latent lik bug absolute

brj1 · Feb 17, 2023 · 8be891c · 8be891c
1 parent 3151483
commit 8be891c
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/dist/BBD.addon.zip b/dist/BBD.addon.zip
diff --git a/src/bbd/distributions/LatencyPrior.java b/src/bbd/distributions/LatencyPrior.java
@@ -89,7 +89,7 @@ public double calculateLogP() {
 
         final double tMRCA = tree.getRoot().getDate();
         final double rate = reactivationRate - latencyRate;
-        final double logRate = Math.log(rate);
+        final double logRate = Math.log(Math.abs(rate));
         final double tMRCAFactor = Math.exp(rate * tMRCA);
 
         for (final int i : taxonIndex) {
@@ -99,7 +99,7 @@ public double calculateLogP() {
                 // likelihood of going latent at `date` given sampling date
                 logP += rate * date +
                     logRate - 
-                    Math.log(Math.exp(rate * oriDate[k]) - tMRCAFactor);
+                    Math.log(Math.abs(Math.exp(rate * oriDate[k]) - tMRCAFactor));
             } else {
                 // not in range
                 return Double.NEGATIVE_INFINITY;