a delegate to handle node height gradient and hessian

src/dr/evomodel/treedatalikelihood/discrete/DiscreteTraitBranchRateGradient.java

@@ -85,13 +85,11 @@ public DiscreteTraitBranchRateGradient(String traitName,
         BranchRateModel brm = treeDataLikelihood.getBranchRateModel();
         this.branchRateModel = (brm instanceof DifferentiableBranchRates) ? (DifferentiableBranchRates) brm : null;
 
-        String name = DiscreteTraitBranchRateDelegate.getName(traitName);
+        String name = getTraitName(traitName);
         TreeTrait test = treeDataLikelihood.getTreeTrait(name);
 
         if (test == null) {
-            ProcessSimulationDelegate gradientDelegate = new DiscreteTraitBranchRateDelegate(traitName,
-                    treeDataLikelihood.getTree(),
-                    likelihoodDelegate);
+            ProcessSimulationDelegate gradientDelegate = makeGradientDelegate(traitName, tree, likelihoodDelegate);
             TreeTraitProvider traitProvider = new ProcessSimulation(treeDataLikelihood, gradientDelegate);
             treeDataLikelihood.addTraits(traitProvider.getTreeTraits());
         }
@@ -106,6 +104,16 @@ public DiscreteTraitBranchRateGradient(String traitName,
 //        dim = treeDataLikelihood.getDataLikelihoodDelegate().getTraitDim();
     }
 
+    protected String getTraitName(String traitName) {
+        return DiscreteTraitBranchRateDelegate.getName(null);
+    }
+
+    protected ProcessSimulationDelegate makeGradientDelegate(String traitName, Tree tree, BeagleDataLikelihoodDelegate likelihoodDelegate) {
+        return new DiscreteTraitBranchRateDelegate(traitName,
+                tree,
+                likelihoodDelegate);
+    }
+
     @Override
     public Likelihood getLikelihood() {
         return treeDataLikelihood;

src/dr/evomodel/treedatalikelihood/discrete/DiscreteTraitNodeHeightDelegate.java

@@ -0,0 +1,72 @@
+/*
+ * DiscreteTraitNodeHeightDelegate.java
+ *
+ * Copyright (c) 2002-2017 Alexei Drummond, Andrew Rambaut and Marc Suchard
+ *
+ * This file is part of BEAST.
+ * See the NOTICE file distributed with this work for additional
+ * information regarding copyright ownership and licensing.
+ *
+ * BEAST is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as
+ * published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ *  BEAST is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with BEAST; if not, write to the
+ * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
+ * Boston, MA  02110-1301  USA
+ */
+
+
+package dr.evomodel.treedatalikelihood.discrete;
+
+import beagle.Beagle;
+import dr.evolution.tree.Tree;
+import dr.evomodel.treedatalikelihood.BeagleDataLikelihoodDelegate;
+
+/**
+ * @author Xiang Ji
+ * @author Marc A. Suchard
+ */
+public class DiscreteTraitNodeHeightDelegate extends DiscreteTraitBranchRateDelegate {
+
+    static final String GRADIENT_TRAIT_NAME = "NodeHeightGradient";
+
+    static final String HESSIAN_TRAIT_NAME = "NodeHeightHessian";
+
+    DiscreteTraitNodeHeightDelegate(String name, Tree tree, BeagleDataLikelihoodDelegate likelihoodDelegate) {
+        super(name, tree, likelihoodDelegate);
+    }
+
+
+    protected void getNodeDerivatives(Tree tree, double[] first, double[] second) {
+        super.getNodeDerivatives(tree, first, second);
+        final int internalNodeCount = tree.getInternalNodeCount();
+
+        double[][] prePartials = new double[internalNodeCount][patternCount * stateCount * categoryCount];
+        double[][] postPartials = new double[internalNodeCount][patternCount * stateCount * categoryCount];
+        double[][] transitionMatrices = new double[internalNodeCount][stateCount * stateCount * categoryCount];
+
+        for (int i = 0; i < internalNodeCount; i++) {
+            beagle.getPartials(getPostOrderPartialIndex(i + tree.getExternalNodeCount()), Beagle.NONE, postPartials[i]);
+            beagle.getPartials(getPreOrderPartialIndex(i + tree.getExternalNodeCount()), Beagle.NONE, prePartials[i]);
+            beagle.getTransitionMatrix(evolutionaryProcessDelegate.getMatrixIndex(i + tree.getExternalNodeCount()), transitionMatrices[i]);
+        }
+
+    }
+
+    protected String getGradientTraitName() {
+        return GRADIENT_TRAIT_NAME;
+    }
+
+    protected String getHessianTraitName() {
+        return HESSIAN_TRAIT_NAME;
+    }
+
+}

src/dr/evomodel/treedatalikelihood/discrete/NodeHeightGradientForDiscreteTrait.java

@@ -31,6 +31,7 @@
 import dr.evomodel.tree.TreeParameterModel;
 import dr.evomodel.treedatalikelihood.BeagleDataLikelihoodDelegate;
 import dr.evomodel.treedatalikelihood.TreeDataLikelihood;
+import dr.evomodel.treedatalikelihood.preorder.ProcessSimulationDelegate;
 import dr.inference.hmc.GradientWrtParameterProvider;
 import dr.inference.loggers.Loggable;
 import dr.inference.model.Parameter;
@@ -67,6 +68,15 @@ public NodeHeightGradientForDiscreteTrait(String traitName,
         this.nodeHeightProxyParameter = new NodeHeightProxyParameter("internalNodeHeights", treeModel, true);
     }
 
+    protected String getTraitName(String traitName) {
+        return DiscreteTraitNodeHeightDelegate.GRADIENT_TRAIT_NAME;
+    }
+
+    protected ProcessSimulationDelegate makeGradientDelegate(String traitName, Tree tree, BeagleDataLikelihoodDelegate likelihoodDelegate) {
+        return new DiscreteTraitNodeHeightDelegate(traitName,
+                tree,
+                likelihoodDelegate);
+    }
     @Override
     public Parameter getParameter() {
         return nodeHeightProxyParameter;