beast.evolution.speciation.BirthDeathGernhard08Model.java Source code

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Here is the source code for beast.evolution.speciation.BirthDeathGernhard08Model.java

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/*
 * BirthDeathGernhard08Model.java
 *
 * Copyright (C) 2002-2009 Alexei Drummond and Andrew Rambaut
 *
 * 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 beast.evolution.speciation;

import static org.apache.commons.math.special.Gamma.logGamma;

import java.util.Arrays;

import beast.core.Citation;
import beast.core.Description;
import beast.core.Input;
import beast.core.Input.Validate;
import beast.core.parameter.RealParameter;
import beast.evolution.tree.TreeInterface;

/* Ported from Beast 1.6
 * @author Joseph Heled
 *         Date: 24/02/2008
 */
@Description("Birth Death model based on Gernhard 2008. <br/>"
        + "This derivation conditions directly on fixed N taxa. <br/>"
        + "The inference is directly on b-d (strictly positive) and d/b (constrained in [0,1)) <br/>"
        + "Verified using simulated trees generated by Klass tree sample. (http://www.klaashartmann.com/treesample/) <br/>"
        + "Sampling proportion not verified via simulation. Proportion set by default to 1, an assignment which makes "
        + "the expressions identical to the expressions before the change.")

@Citation(value = "Gernhard 2008. The conditioned reconstructed process. Journal of Theoretical Biology Volume 253, "
        + "Issue 4, 21 August 2008, Pages 769-778", DOI = "doi:10.1016/j.jtbi.2008.04.005", // (http://dx.doi.org/10.1016/j.jtbi.2008.04.005)
        year = 2008, firstAuthorSurname = "gernhard")

public class BirthDeathGernhard08Model extends YuleModel {

    final static String[] TYPES = { "unscaled", "timesonly", "oriented", "labeled" };

    final public Input<String> typeInput = new Input<>("type",
            "tree type, should be one of " + Arrays.toString(TYPES) + " (default unscaled)", "unscaled", TYPES);
    final public Input<RealParameter> relativeDeathRateParameterInput = new Input<>("relativeDeathRate",
            "relative death rate parameter, mu/lambda in birth death model", Validate.REQUIRED);
    final public Input<RealParameter> sampleProbabilityInput = new Input<>("sampleProbability",
            "sample probability, rho in birth/death model");

    @Override
    public void initAndValidate() {
        super.initAndValidate();
        final String typeName = typeInput.get().toLowerCase();
        if (typeName.equals("unscaled")) {
            type = TreeType.UNSCALED;
        } else if (typeName.equals("timesonly")) {
            type = TreeType.TIMESONLY;
        } else if (typeName.equals("oriented")) {
            type = TreeType.ORIENTED;
        } else if (typeName.equals("labeled")) {
            type = TreeType.LABELED;
        } else {
            throw new IllegalArgumentException("type '" + typeName
                    + "' is not recognized. Should be one of unscaled, timesonly, oriented and labeled.");
        }
    }

    @Override
    public double calculateTreeLogLikelihood(final TreeInterface tree) {
        final double a = relativeDeathRateParameterInput.get().getValue();
        final double rho = (sampleProbabilityInput.get() == null ? 1.0 : sampleProbabilityInput.get().getValue());
        return calculateTreeLogLikelihood(tree, rho, a);
    }

    private TreeType type;

    public enum TreeType {
        UNSCALED, // no coefficient 
        TIMESONLY, // n!
        ORIENTED, // n
        LABELED, // 2^(n-1)/(n-1)!
                 // conditional on root: 2^(n-1)/n!(n-1)
                 // conditional on origin: 2^(n-1)/n!
    }

    /**
     * scaling coefficient of tree *
     */
    @Override
    protected double logCoeff(final int taxonCount) {
        switch (type) {
        case UNSCALED:
            break;
        case TIMESONLY:
            return logGamma(taxonCount + 1);
        case ORIENTED:
            return Math.log(taxonCount);
        case LABELED: {
            final double two2nm1 = (taxonCount - 1) * Math.log(2.0);
            if (conditionalOnRoot) {
                return two2nm1 - Math.log(taxonCount - 1) - logGamma(taxonCount + 1);
            } else if (conditionalOnOrigin) {
                return two2nm1 - logGamma(taxonCount + 1);
            } else {
                return two2nm1 - logGamma(taxonCount);
            }
        }
        }
        return 0.0;
    }

    //    @Override
    //    public boolean includeExternalNodesInLikelihoodCalculation() {
    //        return true;
    //    }

    @Override
    protected boolean requiresRecalculation() {
        return super.requiresRecalculation() || relativeDeathRateParameterInput.get().somethingIsDirty()
                || sampleProbabilityInput.get().somethingIsDirty();
    }
} // class BirthDeathGernhard08Model