From de281bd0aebfacb57db19a6b1c5b2fc5690b6acb Mon Sep 17 00:00:00 2001
From: jordandouglas <jordandouglas@windowslive.com>
Date: Tue, 9 Aug 2022 11:26:41 +1200
Subject: [PATCH] clock rate fix first entry; extinction fraction beta prior

---
 fxtemplates/StarBeast3.xml                    |  3 ++
 fxtemplates/sb3TreePriors.xml                 |  5 ++-
 .../branchratemodel/StarBeast3Clock.java      | 37 ++++++++++++-------
 3 files changed, 31 insertions(+), 14 deletions(-)

diff --git a/fxtemplates/StarBeast3.xml b/fxtemplates/StarBeast3.xml
index 4589838..10987d0 100644
--- 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
index a820a5c..ddb0374 100644
--- 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
index 445e963..705cf2b 100644
--- 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;
@@ -205,6 +207,7 @@ public double getRateForBranch(Node node) {
     public static void estimateGeneClockRates(BeautiDoc doc) {
     	
     	
+    	
     	boolean first = true;
     	for (String str : doc.pluginmap.keySet()) {
     		
@@ -212,18 +215,26 @@ public static void estimateGeneClockRates(BeautiDoc doc) {
     		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);
+        			}
+    				
+    				
+				}
+    			
+    			
     			
     			
     		}