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src/dr/evomodel/treedatalikelihood/discrete/CtmcFrequencyModelGradient.java
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| /* | ||
| * CtmcFrequencyDistributionGradient.java | ||
| * | ||
| * Copyright (c) 2002-2024 Alexei Drummond, Andrew Rambaut and Marc Suchard | ||
| * | ||
| * This file is part of BEAST. | ||
| * See the NOTICE file distributed with this work for additional | ||
| * information regarding copyright ownership and licensing. | ||
| * | ||
| * BEAST is free software; you can redistribute it and/or modify | ||
| * it under the terms of the GNU Lesser General Public License as | ||
| * published by the Free Software Foundation; either version 2 | ||
| * of the License, or (at your option) any later version. | ||
| * | ||
| * BEAST is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Lesser General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Lesser General Public | ||
| * License along with BEAST; if not, write to the | ||
| * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, | ||
| * Boston, MA 02110-1301 USA | ||
| */ | ||
|
|
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| package dr.evomodel.treedatalikelihood.discrete; | ||
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| import dr.evomodel.substmodel.FrequencyModel; | ||
| import dr.evomodel.substmodel.GlmSubstitutionModel; | ||
| import dr.evomodel.substmodel.SubstitutionModel; | ||
| import dr.evomodel.treedatalikelihood.BeagleDataLikelihoodDelegate; | ||
| import dr.evomodel.treedatalikelihood.TreeDataLikelihood; | ||
| import dr.inference.loggers.LogColumn; | ||
| import dr.inference.model.Parameter; | ||
| import dr.util.Citation; | ||
|
|
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| import java.util.List; | ||
|
|
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| /** | ||
| * @author Marc A. Suchard | ||
| */ | ||
|
|
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| public class CtmcFrequencyModelGradient extends AbstractLogAdditiveSubstitutionModelGradient { | ||
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| private final FrequencyModel frequencyModel; | ||
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| public CtmcFrequencyModelGradient(String traitName, | ||
| TreeDataLikelihood treeDataLikelihood, | ||
| BeagleDataLikelihoodDelegate likelihoodDelegate, | ||
| GlmSubstitutionModel substitutionModel) { | ||
| super(traitName, treeDataLikelihood, likelihoodDelegate, substitutionModel, | ||
| ApproximationMode.FIRST_ORDER); | ||
|
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| List<SubstitutionModel> substitutionModels = likelihoodDelegate.getBranchModel().getSubstitutionModels(); | ||
| this.frequencyModel = likelihoodDelegate.getBranchModel().getRootFrequencyModel(); | ||
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| for (SubstitutionModel model : substitutionModels) { | ||
| if (frequencyModel != model.getFrequencyModel()) { | ||
| throw new RuntimeException("Not yet implemented"); | ||
| } | ||
| } | ||
| } | ||
|
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| @Override | ||
| protected double preProcessNormalization(double[] differentials, double[] generator, | ||
| boolean normalize) { | ||
| double total = 0.0; | ||
| if (normalize) { | ||
| for (int i = 0; i < stateCount; ++i) { | ||
| for (int j = 0; j < stateCount; ++j) { | ||
| final int ij = i * stateCount + j; | ||
| total += differentials[ij] * generator[ij]; | ||
| } | ||
| } | ||
| } | ||
| return total; | ||
| } | ||
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| @Override | ||
| double processSingleGradientDimension(int j, double[] differentials, double[] generator, double[] pi, | ||
| boolean normalize, double normalizationConstant) { | ||
| // derivative wrt pi[j] | ||
| double total = 0.0; | ||
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| for (int i = 0; i < stateCount; ++i) { | ||
| final int ii = i * stateCount + i; | ||
| final int ij = i * stateCount + j; | ||
| total += (differentials[ij] - differentials[ii]) * generator[ij]; | ||
| } | ||
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| if (normalize) { | ||
| for (int i = 0; i < stateCount; ++i) { | ||
| final int ij = i * stateCount + j; | ||
| total -= generator[ij] * pi[j] * normalizationConstant; | ||
| } | ||
| } | ||
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| return total; | ||
| } | ||
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| @Override | ||
| public Parameter getParameter() { | ||
| return frequencyModel.getFrequencyParameter(); | ||
| } | ||
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| @Override | ||
| public LogColumn[] getColumns() { | ||
| throw new RuntimeException("Not yet implemented"); | ||
| } | ||
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| @Override | ||
| public Citation.Category getCategory() { | ||
| return Citation.Category.SUBSTITUTION_MODELS; | ||
| } | ||
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| @Override | ||
| public String getDescription() { | ||
| return null; // TODO | ||
| } | ||
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| @Override | ||
| public List<Citation> getCitations() { | ||
| // TODO Update | ||
| return null; | ||
| } | ||
| } |
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