begin template for marginal likelihood

src/dr/app/beast/development_parsers.properties

@@ -434,4 +434,7 @@ dr.inferencexml.distribution.WeightsParser
 
 # Tip state integration
 dr.evomodelxml.tipstatesmodel.TimeVaryingFrequenciesModelParser
-dr.evomodelxml.operators.TipStateOperatorParser
+dr.evomodelxml.operators.TipStateOperatorParser
+
+# Marginal likelihoods
+dr.evomodel.treedatalikelihood.ApproximateTreeDataLikelihood

src/dr/evomodel/treedatalikelihood/ApproximateTreeDataLikelihood.java

@@ -0,0 +1,128 @@
+/*
+ * TreeDataLikelihood.java
+ *
+ * Copyright © 2002-2024 the BEAST Development Team
+ * http://beast.community/about
+ *
+ * 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;
+
+import dr.evomodel.treedatalikelihood.discrete.MaximizerWrtParameter;
+import dr.inference.hmc.GradientWrtParameterProvider;
+import dr.inference.model.Likelihood;
+import dr.inference.model.Parameter;
+import dr.util.Transform;
+import dr.xml.*;
+import dr.math.NumericalDerivative;
+
+/**
+ *  @author Alexander Fisher
+ */
+
+public class ApproximateTreeDataLikelihood {
+    private double marginalLikelihood;
+    private double[] parameterMAP;
+    private MaximizerWrtParameter maximizer;
+    private double[] numericalHessian;
+    private Parameter parameter;
+
+
+    // begin parser stuff
+    public static final String APPROXIMATE_LIKELIHOOD = "approximateTreeDataLikelihood";
+    // end parser stuff
+public ApproximateTreeDataLikelihood(MaximizerWrtParameter maximizer) {
+
+    this.maximizer = maximizer;
+    this.parameter = maximizer.getGradient().getParameter();
+    this.numericalHessian = new double[parameter.getDimension()];
+    // todo: get Numerical Hessian.
+//    NumericalDerivative.getNumericalHessian();
+        updateParameterMAP();
+        updateMarginalLikelihood();
+
+    }
+
+    private void updateMarginalLikelihood() {
+     double diagonalDeterminant = 1;
+             for(int i = 0; i < parameter.getDimension(); i++) {
+                 diagonalDeterminant *= numericalHessian[i];
+             }
+        // 2pi^{-k/2} * det(Sigma)^{-1/2} * likelihood(map) * prior(map)
+        // todo: eval posterior(map)
+        // todo: log likelihood
+      this.marginalLikelihood = 2 / (Math.pow(Math.PI, -1 * parameter.getDimension() / 2) * Math.sqrt(diagonalDeterminant));
+    }
+
+    private void updateParameterMAP() {
+        this.parameterMAP = maximizer.getMinimumPoint(true);
+    }
+
+    public double getMarginalLikelihood() {
+        return marginalLikelihood;
+    }
+    public double[] getParameterMAP() {
+        return parameterMAP;
+    }
+
+    // **************************************************************
+    // XMLObjectParser
+    // **************************************************************
+
+    public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
+
+        public String getParserName() {
+            return APPROXIMATE_LIKELIHOOD;
+        }
+
+        public Object parseXMLObject(XMLObject xo) throws XMLParseException {
+
+            MaximizerWrtParameter maximizer =
+                    (MaximizerWrtParameter) xo.getChild(MaximizerWrtParameter.class);
+
+            return new ApproximateTreeDataLikelihood(maximizer);
+        }
+
+        //************************************************************************
+        // AbstractXMLObjectParser implementation
+        //************************************************************************
+
+        public XMLSyntaxRule[] getSyntaxRules() {
+            return rules;
+        }
+
+        @Override
+        public String getParserDescription() {
+            return "Approximates the marginal likelihood of the data given the tree using Laplace approximation";
+        }
+
+        @SuppressWarnings("rawtypes")
+        @Override
+        public Class getReturnType() {
+            return ApproximateTreeDataLikelihood.class;
+        }
+
+        private final XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
+                new ElementRule(MaximizerWrtParameter.class)
+        };
+    };
+}