Merge branch 'hmc-clock' of https://github.com/beast-dev/beast-mcmc i…

…nto hmc-clock
beast-dev · Apr 19, 2024 · d82b6d2 · d82b6d2
2 parents 4e405f2 + 1d52329
commit d82b6d2
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Showing 2 changed files with 11 additions and 1 deletion.
diff --git a/src/dr/evomodel/speciation/CachedGradientDelegate.java b/src/dr/evomodel/speciation/CachedGradientDelegate.java
@@ -82,6 +82,11 @@ private double[] getGradientLogDensityImpl() {
 
         int currentModelSegment = 0;
 
+        while (treeIntervals.getStartTime() >= modelBreakPoints[currentModelSegment]) { // TODO Maybe it's >= ?
+            ++currentModelSegment;
+            speciationModel.updateLikelihoodModelValues(currentModelSegment);
+        }
+
         provider.processGradientSampling(gradient, currentModelSegment, treeIntervals.getStartTime()); // TODO Fix for getStartTime() != 0.0
 
         for (int i = 0; i < treeIntervals.getIntervalCount(); ++i) {

diff --git a/src/dr/evomodel/speciation/EfficientSpeciationLikelihood.java b/src/dr/evomodel/speciation/EfficientSpeciationLikelihood.java
@@ -104,7 +104,12 @@ final BigFastTreeIntervals getTreeIntervals() {
 
         int currentModelSegment = 0;
 
-        double logL = speciationModel.processSampling(0, treeIntervals.getStartTime()); // TODO Fix for getStartTime() != 0.0
+        while (treeIntervals.getStartTime() >= modelBreakPoints[currentModelSegment]) { // TODO Maybe it's >= ?
+            ++currentModelSegment;
+            speciationModel.updateLikelihoodModelValues(currentModelSegment);
+        }
+
+        double logL = speciationModel.processSampling(currentModelSegment, treeIntervals.getStartTime()); // TODO Fix for getStartTime() != 0.0
 
         for (int i = 0; i < treeIntervals.getIntervalCount(); ++i) {