Examples with BayesianSkyline beast.evolution.tree.coalescent.BayesianSkyline used on opensource projects

Example 1 with BayesianSkyline

use of beast.evolution.tree.coalescent.BayesianSkyline in project beast2 by CompEvol.

the class BayesianSkylineTest method testSkyline.

@Test
public void testSkyline() throws Exception {
    // RealParameter popSize = new RealParameter("1.0", 0.0, 10.0, 2);
    // IntegerParameter groupSize = new IntegerParameter("2", 1, 4, 2);
    // popSize.setValue(1, 2.0);
    Tree tree = new Tree("(((1:1,2:1):2.5,(3:1.5,4:1.5):2):2,5:5.5);");
    TreeIntervals intervals = new TreeIntervals(tree);
    BayesianSkyline skyline = new BayesianSkyline();
    // skyline.init(popSize, groupSize, intervals);
    skyline.initByName("popSizes", "1.0 2.0", "groupSizes", "2 2", "treeIntervals", intervals);
    assertEquals(skyline.getPopSize(0.01), 1.0);
    assertEquals(skyline.getPopSize(1.49), 1.0);
    assertEquals(skyline.getPopSize(1.51), 2.0);
    assertEquals(skyline.getPopSize(5.51), 2.0);
}