issue #3 more sensible BEAUti defaults

BEAST2-Dev · Apr 30, 2015 · 9d1a27a · 9d1a27a
1 parent 6d8e1ba
commit 9d1a27a
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Showing 3 changed files with 15 additions and 6 deletions.
diff --git a/src/snap/likelihood/SnAPTreeLikelihood.java b/src/snap/likelihood/SnAPTreeLikelihood.java
@@ -67,7 +67,7 @@ public class SnAPTreeLikelihood extends TreeLikelihood {
 			//"If true, constant-sites in the data will be used as part of the likelihood calculation. " +
 			//"If false (the default) constant sites will be removed from the sequence data and a normalization factor is " +
 			//"calculated for the likelihood.", 
-			false);
+			true);
 	public Input<IntegerParameter> ascSiteCountInput = new Input<IntegerParameter>("ascSiteCount", "Counts for number of ascertained sites");
 
 

diff --git a/src/snap/likelihood/SnapSubstitutionModel.java b/src/snap/likelihood/SnapSubstitutionModel.java
@@ -3,6 +3,7 @@
 import beast.core.Input;
 import beast.core.Input.Validate;
 import beast.core.parameter.RealParameter;
+import beast.core.util.Log;
 import beast.evolution.datatype.DataType;
 import beast.evolution.substitutionmodel.EigenDecomposition;
 import beast.evolution.substitutionmodel.SubstitutionModel;
@@ -18,7 +19,15 @@ public SnapSubstitutionModel() {
 	}
 
     @Override
-    public void initAndValidate() {}
+    public void initAndValidate() {
+    	double u = m_pU.get().getValue();
+    	double v  = m_pV.get().getValue();
+    	if (Math.abs(2*u*v-u-v) > 1e-6) {
+    		Log.warning.println("WARNING: Mutation rates are not normalised. "
+    				+ "This means that the tree height may not be in units of substitution any more. "
+    				+ "To ensure mutation rates are normalised, check that 2 * u * v = u + v, where v and u are the mutation rates.");
+    	}
+    }
 
 	@Override
     public void getTransitionProbabilities(Node node, double fStartTime, double fEndTime, double fRate, double[] matrix) {}

diff --git a/templates/SNAPP.xml b/templates/SNAPP.xml
@@ -131,7 +131,7 @@
         <distribution spec='snap.likelihood.SnAPPrior' name='distribution' id='snapprior.$(n)' rateprior='gamma'>
 			  <parameter name='alpha' id='alpha'  value='11.750' lower='0.0' estimate='false'/>
 			  <parameter name='beta' id='beta'   value='109.73' lower='0.0' estimate='false'/>
-			  <parameter name='lambda' id='lambda' value='0.00765' lower='0.0' estimate='false'/>
+			  <parameter name='lambda' id='lambda' value='0.01' lower='0.0' estimate='true'/>
 	          <parameter name='kappa' id='kappa' value='1.0' lower='0.0' estimate='false'/>
 		      <tree spec='beast.util.ClusterTree' id='Tree.$(n)' nodetype='snap.NodeData' clusterType='upgma' clock.rate="1.0">
 		            <input name='taxa' idref='snap.$(n)'/>
@@ -146,14 +146,14 @@
         <distribution id='vPrior.$(n)' spec='Prior' x='@v'><distr spec='OneOnX'/></distribution>
 
 
-         <snaptreelikelihood spec='snap.likelihood.SnAPTreeLikelihood' name='distribution' id='treeLikelihood.$(n)' initFromTree='false' pattern='coalescenceRate'>
+         <snaptreelikelihood spec='snap.likelihood.SnAPTreeLikelihood' name='distribution' id='treeLikelihood.$(n)' initFromTree='false' pattern='coalescenceRate' non-polymorphic='true'>
             <siteModel spec='sitemodel.SiteModel' id="MutationSiteModel.$(n)">
                 <parameter name='mutationRate' id='mutationRate' value='1.0' estimate='false'/>
                 <parameter name='proportionInvariant' id='proportionInvariant' value='0.0' estimate='false'/>
                 <parameter name='shape' value='2.0' id='shape' estimate='false'/>
                 <substModel spec='snap.likelihood.SnapSubstitutionModel' id='MutationModel' coalescenceRate='@coalescenceRate'>
-					  <parameter name='mutationRateV' id='v' value='0.588235' lower='0.0' estimate='false'/>
-					  <parameter name='mutationRateU' id='u' value='3.33333' lower='0.0' estimate='false'/>
+					  <parameter name='mutationRateV' id='v' value='1.0' lower='0.0' estimate='true'/>
+					  <parameter name='mutationRateU' id='u' value='1.0' lower='0.0' estimate='true'/>
                 </substModel>
             </siteModel>
             <data idref='snap.$(n)'/>