteTetradTest method piHat2.

/**
 * For two factor models.
 */
private double piHat2(int[] indices, int[] v, SemIm semIm) {
    SemGraph graph = semIm.getSemPm().getGraph();
    graph.setShowErrorTerms(true);
    Node etaNode1 = graph.getNode("eta1");
    double varEta1 = semIm.getParamValue(etaNode1, etaNode1);
    double stdEta1 = Math.sqrt(semIm.getParamValue(etaNode1, etaNode1));
    Node etaNode2 = graph.getNode("eta2");
    double coeffEta = semIm.getParamValue(etaNode1, etaNode2);
    Node errorEta2;
    if (graph.getParents(etaNode2).get(0) == etaNode1) {
        errorEta2 = graph.getParents(etaNode2).get(1);
    } else {
        errorEta2 = graph.getParents(etaNode2).get(0);
    }
    double varEta2 = coeffEta * coeffEta * varEta1 + semIm.getParamValue(errorEta2, errorEta2);
    double stdEtaError2 = Math.sqrt(semIm.getParamValue(errorEta2, errorEta2));
    double[] stdE = new double[indices.length];
    double[] varEta = new double[indices.length];
    double[] stdU = new double[indices.length];
    double[] coeff = new double[indices.length];
    for (int i = 0; i < indices.length; i++) {
        Node uNode = graph.getNode("xi" + i);
        Node uParent = null, uError = null;
        for (Node node : graph.getParents(uNode)) {
            Node parent = node;
            if (parent.getNodeType() == NodeType.LATENT) {
                uParent = parent;
            } else {
                uError = parent;
            }
        }
        if (i == 0 || (i == 2 && indices.length == 4) || (i == 3 && indices.length > 4)) {
            coeff[i] = 1.;
        } else {
            coeff[i] = semIm.getParamValue(uParent, uNode);
        }
        if (uParent == etaNode1) {
            varEta[i] = varEta1;
        } else {
            varEta[i] = varEta2;
        }
        stdE[i] = Math.sqrt(semIm.getParamValue(uError, uError));
        stdU[i] = Math.sqrt(coeff[i] * coeff[i] * varEta[i] + semIm.getParamValue(uError, uError));
    }
    double l = 0.;
    for (int t1 = 0; t1 < GHY.length; t1++) {
        for (int t2 = 0; t2 < GHY.length; t2++) {
            double tValue = GHW[t1] * GHW[t2];
            double eta1 = GHY[t1] * stdEta1;
            double eta2 = eta1 * coeffEta + GHY[t2] * stdEtaError2;
            for (int i = 0; i < indices.length; i++) {
                double eta;
                if (indices.length == 4) {
                    if (i < 2) {
                        eta = eta1;
                    } else {
                        eta = eta2;
                    }
                } else {
                    if (i < 3) {
                        eta = eta1;
                    } else {
                        eta = eta2;
                    }
                }
                int numValues = this.values[indices[i]].length;
                if (v[i] == 0) {
                    tValue *= ProbUtils.normalCdf((this.thresholds[indices[i]][0] * stdU[i] - coeff[i] * eta) / stdE[i]);
                } else if (v[i] == numValues - 1) {
                    tValue *= (1. - ProbUtils.normalCdf((this.thresholds[indices[i]][numValues - 2] * stdU[i] - coeff[i] * eta) / stdE[i]));
                } else {
                    tValue *= ProbUtils.normalCdf((this.thresholds[indices[i]][v[i]] * stdU[i] - coeff[i] * eta) / stdE[i]) - ProbUtils.normalCdf((this.thresholds[indices[i]][v[i] - 1] * stdU[i] - coeff[i] * eta) / stdE[i]);
                }
            }
            l += tValue;
        }
    }
    return l;
}

Example 7 with SemGraph

use of edu.cmu.tetrad.graph.SemGraph in project tetrad by cmu-phil.

the class StandardizedSemImImpliedMatricesPanel method layoutByKnowledge.

/**
 * Lays the workbench graph out using knowledge tiers.
 */
public void layoutByKnowledge() {
    SemGraph _graph = (SemGraph) standardizedSemImGraphicalEditor.getWorkbench().getGraph();
    _graph.setShowErrorTerms(false);
    standardizedSemImGraphicalEditor.getWorkbench().layoutByKnowledge();
    _graph.resetErrorPositions();
    standardizedSemImGraphicalEditor.getWorkbench().setGraph(_graph);
    errorTerms.setText("Show Error Terms");
}

Example 8 with SemGraph

use of edu.cmu.tetrad.graph.SemGraph in project tetrad by cmu-phil.

the class StandardizedSemImImpliedMatricesPanel method layoutByGraph.

/**
 * Lays out the graph in the workbench.
 * @param graph The graph whose layout is to be mimicked.
 */
public void layoutByGraph(Graph graph) {
    SemGraph _graph = (SemGraph) standardizedSemImGraphicalEditor.getWorkbench().getGraph();
    _graph.setShowErrorTerms(false);
    standardizedSemImGraphicalEditor.getWorkbench().layoutByGraph(graph);
    _graph.resetErrorPositions();
    // standardizedSemImGraphicalEditor.getWorkbench().setGraph(_graph);
    errorTerms.setText("Show Error Terms");
}

Example 9 with SemGraph

use of edu.cmu.tetrad.graph.SemGraph in project tetrad by cmu-phil.

the class SemUpdater method createManipulatedGraph.

/**
 * Alters the graph by removing edges from parents to manipulated variables.
 */
private SemGraph createManipulatedGraph(Graph graph) {
    SemGraph updatedGraph = new SemGraph(graph);
    for (int i = 0; i < evidence.getNumNodes(); ++i) {
        if (evidence.isManipulated(i)) {
            Node node = evidence.getNode(i);
            List<Node> parents = updatedGraph.getParents(node);
            for (Node parent : parents) {
                if (parent.getNodeType() == NodeType.ERROR) {
                    continue;
                }
                updatedGraph.removeEdge(node, parent);
            }
        }
    }
    return updatedGraph;
}

Example 10 with SemGraph

use of edu.cmu.tetrad.graph.SemGraph in project tetrad by cmu-phil.

the class SemUpdater method getManipulatedSemIm.

public SemIm getManipulatedSemIm() {
    SemGraph graph = getSemIm().getSemPm().getGraph();
    SemGraph manipulatedGraph = createManipulatedGraph(graph);
    return SemIm.retainValues(getSemIm(), manipulatedGraph);
}