public GeneralizedSemPm(SemPm semPm) {
this(semPm.getGraph());
// Write down equations.
try {
List<Node> variableNodes = getVariableNodes();
for (int i = 0; i < variableNodes.size(); i++) {
Node node = variableNodes.get(i);
List<Node> parents = getVariableParents(node);
StringBuilder buf = new StringBuilder();
for (int j = 0; j < parents.size(); j++) {
if (!(variableNodes.contains(parents.get(j)))) {
continue;
}
Node parent = parents.get(j);
Parameter _parameter = semPm.getParameter(parent, node);
String parameter = _parameter.getName();
Set<Node> nodes = new HashSet<>();
nodes.add(node);
referencedParameters.put(parameter, nodes);
buf.append(parameter);
buf.append("*");
buf.append(parents.get(j).getName());
setParameterExpression(parameter, "Split(-1.5, -.5, .5, 1.5)");
setStartsWithParametersTemplate(parameter.substring(0, 1), "Split(-1.5, -.5, .5, 1.5)");
setStartsWithParametersEstimationInitializaationTemplate(
parameter.substring(0, 1), "Split(-1.5, -.5, .5, 1.5)");
if (j < parents.size() - 1) {
buf.append(" + ");
}
}
if (buf.toString().trim().length() != 0) {
buf.append(" + ");
}
buf.append(errorNodes.get(i));
setNodeExpression(node, buf.toString());
}
for (Node node : variableNodes) {
Parameter _parameter = semPm.getParameter(node, node);
String parameter = _parameter.getName();
String distributionFormula = "N(0," + parameter + ")";
setNodeExpression(getErrorNode(node), distributionFormula);
setParameterExpression(parameter, "U(0, 1)");
setStartsWithParametersTemplate(parameter.substring(0, 1), "U(0, 1)");
setStartsWithParametersEstimationInitializaationTemplate(
parameter.substring(0, 1), "U(0, 1)");
}
variableNames = new ArrayList<>();
for (Node _node : variableNodes) variableNames.add(_node.getName());
for (Node _node : errorNodes) variableNames.add(_node.getName());
} catch (ParseException e) {
throw new IllegalStateException("Parse error in constructing initial model.", e);
}
}
/** Constructs a new SemPm from the given SemGraph. */
public GeneralizedSemPm(SemGraph graph) {
if (graph == null) {
throw new NullPointerException("Graph must not be null.");
}
// if (graph.existsDirectedCycle()) {
// throw new IllegalArgumentExcneption("Cycles are not supported.");
// }
// Cannot afford to allow error terms on this graph to be shown or hidden from the outside; must
// make a
// hidden copy of it and make sure error terms are shown.
this.graph = new SemGraph(graph);
this.graph.setShowErrorTerms(true);
for (Edge edge : this.graph.getEdges()) {
if (Edges.isBidirectedEdge(edge)) {
throw new IllegalArgumentException(
"The generalized SEM PM cannot currently deal with bidirected " + "edges. Sorry.");
}
}
this.nodes = Collections.unmodifiableList(this.graph.getNodes());
for (Node node : nodes) {
namesToNodes.put(node.getName(), node);
}
this.variableNodes = new ArrayList<>();
this.measuredNodes = new ArrayList<>();
for (Node variable : this.nodes) {
if (variable.getNodeType() == NodeType.MEASURED
|| variable.getNodeType() == NodeType.LATENT) {
variableNodes.add(variable);
}
if (variable.getNodeType() == NodeType.MEASURED) {
measuredNodes.add(variable);
}
}
this.errorNodes = new ArrayList<>();
for (Node variable : this.variableNodes) {
List<Node> parents = this.graph.getParents(variable);
boolean added = false;
for (Node _node : parents) {
if (_node.getNodeType() == NodeType.ERROR) {
errorNodes.add(_node);
added = true;
break;
}
}
if (!added) {
errorNodes.add(null);
}
}
this.referencedParameters = new HashMap<>();
this.referencedNodes = new HashMap<>();
this.nodeExpressions = new HashMap<>();
this.nodeExpressionStrings = new HashMap<>();
this.parameterExpressions = new HashMap<>();
this.parameterExpressionStrings = new HashMap<>();
this.parameterEstimationInitializationExpressions = new HashMap<>();
this.parameterEstimationInitializationExpressionStrings = new HashMap<>();
this.startsWithParametersTemplates = new HashMap<>();
this.startsWithParametersEstimationInitializationTemplates = new HashMap<>();
this.variableNames = new ArrayList<>();
for (Node _node : variableNodes) variableNames.add(_node.getName());
for (Node _node : errorNodes) variableNames.add(_node.getName());
try {
List<Node> variableNodes = getVariableNodes();
for (Node node : variableNodes) {
if (!this.graph.isParameterizable(node)) continue;
if (nodeExpressions.get(node) != null) {
continue;
}
String variablestemplate = getVariablesTemplate();
String formula =
TemplateExpander.getInstance().expandTemplate(variablestemplate, this, node);
setNodeExpression(node, formula);
Set<String> parameters = getReferencedParameters(node);
String parametersTemplate = getParametersTemplate();
for (String parameter : parameters) {
if (parameterExpressions.get(parameter) == null) {
if (parametersTemplate != null) {
setParameterExpression(parameter, parametersTemplate);
} else if (this.graph.isTimeLagModel()) {
String expressionString = "Split(-0.9, -.1, .1, 0.9)";
setParameterExpression(parameter, expressionString);
setParametersTemplate(expressionString);
} else {
String expressionString = "Split(-1.5, -.5, .5, 1.5)";
setParameterExpression(parameter, expressionString);
setParametersTemplate(expressionString);
}
}
}
for (String parameter : parameters) {
if (parameterEstimationInitializationExpressions.get(parameter) == null) {
if (parametersTemplate != null) {
setParameterEstimationInitializationExpression(parameter, parametersTemplate);
} else if (this.graph.isTimeLagModel()) {
String expressionString = "Split(-0.9, -.1, .1, 0.9)";
setParameterEstimationInitializationExpression(parameter, expressionString);
} else {
String expressionString = "Split(-1.5, -.5, .5, 1.5)";
setParameterEstimationInitializationExpression(parameter, expressionString);
}
}
setStartsWithParametersTemplate("s", "Split(-1.5, -.5, .5, 1.5)");
setStartsWithParametersEstimationInitializaationTemplate(
"s", "Split(-1.5, -.5, .5, 1.5)");
}
}
for (Node node : errorNodes) {
if (node == null) continue;
String template = getErrorsTemplate();
String formula = TemplateExpander.getInstance().expandTemplate(template, this, node);
setNodeExpression(node, formula);
Set<String> parameters = getReferencedParameters(node);
setStartsWithParametersTemplate("s", "U(1, 3)");
setStartsWithParametersEstimationInitializaationTemplate("s", "U(1, 3)");
for (String parameter : parameters) {
setParameterExpression(parameter, "U(1, 3)");
}
}
} catch (ParseException e) {
throw new IllegalStateException("Parse error in constructing initial model.", e);
}
}