/**
* @param name the name of the covarion substitution model
* @param dataType the data type
* @param freqModel the equlibrium frequencies
* @param hiddenClassRates the relative rates of the hidden categories (first hidden category has
* rate 1.0 so this parameter has dimension one less than number of hidden categories. each
* hidden category.
* @param switchingRates rate of switching between hidden categories
*/
public AbstractCovarionDNAModel(
String name,
HiddenNucleotides dataType,
Parameter hiddenClassRates,
Parameter switchingRates,
FrequencyModel freqModel) {
super(name, dataType, freqModel);
hiddenClassCount = dataType.getHiddenClassCount();
this.hiddenClassRates = hiddenClassRates;
this.switchingRates = switchingRates;
assert hiddenClassRates.getDimension() == hiddenClassCount - 1;
int hiddenClassCount = getHiddenClassCount();
int switchingClassCount = hiddenClassCount * (hiddenClassCount - 1) / 2;
if (switchingRates.getDimension() != switchingClassCount) {
throw new IllegalArgumentException(
"switching rate parameter must have "
+ switchingClassCount
+ " rates for "
+ hiddenClassCount
+ " classes");
}
addVariable(switchingRates);
addVariable(hiddenClassRates);
constructRateMatrixMap();
}
protected double calculateLogFieldLikelihood() {
if (!intervalsKnown) {
// intervalsKnown -> false when handleModelChanged event occurs in super.
wrapSetupIntervals();
setupGMRFWeights();
intervalsKnown = true;
}
double currentLike = 0;
DenseVector diagonal1 = new DenseVector(fieldLength);
DenseVector currentGamma = new DenseVector(popSizeParameter.getParameterValues());
SymmTridiagMatrix currentQ =
getScaledWeightMatrix(
precisionParameter.getParameterValue(0), lambdaParameter.getParameterValue(0));
currentQ.mult(currentGamma, diagonal1);
// currentLike += 0.5 * logGeneralizedDeterminant(currentQ) - 0.5 *
// currentGamma.dot(diagonal1);
currentLike +=
0.5 * (fieldLength - 1) * Math.log(precisionParameter.getParameterValue(0))
- 0.5 * currentGamma.dot(diagonal1);
if (lambdaParameter.getParameterValue(0) == 1) {
currentLike -= (fieldLength - 1) / 2.0 * LOG_TWO_TIMES_PI;
} else {
currentLike -= fieldLength / 2.0 * LOG_TWO_TIMES_PI;
}
return currentLike;
}
private void printInformtion(Parameter par) {
StringBuffer sb = new StringBuffer("parameter \n");
for (int j = 0; j < par.getDimension(); j++) {
sb.append(par.getParameterValue(j));
}
Logger.getLogger("dr.evomodel").info(sb.toString());
};
public DriftedLocationsStatistic(
MatrixParameter locationsParameter,
Parameter offsetsParameter,
Parameter locationDriftParameter) {
this.locationsParameter = locationsParameter;
locationsParameter.addParameterListener(this);
this.offsetsParameter = offsetsParameter;
offsetsParameter.addParameterListener(this);
this.locationDriftParameter = locationDriftParameter;
locationDriftParameter.addParameterListener(this);
}
public double calculateWeightedSSE() {
double weightedSSE = 0;
double currentPopSize = popSizeParameter.getParameterValue(0);
double currentInterval = coalescentIntervals[0];
for (int j = 1; j < fieldLength; j++) {
double nextPopSize = popSizeParameter.getParameterValue(j);
double nextInterval = coalescentIntervals[j];
double delta = nextPopSize - currentPopSize;
double weight = (currentInterval + nextInterval) / 2.0;
weightedSSE += delta * delta / weight;
currentPopSize = nextPopSize;
currentInterval = nextInterval;
}
return weightedSSE;
}
/** Constructor */
public SampleStateAndCategoryModel(
Parameter muParameter, Parameter categoriesParameter, Vector substitutionModels) {
super(SampleStateAndCategoryModelParser.SAMPLE_STATE_AND_CATEGORY_MODEL);
this.substitutionModels = substitutionModels;
for (int i = 0; i < substitutionModels.size(); i++) {
addModel((SubstitutionModel) substitutionModels.elementAt(i));
}
this.categoryCount = substitutionModels.size();
sitesInCategory = new int[categoryCount];
// stateCount =
// ((SubstitutionModel)substitutionModels.elementAt(0)).getDataType().getStateCount();
this.muParameter = muParameter;
addVariable(muParameter);
muParameter.addBounds(new Parameter.DefaultBounds(1000.0, 0.0, 1));
this.categoriesParameter = categoriesParameter;
addVariable(categoriesParameter);
if (categoryCount > 1) {
for (int i = 0; i < categoryCount; i++) {
Parameter p = (Parameter) ((YangCodonModel) substitutionModels.elementAt(i)).getVariable(0);
Parameter lower = null;
Parameter upper = null;
if (i == 0) {
upper = (Parameter) ((YangCodonModel) substitutionModels.elementAt(i + 1)).getVariable(0);
p.addBounds(new omegaBounds(lower, upper));
} else {
if (i == (categoryCount - 1)) {
lower =
(Parameter) ((YangCodonModel) substitutionModels.elementAt(i - 1)).getVariable(0);
p.addBounds(new omegaBounds(lower, upper));
} else {
upper =
(Parameter) ((YangCodonModel) substitutionModels.elementAt(i + 1)).getVariable(0);
lower =
(Parameter) ((YangCodonModel) substitutionModels.elementAt(i - 1)).getVariable(0);
p.addBounds(new omegaBounds(lower, upper));
}
}
}
}
}
/** Calculates the actual rates corresponding to the category indices. */
protected void setupRates() {
// System.out.println("BRRRTTZZZ " + distributionIndexParameter.getValue(0));
for (int i = 0; i < tree.getNodeCount(); i++) {
// rates[i] = distributionModel.quantile(rateCategoryQuantiles.getNodeValue(
// rateCategoryQuantiles.getTreeModel(), rateCategoryQuantiles.getTreeModel().getNode(i) ));
if (!tree.isRoot(tree.getNode(i))) {
if (useQuantilesForRates) {
/* Using quantiles to represent rates */
rates[tree.getNode(i).getNumber()] =
distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].quantile(
rateCategoryQuantiles.getNodeValue(tree, tree.getNode(i)));
} else {
/* Not using quantiles to represent rates. This is practically useless for anything else other than simulation */
rates[tree.getNode(i).getNumber()] =
rateCategoryQuantiles.getNodeValue(tree, tree.getNode(i));
}
}
}
/*System.out.print(distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].getClass().getName() + "\t" + (int) Math.round(distributionIndexParameter.getValue(0)) + "\t" + rates[1] + "\t" + rateCategoryQuantiles.getNodeValue(tree, tree.getNode(1)));// + "\t" + distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].);
if(distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].getClass().getName().equals("dr.inference.distribution.LogNormalDistributionModel")) {
LogNormalDistributionModel lndm = (LogNormalDistributionModel) distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))];
System.out.println("\t" + lndm.getS());
}
else if (distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))].getClass().getName().equals("dr.inference.distribution.InverseGaussianDistributionModel")) {
InverseGaussianDistributionModel lndm = (InverseGaussianDistributionModel) distributionModels[(int) Math.round(distributionIndexParameter.getValue(0))];
System.out.println("\t" + lndm.getS());
}*/
if (normalize) computeFactor();
}
/** @return the lower limit of this hypervolume in the given dimension. */
public Double getLowerLimit(int dimension) {
if (dimension != 0)
throw new RuntimeException("omega parameters have wrong dimension " + dimension);
if (lowerOmega == null) return OMEGA_MIN_VALUE;
else return lowerOmega.getParameterValue(dimension);
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
// final int overSampling = xo.getAttribute(OVERSAMPLING, 1);
final boolean normalize = xo.getAttribute(NORMALIZE, false);
final double normalizeBranchRateTo = xo.getAttribute(NORMALIZE_BRANCH_RATE_TO, Double.NaN);
TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
ParametricDistributionModel distributionModel =
(ParametricDistributionModel) xo.getElementFirstChild(DISTRIBUTION);
// Parameter rateCategoryParameter = (Parameter) xo.getElementFirstChild(RATE_CATEGORIES);
Parameter rateCategoryQuantilesParameter =
(Parameter) xo.getElementFirstChild(RATE_CATEGORY_QUANTILES);
Logger.getLogger("dr.evomodel").info("Using continuous relaxed clock model.");
// Logger.getLogger("dr.evomodel").info(" over sampling = " + overSampling);
Logger.getLogger("dr.evomodel")
.info(" parametric model = " + distributionModel.getModelName());
// Logger.getLogger("dr.evomodel").info(" rate categories = " +
// rateCategoryParameter.getDimension());
Logger.getLogger("dr.evomodel")
.info(" rate categories = " + rateCategoryQuantilesParameter.getDimension());
if (normalize) {
Logger.getLogger("dr.evomodel")
.info(" mean rate is normalized to " + normalizeBranchRateTo);
}
if (xo.hasAttribute(SINGLE_ROOT_RATE)) {
// singleRootRate = xo.getBooleanAttribute(SINGLE_ROOT_RATE);
Logger.getLogger("dr.evomodel").warning(" WARNING: single root rate is not implemented!");
}
/* if (xo.hasAttribute(NORMALIZED_MEAN)) {
dbr.setNormalizedMean(xo.getDoubleAttribute(NORMALIZED_MEAN));
}*/
return new ContinuousBranchRates(
tree, /*rateCategoryParameter, */
rateCategoryQuantilesParameter,
distributionModel, /*overSampling,*/
normalize,
normalizeBranchRateTo);
}
public int[] connected(int i, Parameter clusteringParameter) {
int n = clusteringParameter.getDimension();
int[] visited = new int[n + 1];
visited[0] = i + 1;
int tv = 1;
for (int j = 0; j < n; j++) {
if (visited[j] != 0) {
int curr = visited[j] - 1;
/*look forward
*/
int forward = (int) clusteringParameter.getParameterValue(curr);
visited[tv] = forward + 1;
tv++;
// Check to see if is isn't already on the list
for (int ii = 0; ii < tv - 1; ii++) {
if (visited[ii] == forward + 1) {
tv--;
visited[tv] = 0;
}
}
/*look back
*/
for (int jj = 0; jj < n; jj++) {
if ((int) clusteringParameter.getParameterValue(jj) == curr) {
visited[tv] = jj + 1;
tv++;
for (int ii = 0; ii < tv - 1; ii++) {
if (visited[ii] == jj + 1) {
tv--;
visited[tv] = 0;
}
}
}
}
}
}
return visited;
}
public double getStatisticValue(int dim) {
double val;
// x is location count, y is location dimension
int x = getColumnIndex(dim);
int y = getRowIndex(dim);
Parameter loc = locationsParameter.getParameter(x);
if (y == 0) {
val =
loc.getParameterValue(y)
+ locationDriftParameter.getParameterValue(0) * offsetsParameter.getParameterValue(x);
} else {
val = loc.getParameterValue(y);
}
return val;
}
/** Construct demographic model with default settings */
public ExponentialLogisticModel(
String name,
Parameter N0Parameter,
Parameter logisticGrowthParameter,
Parameter logisticShapeParameter,
Parameter exponentialGrowthParameter,
Parameter transistionTimeParameter,
double alpha,
Type units) {
super(name);
exponentialLogistic = new ExponentialLogistic(units);
this.N0Parameter = N0Parameter;
addVariable(N0Parameter);
N0Parameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));
this.logisticGrowthParameter = logisticGrowthParameter;
addVariable(logisticGrowthParameter);
logisticGrowthParameter.addBounds(
new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));
this.logisticShapeParameter = logisticShapeParameter;
addVariable(logisticShapeParameter);
logisticShapeParameter.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));
this.exponentialGrowthParameter = exponentialGrowthParameter;
addVariable(exponentialGrowthParameter);
exponentialGrowthParameter.addBounds(
new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));
this.transistionTimeParameter = transistionTimeParameter;
addVariable(transistionTimeParameter);
transistionTimeParameter.addBounds(
new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));
this.alpha = alpha;
setUnits(units);
}
public PopsIOSpeciesTreeModel(
PopsIOSpeciesBindings piosb, Parameter popPriorScale, PriorComponent[] priorComponents) {
super(PopsIOSpeciesTreeModelParser.PIO_SPECIES_TREE);
this.piosb = piosb;
this.popPriorScale = popPriorScale;
addVariable(popPriorScale);
popPriorScale.addBounds(new Parameter.DefaultBounds(Double.POSITIVE_INFINITY, 0.0, 1));
this.priorComponents = priorComponents;
PopsIOSpeciesBindings.SpInfo[] species = piosb.getSpecies();
int nTaxa = species.length;
int nNodes = 2 * nTaxa - 1;
pionodes = new PopsIONode[nNodes];
for (int n = 0; n < nNodes; n++) {
pionodes[n] = new PopsIONode(n);
}
ArrayList<Integer> tojoin = new ArrayList<Integer>(nTaxa);
for (int n = 0; n < nTaxa; n++) {
pionodes[n].setTaxon(species[n].name);
pionodes[n].setHeight(0.0);
pionodes[n].setUnion(piosb.tipUnionFromTaxon(pionodes[n].getTaxon()));
tojoin.add(n);
}
double rate = 1.0;
double treeheight = 0.0;
for (int i = 0; i < nTaxa - 1; i++) {
int numtojoin = tojoin.size();
int j = MathUtils.nextInt(numtojoin);
Integer child0 = tojoin.get(j);
tojoin.remove(j);
int k = MathUtils.nextInt(numtojoin - 1);
Integer child1 = tojoin.get(k);
tojoin.remove(k);
pionodes[nTaxa + i].addChildren(pionodes[child0], pionodes[child1]);
pionodes[nTaxa + i].setHeight(treeheight + randomnodeheight(numtojoin * rate));
treeheight = pionodes[nTaxa + i].getHeight();
tojoin.add(nTaxa + i);
}
rootn = pionodes.length - 1;
double scale = 0.99 * piosb.initialMinGeneNodeHeight() / pionodes[rootn].height;
scaleAllHeights(scale);
pionodes[rootn].fillinUnionsInSubtree(piosb.getSpecies().length);
stree = makeSimpleTree();
Logger.getLogger("dr.evomodel.speciation.popsio")
.info(
"\tConstructing a PopsIO Species Tree Model, please cite:\n"
+ Citable.Utils.getCitationString(this));
}
protected double getRawBranchRate(final Tree tree, final NodeRef node) {
double rate = 0.0;
double[] processValues = getProcessValues(tree, node);
double totalTime = 0;
if (indicatorParameter != null) {
double absRate = rateParameter.getParameterValue(0);
for (int i = 0; i < indicatorParameter.getDimension(); i++) {
int index = (int) indicatorParameter.getParameterValue(i);
if (index == 0) {
rate += absRate * processValues[i];
} else {
rate +=
(absRate * (1.0 + relativeRatesParameter.getParameterValue(index - 1)))
* processValues[i];
}
totalTime += processValues[i];
}
} else {
for (int i = 0; i < rateParameter.getDimension(); i++) {
rate += rateParameter.getParameterValue(i) * processValues[i];
totalTime += processValues[i];
}
}
rate /= totalTime;
return rate;
}
public DistanceDependentCRPGibbsOperator(
Parameter links,
Parameter assignments,
Parameter chiParameter,
NPAntigenicLikelihood Likelihood,
double weight) {
this.links = links;
this.assignments = assignments;
this.modelLikelihood = Likelihood;
this.chiParameter = chiParameter;
this.depMatrix = Likelihood.getLogDepMatrix();
for (int i = 0; i < links.getDimension(); i++) {
links.setParameterValue(i, i);
}
setWeight(weight);
// double[][] x=modelLikelihood.getData();
// modelLikelihood.printInformtion(x[0][0]);
this.m = new double[2];
m[0] = modelLikelihood.priorMean.getParameterValue(0);
m[1] = modelLikelihood.priorMean.getParameterValue(1);
this.v0 = 2;
this.k0 =
modelLikelihood.priorPrec.getParameterValue(0)
/ modelLikelihood.clusterPrec.getParameterValue(0);
this.T0Inv = new double[2][2];
T0Inv[0][0] = v0 / modelLikelihood.clusterPrec.getParameterValue(0);
T0Inv[1][1] = v0 / modelLikelihood.clusterPrec.getParameterValue(0);
T0Inv[1][0] = 0.0;
T0Inv[0][1] = 0.0;
this.logDetT0 = -Math.log(T0Inv[0][0] * T0Inv[1][1]);
}
private void restrictNodePartials(int nodeIndex) {
Parameter restrictionParameter = partialsMap[nodeIndex];
if (restrictionParameter == null) {
return;
}
getPartials(nodeIndex, partials);
double[] restriction = restrictionParameter.getParameterValues();
final int partialsLengthPerCategory = stateCount * patternCount;
if (restriction.length == partialsLengthPerCategory) {
for (int i = 0; i < categoryCount; i++) {
componentwiseMultiply(
partials, partialsLengthPerCategory * i, restriction, 0, partialsLengthPerCategory);
}
} else {
componentwiseMultiply(partials, 0, restriction, 0, partialsLengthPerCategory * categoryCount);
}
setPartials(nodeIndex, partials);
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
XMLObject cxo = xo.getChild(COUNTS);
Parameter counts = (Parameter) cxo.getChild(Parameter.class);
DirichletDistribution dirichlet = new DirichletDistribution(counts.getParameterValues());
MultivariateDistributionLikelihood likelihood =
new MultivariateDistributionLikelihood(dirichlet);
cxo = xo.getChild(DATA);
for (int j = 0; j < cxo.getChildCount(); j++) {
if (cxo.getChild(j) instanceof Parameter) {
likelihood.addData((Parameter) cxo.getChild(j));
} else {
throw new XMLParseException(
"illegal element in " + xo.getName() + " element " + cxo.getName());
}
}
return likelihood;
}
protected void getDiagonalRates(double[] diagonalRates) {
double kappa = substitutionModel.getKappa();
double[] freq = substitutionModel.getFrequencyModel().getFrequencies();
double mutationRate = mutationParameter.getParameterValue(0);
double beta =
0.5
/ ((freq[0] + freq[2]) * (freq[1] + freq[3])
+ kappa * (freq[0] * freq[2] + freq[1] * freq[3]));
diagonalRates[0] = ((freq[1] + freq[3]) + freq[2] * kappa) * mutationRate * beta;
diagonalRates[1] = ((freq[0] + freq[2]) + freq[3] * kappa) * mutationRate * beta;
diagonalRates[2] = ((freq[1] + freq[3]) + freq[0] * kappa) * mutationRate * beta;
diagonalRates[3] = ((freq[0] + freq[2]) + freq[1] * kappa) * mutationRate * beta;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Parameter kappaParam;
Parameter switchingRates;
Parameter hiddenClassRates;
FrequencyModel freqModel;
kappaParam = (Parameter) xo.getElementFirstChild(KAPPA);
switchingRates = (Parameter) xo.getElementFirstChild(AbstractCovarionDNAModel.SWITCHING_RATES);
hiddenClassRates =
(Parameter) xo.getElementFirstChild(AbstractCovarionDNAModel.HIDDEN_CLASS_RATES);
freqModel = (FrequencyModel) xo.getElementFirstChild(AbstractCovarionDNAModel.FREQUENCIES);
if (!(freqModel.getDataType() instanceof HiddenNucleotides)) {
throw new IllegalArgumentException("Datatype must be hidden nucleotides!!");
}
HiddenNucleotides dataType = (HiddenNucleotides) freqModel.getDataType();
int hiddenStateCount = dataType.getHiddenClassCount();
int switchingRatesCount = hiddenStateCount * (hiddenStateCount - 1) / 2;
if (switchingRates.getDimension() != switchingRatesCount) {
throw new IllegalArgumentException(
"switching rates parameter must have "
+ switchingRatesCount
+ " dimensions, for "
+ hiddenStateCount
+ " hidden categories");
}
CovarionHKY model =
new CovarionHKY(dataType, kappaParam, hiddenClassRates, switchingRates, freqModel);
System.out.println(model);
return model;
}
/** Construct demographic model with default settings */
public EmergingEpidemicModel(
String name,
Parameter growthRateParameter,
Parameter generationTimeParameter,
Parameter generationShapeParameter,
Parameter offspringDispersionParameter,
TreeModel treeModel,
Type units) {
super(name);
exponentialGrowth = new ExponentialGrowth(units);
this.growthRateParameter = growthRateParameter;
addVariable(growthRateParameter);
growthRateParameter.addBounds(new Parameter.DefaultBounds(Double.MAX_VALUE, 0.0, 1));
this.generationTimeParameter = generationTimeParameter;
addVariable(generationTimeParameter);
generationTimeParameter.addBounds(new Parameter.DefaultBounds(Double.MAX_VALUE, 0.0, 1));
this.generationShapeParameter = generationShapeParameter;
addVariable(generationShapeParameter);
generationShapeParameter.addBounds(new Parameter.DefaultBounds(Double.MAX_VALUE, 0.0, 1));
this.offspringDispersionParameter = offspringDispersionParameter;
addVariable(offspringDispersionParameter);
offspringDispersionParameter.addBounds(new Parameter.DefaultBounds(Double.MAX_VALUE, 0.0, 1));
this.treeModel = treeModel;
addModel(treeModel);
addStatistic(new N0Statistic("N0"));
addStatistic(new RStatistic("R"));
setUnits(units);
}
public MultivariateNormalIndependenceSampler(
Parameter parameter,
SelfControlledCaseSeries sccs,
double setSizeMean,
double weight,
double scaleFactor,
CoercionMode mode) {
super(mode);
this.scaleFactor = scaleFactor;
this.parameter = parameter;
setWeight(weight);
dim = parameter.getDimension();
setWeight(weight);
this.sccs = sccs;
this.setSizeMean = setSizeMean;
}
public double logLhoodAllGeneTreesInSpeciesTree() {
double[] llhoodcpts = new double[priorComponents.length];
double totalweight = 0.0;
for (int i = 0; i < priorComponents.length; i++) {
totalweight += priorComponents[i].weight;
}
for (int i = 0; i < priorComponents.length; i++) {
llhoodcpts[i] = Math.log(priorComponents[i].weight / totalweight);
double sigma = popPriorScale.getParameterValue(0);
double alpha = priorComponents[i].alpha;
double beta = sigma * priorComponents[i].beta;
llhoodcpts[i] += logLhoodAllGeneTreesInSpeciesSubtree(pionodes[rootn], alpha, beta);
}
return logsumexp(llhoodcpts);
}
/**
* Calculates the log likelihood of this set of coalescent intervals, given a demographic model.
*
* @return coalescent part of density
*/
protected double calculateLogCoalescentLikelihood() {
if (!intervalsKnown) {
// intervalsKnown -> false when handleModelChanged event occurs in super.
wrapSetupIntervals();
setupGMRFWeights();
intervalsKnown = true;
}
// Matrix operations taken from block update sampler to calculate data likelihood and field
// prior
double currentLike = 0;
double[] currentGamma = popSizeParameter.getParameterValues();
for (int i = 0; i < fieldLength; i++) {
currentLike += -currentGamma[i] - sufficientStatistics[i] * Math.exp(-currentGamma[i]);
}
return currentLike; // +
// LogNormalDistribution.logPdf(Math.exp(popSizeParameter.getParameterValue(coalescentIntervals.length - 1)), mu, sigma);
}
/** change the parameter and return the hastings ratio. */
public double doOperation() throws OperatorFailedException {
double[] mean = sccs.getMode();
double[] currentValue = parameter.getParameterValues();
double[] newValue = new double[dim];
Set<Integer> updateSet = new HashSet<Integer>();
if (setSizeMean != -1.0) {
final int listLength = Poisson.nextPoisson(setSizeMean);
while (updateSet.size() < listLength) {
int newInt = MathUtils.nextInt(parameter.getDimension());
if (!updateSet.contains(newInt)) {
updateSet.add(newInt);
}
}
} else {
for (int i = 0; i < dim; ++i) {
updateSet.add(i);
}
}
double logq = 0;
for (Integer i : updateSet) {
newValue[i] = mean[i] + scaleFactor * MathUtils.nextGaussian();
if (UPDATE_ALL) {
parameter.setParameterValueQuietly(i, newValue[i]);
} else {
parameter.setParameterValue(i, newValue[i]);
}
logq +=
(NormalDistribution.logPdf(currentValue[i], mean[i], scaleFactor)
- NormalDistribution.logPdf(newValue[i], mean[i], scaleFactor));
}
// for (Integer i : updateSet) {
// parameter.setParameterValueQuietly(i, newValue[i]);
// }
if (UPDATE_ALL) {
parameter.setParameterValueNotifyChangedAll(0, parameter.getParameterValue(0));
}
return logq;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
final boolean onLogitScale = xo.getAttribute(ON_LOGIT_SCALE, false);
XMLObject cxo = xo.getChild(COUNTS);
Parameter countsParam = (Parameter) cxo.getChild(Parameter.class);
cxo = xo.getChild(PROPORTION);
Parameter proportionParam = (Parameter) cxo.getChild(Parameter.class);
if (proportionParam.getDimension() != 1
&& proportionParam.getDimension() != countsParam.getDimension()) {
throw new XMLParseException(
"Proportion dimension ("
+ proportionParam.getDimension()
+ ") "
+ "must equal 1 or counts dimension ("
+ countsParam.getDimension()
+ ")");
}
cxo = xo.getChild(TRIALS);
Parameter trialsParam;
if (cxo.hasAttribute(VALUES)) {
int[] tmp = cxo.getIntegerArrayAttribute(VALUES);
double[] v = new double[tmp.length];
for (int i = 0; i < tmp.length; ++i) {
v[i] = tmp[i];
}
trialsParam = new Parameter.Default(v);
} else {
trialsParam = (Parameter) cxo.getChild(Parameter.class);
}
if (trialsParam.getDimension() != countsParam.getDimension()) {
throw new XMLParseException(
"Trials dimension ("
+ trialsParam.getDimension()
+ ") must equal counts dimension ("
+ countsParam.getDimension()
+ ")");
}
return new BinomialLikelihood(trialsParam, proportionParam, countsParam, onLogitScale);
}
public void initializationReport() {
System.out.println("Creating a GMRF smoothed skyride model:");
System.out.println("\tPopulation sizes: " + popSizeParameter.getDimension());
System.out.println(
"\tIf you publish results using this model, please reference: Minin, Bloomquist and Suchard (2008) Molecular Biology and Evolution, 25, 1459-1471.");
}
public GMRFSkyrideLikelihood(
List<Tree> treeList,
Parameter popParameter,
Parameter groupParameter,
Parameter precParameter,
Parameter lambda,
Parameter beta,
MatrixParameter dMatrix,
boolean timeAwareSmoothing,
boolean rescaleByRootHeight) {
super(GMRFSkyrideLikelihoodParser.SKYLINE_LIKELIHOOD);
this.popSizeParameter = popParameter;
this.groupSizeParameter = groupParameter;
this.precisionParameter = precParameter;
this.lambdaParameter = lambda;
this.betaParameter = beta;
this.dMatrix = dMatrix;
this.timeAwareSmoothing = timeAwareSmoothing;
this.rescaleByRootHeight = rescaleByRootHeight;
addVariable(popSizeParameter);
addVariable(precisionParameter);
addVariable(lambdaParameter);
if (betaParameter != null) {
addVariable(betaParameter);
}
setTree(treeList);
int correctFieldLength = getCorrectFieldLength();
if (popSizeParameter.getDimension() <= 1) {
// popSize dimension hasn't been set yet, set it here:
popSizeParameter.setDimension(correctFieldLength);
}
fieldLength = popSizeParameter.getDimension();
if (correctFieldLength != fieldLength) {
throw new IllegalArgumentException(
"Population size parameter should have length " + correctFieldLength);
}
// Field length must be set by this point
wrapSetupIntervals();
coalescentIntervals = new double[fieldLength];
storedCoalescentIntervals = new double[fieldLength];
sufficientStatistics = new double[fieldLength];
storedSufficientStatistics = new double[fieldLength];
setupGMRFWeights();
addStatistic(new DeltaStatistic());
initializationReport();
/* Force all entries in groupSizeParameter = 1 for compatibility with Tracer */
if (groupSizeParameter != null) {
for (int i = 0; i < groupSizeParameter.getDimension(); i++)
groupSizeParameter.setParameterValue(i, 1.0);
}
}
public String getOperatorName() {
return "independentNormalDistribution(" + parameter.getVariableName() + ")";
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
Parameter ratesParameter = null;
FrequencyModel freqModel = null;
if (xo.hasChildNamed(FREQUENCIES)) {
XMLObject cxo = xo.getChild(FREQUENCIES);
freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);
}
DataType dataType = DataTypeUtils.getDataType(xo);
if (dataType == null) dataType = (DataType) xo.getChild(DataType.class);
// if (xo.hasAttribute(DataType.DATA_TYPE)) {
// String dataTypeStr = xo.getStringAttribute(DataType.DATA_TYPE);
// if (dataTypeStr.equals(Nucleotides.DESCRIPTION)) {
// dataType = Nucleotides.INSTANCE;
// } else if (dataTypeStr.equals(AminoAcids.DESCRIPTION)) {
// dataType = AminoAcids.INSTANCE;
// } else if (dataTypeStr.equals(Codons.DESCRIPTION)) {
// dataType = Codons.UNIVERSAL;
// } else if (dataTypeStr.equals(TwoStates.DESCRIPTION)) {
// dataType = TwoStates.INSTANCE;
// }
// }
if (dataType == null) dataType = freqModel.getDataType();
if (dataType != freqModel.getDataType()) {
throw new XMLParseException(
"Data type of "
+ getParserName()
+ " element does not match that of its frequencyModel.");
}
XMLObject cxo = xo.getChild(RATES);
ratesParameter = (Parameter) cxo.getChild(Parameter.class);
int states = dataType.getStateCount();
Logger.getLogger("dr.evomodel")
.info(" General Substitution Model (stateCount=" + states + ")");
boolean hasRelativeRates =
cxo.hasChildNamed(RELATIVE_TO)
|| (cxo.hasAttribute(RELATIVE_TO) && cxo.getIntegerAttribute(RELATIVE_TO) > 0);
int nonReversibleRateCount = ((dataType.getStateCount() - 1) * dataType.getStateCount());
int reversibleRateCount = (nonReversibleRateCount / 2);
boolean isNonReversible = ratesParameter.getDimension() == nonReversibleRateCount;
boolean hasIndicator = xo.hasChildNamed(INDICATOR);
if (!hasRelativeRates) {
Parameter indicatorParameter = null;
if (ratesParameter.getDimension() != reversibleRateCount
&& ratesParameter.getDimension() != nonReversibleRateCount) {
throw new XMLParseException(
"Rates parameter in "
+ getParserName()
+ " element should have "
+ (reversibleRateCount)
+ " dimensions for reversible model or "
+ nonReversibleRateCount
+ " dimensions for non-reversible. "
+ "However parameter dimension is "
+ ratesParameter.getDimension());
}
if (hasIndicator) { // this is using BSSVS
cxo = xo.getChild(INDICATOR);
indicatorParameter = (Parameter) cxo.getChild(Parameter.class);
if (indicatorParameter.getDimension() != ratesParameter.getDimension()) {
throw new XMLParseException(
"Rates and indicator parameters in "
+ getParserName()
+ " element must be the same dimension.");
}
boolean randomize =
xo.getAttribute(
dr.evomodelxml.substmodel.ComplexSubstitutionModelParser.RANDOMIZE, false);
if (randomize) {
BayesianStochasticSearchVariableSelection.Utils.randomize(
indicatorParameter, dataType.getStateCount(), !isNonReversible);
}
}
if (isNonReversible) {
// if (xo.hasChildNamed(ROOT_FREQ)) {
// cxo = xo.getChild(ROOT_FREQ);
// FrequencyModel rootFreq = (FrequencyModel)
// cxo.getChild(FrequencyModel.class);
//
// if (dataType != rootFreq.getDataType()) {
// throw new XMLParseException("Data type of " + getParserName() + "
// element does not match that of its rootFrequencyModel.");
// }
//
// Logger.getLogger("dr.evomodel").info(" Using BSSVS Complex
// Substitution Model");
// return new SVSComplexSubstitutionModel(getParserName(), dataType,
// freqModel, ratesParameter, indicatorParameter);
//
// } else {
// throw new XMLParseException("Non-reversible model missing " +
// ROOT_FREQ + " element");
// }
Logger.getLogger("dr.evomodel").info(" Using BSSVS Complex Substitution Model");
return new SVSComplexSubstitutionModel(
getParserName(), dataType, freqModel, ratesParameter, indicatorParameter);
} else {
Logger.getLogger("dr.evomodel").info(" Using BSSVS General Substitution Model");
return new SVSGeneralSubstitutionModel(
getParserName(), dataType, freqModel, ratesParameter, indicatorParameter);
}
} else {
// if we have relativeTo attribute then we use the old GeneralSubstitutionModel
if (ratesParameter.getDimension() != reversibleRateCount - 1) {
throw new XMLParseException(
"Rates parameter in "
+ getParserName()
+ " element should have "
+ (reversibleRateCount - 1)
+ " dimensions. However parameter dimension is "
+ ratesParameter.getDimension());
}
int relativeTo = 0;
if (hasRelativeRates) {
relativeTo = cxo.getIntegerAttribute(RELATIVE_TO) - 1;
}
if (relativeTo < 0 || relativeTo >= reversibleRateCount) {
throw new XMLParseException(RELATIVE_TO + " must be 1 or greater");
} else {
int t = relativeTo;
int s = states - 1;
int row = 0;
while (t >= s) {
t -= s;
s -= 1;
row += 1;
}
int col = t + row + 1;
Logger.getLogger("dr.evomodel")
.info(" Rates relative to " + dataType.getCode(row) + "<->" + dataType.getCode(col));
}
if (ratesParameter == null) {
if (reversibleRateCount == 1) {
// simplest model for binary traits...
} else {
throw new XMLParseException("No rates parameter found in " + getParserName());
}
}
return new GeneralSubstitutionModel(
getParserName(), dataType, freqModel, ratesParameter, relativeTo);
}
}
public double getBranchRate(final Tree tree, final NodeRef node) {
return rateParameter.getParameterValue(0);
}
