use of beast.core.State in project MultiTypeTree by tgvaughan.
the class STX_NR_MTU_TS_Test method test.
@Test
public void test() throws Exception {
System.out.println("STX_NR_MTU_TS test");
// Test passing locally, not on Travis. WHY!?
// Fix seed.
Randomizer.setSeed(53);
// 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 operatorSTX = new TypedSubtreeExchange();
operatorSTX.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel);
Operator operatorNR = new NodeRetype();
operatorNR.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel);
Operator operatorMTU = new MultiTypeUniform();
operatorMTU.initByName("weight", 1.0, "migrationModel", migModel, "multiTypeTree", mtTree);
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", "1000000", "state", state, "distribution", distribution, "operator", operatorSTX, "operator", operatorNR, "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());
// Direct simulation:
double[] heights = UtilMethods.getSimulatedHeights(migModel, new IntegerParameter("1 1 0 0"));
double simHeightMean = DiscreteStatistics.mean(heights);
double simHeightVar = DiscreteStatistics.variance(heights);
// Compare analysis results with truth:
boolean withinTol = (logger.getHeightESS() > 500) && (Math.abs(logger.getHeightMean() - simHeightMean) < 2.0) && (Math.abs(logger.getHeightVar() - simHeightVar) < 50);
Assert.assertTrue(withinTol);
}
use of beast.core.State in project MultiTypeTree by tgvaughan.
the class TWB_TS_Test method test1.
@Test
public void test1() throws Exception {
System.out.println("TWB_test 1");
// Fix seed.
Randomizer.setSeed(42);
// Assemble initial MultiTypeTree
String newickStr = "((1[&deme=0]: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:
TypedWilsonBalding operatorTWB = new TypedWilsonBalding();
operatorTWB.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel, "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", 0.2, "logEvery", 1000);
// Set up MCMC:
MCMC mcmc = new MCMC();
mcmc.initByName("chainLength", "1000000", "state", state, "distribution", distribution, "operator", operatorTWB, "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());
// Direct simulation:
double[] heights = UtilMethods.getSimulatedHeights(migModel, new IntegerParameter("0 0 0"));
double simHeightMean = DiscreteStatistics.mean(heights);
double simHeightVar = DiscreteStatistics.variance(heights);
// Compare results with simulation results:
boolean withinTol = (logger.getHeightESS() > 400) && (Math.abs(logger.getHeightMean() - simHeightMean) < 1.0) && (Math.abs(logger.getHeightVar() - simHeightVar) < 30);
Assert.assertTrue(withinTol);
}
use of beast.core.State in project MultiTypeTree by tgvaughan.
the class TWB_TS_Test method testTWB2.
@Test
public void testTWB2() throws Exception {
System.out.println("TWB_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:
TypedWilsonBalding operatorTWB = new TypedWilsonBalding();
operatorTWB.initByName("weight", 1.0, "multiTypeTree", mtTree, "migrationModel", migModel, "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", operatorTWB, "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());
// Direct simulation:
double[] heights = UtilMethods.getSimulatedHeights(migModel, new IntegerParameter("1 0 0"));
double simHeightMean = DiscreteStatistics.mean(heights);
double simHeightVar = DiscreteStatistics.variance(heights);
// Compare analysis results with truth:
boolean withinTol = (logger.getHeightESS() > 400) && (Math.abs(logger.getHeightMean() - simHeightMean) < 1.0) && (Math.abs(logger.getHeightVar() - simHeightVar) < 30);
Assert.assertTrue(withinTol);
}
use of beast.core.State in project beast2 by CompEvol.
the class XMLParser method createBeastObject.
// createObject
/**
* create BEASTInterface either using Inputs, or using annotated constructor *
*/
private BEASTInterface createBeastObject(Node node, String ID, String clazzName, List<NameValuePair> inputInfo) throws XMLParserException {
BEASTInterface beastObject = useAnnotatedConstructor(node, ID, clazzName, inputInfo);
if (beastObject != null) {
return beastObject;
}
// create new instance using class name
Object o = null;
try {
Class<?> c = Class.forName(clazzName);
o = c.newInstance();
} catch (InstantiationException e) {
// created for instance because it is abstract
throw new XMLParserException(node, "Cannot instantiate class. Please check the spec attribute.", 1006);
} catch (ClassNotFoundException e) {
// ignore -- class was found in beastObjectNames before
} catch (IllegalAccessException e) {
// T O D O Auto-generated catch block
e.printStackTrace();
throw new XMLParserException(node, "Cannot access class. Please check the spec attribute.", 1011);
}
// set id
beastObject = (BEASTInterface) o;
beastObject.setID(ID);
// hack required to make log-parsing easier
if (o instanceof State) {
m_state = (State) o;
}
// process inputs for annotated constructors
for (NameValuePair pair : inputInfo) {
if (pair.value instanceof BEASTInterface) {
setInput(node, beastObject, pair.name, (BEASTInterface) pair.value);
} else if (pair.value instanceof String) {
setInput(node, beastObject, pair.name, (String) pair.value);
} else {
throw new RuntimeException("Programmer error: value should be String or BEASTInterface");
}
}
// fill in missing inputs, if an input provider is available
try {
if (requiredInputProvider != null) {
for (Input<?> input : beastObject.listInputs()) {
if (input.get() == null && input.getRule() == Validate.REQUIRED) {
Object o2 = requiredInputProvider.createInput(beastObject, input, partitionContext);
if (o2 != null) {
input.setValue(o2, beastObject);
}
}
}
}
} catch (Exception e) {
throw new XMLParserException(node, e.getMessage(), 1008);
}
// sanity check: all attributes should be valid input names
if (!(beastObject instanceof Map)) {
for (NameValuePair pair : inputInfo) {
String name = pair.name;
if (!(name.equals("id") || name.equals("idref") || name.equals("spec") || name.equals("name"))) {
try {
beastObject.getInput(name);
} catch (Exception e) {
throw new XMLParserException(node, e.getMessage(), 1009);
}
}
}
}
// make sure object o is in outputs of inputs
for (NameValuePair pair : inputInfo) {
if (pair.value instanceof BEASTInterface) {
((BEASTInterface) pair.value).getOutputs().add((BEASTInterface) o);
}
}
register(node, beastObject);
return beastObject;
}
use of beast.core.State in project beast2 by CompEvol.
the class BeautiBase method stateAsString.
String stateAsString() {
State state = (State) doc.pluginmap.get("state");
List<StateNode> stateNodes = state.stateNodeInput.get();
return "assertStateEquals" + pluginListAsString(stateNodes);
}
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