Merged changes in BetaApproximationLikelihood.java

BEAST2-Dev · May 12, 2015 · 8ab4d5d · 8ab4d5d
2 parents 56ecc28 + 9985244
commit 8ab4d5d
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Showing 2 changed files with 13 additions and 1 deletion.
diff --git a/src/snap/Data.java b/src/snap/Data.java
@@ -510,7 +510,7 @@ public double getProportionZeros() {
     		int w = getPatternWeight(i);
     		for (int j = 0; j < p.length; j++) {
     			oneCount += w * p[j];
-    			zeroCount += w * (n[j] - p[j]);
+    			zeroCount += w * (n[j] - 1 - p[j]);
     		}
     	}
     	return (double) zeroCount / ((double) zeroCount + oneCount);

diff --git a/src/snap/likelihood/BetaApproximationLikelihood.java b/src/snap/likelihood/BetaApproximationLikelihood.java
@@ -22,7 +22,11 @@ public class BetaApproximationLikelihood extends GenericTreeLikelihood {
 
 
 	Tree tree;
+<<<<<<< HEAD
 	Double rootAlpha; //Parameter for root distribution. 
+=======
+	Double rootTheta; //Parameter for root distribution. 
+>>>>>>> 998524460c43138ca5124e4ba57b30d99803bf95
 	Data data;	
 
 	int nPoints;    //Size of mesh used in integration
@@ -62,6 +66,10 @@ public void initAndValidate() throws Exception {
         nPoints = 20; //TODO: read this from the xml
         int nNodes = tree.getNodeCount();
         partialIntegral = new double[nPoints][nNodes];
+<<<<<<< HEAD
+=======
+        rootTheta = 0.5; //We should get this from the PARAMETERS.
+>>>>>>> 998524460c43138ca5124e4ba57b30d99803bf95
 
         hasDirt = Tree.IS_FILTHY;
 	}
@@ -231,7 +239,11 @@ private double transProb(double x,double y, double t) {
 	}
 
 	private double rootProb(double x) {
+<<<<<<< HEAD
 		return betaDensity(x,rootAlpha,rootAlpha);
+=======
+		return betaDensity(x,rootTheta,rootTheta);
+>>>>>>> 998524460c43138ca5124e4ba57b30d99803bf95
 	}