clock rate fix first entry; extinction fraction beta prior

rbouckaert · Aug 8, 2022 · de281bd · de281bd
1 parent c631655
commit de281bd
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Showing 3 changed files with 31 additions and 14 deletions.
diff --git a/fxtemplates/StarBeast3.xml b/fxtemplates/StarBeast3.xml
@@ -445,6 +445,9 @@ ClusterTree/clusterType//'>
 			<mergepoint id="aux-sb3-partitiontemplate"/>
 
 
+			<connect method="starbeast3.evolution.branchratemodel.StarBeast3Clock.estimateGeneClockRates" />
+
+
 
 
 

diff --git a/fxtemplates/sb3TreePriors.xml b/fxtemplates/sb3TreePriors.xml
@@ -116,7 +116,10 @@ ExtinctionFractionPrior/index/=Priors/DeathRatePrior/'>
 				 <distr spec="beast.base.inference.distribution.Uniform" lower="0.0" upper="10000.0"/>
 			</prior>
 			<prior id="ExtinctionFractionPrior.t:$(n)" x="@ExtinctionFraction.t:$(n)">
-				 <distr spec="beast.base.inference.distribution.Uniform" lower="0.0" upper="1.0"/>
+			 	<Beta name="distr">
+                    <alpha spec="parameter.RealParameter" lower="0.0">5.0</alpha>
+                    <beta spec="parameter.RealParameter" lower="0.0">1.0</beta>
+                </Beta>
 			</prior>
 
 

diff --git a/src/starbeast3/evolution/branchratemodel/StarBeast3Clock.java b/src/starbeast3/evolution/branchratemodel/StarBeast3Clock.java
@@ -12,16 +12,18 @@
 package starbeast3.evolution.branchratemodel;
 
 
+
+import beastfx.app.inputeditor.BeautiDoc;
+
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
+import java.util.Set;
 
-import beastfx.app.inputeditor.BeautiDoc;
 import beast.base.core.BEASTInterface;
 import beast.base.core.Function;
 import beast.base.core.Input;
-import beast.base.inference.CalculationNode;
 import beast.base.inference.StateNode;
-import beast.base.inference.parameter.RealParameter;
 import beast.base.inference.util.InputUtil;
 import beast.base.core.Log;
 import beast.base.evolution.branchratemodel.BranchRateModel;
@@ -205,25 +207,34 @@ public double getRateForBranch(Node node) {
     public static void estimateGeneClockRates(BeautiDoc doc) {
 
 
+
     	boolean first = true;
     	for (String str : doc.pluginmap.keySet()) {
 
     		// Find the StarBeast3Clocks
     		BEASTInterface obj = doc.pluginmap.get(str);
     		if (obj instanceof StarBeast3Clock) {
 
-    			// Get the clock rate
     			StarBeast3Clock clock = (StarBeast3Clock)obj;
-    			//if (first) {
-    				//first=false;
-    				//clock.meanRateInput.get().isEstimatedInput.set(false);
-    			//}else {
-    				if (clock.meanRateInput.get() instanceof StateNode) {
-    					StateNode rp = (StateNode)clock.meanRateInput.get();
-    					//rp.isEstimatedInput.set(true);
-    				}
+    			if (clock.meanRateInput.get() != null && clock.meanRateInput.get() instanceof StateNode) {
+
+    				StateNode rp = (StateNode)clock.meanRateInput.get();
 
-    			//}
+    				//rp.isEstimatedInput.set(true);
+
+
+    				// Get the clock rate
+        			if (first) {
+        				first=false;
+        				rp.isEstimatedInput.set(false);
+        			}else {
+    					rp.isEstimatedInput.set(true);
+        			}
+
+
+				}
+
+
 
 
     		}