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uniquify operator IDs
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@denisekuehnert
denisekuehnert committed Feb 18, 2019
1 parent 6f6e6d4 commit 356508b
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Showing 4 changed files with 105 additions and 105 deletions.
50 changes: 25 additions & 25 deletions templates/BDSKY_contemp.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -63,25 +63,25 @@ suppressInputs='beast.evolution.speciation.BirthDeathSkylineModel.intervalTimes,
</distribution>
<!-- tree operators -->
<operator id='BDSKY_contemptreeScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="3" tree="@Tree.t:$(n)"/>
<operator id='BDSKY_contemptreeRootScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="3" tree="@Tree.t:$(n)" rootOnly='true'/>
<operator id='BDSKY_contempUniformOperator.t:$(n)' spec='Uniform' weight="30" tree="@Tree.t:$(n)"/>
<operator id='BDSKY_contempSubtreeSlide.t:$(n)' spec='SubtreeSlide' weight="15" gaussian="true" size="1.0" tree="@Tree.t:$(n)"/>
<operator id='BDSKY_contempnarrow.t:$(n)' spec='Exchange' isNarrow='true' weight="15" tree="@Tree.t:$(n)"/>
<operator id='BDSKY_contempwide.t:$(n)' spec='Exchange' isNarrow='false' weight="3" tree="@Tree.t:$(n)"/>
<operator id='BDSKY_contempWilsonBalding.t:$(n)' spec='WilsonBalding' weight="3" tree="@Tree.t:$(n)"/>
<operator id='BDSKY_contemp_treeScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="3" tree="@Tree.t:$(n)"/>
<operator id='BDSKY_contemp_treeRootScaler.t:$(n)' spec='ScaleOperator' scaleFactor="0.5" weight="3" tree="@Tree.t:$(n)" rootOnly='true'/>
<operator id='BDSKY_contemp_UniformOperator.t:$(n)' spec='Uniform' weight="30" tree="@Tree.t:$(n)"/>
<operator id='BDSKY_contemp_SubtreeSlide.t:$(n)' spec='SubtreeSlide' weight="15" gaussian="true" size="1.0" tree="@Tree.t:$(n)"/>
<operator id='BDSKY_contemp_narrow.t:$(n)' spec='Exchange' isNarrow='true' weight="15" tree="@Tree.t:$(n)"/>
<operator id='BDSKY_contemp_wide.t:$(n)' spec='Exchange' isNarrow='false' weight="3" tree="@Tree.t:$(n)"/>
<operator id='BDSKY_contemp_WilsonBalding.t:$(n)' spec='WilsonBalding' weight="3" tree="@Tree.t:$(n)"/>
<!-- BDSKY operators -->
<operator id='becomeUninfectiousRateScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="2" parameter="@becomeUninfectiousRate.t:$(n)"/>
<operator id='rhoScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="1" parameter="@rho.t:$(n)"/>
<operator id='reproductiveNumberScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="10" parameter="@reproductiveNumber.t:$(n)"/>
<operator id='BDSKY_contemp_becomeUninfectiousRateScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="2" parameter="@becomeUninfectiousRate.t:$(n)"/>
<operator id='BDSKY_contemp_rhoScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="1" parameter="@rho.t:$(n)"/>
<operator id='BDSKY_contemp_reproductiveNumberScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="10" parameter="@reproductiveNumber.t:$(n)"/>
<operator id="updownBD.t:$(n)" spec="UpDownOperator" scaleFactor=".75" weight="2">
<operator id="BDSKY_contemp_updownBD.t:$(n)" spec="UpDownOperator" scaleFactor=".75" weight="2">
<up idref="reproductiveNumber.t:$(n)"/>
<down idref="becomeUninfectiousRate.t:$(n)"/>
</operator>
<operator id='origScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="1" parameter="@origin.t:$(n)"/>
<operator id='BDSKY_contemp_origScaler.t:$(n)' spec='ScaleOperator' scaleFactor=".75" weight="1" parameter="@origin.t:$(n)"/>
]]>
<connect srcID='BirthDeathSkyContemporary.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inlikelihood(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'/>
<connect srcID='RandomTree.t:$(n)' targetID='mcmc' inputName='init' if='inposterior(Tree.t:$(n))'/>
Expand All @@ -91,19 +91,19 @@ suppressInputs='beast.evolution.speciation.BirthDeathSkylineModel.intervalTimes,
<connect srcID='becomeUninfectiousRatePriorContemp.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and becomeUninfectiousRate.t:$(n)/estimate=true'>prior on becomeUninfectiousRate.t:$(n)</connect>
<connect srcID='reproductiveNumberPriorContemp.t:$(n)' targetID='prior' inputName='distribution' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and reproductiveNumber.t:$(n)/estimate=true'>prior on reproductiveNumber.t:$(n)</connect>

<connect srcID='BDSKY_contemptreeScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Scales all internal nodes for tree t:$(n)</connect>
<connect srcID='BDSKY_contemptreeRootScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Scales root node for tree t:$(n)</connect>
<connect srcID='BDSKY_contempUniformOperator.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Draws new internal node heights uniformally for tree t:$(n)</connect>
<connect srcID='BDSKY_contempSubtreeSlide.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Performs subtree slide rearrangement of tree t:$(n)</connect>
<connect srcID='BDSKY_contempnarrow.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Narrow exchange performs local rearrangement of tree t:$(n)</connect>
<connect srcID='BDSKY_contempwide.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Wide exchange performs global rearrangement of tree t:$(n)</connect>
<connect srcID='BDSKY_contempWilsonBalding.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Performs Wilson-Balding global rearrangement of tree t:$(n)</connect>

<connect srcID='becomeUninfectiousRateScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and becomeUninfectiousRate.t:$(n)/estimate=true'/>
<connect srcID='rhoScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and rho.t:$(n)/estimate=true'/>
<connect srcID='reproductiveNumberScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and reproductiveNumber.t:$(n)/estimate=true'/>
<connect srcID='updownBD.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and reproductiveNumber.t:$(n)/estimate=true and becomeUninfectiousRate.t:$(n)/estimate=true'/>
<connect srcID='origScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and origin.t:$(n)/estimate=true'/>
<connect srcID='BDSKY_contemp_treeScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Scales all internal nodes for tree t:$(n)</connect>
<connect srcID='BDSKY_contemp_treeRootScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Scales root node for tree t:$(n)</connect>
<connect srcID='BDSKY_contemp_UniformOperator.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Draws new internal node heights uniformally for tree t:$(n)</connect>
<connect srcID='BDSKY_contemp_SubtreeSlide.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Performs subtree slide rearrangement of tree t:$(n)</connect>
<connect srcID='BDSKY_contemp_narrow.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Narrow exchange performs local rearrangement of tree t:$(n)</connect>
<connect srcID='BDSKY_contemp_wide.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Wide exchange performs global rearrangement of tree t:$(n)</connect>
<connect srcID='BDSKY_contemp_WilsonBalding.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and inposterior(Tree.t:$(n)) and Tree.t:$(n)/estimate=true'>Performs Wilson-Balding global rearrangement of tree t:$(n)</connect>

<connect srcID='BDSKY_contemp_becomeUninfectiousRateScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and becomeUninfectiousRate.t:$(n)/estimate=true'/>
<connect srcID='BDSKY_contemp_rhoScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and rho.t:$(n)/estimate=true'/>
<connect srcID='BDSKY_contemp_reproductiveNumberScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and reproductiveNumber.t:$(n)/estimate=true'/>
<connect srcID='BDSKY_contemp_updownBD.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and reproductiveNumber.t:$(n)/estimate=true and becomeUninfectiousRate.t:$(n)/estimate=true'/>
<connect srcID='BDSKY_contemp_origScaler.t:$(n)' targetID='mcmc' inputName='operator' if='inposterior(BirthDeathSkyContemporary.t:$(n)) and origin.t:$(n)/estimate=true'/>



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