Add rates prior for UCLN, and TODO for logging LinguaPhylo/linguaPhyl…

…o#488
LinguaPhylo · Oct 4, 2024 · 17d7c93 · 17d7c93
1 parent 3e3c1ef
commit 17d7c93
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Showing 2 changed files with 14 additions and 2 deletions.
diff --git a/lphybeast/src/main/java/lphybeast/tobeast/generators/PhyloCTMCToBEAST.java b/lphybeast/src/main/java/lphybeast/tobeast/generators/PhyloCTMCToBEAST.java
@@ -176,8 +176,6 @@ public static void constructTreeAndBranchRate(PhyloCTMC phyloCTMC, GenericTreeLi
             if (generator instanceof UCLN ucln) {
 
                 UCRelaxedClockModel relaxedClockModel = (UCRelaxedClockModel) context.getBEASTObject(generator);
-                relaxedClockModel.setID(branchRates.getCanonicalId());
-
                 treeLikelihood.setInputValue("branchRateModel", relaxedClockModel);
 
                 if (skipBranchOperators == false) {

diff --git a/lphybeast/src/main/java/lphybeast/tobeast/generators/UCLNRelaxedClockToBEAST.java b/lphybeast/src/main/java/lphybeast/tobeast/generators/UCLNRelaxedClockToBEAST.java
@@ -3,9 +3,11 @@
 import beast.base.core.BEASTInterface;
 import beast.base.evolution.branchratemodel.UCRelaxedClockModel;
 import beast.base.inference.distribution.LogNormalDistributionModel;
+import beast.base.inference.distribution.Prior;
 import beast.base.inference.parameter.RealParameter;
 import lphy.base.distribution.UCLN;
 import lphy.base.evolution.tree.TimeTree;
+import lphy.core.model.GraphicalModelNode;
 import lphy.core.model.Value;
 import lphybeast.BEASTContext;
 import lphybeast.GeneratorToBEAST;
@@ -27,9 +29,21 @@ public UCRelaxedClockModel generatorToBEAST(UCLN ucln, BEASTInterface value, BEA
 
         if (value instanceof RealParameter rates) {
             ucRelaxedClockModel.setInputValue("rates", rates);
+
+            // rates prior, which is same LogNormal as UCLN
+            Prior ratesPrior = BEASTContext.createPrior(logNormDist, rates);
+            context.addBEASTObject(ratesPrior, ucln);
+
         } else throw new IllegalArgumentException("Value sampled from LPhy UCLN should be mapped to RealParameter ! " + value);
 
         ucRelaxedClockModel.initAndValidate();
+        GraphicalModelNode branchRates = context.getGraphicalModelNode(value);
+        // in case to duplicate with RandomValue id also called "branchRates"
+        ucRelaxedClockModel.setID(branchRates.getUniqueId() + ".model");
+
+        //TODO rm rates from log, replaced by
+        // <log id="ORCRatesStat" spec="beast.base.evolution.RateStatistic" branchratemodel="@OptimisedRelaxedClock" tree="@Tree"/>
+
         return ucRelaxedClockModel;
     }