further preparation for v0.0.3

jordandouglas · Oct 23, 2024 · e334581 · e334581
1 parent fb67451
commit e334581
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/examples/DS/DS9.xml b/examples/DS/DS9.xml
@@ -110,7 +110,7 @@ name="alignment">
             <parameter id="kappa.s:DS9" spec="parameter.RealParameter" lower="0.0" name="stateNode">2.0</parameter>
             <parameter id="freqParameter.s:DS9" spec="parameter.RealParameter" dimension="4" lower="0.0" name="stateNode" upper="1.0">0.25</parameter>
             <parameter id="gammaShape.s:DS9" spec="parameter.RealParameter" lower="0.1" name="stateNode">1.0</parameter>
-            <stateNode id="GSMuseSpikeModel.c:DS9" spec="parameter.BooleanParameter">true</stateNode>
+            <stateNode id="GSMuseSpikeModel.c:DS9" spec="parameter.BooleanParameter">false</stateNode>
         </state>
         <init id="RandomTree.t:DS9" spec="RandomTree" estimate="false" initial="@Tree.t:DS9" taxa="@DS9">
             <populationModel id="ConstantPopulation0.t:DS9" spec="ConstantPopulation">
@@ -254,7 +254,7 @@ name="alignment">
         <operator id="GSMUpDownSpikeTree.c:DS9" spec="gammaspike.operator.StumpedTreeScaler" scaleFactor="0.1" tree="@Tree.t:DS9" weight="5.0">
             <down idref="GSMspikeMean.c:DS9"/>
         </operator>
-        <!-- <operator id="GSMBitFlipOperator.c:DS9" spec="operator.BitFlipOperator" parameter="@GSMuseSpikeModel.c:DS9" weight="1.0"/> -->
+        <operator id="GSMBitFlipOperator.c:DS9" spec="operator.BitFlipOperator" parameter="@GSMuseSpikeModel.c:DS9" weight="1.0"/>
         <logger id="tracelog" spec="Logger" fileName="$(filebase).log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
             <log idref="posterior"/>
             <log idref="likelihood"/>

diff --git a/fxtemplates/GammaSpikeClockModel.xml b/fxtemplates/GammaSpikeClockModel.xml
@@ -108,6 +108,7 @@
         </operator>
 
 		<log id="GSMrateStat.c:$(n)" spec="beast.base.evolution.RateStatistic" tree="@Tree.t:$(n)" branchratemodel="@GammaSpikeRelaxedClock.c:$(n)"/>
+      <log id="GSMSaltativeProportionLogger.c:$(n)" spec="gammaspike.logger.SaltativeProportionLogger" tree="@Tree.t:$(n)" clock="@GammaSpikeRelaxedClock.c:$(n)"/>
 
 			]]>
 
@@ -159,7 +160,9 @@
             <connect srcID='GSMspikeMean.c:$(n)' targetID='tracelog' inputName='log' if='inposterior(GSMspikeMean.c:$(n))'/>
             <connect srcID='GSMStumpedTreePrior.c:$(n)' targetID='tracelog' inputName='log' if='inposterior(GSMStumpedTreePrior.c:$(n))'/>
             <connect srcID='GSMrateStat.c:$(n)' targetID='tracelog' inputName='log' if='inlikelihood(GammaSpikeRelaxedClock.c:$(n))'/>
-
+            <connect srcID='GSMSaltativeProportionLogger.c:$(n)' targetID='tracelog' inputName='log' if='inlikelihood(GammaSpikeRelaxedClock.c:$(n))'/>
+
+
             <connect srcID='GammaSpikeRelaxedClock.c:$(n)' targetID='TreeWithMetaDataLogger.t:$(n)' inputName='branchratemodel'
                      if='inposterior(GammaSpikeRelaxedClock.c:$(n))'/>
             <connect srcID='GSMweightedSpikes.c:$(n)' targetID='TreeWithMetaDataLogger.t:$(n)' inputName='metadata' 
@@ -202,6 +205,7 @@
 
             <connect srcID='Tree.t:$(n)' targetID='GammaSpikeRelaxedClock.c:$(n)' inputName='tree' if='inlikelihood(GammaSpikeRelaxedClock.c:$(n))'/>
             <connect srcID='Tree.t:$(n)' targetID='GSMrateStat.c:$(n)' inputName='tree' if='inlikelihood(GammaSpikeRelaxedClock.c:$(n))'/>
+            <connect srcID='Tree.t:$(n)' targetID='GSMSaltativeProportionLogger.c:$(n)' inputName='tree' if='inlikelihood(GammaSpikeRelaxedClock.c:$(n))'/>
 
         </subtemplate>
 	</mergewith>