Added operator for inferring negative diversification rates.

src/bdsky/JointDiversificationTurnoverOperator.java

@@ -0,0 +1,48 @@
+package bdsky;
+
+import beast.core.Description;
+import beast.core.Input;
+import beast.core.Operator;
+import beast.core.parameter.RealParameter;
+import beast.util.Randomizer;
+
+@Description("Operator necessary for inferring negative diversification rates.")
+public class JointDiversificationTurnoverOperator extends Operator {
+
+    public Input<RealParameter> divRateInput = new Input<>("netDiversification",
+            "Net diversification rate parameter.", Input.Validate.REQUIRED);
+
+    public Input<RealParameter> turnOverInput = new Input<>("turnOver",
+            "Turnover parameter.", Input.Validate.REQUIRED);
+
+    RealParameter divRate, turnOver;
+
+    @Override
+    public void initAndValidate() {
+        divRate = divRateInput.get();
+        turnOver = turnOverInput.get();
+
+        if (divRate.getDimension() != turnOver.getDimension())
+            throw new IllegalArgumentException("JointDiversificationTurnoverOperator " +
+                    "requires that the dimension of diversification rate and " +
+                    "turnover are identical.");
+    }
+
+    @Override
+    public double proposal() {
+
+        int idx = Randomizer.nextInt(divRate.getDimension());
+
+        double newDiv = -divRate.getValue(idx);
+        double newTurnOver = 1.0/turnOver.getValue(idx);
+
+        if (newDiv < divRate.getLower() || newDiv > divRate.getUpper()
+                || newTurnOver < turnOver.getLower() || newTurnOver > turnOver.getUpper())
+            return Double.NEGATIVE_INFINITY;
+
+        divRate.setValue(idx, newDiv);
+        turnOver.setValue(idx, newTurnOver);
+
+        return 2*Math.log(newTurnOver);
+    }
+}