MeanOfParametricDistributionTest.java

package test.beast.math.distributions;



import org.junit.Test;

import beast.core.BEASTInterface;
import beast.math.distributions.Exponential;
import beast.math.distributions.Gamma;
import beast.math.distributions.LogNormalDistributionModel;
import beast.math.distributions.Normal;
import beast.math.distributions.Uniform;
import beast.util.XMLParser;
import junit.framework.TestCase;

public class MeanOfParametricDistributionTest extends TestCase {

	@Test
    public void testMeanOfNormal() throws Exception {
		Normal normal = new Normal();
		normal.initByName("mean","123.0","sigma","3.0");
		double mean = normal.getMean();
        assertEquals(mean, 123, 1e-10);

        normal = new Normal();
		normal.initByName("mean","123.0","sigma","30.0");
		mean = normal.getMean();
        assertEquals(mean, 123, 1e-10);

        normal = new Normal();
		normal.initByName("mean","123.0","sigma","3.0","offset","3.0");
		mean = normal.getMean();
        assertEquals(mean, 126, 1e-10);
	}

	@Test
    public void testMeanOfGamma() throws Exception {
		Gamma gamma = new Gamma();
		gamma.initByName("alpha", "100", "beta", "10");
		double mean = gamma.getMean();
        assertEquals(mean, 1000, 1e-10);

        gamma = new Gamma();
		gamma.initByName("alpha", "100", "beta", "100");
		mean = gamma.getMean();
        assertEquals(mean, 10000, 1e-10);

        gamma = new Gamma();
		gamma.initByName("alpha", "100", "beta", "10", "offset", "3");
		mean = gamma.getMean();
        assertEquals(mean, 1003, 1e-10);
	}


	@Test
    public void testMeanOfExponential() throws Exception {
		Exponential exp = new Exponential();
		exp.initByName("mean", "10");
		double mean = exp.getMean();
        assertEquals(mean, 10, 1e-10);

        exp = new Exponential();
		exp.initByName("mean", "1");
		mean = exp.getMean();
        assertEquals(mean, 1, 1e-10);

        exp = new Exponential();
		exp.initByName("mean", "1", "offset", "3");
		mean = exp.getMean();
        assertEquals(mean, 4, 1e-10);
	}

	@Test
    public void testMeanOfLogNormal() throws Exception {
		LogNormalDistributionModel exp = new LogNormalDistributionModel();
		exp.initByName("M", "10" , "S", "1", "meanInRealSpace", true);
		double mean = exp.getMean();
        assertEquals(mean, 10, 1e-10);

        exp = new LogNormalDistributionModel();
		exp.initByName("M", "1", "S", "1", "meanInRealSpace", true);
		mean = exp.getMean();
        assertEquals(mean, 1, 1e-10);

        exp = new LogNormalDistributionModel();
		exp.initByName("M", "1", "S", "1", "meanInRealSpace", true, "offset", "3");
		mean = exp.getMean();
        assertEquals(mean, 4, 1e-10);

        try {
            exp = new LogNormalDistributionModel();
    		exp.initByName("M", "1", "S", "1", "meanInRealSpace", false, "offset", "3");
    		mean = exp.getMean();
            assertEquals(mean, 4.4816890703380645, 1e-10);
        } catch (RuntimeException e) {
        	// we are fine here
        }
	}
	
	@Test
	public void testMeanOfUniform() throws Exception {
        Uniform dist = (Uniform) fromXML("<input spec='beast.math.distributions.Uniform' lower='0' upper='1.0' offset='0'/>");
        assertEquals(0.5, dist.getMean(), 1e-10);
        
        dist = (Uniform) fromXML("<input spec='beast.math.distributions.Uniform'/>");
        assertEquals(0.5, dist.getMean(), 1e-10);

        dist = (Uniform) fromXML("<input spec='beast.math.distributions.Uniform' lower='0' upper='1.0' offset='10'/>");
        assertEquals(10.5, dist.getMean(), 1e-10);

        dist = (Uniform) fromXML("<input spec='beast.math.distributions.Uniform' upper='Infinity'/>");
        assertEquals(Double.NaN, dist.getMean(), 1e-10);

        dist = (Uniform) fromXML("<input spec='beast.math.distributions.Uniform' lower='-Infinity' offset='10'/>");
        assertEquals(Double.NaN, dist.getMean(), 1e-10);

        dist = (Uniform) fromXML("<input spec='beast.math.distributions.Uniform' lower='-10' upper='10.0' offset='10'/>");
        assertEquals(10, dist.getMean(), 1e-10);
        
        dist = new Uniform();
        dist.initByName("lower", "-1.0", "upper", "0.0");
        assertEquals(-0.5, dist.getMean(), 1e-10);
        
	}
	
	BEASTInterface fromXML(String xml) throws Exception {
		return (new XMLParser()).parseBareFragment(xml, true);
	}

}