set upper boundary manually for RealParameter #169

LinguaPhylo · Nov 19, 2024 · 000f24f · 000f24f
1 parent 0a71ee9
commit 000f24f
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/lphybeast-flc/src/main/java/flc/lphybeast/tobeast/generators/LocalClockToBeast.java b/lphybeast-flc/src/main/java/flc/lphybeast/tobeast/generators/LocalClockToBeast.java
@@ -26,7 +26,12 @@ public FlexibleLocalClockModel generatorToBEAST(LocalClock localClock, BEASTInte
 
         Value<Double> rootRate = localClock.getRootRate();
         StrictLineageClockModel rootCladeModel = new StrictLineageClockModel();
-        rootCladeModel.initByName("clock.rate", new RealParameter(rootRate.valueToString()));
+
+        RealParameter rootRateParameter = new RealParameter(rootRate.valueToString());
+        // specify the parameter has the upper bound at 1.0
+        rootRateParameter.setInputValue("upper", 1.0);
+
+        rootCladeModel.initByName("clock.rate", rootRateParameter);
 
         Value<Object[]> clades = localClock.getClades();
         Value<Double[]> cladeRates = localClock.getCladeRates();