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Rong419Rong419
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Merge pull request #1 from walterxie/master
migrate to 2.7
2 parents f084f52 + 54629b0 commit 49889f3

79 files changed

Lines changed: 1532 additions & 1476 deletions

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‎.classpath‎

Lines changed: 3 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -2,16 +2,14 @@
22
<classpath>
33
<classpathentry kind="src" path="src"/>
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<classpathentry combineaccessrules="false" kind="src" path="/beast2"/>
5-
<classpathentry combineaccessrules="false" kind="src" path="/BEASTLabs"/>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER">
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<attributes>
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<attribute name="module" value="true"/>
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</attributes>
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</classpathentry>
11-
<classpathentry kind="lib" path="/beast2/lib/commons-math3-3.1.1.jar"/>
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<classpathentry kind="lib" path="/beast2/lib/fest.jar"/>
13-
<classpathentry kind="lib" path="/beast2/lib/jam.jar"/>
14-
<classpathentry kind="lib" path="/beast2/lib/junit-4.8.2.jar"/>
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<classpathentry kind="lib" path="/beast2/lib/beagle.jar"/>
11+
<classpathentry combineaccessrules="false" kind="src" path="/BeastFX"/>
12+
<classpathentry kind="lib" path="/beast2/lib/commons-math3-3.6.1.jar"/>
13+
<classpathentry kind="lib" path="/beast2/lib/junit/junit-platform-console-standalone-1.8.2.jar"/>
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<classpathentry kind="output" path="bin"/>
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</classpath>

‎build.xml‎

Lines changed: 7 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@
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<property name="srcBeast2" location="${beast2path}/src" />
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<property name="beast2classpath" location="${beast2path}/build" />
2020
<property name="Add_on_dir" value="${release_dir}/add-on" />
21-
<property name="version" value="1.1.1" />
21+
<property name="version" value="1.2.0" />
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<import file="${beast2path}/build.xml" />
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@@ -27,15 +27,11 @@
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<path id="classpath">
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<pathelement path="${buildFastRelaxedClockLogNormal}"/>
30-
<fileset dir="${libBeast2}" includes="commons-math3-3.1.1.jar"/>
31-
<fileset dir="${libBeast2}" includes="junit-4.8.2.jar"/>
32-
<fileset dir="${libBeast2}" includes="antlr-runtime-4.7.jar"/>
30+
<fileset dir="${libBeast2}" includes="commons-math3-3.6.1.jar"/>
31+
<fileset dir="${libBeast2}" includes="junit/*.jar"/>
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<pathelement path="${beast2classpath}"/>
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<fileset dir="${beast2path}/lib" includes="jam.jar"/>
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<fileset dir="${beast2path}/lib" includes="beagle.jar"/>
36-
<fileset dir="${beast2path}/lib" includes="fest.jar"/>
37-
<fileset dir="${beast2path}/lib" includes="colt.jar"/>
38-
<pathelement path="../BEASTLabs/build"/>
34+
<pathelement path="../BeastFX/build"/>
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</path>
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<!-- start -->
@@ -173,7 +169,7 @@
173169
<mkdir dir="${Add_on_dir}" />
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<mkdir dir="${Add_on_dir}/lib" />
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<mkdir dir="${Add_on_dir}/examples" />
176-
<mkdir dir="${Add_on_dir}/templates" />
172+
<mkdir dir="${Add_on_dir}/fxtemplates" />
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<copy todir="${Add_on_dir}">
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<fileset file="version.xml"/>
@@ -187,8 +183,8 @@
187183
<copy todir="${Add_on_dir}">
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<fileset dir="${distFastRelaxedClockLogNormal}" includes="FastRelaxedClockLogNormal.src.jar" />
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</copy>
190-
<copy todir="${Add_on_dir}/templates">
191-
<fileset file="templates/*.xml" />
186+
<copy todir="${Add_on_dir}/fxtemplates">
187+
<fileset file="fxtemplates/*.xml" />
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</copy>
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<jar jarfile="${distFastRelaxedClockLogNormal}/FastRelaxedClockLogNormal.addon.v${version}.zip">

‎examples/Dengue4.xml‎

Lines changed: 36 additions & 36 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='Standard' beautistatus='' namespace="beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood" required="" version="2.6">
1+
<?xml version="1.0" encoding="UTF-8" standalone="no"?><beast beautitemplate='Standard' beautistatus='' namespace="beast.pkgmgmt:beast.base.core:beast.base.inference:beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:beast.pkgmgmt:beast.base.core:beast.base.inference.util:beast.evolution.nuc:beast.base.evolution.operator:beast.base.inference.operator:beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:beast.base.evolution.likelihood" required="" version="2.6">
22

33

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<data id="Dengue4" spec="Alignment" name="alignment">
@@ -21,22 +21,22 @@
2121
<sequence id="seq_D4Thai84" spec="Sequence" taxon="D4Thai84" totalcount="4" value="ATGCGATGCGTAGGAGTAGGGAACAGAGACTTTGTAGAAGGAGTCTCAGGTGGAGCATGGGTCGATCTGGTGCTAGAACATGGAGGATGTGTCACAACCATGGCCCAGGGAAAACCAACCCTGGATTTTGAACTGATCAAGACAACAGCCAAGGAAGTGGCTCTGTTAAGAACCTATTGCATTGAAGCCTCCATATCAAACATAACCACGGCAACAAGATGTCCAACGCAAGGAGAGCCTTACCTCAAAGAGGAACAAGATCAACAGTACATCTGCCGGAGAGACGTGGTAGACAGAGGGTGGGGCAACGGCTGTGGCTTGTTTGGGAAAGGAGGAGTTGTGACATGTGCGAAGTTTTCATGCTCGGGGAAGATAACGGGCAACTTAGTCCAAATTGAGAACCTTGAATACACAGTGGTTGTAACAGTCCACAATGGAGACACCCATGCTGTAGGAAATGATACATCCAACCACGGAGTGACAGCCACGATAACCCCCAGGTCACCATCGGTAGAAGTTAAATTACCGGACTATGGAGAATTAACACTTGATTGTGAACCTAGGTCCGGAATTGATTTTAATGAGATGATTCTGATGAAAATGAAAAAGAAAACGTGGCTCGTGCACAAGCAATGGTTTTTGGATCTACCTCTACCATGGACAGCAGGAGCAGACACGTCAGAAGTTCACTGGAATCACAAAGAGAGAATGGTGACATTCAAGGTTCCTCATGCCAAGAGACAGGATGTGACAGTGCTAGGATCTCAGGAAGGAGCCATGCATTCAGCCCTCGCCGGAGCCACAGAAGTGGATTCCGGTGATGGAAACCATATGTTTGCAGGACACTTAAAGTGTAAAGTTCGTATGGAGAAATTGAGAATCAAGGGAATGTCATACACGATGTGCTCAGGAAAGTTCTCAATTGATAAAGAGATGGCAGAAACACAGCATGGAACAACAGTGGTAAAGGTCAAGTATGAAGGCACTGGAGCTCCATGTAAAGTCCCCATAGAGATAAGAGATGTGAACAAGGAAAAAGTGGTTGGGCGTATCATCTCATCTACCCCTTTGGCTGAGAATACCAACAGTGTGACCAATATAGAATTGGAACCTCCTTTTGGGGATAGCTACATAGTGATAGGTGTGGGAGACAGTGCATTAACACTCCATTGGTTCAGGAAAGGGAGCTCCATTGGCAAGATGTTTGAGTCCACATACAGAGGTGCAAAGCGCATGGCCATTCTAGGTGAAACAGCTTGGGATTTTGGTTCTGTTGGCGGACTGCTCACATCATTGGGAAAGGCTGTACACCAGGTTTTTGGCAGTGTGTATACAACTATGTTTGGAGGAGTCTCATGGATGGTTAGAATCCTAATCGGGTTCTTAGTGTTGTGGATTGGCACGAATTCAAGAAACACTTCAATGGCTATGTCGTGCATAGCTGTTGGAGGAATTACTCTGTTTCTGGGCTTCACAGTTCATGCA"/>
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</data>
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24-
<map name="Uniform" >beast.math.distributions.Uniform</map>
25-
<map name="Exponential" >beast.math.distributions.Exponential</map>
26-
<map name="LogNormal" >beast.math.distributions.LogNormalDistributionModel</map>
27-
<map name="Normal" >beast.math.distributions.Normal</map>
28-
<map name="Beta" >beast.math.distributions.Beta</map>
29-
<map name="Gamma" >beast.math.distributions.Gamma</map>
30-
<map name="LaplaceDistribution" >beast.math.distributions.LaplaceDistribution</map>
31-
<map name="prior" >beast.math.distributions.Prior</map>
32-
<map name="InverseGamma" >beast.math.distributions.InverseGamma</map>
33-
<map name="OneOnX" >beast.math.distributions.OneOnX</map>
24+
<map name="Uniform" >beast.base.inference.distribution.Uniform</map>
25+
<map name="Exponential" >beast.base.inference.distribution.Exponential</map>
26+
<map name="LogNormal" >beast.base.inference.distribution.LogNormalDistributionModel</map>
27+
<map name="Normal" >beast.base.inference.distribution.Normal</map>
28+
<map name="Beta" >beast.base.inference.distribution.Beta</map>
29+
<map name="Gamma" >beast.base.inference.distribution.Gamma</map>
30+
<map name="LaplaceDistribution" >beast.base.inference.distribution.LaplaceDistribution</map>
31+
<map name="prior" >beast.base.inference.distribution.Prior</map>
32+
<map name="InverseGamma" >beast.base.inference.distribution.InverseGamma</map>
33+
<map name="OneOnX" >beast.base.inference.distribution.OneOnX</map>
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<run id="mcmc" spec="MCMC" chainLength="3000000">
3737
<state id="state" spec="State" storeEvery="5000">
38-
<tree id="Tree.t:Dengue4" spec="beast.evolution.tree.Tree" name="stateNode">
39-
<trait id="dateTrait.t:Dengue4" spec="beast.evolution.tree.TraitSet" traitname="date" value="D4Brazi82=82,D4ElSal83=83,D4ElSal94=94,D4Indon76=76,D4Indon77=77,D4Mexico84=84,D4NewCal81=81,D4Philip64=64,D4Philip56=56,D4Philip84=84,D4PRico86=86,D4SLanka78=78,D4Tahiti79=79,D4Tahiti85=85,D4Thai63=63,D4Thai78=78,D4Thai84=84">
38+
<tree id="Tree.t:Dengue4" spec="beast.base.evolution.tree.Tree" name="stateNode">
39+
<trait id="dateTrait.t:Dengue4" spec="beast.base.evolution.tree.TraitSet" traitname="date" value="D4Brazi82=82,D4ElSal83=83,D4ElSal94=94,D4Indon76=76,D4Indon77=77,D4Mexico84=84,D4NewCal81=81,D4Philip64=64,D4Philip56=56,D4Philip84=84,D4PRico86=86,D4SLanka78=78,D4Tahiti79=79,D4Tahiti85=85,D4Thai63=63,D4Thai78=78,D4Thai84=84">
4040
<taxa id="TaxonSet.Dengue4" spec="TaxonSet">
4141
<alignment idref="Dengue4"/>
4242
</taxa>
@@ -54,33 +54,33 @@
5454
<parameter id="rateCategories.c:Dengue4" spec="parameter.IntegerParameter" name="stateNode">1</parameter>
5555
</state>
5656

57-
<init id="RandomTree.t:Dengue4" spec="beast.evolution.tree.RandomTree" estimate="false" initial="@Tree.t:Dengue4" taxa="@Dengue4">
57+
<init id="RandomTree.t:Dengue4" spec="beast.base.evolution.tree.coalescent.RandomTree" estimate="false" initial="@Tree.t:Dengue4" taxa="@Dengue4">
5858
<populationModel id="ConstantPopulation0.t:Dengue4" spec="ConstantPopulation">
5959
<parameter id="randomPopSize.t:Dengue4" spec="parameter.RealParameter" name="popSize">1.0</parameter>
6060
</populationModel>
6161
</init>
6262

63-
<distribution id="posterior" spec="util.CompoundDistribution">
64-
<distribution id="prior" spec="util.CompoundDistribution">
63+
<distribution id="posterior" spec="beast.base.inference.CompoundDistribution">
64+
<distribution id="prior" spec="beast.base.inference.CompoundDistribution">
6565
<distribution id="FBD" spec="beast.evolution.speciation.SABirthDeathModel" conditionOnRhoSampling="true" birthRate="@FBDbirthRate" deathRate="@FBDdeathRate" samplingRate="@FBDsamplingRate" origin="@FBDorigin" tree="@Tree.t:Dengue4">
6666
<parameter id="FBDremovalProb" lower="0.0" name="removalProbability" upper="1.0">0.0</parameter>
6767
<parameter id="FBDrho" estimate="false" lower="0.0" name="rho" upper="1.0">1.0</parameter>
6868
</distribution>
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70-
<distribution id="FBDbirthRatePrior" spec="beast.math.distributions.Prior" x="@FBDbirthRate">
71-
<distr id="FBDbirthRateExponential" spec="beast.math.distributions.Exponential" offset="0.0" mean="0.0125"/>
70+
<distribution id="FBDbirthRatePrior" spec="beast.base.inference.distribution.Prior" x="@FBDbirthRate">
71+
<distr id="FBDbirthRateExponential" spec="beast.base.inference.distribution.Exponential" offset="0.0" mean="0.0125"/>
7272
</distribution>
7373

74-
<distribution id="FBDdeathRatePrior" spec="beast.math.distributions.Prior" x="@FBDdeathRate">
75-
<distr id="FBDdeathRateExponential" spec="beast.math.distributions.Exponential" offset="0.0" mean="0.01"/>
74+
<distribution id="FBDdeathRatePrior" spec="beast.base.inference.distribution.Prior" x="@FBDdeathRate">
75+
<distr id="FBDdeathRateExponential" spec="beast.base.inference.distribution.Exponential" offset="0.0" mean="0.01"/>
7676
</distribution>
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78-
<distribution id="FBDsamplingRatePrior" spec="beast.math.distributions.Prior" x="@FBDsamplingRate">
79-
<distr id="FBDsamplingRateExponential" spec="beast.math.distributions.Exponential" offset="0.0" mean="0.0066666"/>
78+
<distribution id="FBDsamplingRatePrior" spec="beast.base.inference.distribution.Prior" x="@FBDsamplingRate">
79+
<distr id="FBDsamplingRateExponential" spec="beast.base.inference.distribution.Exponential" offset="0.0" mean="0.0066666"/>
8080
</distribution>
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82-
<distribution id="FBDoriginPrior" spec="beast.math.distributions.Prior" x="@FBDorigin">
83-
<distr id="FBDoriginExponential" spec="beast.math.distributions.Exponential" offset="0.0" mean="298.935669052568"/>
82+
<distribution id="FBDoriginPrior" spec="beast.base.inference.distribution.Prior" x="@FBDorigin">
83+
<distr id="FBDoriginExponential" spec="beast.base.inference.distribution.Exponential" offset="0.0" mean="298.935669052568"/>
8484
</distribution>
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<prior id="FrequenciesPrior.s:Dengue4" name="distribution" x="@freqParameter.s:Dengue4">
@@ -108,7 +108,7 @@
108108
</prior>
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110110
</distribution>
111-
<distribution id="likelihood" spec="util.CompoundDistribution" useThreads="true">
111+
<distribution id="likelihood" spec="beast.base.inference.CompoundDistribution" useThreads="true">
112112
<distribution id="treeLikelihood.Dengue4" spec="ThreadedTreeLikelihood" data="@Dengue4" tree="@Tree.t:Dengue4">
113113
<siteModel id="SiteModel.s:Dengue4" spec="SiteModel">
114114
<parameter id="mutationRate.s:Dengue4" spec="parameter.RealParameter" estimate="false" name="mutationRate">1.0</parameter>
@@ -118,7 +118,7 @@
118118
<frequencies id="estimatedFreqs.s:Dengue4" spec="Frequencies" frequencies="@freqParameter.s:Dengue4"/>
119119
</substModel>
120120
</siteModel>
121-
<branchRateModel id="FastRelaxedClock.c:Dengue4" spec="beast.evolution.branchratemodel.UCRelaxedClockModel" clock.rate="@fastUcldMean.c:Dengue4"
121+
<branchRateModel id="FastRelaxedClock.c:Dengue4" spec="beast.base.evolution.branchratemodel.UCRelaxedClockModel" clock.rate="@fastUcldMean.c:Dengue4"
122122
rateCategories="@rateCategories.c:Dengue4" tree="@Tree.t:Dengue4">
123123
<LogNormal id="LogNormal.3" S="@fastUcldStdev.c:Dengue4" M="1.0" meanInRealSpace="true" name="distr"/>
124124
</branchRateModel>
@@ -131,13 +131,13 @@
131131
<operator id="FBDbirthRateScaler" spec="ScaleOperator" parameter="@FBDbirthRate" scaleFactor="0.75" weight="1.0"/>
132132
<operator id="FBDdeathRateScaler" spec="ScaleOperator" parameter="@FBDdeathRate" scaleFactor="0.75" weight="1.0"/>
133133
<operator id="FBDsamplingRateScaler" spec="ScaleOperator" parameter="@FBDsamplingRate" scaleFactor="0.75" weight="10.0"/>
134-
<operator id="FBDLeafToSA" spec="LeafToSampledAncestorJump" tree="@Tree.t:Dengue4" weight="10.0"/>
135-
<operator id="FBDSAWilsonBalding" spec="SAWilsonBalding" tree="@Tree.t:Dengue4" weight="10.0"/>
136-
<operator id="FBDSAWide" spec="SAExchange" isNarrow="false" tree="@Tree.t:Dengue4" weight="10.0"/>
137-
<operator id="FBDSANarrow" spec="SAExchange" tree="@Tree.t:Dengue4" weight="10.0"/>
138-
<operator id="FBDSAUniformOperator" spec="SAUniform" tree="@Tree.t:Dengue4" weight="20.0"/>
139-
<operator id="FBDSATreeRootScaler" spec="SAScaleOperator" rootOnly="true" scaleFactor="0.95" tree="@Tree.t:Dengue4" weight="1.0"/>
140-
<operator id="FBDSATreeScaler" spec="SAScaleOperator" scaleFactor="0.95" tree="@Tree.t:Dengue4" weight="3.0"/>
134+
<operator id="FBDLeafToSA" spec="sa.evolution.operators.LeafToSampledAncestorJump" tree="@Tree.t:Dengue4" weight="10.0"/>
135+
<operator id="FBDSAWilsonBalding" spec="sa.evolution.operators.SAWilsonBalding" tree="@Tree.t:Dengue4" weight="10.0"/>
136+
<operator id="FBDSAWide" spec="sa.evolution.operators.SAExchange" isNarrow="false" tree="@Tree.t:Dengue4" weight="10.0"/>
137+
<operator id="FBDSANarrow" spec="sa.evolution.operators.SAExchange" tree="@Tree.t:Dengue4" weight="10.0"/>
138+
<operator id="FBDSAUniformOperator" spec="sa.evolution.operators.SAUniform" tree="@Tree.t:Dengue4" weight="20.0"/>
139+
<operator id="FBDSATreeRootScaler" spec="sa.evolution.operators.SAScaleOperator" rootOnly="true" scaleFactor="0.95" tree="@Tree.t:Dengue4" weight="1.0"/>
140+
<operator id="FBDSATreeScaler" spec="sa.evolution.operators.SAScaleOperator" scaleFactor="0.95" tree="@Tree.t:Dengue4" weight="3.0"/>
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<operator id="FrequenciesExchanger.s:Dengue4" spec="DeltaExchangeOperator" delta="0.01" weight="0.5">
143143
<parameter idref="freqParameter.s:Dengue4"/>
@@ -166,7 +166,7 @@
166166
<log idref="likelihood"/>
167167
<log idref="prior"/>
168168
<log idref="treeLikelihood.Dengue4"/>
169-
<log id="TreeHeight.t:Dengue4" spec="beast.evolution.tree.TreeHeightLogger" tree="@Tree.t:Dengue4"/>
169+
<log id="TreeHeight.t:Dengue4" spec="beast.base.evolution.tree.TreeHeightLogger" tree="@Tree.t:Dengue4"/>
170170
<log idref="FBD"/>
171171
<log idref="FBDbirthRate"/>
172172
<log idref="FBDdeathRate"/>
@@ -177,7 +177,7 @@
177177
<log idref="fastUcldMean.c:Dengue4"/>
178178
<log idref="fastUcldStdev.c:Dengue4"/>
179179
<log idref="freqParameter.s:Dengue4"/>
180-
<log id="ratesStat.c:Dengue4" spec="beast.evolution.branchratemodel.RateStatistic" branchratemodel="@FastRelaxedClock.c:Dengue4" tree="@Tree.t:Dengue4"/>
180+
<log id="ratesStat.c:Dengue4" spec="beast.base.evolution.RateStatistic" branchratemodel="@FastRelaxedClock.c:Dengue4" tree="@Tree.t:Dengue4"/>
181181
</logger>
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183183
<logger id="screenlog" spec="Logger" logEvery="100000">
@@ -187,7 +187,7 @@
187187
</logger>
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189189
<logger id="treelog.t:Dengue4" spec="Logger" fileName="$(tree).trees" logEvery="1000" mode="tree">
190-
<log id="TreeWithMetaDataLogger.t:Dengue4" spec="beast.evolution.tree.TreeWithMetaDataLogger" branchratemodel="@FastRelaxedClock.c:Dengue4" tree="@Tree.t:Dengue4"/>
190+
<log id="TreeWithMetaDataLogger.t:Dengue4" spec="beast.base.evolution.TreeWithMetaDataLogger" branchratemodel="@FastRelaxedClock.c:Dengue4" tree="@Tree.t:Dengue4"/>
191191
</logger>
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</run>

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