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add scalar support in IntRandomWalkOperator #176

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Merged
walterxie merged 1 commit into from
Oct 6, 2026
Merged

add scalar support in IntRandomWalkOperator #176

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51 changes: 36 additions & 15 deletions beast-base/src/main/java/beast/base/spec/inference/operator/IntRandomWalkOperator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,13 @@
import beast.base.core.Input;
import beast.base.core.Input.Validate;
import beast.base.inference.Operator;
import beast.base.spec.inference.parameter.IntScalarParam;
import beast.base.spec.inference.parameter.IntVectorParam;
import beast.base.util.Randomizer;


/**
* Random walk operator for integer-valued vector parameters.
* Random walk operator for integer-valued scalar or vector parameters.
* Selects a random dimension and perturbs it by a uniform integer
* amount within the specified window size.
*/
Expand All @@ -19,7 +20,9 @@ public class IntRandomWalkOperator extends Operator {
final public Input<Integer> windowSizeInput =
new Input<>("windowSize", "the size of the window both up and down", Validate.REQUIRED);
final public Input<IntVectorParam<?>> parameterInput =
new Input<>("parameter", "the parameter to operate a random walk on.", Validate.REQUIRED);
new Input<>("parameter", "the vector parameter to operate a random walk on.");
final public Input<IntScalarParam<?>> scalarInput =
new Input<>("scalar", "the scalar parameter to operate a random walk on.", Validate.XOR, parameterInput);

int windowSize = 1;

Expand All @@ -35,22 +38,40 @@ public void initAndValidate() {
@Override
public double proposal() {

final IntVectorParam<?> param = parameterInput.get();
if (parameterInput.get() != null) {
final IntVectorParam<?> param = parameterInput.get();

final int i = Randomizer.nextInt(param.size());
final int value = param.get(i);
final int newValue = value + Randomizer.nextInt(2 * windowSize + 1) - windowSize;
final int i = Randomizer.nextInt(param.size());
final int value = param.get(i);
final int newValue = value + Randomizer.nextInt(2 * windowSize + 1) - windowSize;

if (newValue < param.getLower() || newValue > param.getUpper()) {
// invalid move, can be rejected immediately
return Double.NEGATIVE_INFINITY;
}
if (newValue == value) {
// this saves calculating the posterior
return Double.NEGATIVE_INFINITY;
}
if (newValue < param.getLower() || newValue > param.getUpper()) {
// invalid move, can be rejected immediately
return Double.NEGATIVE_INFINITY;
}
if (newValue == value) {
// this saves calculating the posterior
return Double.NEGATIVE_INFINITY;
}

param.set(i, newValue);
} else {
final IntScalarParam<?> param = scalarInput.get();

param.set(i, newValue);
final int value = param.get();
final int newValue = value + Randomizer.nextInt(2 * windowSize + 1) - windowSize;

if (newValue < param.getLower() || newValue > param.getUpper()) {
// invalid move, can be rejected immediately
return Double.NEGATIVE_INFINITY;
}
if (newValue == value) {
// this saves calculating the posterior
return Double.NEGATIVE_INFINITY;
}

param.set(newValue);
}

return 0.0;
}
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