Examples with RealParameter beast.core.parameter.RealParameter used on opensource projects

Example 26 with RealParameter

use of beast.core.parameter.RealParameter in project beast2 by CompEvol.

the class InputForAnnotatedConstructor method setStringValue.

/**
 * Try to parse value of string into Integer, Double or Boolean,
 * or it this types differs, just assign as string.
 *
 * @param valueString value representation
 * @throws IllegalArgumentException when all conversions fail
 */
@SuppressWarnings({ "unchecked", "rawtypes" })
private void setStringValue(final String valueString) {
    // figure out the type of T and create object based on T=Integer, T=Double, T=Boolean, T=Valuable
    if (value instanceof List<?>) {
        List list = (List) get();
        list.clear();
        // remove start and end spaces
        String valueString2 = valueString.replaceAll("^\\s+", "");
        valueString2 = valueString2.replaceAll("\\s+$", "");
        // split into space-separated bits
        String[] valuesString = valueString2.split("\\s+");
        for (int i = 0; i < valuesString.length; i++) {
            if (theClass.equals(Integer.class)) {
                list.add(new Integer(valuesString[i % valuesString.length]));
            } else if (theClass.equals(Double.class)) {
                list.add(new Double(valuesString[i % valuesString.length]));
            } else if (theClass.equals(Boolean.class)) {
                String str = valuesString[i % valuesString.length].toLowerCase();
                list.add(str.equals("1") || str.equals("true") || str.equals("yes"));
            } else if (theClass.equals(String.class)) {
                list.add(new String(valuesString[i % valuesString.length]));
            }
        }
        return;
    }
    if (theClass.equals(Integer.class)) {
        setValue(new Integer(valueString));
        return;
    }
    if (theClass.equals(Double.class)) {
        setValue(new Double(valueString));
        return;
    }
    if (theClass.equals(Boolean.class)) {
        final String valueString2 = valueString.toLowerCase();
        if (valueString2.equals("yes") || valueString2.equals("true")) {
            setValue(Boolean.TRUE);
            return;
        } else if (valueString2.equals("no") || valueString2.equals("false")) {
            setValue(Boolean.FALSE);
            return;
        }
    }
    if (theClass.equals(Function.class)) {
        final RealParameter param = new RealParameter();
        param.initByName("value", valueString, "upper", 0.0, "lower", 0.0, "dimension", 1);
        param.initAndValidate();
        setValue(param);
        param.getOutputs().add(beastObject);
        return;
    }
    if (theClass.isEnum()) {
        if (possibleValues == null) {
            possibleValues = (T[]) theClass.getDeclaringClass().getEnumConstants();
        }
        for (final T t : possibleValues) {
            if (valueString.equals(t.toString())) {
                setValue(t);
                return;
            }
        }
        throw new IllegalArgumentException("Input 104: value " + valueString + " not found. Select one of " + Arrays.toString(possibleValues));
    }
    // call a string constructor of theClass
    try {
        Constructor ctor;
        Object v = valueString;
        try {
            ctor = theClass.getDeclaredConstructor(String.class);
        } catch (NoSuchMethodException e) {
            // try integer constructor instead
            try {
                if (valueString.startsWith("0x")) {
                    v = Integer.parseInt(valueString.substring(2), 16);
                } else {
                    v = Integer.parseInt(valueString);
                }
                ctor = theClass.getDeclaredConstructor(int.class);
            } catch (NumberFormatException e2) {
                // could not parse as integer, try double instead
                v = Double.parseDouble(valueString);
                ctor = theClass.getDeclaredConstructor(double.class);
            }
        }
        ctor.setAccessible(true);
        final Object o = ctor.newInstance(v);
        setValue(o);
        if (o instanceof BEASTInterface) {
            ((BEASTInterface) o).getOutputs().add(beastObject);
        }
    } catch (Exception e) {
        throw new IllegalArgumentException("Input 103: type mismatch, cannot initialize input '" + getName() + "' with value '" + valueString + "'.\nExpected something of type " + getType().getName() + ". " + (e.getMessage() != null ? e.getMessage() : ""));
    }
}

Example 27 with RealParameter

use of beast.core.parameter.RealParameter in project MultiTypeTree by tgvaughan.

the class SCLikelihoodTest method testCalculateLogP.

/**
 * Test of calculateLogP method, of class StructuredCoalescentLikelihood.
 */
@Test
public void testCalculateLogP() throws Exception {
    System.out.println("SCLikelihoodTest");
    // Assemble test MultiTypeTree:
    String newickStr = "(((A[&state=1]:0.25)[&state=0]:0.25,B[&state=0]:0.5)[&state=0]:1.5," + "(C[&state=0]:1.0,D[&state=0]:1.0)[&state=0]:1.0)[&state=0]:0.0;";
    MultiTypeTreeFromNewick mtTree = new MultiTypeTreeFromNewick();
    mtTree.initByName("value", newickStr, "typeLabel", "state");
    // Assemble migration model:
    RealParameter rateMatrix = new RealParameter();
    rateMatrix.initByName("value", "2.0 1.0");
    RealParameter popSizes = new RealParameter();
    popSizes.initByName("value", "5.0 10.0");
    SCMigrationModel migrationModel = new SCMigrationModel();
    migrationModel.initByName("rateMatrix", rateMatrix, "popSizes", popSizes, "typeSet", new TypeSet("A", "B"));
    // Set up likelihood instance:
    StructuredCoalescentTreeDensity likelihood = new StructuredCoalescentTreeDensity();
    likelihood.initByName("migrationModel", migrationModel, "multiTypeTree", mtTree);
    // Calculated by hand
    double expResult = -16.52831;
    double result = likelihood.calculateLogP();
    System.out.println(result);
    assertEquals(expResult, result, 1e-5);
}

Example 28 with RealParameter

use of beast.core.parameter.RealParameter in project MultiTypeTree by tgvaughan.

the class NSR_Test method test.

@Test
public void test() throws Exception {
    System.out.println("NSR test");
    // Fix seed.
    Randomizer.setSeed(42);
    // Assemble migration model:
    RealParameter rateMatrix = new RealParameter("0.1 0.1");
    RealParameter popSizes = new RealParameter("7.0 7.0");
    SCMigrationModel migModel = new SCMigrationModel();
    migModel.initByName("rateMatrix", rateMatrix, "popSizes", popSizes, "typeSet", new TypeSet("A", "B"));
    // Assemble initial MultiTypeTree
    MultiTypeTree mtTree = new StructuredCoalescentMultiTypeTree();
    mtTree.initByName("typeLabel", "deme", "migrationModel", migModel, "leafTypes", "1 0");
    // Set up state:
    State state = new State();
    state.initByName("stateNode", mtTree);
    // Assemble distribution:
    StructuredCoalescentTreeDensity distribution = new StructuredCoalescentTreeDensity();
    distribution.initByName("migrationModel", migModel, "multiTypeTree", mtTree);
    // Set up operators:
    Operator operatorNSR = new NodeShiftRetype();
    operatorNSR.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel);
    // Set up stat analysis logger:
    MultiTypeTreeStatLogger logger = new MultiTypeTreeStatLogger();
    logger.initByName("multiTypeTree", mtTree, "burninFrac", 0.1, "logEvery", 100);
    // Set up MCMC:
    MCMC mcmc = new MCMC();
    mcmc.initByName("chainLength", "1000000", "state", state, "distribution", distribution, "operator", operatorNSR, "logger", logger);
    // Run MCMC:
    mcmc.run();
    System.out.format("height mean = %s\n", logger.getHeightMean());
    System.out.format("height var = %s\n", logger.getHeightVar());
    System.out.format("height ESS = %s\n", logger.getHeightESS());
    // Compare analysis results with truth:
    boolean withinTol = (logger.getHeightESS() > 2000) && (Math.abs(logger.getHeightMean() - 19.0) < 0.5) && (Math.abs(logger.getHeightVar() - 291) < 30);
    Assert.assertTrue(withinTol);
}

Example 29 with RealParameter

use of beast.core.parameter.RealParameter in project MultiTypeTree by tgvaughan.

the class STXR_NRR_MTU_TS_Test method test.

@Test
public void test() throws Exception {
    System.out.println("STXR_NRR_MTU_TS test");
    // Fix seed.
    Randomizer.setSeed(42);
    // Assemble migration model:
    RealParameter rateMatrix = new RealParameter("0.1 0.1");
    RealParameter popSizes = new RealParameter("7.0 7.0");
    SCMigrationModel migModel = new SCMigrationModel();
    migModel.initByName("rateMatrix", rateMatrix, "popSizes", popSizes, "typeSet", new TypeSet("A", "B"));
    // Assemble initial MultiTypeTree
    MultiTypeTree mtTree = new StructuredCoalescentMultiTypeTree();
    mtTree.initByName("typeLabel", "deme", "migrationModel", migModel, "leafTypes", "1 1 0 0");
    // Set up state:
    State state = new State();
    state.initByName("stateNode", mtTree);
    // Assemble distribution:
    StructuredCoalescentTreeDensity distribution = new StructuredCoalescentTreeDensity();
    distribution.initByName("migrationModel", migModel, "multiTypeTree", mtTree);
    // Set up operators:
    Operator operatorSTXR = new TypedSubtreeExchangeRandom();
    operatorSTXR.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel, "mu", 0.2);
    Operator operatorNRR = new NodeRetypeRandom();
    operatorNRR.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel, "mu", 0.2);
    Operator operatorMTU = new MultiTypeUniform();
    operatorMTU.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel);
    Operator operatorMTTS = new MultiTypeTreeScale();
    operatorMTTS.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel, "scaleFactor", 1.5, "useOldTreeScaler", false);
    // Set up stat analysis logger:
    MultiTypeTreeStatLogger logger = new MultiTypeTreeStatLogger();
    logger.initByName("multiTypeTree", mtTree, "burninFrac", 0.1, "logEvery", 1000);
    // Set up MCMC:
    MCMC mcmc = new MCMC();
    mcmc.initByName("chainLength", "10000000", "state", state, "distribution", distribution, "operator", operatorSTXR, "operator", operatorNRR, "operator", operatorMTU, "operator", operatorMTTS, "logger", logger);
    // Run MCMC:
    mcmc.run();
    System.out.format("height mean = %s\n", logger.getHeightMean());
    System.out.format("height var = %s\n", logger.getHeightVar());
    System.out.format("height ESS = %s\n", logger.getHeightESS());
    // Compare analysis results with truth:
    boolean withinTol = (logger.getHeightESS() > 2000) && (Math.abs(logger.getHeightMean() - 25.8) < 0.5) && (Math.abs(logger.getHeightVar() - 320) < 30);
    Assert.assertTrue(withinTol);
}

Example 30 with RealParameter

use of beast.core.parameter.RealParameter in project MultiTypeTree by tgvaughan.

the class TWBR_TS_Test method test2.

@Test
public void test2() throws Exception {
    System.out.println("TWBR_test 2");
    // Fix seed.
    Randomizer.setSeed(42);
    // Assemble initial MultiTypeTree
    String newickStr = "((1[&deme=1]:1,2[&deme=0]:1)[&deme=0]:1," + "3[&deme=0]:2)[&deme=0]:0;";
    MultiTypeTreeFromNewick mtTree = new MultiTypeTreeFromNewick();
    mtTree.initByName("value", newickStr, "typeLabel", "deme");
    // Assemble migration model:
    RealParameter rateMatrix = new RealParameter("0.1 0.1");
    RealParameter popSizes = new RealParameter("7.0 7.0");
    SCMigrationModel migModel = new SCMigrationModel();
    migModel.initByName("rateMatrix", rateMatrix, "popSizes", popSizes, "typeSet", new TypeSet("A", "B"));
    // Assemble distribution:
    StructuredCoalescentTreeDensity distribution = new StructuredCoalescentTreeDensity();
    distribution.initByName("migrationModel", migModel, "multiTypeTree", mtTree);
    // Set up state:
    State state = new State();
    state.initByName("stateNode", mtTree);
    // Set up operator:
    TypedWilsonBaldingRandom operatorTWBR = new TypedWilsonBaldingRandom();
    operatorTWBR.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel, "mu", 0.2, "alpha", 0.2);
    Operator operatorMTTS = new MultiTypeTreeScale();
    operatorMTTS.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel, "scaleFactor", 0.8, "useOldTreeScaler", false);
    // Set up stat analysis logger:
    MultiTypeTreeStatLogger logger = new MultiTypeTreeStatLogger();
    logger.initByName("multiTypeTree", mtTree, "burninFrac", 0.1, "logEvery", 1000);
    // Set up MCMC:
    MCMC mcmc = new MCMC();
    mcmc.initByName("chainLength", "1000000", "state", state, "distribution", distribution, "operator", operatorTWBR, "operator", operatorMTTS, "logger", logger);
    // Run MCMC:
    mcmc.run();
    System.out.format("height mean = %s\n", logger.getHeightMean());
    System.out.format("height var = %s\n", logger.getHeightVar());
    System.out.format("height ESS = %s\n", logger.getHeightESS());
    // Compare analysis results with truth:
    boolean withinTol = (logger.getHeightESS() > 200) && (Math.abs(logger.getHeightMean() - 23) < 1) && (Math.abs(logger.getHeightVar() - 300) < 30);
    Assert.assertTrue(withinTol);
}