Examples with CladeNodeModel dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel used on opensource projects

Example 11 with CladeNodeModel

use of dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel in project beast-mcmc by beast-dev.

the class ApproximatePoissonTreeLikelihoodTest method testRootPolytomy.

public void testRootPolytomy() throws IOException, Importer.ImportException, TreeUtils.MissingTaxonException {
    branchRateModel = new StrictClockBranchRates(new Parameter.Default(1.0));
    NewickImporter importer = new NewickImporter("((1:1.0,2:1.0):1.0,3:1.0,4:1.0);");
    NewickImporter importer2 = new NewickImporter("(((1:1.0,2:1.0):1.0,3:1.1):0.1,4:1.0);");
    tree = importer.importTree(null);
    treeModel = new BigFastTreeModel(importer2.importTree(null));
    CladeNodeModel cladeModel = new CladeNodeModel(tree, treeModel);
    BranchLengthProvider constrainedBranchLengthProvider = new ConstrainedTreeBranchLengthProvider(cladeModel);
    approximatePoissonTreeLikelihood = new ApproximatePoissonTreeLikelihood("approximateTreeLikelihood", 1, treeModel, branchRateModel, constrainedBranchLengthProvider);
    approximatePoissonTreeLikelihood.getLogLikelihood();
    expectedLL = 0;
    double[] expectations = { 1d, 1d, 1d, 1.1, 1.1 };
    // time
    double[] mutations = { 1d, 1d, 1d, 1.0, 1 };
    for (int i = 0; i < expectations.length; i++) {
        PoissonDistribution p = new PoissonDistribution(expectations[i]);
        expectedLL += p.logPdf(mutations[i]);
    }
    NodeRef rootNode = treeModel.getRoot();
    NodeRef rootNode1 = treeModel.getNode(5);
    NodeRef tip3 = treeModel.getNode(2);
    CladeRef clade = cladeModel.getClade(rootNode);
    treeModel.beginTreeEdit();
    treeModel.removeChild(rootNode, rootNode1);
    treeModel.setRoot(rootNode1);
    treeModel.removeChild(rootNode1, tip3);
    treeModel.addChild(rootNode, tip3);
    treeModel.addChild(rootNode1, rootNode);
    treeModel.setNodeHeight(rootNode1, treeModel.getNodeHeight(rootNode) + 1);
    treeModel.endTreeEdit();
    // cladeModel.setRootNode(clade,rootNode1);
    double LL = approximatePoissonTreeLikelihood.getLogLikelihood();
    approximatePoissonTreeLikelihood.makeDirty();
    double newLL = approximatePoissonTreeLikelihood.getLogLikelihood();
    assertEquals(LL, newLL, 1E-13);
}

Example 12 with CladeNodeModel

use of dr.evomodel.bigfasttree.constrainedtree.CladeNodeModel in project beast-mcmc by beast-dev.

the class CladeAwareSubtreeLeapTest method testFullOperationsOnBigTree.

public void testFullOperationsOnBigTree() throws TreeUtils.MissingTaxonException, IOException, Importer.ImportException {
    MathUtils.setSeed(301);
    NewickImporter importer = new NewickImporter("(Lishui/LS557/2020:0,((Netherlands/Utrecht_10015/2020:0.00006795400000000001,USA/IL-NM073/2020:0.00006799599999999999):0.000033976,England/LOND-D604F/2020:0.000101963):0.000033968,Guangdong/2020XN4459-P0041/2020:0.000000005,(Portugal/PT0063/2020:0,(Spain/Zaragoza2486/2020:0.000102605,Scotland/CVR746/2020:0.000000005,Spain/COV000882/2020:0.000067956,Colombia/INS-79253/2020:0.000101944,Uruguay/UY-4/2020:0.000031515):0.000033979,(Spain/CastillaLaMancha201329/2020:0.000000005,Netherlands/NoordHolland_10011/2020:0.000033987):0.00006799,England/LIVE-9CE87/2020:0.00013727299999999998,Spain/Granada-COV002916/2020:0.000033979999999999997):0.000033968,((USA/VI-CDC-3705/2020:0.000000005,Australia/VIC229/2020:0,USA/MA-MGH-00063/2020:0,(USA/WA-S41/2020:0.000068895,USA/WA-UW114/2020:0.000067978,USA/WA-UW17/2020:0.000000005,(USA/WA-S582/2020:0,USA/WA-UW-1682/2020:0.000000005,USA/WA-S994/2020:0.000101934):0.000033955,USA/WA-S121/2020:0.000000005,USA/WA-S154/2020:0.000067982,USA/WA-UW37/2020:0,USA/WA-S321/2020:0,USA/WA-S445/2020:0,USA/WA-S512/2020:0,USA/WA-S33/2020:0.000033979,Canada/BC_6981299/2020:0.000033972,USA/WA-UW-1294/2020:0.000033972,USA/WA-UW-2247/2020:0.000033988,Australia/VIC140/2020:0.000033984,USA/WA-UW61/2020:0.000033972,Canada/BC_8606204/2020:0.000166157,(USA/WA-S734/2020:0,USA/WA-S844/2020:0.000033983):0.000067965,(USA/WA-S1191/2020:0.000067947,USA/WA-S951/2020:0.000101914):0.000095803,Australia/NSW99/2020:0.000101953,(USA/WA-S317/2020:0.000000005,USA/WA-S721/2020:0.00003397):0.00010195700000000001,USA/WA-UW139/2020:0.000135916,USA/WA-S572/2020:0.000033979999999999997,USA/WA-S279/2020:0.000033972,USA/WA-UW28/2020:0.000034002,USA/WA-S114/2020:0.000033969,(USA/WA-S852/2020:0.000203899,(USA/WA-S568/2020:0,USA/WA-S791/2020:0.00006794599999999999):0.000033983):0.000101964,USA/WA-S842/2020:0.000067951):0.000033986,Singapore/302/2020:0.000101947):0.00016677,(((USA/IL-NM0112/2020:0.00003397,USA/IL-NM053/2020:0.000034229,USA/IL-NM059/2020:0.000101967):0.00003397,USA/WI-UW-218/2020:0.000033995):0.000030539,(USA/UT-QDX-63/2020:0,USA/CA-QDX-111/2020:0,USA/TX-HMH0427/2020:0.000203861):0.000101955):0.00023787300000000002):0.000033959,(((Scotland/CVR3203/2020:0.000000005,Scotland/CVR2246/2020:0.000000005,Scotland/GCVR-1714B2/2020:0.000033975999999999995,Scotland/CVR3514/2020:0.000068628):0.000067954,Australia/NT08/2020:0.000034000999999999995):0.00003397,Spain/COV001440/2020:0,Spain/Alcaniz2449/2020:0.000068985,Spain/COV001548/2020:0,USA/WI-WSLH-200057/2020:0.000000005,Spain/Valencia6/2020:0.0000343,Spain/Granada-COV002944/2020:0.000000005,Spain/COV001929/2020:0.000000005,Spain/COV002049/2020:0.000000005,(Spain/Valencia59/2020:0,Spain/Valencia306/2020:0.000000005):0.000033996,(Spain/COV001117/2020:0.00010265,Spain/COV002055/2020:0.000000005,England/20126000104/2020:0.00006758400000000001):0.000033997,Spain/COV001576/2020:0.000000005,Chile/Santiago-1/2020:0.000000005,Spain/COV000721/2020:0.000000005,(Spain/COV001575/2020:0,Spain/COV001505/2020:0):0.000067968,Spain/Madrid_H12_28/2020:0.000067957,Spain/COV001568/2020:0.000033975,England/CAMB-83357/2020:0.000068619,(Spain/Almeria-COV002842/2020:0.000000005,Spain/Malaga-COV002841/2020:0.000000005):0.000067851):0.000169854,Spain/Madrid_LP16_6193/2020:0.00006795299999999999,Singapore/51/2020:0.000044697,(Thailand/Nonthaburi_193/2020:0,Thailand/Bangkok_237/2020:0,Thailand/Bangkok_238/2020:0,((Thailand/Bangkok-0034/2020:0.000000005,Thailand/Bangkok_2295/2020:0,Thailand/Bangkok-0065/2020:0.000047826,Thailand/Bangkok-CONI-0147/2020:0.000033997):0.000033983,Thailand/SI202769-NT/2020:0.000203899):0.000101951):0.00006797500000000001,Shenzhen/SZTH-002/2020:0.000033999);");
    NewickImporter constraintsImporter = new NewickImporter("(Lishui/LS557/2020:0,((Netherlands/Utrecht_10015/2020:0.00006795400000000001,USA/IL-NM073/2020:0.00006799599999999999):0.000033976,England/LOND-D604F/2020:0.000101963):0.000033968,Guangdong/2020XN4459-P0041/2020:0.000000005,(Portugal/PT0063/2020:0,(Spain/Zaragoza2486/2020:0.000102605,Scotland/CVR746/2020:0.000000005,Spain/COV000882/2020:0.000067956,Colombia/INS-79253/2020:0.000101944,Uruguay/UY-4/2020:0.000031515):0.000033979,(Spain/CastillaLaMancha201329/2020:0.000000005,Netherlands/NoordHolland_10011/2020:0.000033987):0.00006799,England/LIVE-9CE87/2020:0.00013727299999999998,Spain/Granada-COV002916/2020:0.000033979999999999997):0.000033968,((USA/VI-CDC-3705/2020:0.000000005,Australia/VIC229/2020:0,USA/MA-MGH-00063/2020:0,(USA/WA-S41/2020:0.000068895,USA/WA-UW114/2020:0.000067978,USA/WA-UW17/2020:0.000000005,(USA/WA-S582/2020:0,USA/WA-UW-1682/2020:0.000000005,USA/WA-S994/2020:0.000101934):0.000033955,USA/WA-S121/2020:0.000000005,USA/WA-S154/2020:0.000067982,USA/WA-UW37/2020:0,USA/WA-S321/2020:0,USA/WA-S445/2020:0,USA/WA-S512/2020:0,USA/WA-S33/2020:0.000033979,Canada/BC_6981299/2020:0.000033972,USA/WA-UW-1294/2020:0.000033972,USA/WA-UW-2247/2020:0.000033988,Australia/VIC140/2020:0.000033984,USA/WA-UW61/2020:0.000033972,Canada/BC_8606204/2020:0.000166157,(USA/WA-S734/2020:0,USA/WA-S844/2020:0.000033983):0.000067965,(USA/WA-S1191/2020:0.000067947,USA/WA-S951/2020:0.000101914):0.000095803,Australia/NSW99/2020:0.000101953,(USA/WA-S317/2020:0.000000005,USA/WA-S721/2020:0.00003397):0.00010195700000000001,USA/WA-UW139/2020:0.000135916,USA/WA-S572/2020:0.000033979999999999997,USA/WA-S279/2020:0.000033972,USA/WA-UW28/2020:0.000034002,USA/WA-S114/2020:0.000033969,(USA/WA-S852/2020:0.000203899,(USA/WA-S568/2020:0,USA/WA-S791/2020:0.00006794599999999999):0.000033983):0.000101964,USA/WA-S842/2020:0.000067951):0.000033986,Singapore/302/2020:0.000101947):0.00016677,(((USA/IL-NM0112/2020:0.00003397,USA/IL-NM053/2020:0.000034229,USA/IL-NM059/2020:0.000101967):0.00003397,USA/WI-UW-218/2020:0.000033995):0.000030539,(USA/UT-QDX-63/2020:0,USA/CA-QDX-111/2020:0,USA/TX-HMH0427/2020:0.000203861):0.000101955):0.00023787300000000002):0.000033959,(((Scotland/CVR3203/2020:0.000000005,Scotland/CVR2246/2020:0.000000005,Scotland/GCVR-1714B2/2020:0.000033975999999999995,Scotland/CVR3514/2020:0.000068628):0.000067954,Australia/NT08/2020:0.000034000999999999995):0.00003397,Spain/COV001440/2020:0,Spain/Alcaniz2449/2020:0.000068985,Spain/COV001548/2020:0,USA/WI-WSLH-200057/2020:0.000000005,Spain/Valencia6/2020:0.0000343,Spain/Granada-COV002944/2020:0.000000005,Spain/COV001929/2020:0.000000005,Spain/COV002049/2020:0.000000005,(Spain/Valencia59/2020:0,Spain/Valencia306/2020:0.000000005):0.000033996,(Spain/COV001117/2020:0.00010265,Spain/COV002055/2020:0.000000005,England/20126000104/2020:0.00006758400000000001):0.000033997,Spain/COV001576/2020:0.000000005,Chile/Santiago-1/2020:0.000000005,Spain/COV000721/2020:0.000000005,(Spain/COV001575/2020:0,Spain/COV001505/2020:0):0.000067968,Spain/Madrid_H12_28/2020:0.000067957,Spain/COV001568/2020:0.000033975,England/CAMB-83357/2020:0.000068619,(Spain/Almeria-COV002842/2020:0.000000005,Spain/Malaga-COV002841/2020:0.000000005):0.000067851):0.000169854,Spain/Madrid_LP16_6193/2020:0.00006795299999999999,Singapore/51/2020:0.000044697,(Thailand/Nonthaburi_193/2020:0,Thailand/Bangkok_237/2020:0,Thailand/Bangkok_238/2020:0,((Thailand/Bangkok-0034/2020:0.000000005,Thailand/Bangkok_2295/2020:0,Thailand/Bangkok-0065/2020:0.000047826,Thailand/Bangkok-CONI-0147/2020:0.000033997):0.000033983,Thailand/SI202769-NT/2020:0.000203899):0.000101951):0.00006797500000000001,Shenzhen/SZTH-002/2020:0.000033999);");
    // NewickImporter importer = new NewickImporter("(((0:1.0,(1:1.0,2:1.0)n6:1.0)n7:1.0,3:2.0)n8:1.0,(4:3.0,5:1.0)n9:1.0)n10;");
    // NewickImporter constraintsImporter = new NewickImporter("((0:1.0,1:1.0,2:1.0,3:1.0):1.0,4:1.0,5:0.1);");
    Tree tree = importer.importTree(null);
    Tree constraintsTree = constraintsImporter.importTree(null);
    TreeModel treeModel = new BigFastTreeModel(tree);
    CladeNodeModel cladeNodeModel = new CladeNodeModel(constraintsTree, treeModel);
    ConstraintsTreeLikelihood constraintsTreeLikelihood = new ConstraintsTreeLikelihood("constrainedTreeLikelihood", treeModel, constraintsTree);
    CladeAwareSubtreeLeap cladeAwareSubtreeLeap = new CladeAwareSubtreeLeap(cladeNodeModel, 10);
    boolean cladeMaintained = true;
    boolean noNegBranch = true;
    for (int i = 0; i < 10_000; i++) {
        cladeAwareSubtreeLeap.doOperation();
        // check contraints respected
        if (constraintsTreeLikelihood.getLogLikelihood() == Double.NEGATIVE_INFINITY) {
            cladeMaintained = false;
            break;
        }
        noNodeLeftBehind(treeModel);
        for (int j = 0; j < treeModel.getNodeCount(); j++) {
            if (treeModel.getBranchLength(treeModel.getNode(j)) < 0) {
                noNegBranch = false;
                break;
            }
        }
    }
    System.out.println(treeModel.toString());
    assertTrue(cladeMaintained);
    assertTrue(noNegBranch);
}