[beast-mcmc] r6746 committed - Working towards the correct hastings ratio...

[beast...@googlecode.com]

Revision: 6746
Author: rambaut
Date: Thu Apr 23 16:26:49 2015 UTC
Log: Working towards the correct hastings ratio...
https://code.google.com/p/beast-mcmc/source/detail?r=6746

Modified:
/trunk/src/dr/evomodel/operators/SubtreeJumpOperator.java

=======================================
--- /trunk/src/dr/evomodel/operators/SubtreeJumpOperator.java Thu Apr 23
15:57:29 2015 UTC
+++ /trunk/src/dr/evomodel/operators/SubtreeJumpOperator.java Thu Apr 23
16:26:49 2015 UTC
@@ -90,15 +90,15 @@
final double height = tree.getNodeHeight(iP);

// get a list of all edges that intersect this height
- final List<NodeRef> destinations = getIntersectingEdges(tree,
height);
+ final List<NodeRef> destinations = getIntersectingEdges(tree, i,
height);

if (destinations.size() < 1) {
throw new OperatorFailedException("no destinations to jump
to");
}

- double[] weights = getDestinationWeights(tree, iP, height,
destinations);
+ double[] weights = getDestinationWeights(tree, i, height,
destinations);

- // remove the target node and its sibling (shouldn't be there
because their parent's height is exactly equal to the target height).
+ // remove the target node and its sibling (shouldn't be there
because their parent's height is exactly equal to the target height).
destinations.remove(i);
destinations.remove(CiP);

@@ -124,6 +124,8 @@

tree.endTreeEdit();

+ double[] reverseWeights = getDestinationWeights(tree, j, height,
destinations);
+
logq = 0.0;

return logq;
@@ -143,14 +145,21 @@
return MathUtils.randomChoicePDF(weights);
}

- private List<NodeRef> getIntersectingEdges(Tree tree, double height) {
+ /**
+ * Gets a list of edges that subtend the given height, excluding the
original node
+ * @param tree
+ * @param node0
+ * @param height
+ * @return
+ */
+ private List<NodeRef> getIntersectingEdges(Tree tree, NodeRef node0,
double height) {

List<NodeRef> intersectingEdges = new ArrayList<NodeRef>();

for (int i = 0; i < tree.getNodeCount(); i++) {
final NodeRef node = tree.getNode(i);
final NodeRef parent = tree.getParent(node);
- if (parent != null && tree.getNodeHeight(node) < height &&
tree.getNodeHeight(parent) > height) {
+ if (node != node0 && parent != null &&
tree.getNodeHeight(node) < height && tree.getNodeHeight(parent) > height) {
intersectingEdges.add(node);
}
}