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gavryushkinagavryushkina
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example XML and version update
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+51
-33
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4 files changed

+51
-33
lines changed

‎build.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@
1818
<property name="srcBeast2" location="${beast2path}/src" />
1919
<property name="beast2classpath" location="${beast2path}/build" />
2020
<property name="Add_on_dir" value="${release_dir}/add-on" />
21-
<property name="version" value="1.0.2" />
21+
<property name="version" value="1.0.3" />
2222

2323
<import file="${beast2path}/build.xml" />
2424

‎examples/penguins.xml‎

Lines changed: 47 additions & 30 deletions
Original file line numberDiff line numberDiff line change
@@ -345,13 +345,14 @@ Pygoscelis_grandis_4.5=4.5 <taxa id="TaxonSet.penguins_morph2" sp
345345
</trait>
346346
<taxonset idref="TaxonSet.penguins_morph2"/>
347347
</tree>
348+
<parameter id="gammaShape.s:penguins_morph2" name="stateNode">1.0</parameter>
349+
<parameter id="gammaShape.s:penguins_dna" name="stateNode">1.0</parameter>
348350
<parameter id="freqParameter.s:penguins_dna" dimension="4" lower="0.0" name="stateNode" upper="1.0">0.25</parameter>
349351
<parameter id="rateAC.s:penguins_dna" lower="0.0" name="stateNode">1.0</parameter>
350352
<parameter id="rateAG.s:penguins_dna" lower="0.0" name="stateNode">1.0</parameter>
351353
<parameter id="rateAT.s:penguins_dna" lower="0.0" name="stateNode">1.0</parameter>
352354
<parameter id="rateCG.s:penguins_dna" lower="0.0" name="stateNode">1.0</parameter>
353355
<parameter id="rateGT.s:penguins_dna" lower="0.0" name="stateNode">1.0</parameter>
354-
<parameter id="gammaShape.s:penguins_dna" name="stateNode">1.0</parameter>
355356
<parameter id="ucldMean.c:penguins_morph" name="stateNode">1.0</parameter>
356357
<parameter id="ucldStdev.c:penguins_morph" lower="0.0" name="stateNode">0.1</parameter>
357358
<stateNode id="rateCategories.c:penguins_morph" spec="parameter.IntegerParameter" dimension="36">1</stateNode>
@@ -384,6 +385,11 @@ Pygoscelis_grandis_4.5=4.5 <taxa id="TaxonSet.penguins_morph2" sp
384385
<parameter id="RealParameter.0" lower="0.0" name="mean" upper="0.0">1.0</parameter>
385386
</Exponential>
386387
</prior>
388+
<prior id="GammaShapePrior.s:penguins_morph2" name="distribution" x="@gammaShape.s:penguins_morph2">
389+
<Exponential id="Exponential.01" name="distr">
390+
<parameter id="RealParameter.01" lower="0.0" name="mean" upper="0.0">1.0</parameter>
391+
</Exponential>
392+
</prior>
387393
<prior id="originPriorFBD.t:tree" name="distribution" x="@originFBD.t:tree">
388394
<Uniform id="Uniform.01" name="distr" upper="150.0"/>
389395
</prior>
@@ -427,33 +433,39 @@ Pygoscelis_grandis_4.5=4.5 <taxa id="TaxonSet.penguins_morph2" sp
427433
<Uniform id="Uniform.04" name="distr"/>
428434
</prior>
429435
<prior id="MeanRatePrior.c:penguins_dna" name="distribution" x="@ucldMean.c:penguins_dna">
430-
<Uniform id="Uniform.05" name="distr" upper="Infinity"/>
436+
<LogNormal id="LogNormalDistributionModel.0" name="distr">
437+
<parameter id="RealParameter.012" estimate="false" name="M">-3.5</parameter>
438+
<parameter id="RealParameter.013" estimate="false" lower="0.0" name="S" upper="5.0">1.0</parameter>
439+
</LogNormal>
431440
</prior>
432441
<prior id="MeanRatePrior.c:penguins_morph" name="distribution" x="@ucldMean.c:penguins_morph">
433-
<Uniform id="Uniform.06" name="distr" upper="Infinity"/>
442+
<LogNormal id="LogNormalDistributionModel.01" name="distr">
443+
<parameter id="RealParameter.014" estimate="false" name="M">-5.5</parameter>
444+
<parameter id="RealParameter.015" estimate="false" lower="0.0" name="S" upper="5.0">2.0</parameter>
445+
</LogNormal>
434446
</prior>
435447
<prior id="ucldStdevPrior.c:penguins_dna" name="distribution" x="@ucldStdev.c:penguins_dna">
436448
<Gamma id="Gamma.05" name="distr">
437-
<parameter id="RealParameter.012" estimate="false" name="alpha">0.5396</parameter>
438-
<parameter id="RealParameter.013" estimate="false" name="beta">0.3819</parameter>
449+
<parameter id="RealParameter.016" estimate="false" name="alpha">0.5396</parameter>
450+
<parameter id="RealParameter.017" estimate="false" name="beta">0.3819</parameter>
439451
</Gamma>
440452
</prior>
441453
<prior id="ucldStdevPrior.c:penguins_morph" name="distribution" x="@ucldStdev.c:penguins_morph">
442454
<Gamma id="Gamma.06" name="distr">
443-
<parameter id="RealParameter.014" estimate="false" name="alpha">0.5396</parameter>
444-
<parameter id="RealParameter.015" estimate="false" name="beta">0.3819</parameter>
455+
<parameter id="RealParameter.018" estimate="false" name="alpha">0.5396</parameter>
456+
<parameter id="RealParameter.019" estimate="false" name="beta">0.3819</parameter>
445457
</Gamma>
446458
</prior>
447459
</distribution>
448460
<distribution id="likelihood" spec="util.CompoundDistribution">
449461
<distribution id="morphTreeLikelihood.penguins_morph2" spec="TreeLikelihood" data="@penguins_morph2" tree="@Tree.t:tree">
450-
<siteModel id="morphSiteModel.s:penguins_morph2" spec="SiteModel">
462+
<siteModel id="morphSiteModel.s:penguins_morph2" spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape.s:penguins_morph2">
451463
<parameter id="mutationRate.s:penguins_morph2" estimate="false" name="mutationRate">1.0</parameter>
452464
<substModel id="LewisMK.s:penguins_morph2" spec="LewisMK" datatype="@morphDataType.penguins_morph2"/>
453465
</siteModel>
454466
<branchRateModel id="RelaxedClock.c:penguins_morph" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" clock.rate="@ucldMean.c:penguins_morph" rateCategories="@rateCategories.c:penguins_morph" tree="@Tree.t:tree">
455467
<LogNormal id="LogNormalDistributionModel.c:penguins_morph" S="@ucldStdev.c:penguins_morph" meanInRealSpace="true" name="distr">
456-
<parameter id="RealParameter.016" estimate="false" lower="0.0" name="M" upper="1.0">1.0</parameter>
468+
<parameter id="RealParameter.020" estimate="false" lower="0.0" name="M" upper="1.0">1.0</parameter>
457469
</LogNormal>
458470
</branchRateModel>
459471
</distribution>
@@ -465,7 +477,8 @@ data="@penguins_morph"
465477
filter="5,8,12,15,31-32,34,44,56,58,71-74,76,83,86,88,93-94,96-97,104,109,117-118,120,122,126-127,133,137,140,143,151,154,156,158,160,167,169,171,186-187,192,194-195,199-200,206,209-210,214,218,222,227,235,238,245">
466478
<userDataType id="morphDataType.penguins_morph3" spec="beast.evolution.datatype.StandardData" ambiguities="01 12" nrOfStates="3"/>
467479
</data>
468-
<siteModel id="morphSiteModel.s:penguins_morph3" spec="SiteModel">
480+
<!-- 4 gamma categories, gammaShape.s:penguins_morph2 is added and gammaShape.s:penguins_morph3 removed-->
481+
<siteModel id="morphSiteModel.s:penguins_morph3" spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape.s:penguins_morph2">
469482
<parameter id="mutationRate.s:penguins_morph3" estimate="false" name="mutationRate">1.0</parameter>
470483
<substModel id="LewisMK.s:penguins_morph3" spec="LewisMK" datatype="@morphDataType.penguins_morph3"/>
471484
</siteModel>
@@ -478,7 +491,8 @@ data="@penguins_morph"
478491
filter="1,4,35,38-39,42,60,63-64,100,136,166,205">
479492
<userDataType id="morphDataType.penguins_morph4" spec="beast.evolution.datatype.StandardData" ambiguities="01 12" nrOfStates="4"/>
480493
</data>
481-
<siteModel id="morphSiteModel.s:penguins_morph4" spec="SiteModel">
494+
<!-- 4 gamma categories, gammaShape.s:penguins_morph2 is added and gammaShape.s:penguins_morph4 removed-->
495+
<siteModel id="morphSiteModel.s:penguins_morph4" spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape.s:penguins_morph2">
482496
<parameter id="mutationRate.s:penguins_morph4" estimate="false" name="mutationRate">1.0</parameter>
483497
<substModel id="LewisMK.s:penguins_morph4" spec="LewisMK" datatype="@morphDataType.penguins_morph4"/>
484498
</siteModel>
@@ -491,7 +505,8 @@ data="@penguins_morph"
491505
filter="13,16,41,66">
492506
<userDataType id="morphDataType.penguins_morph5" spec="beast.evolution.datatype.StandardData" ambiguities="01 12" nrOfStates="5"/>
493507
</data>
494-
<siteModel id="morphSiteModel.s:penguins_morph5" spec="SiteModel">
508+
<!-- 4 gamma categories, gammaShape.s:penguins_morph2 is added and gammaShape.s:penguins_morph5 removed-->
509+
<siteModel id="morphSiteModel.s:penguins_morph5" spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape.s:penguins_morph2">
495510
<parameter id="mutationRate.s:penguins_morph5" estimate="false" name="mutationRate">1.0</parameter>
496511
<substModel id="LewisMK.s:penguins_morph5" spec="LewisMK" datatype="@morphDataType.penguins_morph5"/>
497512
</siteModel>
@@ -504,7 +519,8 @@ data="@penguins_morph"
504519
filter="11,21,124,173">
505520
<userDataType id="morphDataType.penguins_morph6" spec="beast.evolution.datatype.StandardData" ambiguities="01 12" nrOfStates="6"/>
506521
</data>
507-
<siteModel id="morphSiteModel.s:penguins_morph6" spec="SiteModel">
522+
<!-- 4 gamma categories, gammaShape.s:penguins_morph2 is added and gammaShape.s:penguins_morph6 removed-->
523+
<siteModel id="morphSiteModel.s:penguins_morph6" spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape.s:penguins_morph2">
508524
<parameter id="mutationRate.s:penguins_morph6" estimate="false" name="mutationRate">1.0</parameter>
509525
<substModel id="LewisMK.s:penguins_morph6" spec="LewisMK" datatype="@morphDataType.penguins_morph6"/>
510526
</siteModel>
@@ -517,7 +533,8 @@ data="@penguins_morph"
517533
filter="9">
518534
<userDataType id="morphDataType.penguins_morph7" spec="beast.evolution.datatype.StandardData" ambiguities="01 12" nrOfStates="7"/>
519535
</data>
520-
<siteModel id="morphSiteModel.s:penguins_morph7" spec="SiteModel">
536+
<!-- 4 gamma categories, gammaShape.s:penguins_morph2 is added and gammaShape.s:penguins_morph7 removed-->
537+
<siteModel id="morphSiteModel.s:penguins_morph7" spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape.s:penguins_morph2">
521538
<parameter id="mutationRate.s:penguins_morph7" estimate="false" name="mutationRate">1.0</parameter>
522539
<substModel id="LewisMK.s:penguins_morph7" spec="LewisMK" datatype="@morphDataType.penguins_morph7"/>
523540
</siteModel>
@@ -534,14 +551,18 @@ filter="9">
534551
</siteModel>
535552
<branchRateModel id="RelaxedClock.c:penguins_dna" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" clock.rate="@ucldMean.c:penguins_dna" rateCategories="@rateCategories.c:penguins_dna" tree="@Tree.t:tree">
536553
<LogNormal id="LogNormalDistributionModel.c:penguins_dna" S="@ucldStdev.c:penguins_dna" meanInRealSpace="true" name="distr">
537-
<parameter id="RealParameter.017" estimate="false" lower="0.0" name="M" upper="1.0">1.0</parameter>
554+
<parameter id="RealParameter.021" estimate="false" lower="0.0" name="M" upper="1.0">1.0</parameter>
538555
</LogNormal>
539556
</branchRateModel>
540557
</distribution>
541558
</distribution>
542559
</distribution>
543560

544-
<operator id="FrequenciesExchanger.s:penguins_dna" spec="DeltaExchangeOperator" delta="0.01" weight="1.0">
561+
<operator id="gammaShapeScaler.s:penguins_morph2" spec="ScaleOperator" parameter="@gammaShape.s:penguins_morph2" scaleFactor="0.5" weight="0.1"/>
562+
563+
<operator id="gammaShapeScaler.s:penguins_dna" spec="ScaleOperator" parameter="@gammaShape.s:penguins_dna" scaleFactor="0.5" weight="0.1"/>
564+
565+
<operator id="FrequenciesExchanger.s:penguins_dna" spec="DeltaExchangeOperator" delta="0.01" weight="0.1">
545566
<parameter idref="freqParameter.s:penguins_dna"/>
546567
</operator>
547568

@@ -555,8 +576,6 @@ filter="9">
555576

556577
<operator id="RateGTScaler.s:penguins_dna" spec="ScaleOperator" parameter="@rateGT.s:penguins_dna" scaleFactor="0.5" weight="0.1"/>
557578

558-
<operator id="gammaShapeScaler.s:penguins_dna" spec="ScaleOperator" parameter="@gammaShape.s:penguins_dna" scaleFactor="0.5" weight="1.0"/>
559-
560579
<operator id="ucldMeanScaler.c:penguins_morph" spec="ScaleOperator" parameter="@ucldMean.c:penguins_morph" scaleFactor="0.5" weight="1.0"/>
561580

562581
<operator id="ucldStdevScaler.c:penguins_morph" spec="ScaleOperator" parameter="@ucldStdev.c:penguins_morph" scaleFactor="0.5" weight="3.0"/>
@@ -567,8 +586,10 @@ filter="9">
567586

568587
<operator id="CategoriesUniform.c:penguins_morph" spec="UniformOperator" parameter="@rateCategories.c:penguins_morph" weight="10.0"/>
569588

570-
<operator id="relaxedUpDownOperator.c:penguins_morph" spec="UpDownOperator" scaleFactor="0.75" weight="3.0">
589+
<!-- relaxedUpDownOperator.c:penguins_morph and relaxedUpDownOperator.c:penguins_dna are merged to relaxedUpDownOperator.c:penguins -->
590+
<operator id="relaxedUpDownOperator.c:penguins" spec="UpDownOperator" scaleFactor="0.75" weight="3.0">
571591
<up idref="ucldMean.c:penguins_morph"/>
592+
<up idref="ucldMean.c:penguins_dna"/>
572593
<down idref="Tree.t:tree"/>
573594
</operator>
574595

@@ -582,11 +603,6 @@ filter="9">
582603

583604
<operator id="CategoriesUniform.c:penguins_dna" spec="UniformOperator" parameter="@rateCategories.c:penguins_dna" weight="10.0"/>
584605

585-
<operator id="relaxedUpDownOperator.c:penguins_dna" spec="UpDownOperator" scaleFactor="0.75" weight="3.0">
586-
<up idref="ucldMean.c:penguins_dna"/>
587-
<down idref="Tree.t:tree"/>
588-
</operator>
589-
590606
<operator id="originScalerFBD.t:tree" spec="ScaleOperator" parameter="@originFBD.t:tree" scaleFactor="0.75" weight="3.0"/>
591607

592608
<operator id="divRateScalerFBD.t:tree" spec="ScaleOperator" parameter="@diversificationRateFBD.t:tree" scaleFactor="0.75" weight="10.0"/>
@@ -616,20 +632,21 @@ filter="9">
616632
<log idref="likelihood"/>
617633
<log idref="prior"/>
618634
<log id="TreeHeight.t:tree" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:tree"/>
619-
<log idref="morphTreeLikelihood.penguins_morph5"/>
620-
<log idref="morphTreeLikelihood.penguins_morph7"/>
635+
<log idref="morphTreeLikelihood.penguins_morph3"/>
621636
<log idref="morphTreeLikelihood.penguins_morph2"/>
622-
<log idref="morphTreeLikelihood.penguins_morph4"/>
637+
<log idref="morphTreeLikelihood.penguins_morph7"/>
638+
<log idref="morphTreeLikelihood.penguins_morph5"/>
623639
<log idref="morphTreeLikelihood.penguins_morph6"/>
624-
<log idref="morphTreeLikelihood.penguins_morph3"/>
640+
<log idref="morphTreeLikelihood.penguins_morph4"/>
625641
<log idref="treeLikelihood.penguins_dna"/>
642+
<log idref="gammaShape.s:penguins_morph2"/>
643+
<log idref="gammaShape.s:penguins_dna"/>
626644
<log idref="freqParameter.s:penguins_dna"/>
627645
<log idref="rateAC.s:penguins_dna"/>
628646
<log idref="rateAG.s:penguins_dna"/>
629647
<log idref="rateAT.s:penguins_dna"/>
630648
<log idref="rateCG.s:penguins_dna"/>
631649
<log idref="rateGT.s:penguins_dna"/>
632-
<log idref="gammaShape.s:penguins_dna"/>
633650
<log idref="ucldMean.c:penguins_morph"/>
634651
<log idref="ucldStdev.c:penguins_morph"/>
635652
<log id="rate.c:penguins_morph" spec="beast.evolution.branchratemodel.RateStatistic" branchratemodel="@RelaxedClock.c:penguins_morph" tree="@Tree.t:tree"/>
@@ -652,7 +669,7 @@ filter="9">
652669
<log idref="prior"/>
653670
</logger>
654671

655-
<logger id="treelog.t:tree" fileName="penguins.trees" logEvery="1000" mode="tree">
672+
<logger id="treelog.t:tree" fileName="penguins.trees" logEvery="10000" mode="tree">
656673
<log id="TreeWithMetaDataLogger.t:tree" spec="beast.evolution.tree.TreeWithMetaDataLogger" branchratemodel="@RelaxedClock.c:penguins_morph" tree="@Tree.t:tree"/>
657674
</logger>
658675

‎examples/penguins_Mkv.xml‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -588,7 +588,8 @@ filter="9,246-252">
588588

589589
<operator id="CategoriesUniform.c:penguins_morph" spec="UniformOperator" parameter="@rateCategories.c:penguins_morph" weight="10.0"/>
590590

591-
<operator id="relaxedUpDownOperator.c:penguins_morph" spec="UpDownOperator" scaleFactor="0.75" weight="3.0">
591+
<!-- Merged relaxedUpDownOperator operators -->
592+
<operator id="relaxedUpDownOperator.c:penguins" spec="UpDownOperator" scaleFactor="0.75" weight="3.0">
592593
<up idref="ucldMean.c:penguins_morph"/>
593594
<up idref="ucldMean.c:penguins_dna"/>
594595
<down idref="Tree.t:tree"/>

‎version.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,3 @@
1-
<addon name='MM' version='1.0.2'>
1+
<addon name='MM' version='1.0.3'>
22
<depends on='beast2' atleast='2.3.0'/>
33
</addon>

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