Make origin input not required. Closes #2.

CompEvol · Nov 4, 2016 · 6aae2ba · 6aae2ba
1 parent ac90c16
commit 6aae2ba
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/src/beast/evolution/speciation/SABirthDeathModel.java b/src/beast/evolution/speciation/SABirthDeathModel.java
@@ -38,7 +38,7 @@ public class SABirthDeathModel extends SpeciesTreeDistribution {
 
     //'direct' parameters
     public Input<RealParameter> originInput =
-            new Input<RealParameter>("origin", "The time when the process started", Input.Validate.REQUIRED);
+            new Input<RealParameter>("origin", "The time when the process started", (RealParameter)null);
     public Input<RealParameter> birthRateInput =
             new Input<RealParameter>("birthRate", "Birth rate", Input.Validate.REQUIRED);
     public Input<RealParameter> deathRateInput =
@@ -291,6 +291,10 @@ public double calculateTreeLogLikelihood(TreeInterface tree)
         if (lambdaExceedsMu && lambda <= mu) {
             return Double.NEGATIVE_INFINITY;
         }
+
+        if (lambda < 0 || mu < 0 || psi < 0) {
+            return Double.NEGATIVE_INFINITY;
+        }
         //double x0 = tree.getRoot().getHeight() + origToRootDistance;
         double x0 = origin;
         double x1=tree.getRoot().getHeight();