allow for cognate singletons

jordandouglas · Apr 27, 2023 · a0c45b7 · a0c45b7
1 parent 3ad6e4e
commit a0c45b7
Showing 1 changed file with 11 additions and 3 deletions.
diff --git a/src/indeldollo/StochasticDolloTreeLikelihoodFast.java b/src/indeldollo/StochasticDolloTreeLikelihoodFast.java
@@ -184,12 +184,20 @@ public double calculateLogP() {
 		// Mean birth rate (weighted by branch lengths)
         double totalWeightedRate = 0.0;
         double totalTreeLength = 0.0;
-        for (Node node : root.getAllChildNodesAndSelf()) {
-        	double rate = branchRateModel.getRateForBranch(node);
-        	double length = node == root ? (birthTime - node.getHeight()) : node.getLength();
+        if (root.isLeaf()) {
+        	double rate = branchRateModel.getRateForBranch(root);
+        	double length = birthTime - root.getHeight();
             totalWeightedRate += rate * length;
             totalTreeLength += length;
+        }else {
+        	for (Node node : root.getAllChildNodesAndSelf()) {
+            	double rate = branchRateModel.getRateForBranch(node);
+            	double length = node == root ? (birthTime - node.getHeight()) : node.getLength();
+                totalWeightedRate += rate * length;
+                totalTreeLength += length;
+            }
         }
+
         double meanBranchRate = totalWeightedRate/totalTreeLength;
         double meanBirthRate = lambda * mutationRate * meanBranchRate;