private double proposeNewValue(
QuietRealParameter proposal, ParametricDistribution distr, double upper, double lower)
throws Exception {
Double[] sampleVals = distr.sample(1)[0];
for (int i = 0; i < sampleVals.length; i++) {
proposal.setValueQuietly(i, sampleVals[i]);
}
proposal.setUpper(upper);
proposal.setLower(lower);
return distr.calcLogP(new QuietRealParameter(sampleVals));
}
public double proposeDiscreteValue(
QuietRealParameter proposal,
double oldValue,
ConditionalCategoricalDistribution distr,
double upper,
double lower) {
int oldModel = (int) oldValue;
double newValue =
Randomizer.randomChoicePDF(distr.conditionalDensities(oldModel)) + distr.getOffset();
proposal.setValueQuietly(0, newValue);
proposal.setBounds(lower, upper);
return distr.logConditionalDensity(oldModel, (int) newValue);
}
public double proposeNewValueInLogSpace(
QuietRealParameter proposal,
double oldValue,
ParametricDistribution distr,
double upper,
double lower)
throws Exception {
double sampleVal = distr.sample(1)[0][0];
double newValue = Math.exp(sampleVal + Math.log(oldValue));
proposal.setValueQuietly(0, newValue);
proposal.setBounds(lower, upper);
return distr.calcLogP(new QuietRealParameter(new Double[] {sampleVal})) - Math.log(newValue);
}
private double proposeNewValue(
QuietRealParameter proposal,
Double[] oldValues,
ParametricDistribution distr,
double upper,
double lower)
throws Exception {
Double[] sampleVals = distr.sample(1)[0];
for (int i = 0; i < sampleVals.length; i++) {
// if(distr instanceof DiracDeltaDistribution)
// System.out.println(distr.getClass());
proposal.setValueQuietly(i, oldValues[i] + sampleVals[i]);
}
proposal.setUpper(upper);
proposal.setLower(lower);
return distr.calcLogP(new QuietRealParameter(sampleVals));
}
public double proposalValueInLogSpace(
QuietRealParameter proposal,
double oldValue,
ParametricDistribution distr,
double upper,
double lower)
throws Exception {
double sampleVal = distr.sample(1)[0][0];
double newValue = Math.exp(sampleVal + Math.log(oldValue));
proposal.setValueQuietly(0, newValue);
proposal.setBounds(lower, upper);
/*System.out.println("oldValue: "+oldValue+", newVal: "+newValue+", logpdf: "+(distr.calcLogP(new QuietRealParameter(new Double[]{sampleVal}))-Math.log(newValue)));
System.out.println("sampleValue: "+sampleVal);
System.out.println(distr.calcLogP(new QuietRealParameter(new Double[]{sampleVal})));*/
// System.out.println(oldValue+" "+newValue);
return distr.calcLogP(new QuietRealParameter(new Double[] {sampleVal})) - Math.log(newValue);
}
protected double proposeNewFreqValues(
QuietRealParameter proposal,
Double[] oldValues,
DirichletDistribution distr,
double upper,
double lower)
throws Exception {
// System.out.println(parameterList.getParameter(categoryIndex));
Double[] newValues = DirichletDistribution.nextDirichletScale(oldValues, distr.getScaleValue());
for (int i = 0; i < newValues.length; i++) {
proposal.setValueQuietly(i, newValues[i]);
}
proposal.setBounds(lower, upper);
int validCount = 0;
// while(validCount < 4){
validCount = 0;
for (double newVal : newValues) {
if (newVal == 0.0) {
break;
} else {
validCount++;
}
}
if (validCount < 4) {
return Double.NEGATIVE_INFINITY;
}
// }
if (Double.isNaN(DirichletDistribution.logPDF(newValues, oldValues, distr.getScaleValue()))
|| Double.NEGATIVE_INFINITY
== (DirichletDistribution.logPDF(newValues, oldValues, distr.getScaleValue()))) {
throw new RuntimeException("Crap");
}
return DirichletDistribution.logPDF(newValues, oldValues, distr.getScaleValue());
}