Makes Bacter.xml compatible with beast 2.7 AVMN operators. #34

tgvaughan · Mar 30, 2023 · 9209788 · 9209788
1 parent 1d38c7d
commit 9209788
Showing 1 changed file with 46 additions and 10 deletions.
diff --git a/fxtemplates/Bacter.xml b/fxtemplates/Bacter.xml
@@ -228,6 +228,10 @@
             <operator id="CEslide.t:$(n)" spec="bacter.operators.ConvertedEdgeSlide" weight="1.0"
                 acg="@Tree.t:$(n)" apertureSize="0.05" />
 
+            <!-- Disabled tip-date operator.  (Does this even work with bacter?) -->
+            <operator id='allTipDatesRandomWalker.t:$(n)' spec='TipDatesRandomWalker'
+                windowSize="1" weight="0" tree="@Tree.t:$(n)"/>
+
             <!-- Parameter operators -->
             <operator id='popSizeScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.8"
                 weight="1" parameter="@popSize.t:$(n)"/>
@@ -236,16 +240,48 @@
             <operator id='deltaScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.8"
                 weight="1" parameter="@delta.t:$(n)"/>
 
-            <operator id='proportionInvariantScaler.s:$(n)' spec='ScaleOperator' scaleFactor="0.5"
-                weight="0.1" parameter="@proportionInvariant.s:$(n)"/>
-            <operator id='mutationRateScaler.s:$(n)' spec='ScaleOperator' scaleFactor="0.5"
-                weight="0.1" parameter="@mutationRate.s:$(n)"/>
-            <operator id='gammaShapeScaler.s:$(n)' spec='ScaleOperator' scaleFactor="0.5"
-                weight="0.1" parameter="@gammaShape.s:$(n)"/>
-            <operator id='allTipDatesRandomWalker.t:$(n)' spec='TipDatesRandomWalker'
-                windowSize="1" weight="0" tree="@Tree.t:$(n)"/>
-            <operator id='StrictClockRateScaler.c:$(n)' spec='ScaleOperator' scaleFactor="0.75"
-                weight="3" parameter='@clockRate.c:$(n)'/>
+
+            <operator id="AVMNOperator.$(n)" spec="beast.base.evolution.operator.kernel.AdaptableVarianceMultivariateNormalOperator" weight="0.1"
+                coefficient="1.0"
+                scaleFactor="1"
+                beta="0.05"
+                initial="800"
+                burnin="400"
+                every="1" allowNonsense="true">
+            	<transformations id="AVMNSumTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$LogConstrainedSumTransform" sum="1.0">
+            		<!-- frequencies -->
+            	</transformations>
+            	<transformations id="AVMNLogTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$LogTransform">
+             		<!-- site and substitution model parameters -->
+            	</transformations>
+            	<transformations id="AVMNNoTransform.$(n)" spec="beast.base.inference.operator.kernel.Transform$NoTransform">
+             		<!-- tree -->
+            	</transformations>
+            </operator>
+
+            <operator id="StrictClockRateScaler.c:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="1.5">
+                <parameter idref="clockRate.c:$(n)"/>
+    	        <operator idref="AVMNOperator.$(n)"/>
+        	    <operator id='StrictClockRateScalerX.c:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.75" weight="3" parameter='@clockRate.c:$(n)'/>
+	        </operator>
+
+	        <operator id="proportionInvariantScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
+                <parameter idref="proportionInvariant.s:$(n)"/>
+            	<operator idref="AVMNOperator.$(n)"/>
+            	<operator id='proportionInvariantScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@proportionInvariant.s:$(n)"/>
+        	</operator>
+
+        	<operator id="mutationRateScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
+                <parameter idref="mutationRate.s:$(n)"/>
+            	<operator idref="AVMNOperator.$(n)"/>
+	            <operator id='mutationRateScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@mutationRate.s:$(n)"/>
+        	</operator>
+
+        	<operator id="gammaShapeScaler.s:$(n)" spec="beast.base.evolution.operator.AdaptableOperatorSampler" weight="0.05">
+                <parameter idref="gammaShape.s:$(n)"/>
+            	<operator idref="AVMNOperator.$(n)"/>
+	            <operator id='gammaShapeScalerX.s:$(n)' spec='kernel.BactrianScaleOperator' scaleFactor="0.5" weight="0.1" parameter="@gammaShape.s:$(n)"/>
+        	</operator>
 
             <!-- ACG logger -->
             <plugin id='ACGlogger.t:$(n)' spec='beast.base.inference.Logger' logEvery='10000'