/** * Calculates the error variance for the given error node, given all of the coefficient values in * the model. * * @param error An error term in the model--i.e. a variable with NodeType.ERROR. * @return The value of the error variance, or Double.NaN is the value is undefined. */ private double calculateErrorVarianceFromParams(Node error) { error = semGraph.getNode(error.getName()); Node child = semGraph.getChildren(error).get(0); List<Node> parents = semGraph.getParents(child); double otherVariance = 0; for (Node parent : parents) { if (parent == error) continue; double coef = getEdgeCoefficient(parent, child); otherVariance += coef * coef; } if (parents.size() >= 2) { ChoiceGenerator gen = new ChoiceGenerator(parents.size(), 2); int[] indices; while ((indices = gen.next()) != null) { Node node1 = parents.get(indices[0]); Node node2 = parents.get(indices[1]); double coef1, coef2; if (node1.getNodeType() != NodeType.ERROR) { coef1 = getEdgeCoefficient(node1, child); } else { coef1 = 1; } if (node2.getNodeType() != NodeType.ERROR) { coef2 = getEdgeCoefficient(node2, child); } else { coef2 = 1; } List<List<Node>> treks = GraphUtils.treksIncludingBidirected(semGraph, node1, node2); double cov = 0.0; for (List<Node> trek : treks) { double product = 1.0; for (int i = 1; i < trek.size(); i++) { Node _node1 = trek.get(i - 1); Node _node2 = trek.get(i); Edge edge = semGraph.getEdge(_node1, _node2); double factor; if (Edges.isBidirectedEdge(edge)) { factor = edgeParameters.get(edge); } else if (!edgeParameters.containsKey(edge)) { factor = 1; } else if (semGraph.isParentOf(_node1, _node2)) { factor = getEdgeCoefficient(_node1, _node2); } else { factor = getEdgeCoefficient(_node2, _node1); } product *= factor; } cov += product; } otherVariance += 2 * coef1 * coef2 * cov; } } return 1.0 - otherVariance <= 0 ? Double.NaN : 1.0 - otherVariance; }