<commit_before>package beast.evolution.speciation;


import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import org.apache.commons.math.MathException;

import beast.core.Description;
import beast.core.Distribution;
import beast.core.Input;
import beast.core.Input.Validate;
import beast.core.parameter.RealParameter;
import beast.core.util.CompoundDistribution;
import beast.core.util.Log;
import beast.evolution.alignment.TaxonSet;
import beast.evolution.tree.Node;
import beast.evolution.tree.Tree;
import beast.evolution.tree.TreeInterface;
import beast.math.distributions.MRCAPrior;
import beast.math.statistic.RPNcalculator;

/**
* @author <NAME>
 */


@Description("Birth-Death prior with calibrated monophyletic clades. With this prior, " +
        "the marginal distribution of the" +
        " calibrated nodes (the root age of the clade) is identical to the specified calibration, " +
        "and the density ratio between trees with equal calibration values is equal to the ratio under the " +
        "Birth-Death prior.")
//@Citation(value = "<NAME>, Drummond AJ. Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time " +
//        "Estimation. " +
//        "Syst Biol (2012) 61 (1): 138-149.", DOI = "10.1093/sysbio/syr087")
public class CalibratedBirthDeathModel extends SpeciesTreeDistribution {

    static enum Type {
        NONE("none"),
        OVER_ALL_TOPOS("full"),
        OVER_RANKED_COUNTS("restricted");

        Type(final String name) {<commit_msg>re-added citation annotation.<commit_after>package beast.evolution.speciation;


import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

import beast.core.Citation;
import org.apache.commons.math.MathException;

import beast.core.Description;
import beast.core.Distribution;
import beast.core.Input;
import beast.core.Input.Validate;
import beast.core.parameter.RealParameter;
import beast.core.util.CompoundDistribution;
import beast.core.util.Log;
import beast.evolution.alignment.TaxonSet;
import beast.evolution.tree.Node;
import beast.evolution.tree.Tree;
import beast.evolution.tree.TreeInterface;
import beast.math.distributions.MRCAPrior;
import beast.math.statistic.RPNcalculator;

/**
* @author <NAME>
 */


@Description("Birth-Death prior with calibrated monophyletic clades. With this prior, " +
        "the marginal distribution of the" +
        " calibrated nodes (the root age of the clade) is identical to the specified calibration, " +
        "and the density ratio between trees with equal calibration values is equal to the ratio under the " +
        "Birth-Death prior.")
@Citation(value = "<NAME>, <NAME>. Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time " +
        "Estimation. " +
        "Syst Biol (2012) 61 (1): 138-149.", DOI = "10.1093/sysbio/syr087")
public class CalibratedBirthDeathModel extends SpeciesTreeDistribution {

    static enum Type {
        NONE("none"),
        OVER_ALL_TOPOS("full"),
        OVER_RANKED_COUNTS("restricted");

        Type(final String name) {
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