fix examples #8

BEAST2-Dev · Nov 17, 2022 · 1f8c928 · 1f8c928
1 parent e962fe2
commit 1f8c928
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Showing 12 changed files with 229 additions and 371 deletions.
diff --git a/examples/M0DALikelihood.xml b/examples/M0DALikelihood.xml
@@ -1,7 +1,8 @@
 <beast version="2.7" namespace="beast.base.core:beast.base.inference:beast.base.evolution.alignment:
-                     beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.util:
+                     beast.base.evolution.tree:beast.base.evolution.tree.coalescent:
                      beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:
-                     beast.base.evolution.likelihood:beast.base.evolution.operators:
+                     beast.base.evolution.likelihood:beast.base.util:
+                     beast.base.evolution.operator:beast.base.inference.operator:
                      codonmodels.evolution.alignment:codonmodels.evolution.datatype:
                      codonmodels.evolution.likelihood:codonmodels.evolution.operators:
                      codonmodels.evolution.tree:codonmodels.evolution.operators:
@@ -160,7 +161,6 @@
 
     <nodesStates spec="NodeStatesArray" id="nodesStates" >
         <data idref="codon.alignment"/>
-        <tree idref="tree"/>
     </nodesStates>
 
     <distribution id="daTreeLikelihood" spec="DataAugTreeLikelihood" threads="4">
@@ -242,7 +242,7 @@
 
 <!--        <operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" tree="@tree" weight="3.0"/>-->
 
-        <operator id="GibbsSampler" spec="GibbsSampler" nodesStates="@nodesStates" tree="@tree"
+        <operator id="GibbsSampler" spec="GibbsSamplingOperator" nodesStates="@nodesStates" tree="@tree"
                   DATreeLikelihood="@daTreeLikelihood" weight="15.0"/>
 
         <operator id="TreeRootScaler" spec="ScaleOperator" rootOnly="true" scaleFactor="0.75" tree="@tree" weight="3.0"/>

diff --git a/examples/M0StandardLikelihood.xml b/examples/M0StandardLikelihood.xml
@@ -1,7 +1,8 @@
 <beast version="2.7" namespace="beast.base.core:beast.base.inference:beast.base.evolution.alignment:
-                     beast.base.evolution.tree:beast.base.evolution.tree.coalescent:beast.base.util:
+                     beast.base.evolution.tree:beast.base.evolution.tree.coalescent:
                      beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:
-                     beast.base.evolution.likelihood:beast.base.evolution.operators:
+                     beast.base.evolution.likelihood:beast.base.util:
+                     beast.base.evolution.operator:beast.base.inference.operator:
                      codonmodels.evolution.alignment:codonmodels.evolution.datatype:
                      codonmodels.evolution.likelihood:codonmodels.evolution.operators:
                      codonmodels.evolution.tree:codonmodels.evolution.operators:

diff --git a/examples/beauti.m0.xml b/examples/beauti.m0.xml
diff --git a/examples/benchmarkData1024T1K.xml → examples/data/benchmarkData1024T1K.xml b/examples/benchmarkData1024T1K.xml → examples/data/benchmarkData1024T1K.xml
@@ -1,4 +1,9 @@
-<?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">
+<beast version="2.7" namespace="beast.base.core:beast.base.inference:
+                     beast.base.evolution.alignment:beast.base.evolution.tree.coalescent:
+                     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">
 
 <!-- used as data only for Benchmarking 1 and 2  -->
 <!-- 1024 taxa, 3000 nucleotides, 886 patterns -->

diff --git a/examples/codon.fasta → examples/data/codon.fasta b/examples/codon.fasta → examples/data/codon.fasta
diff --git a/examples/codon.nex → examples/data/codon.nex b/examples/codon.nex → examples/data/codon.nex
diff --git a/examples/testApproxM0.xml b/examples/testApproxM0.xml
@@ -1,6 +1,12 @@
-<beast version="2.7" 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.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood">
-
+<beast version="2.7" namespace="beast.base.core:beast.base.inference:beast.base.evolution.alignment:
+                     beast.base.evolution.tree:beast.base.evolution.tree.coalescent:
+                     beast.base.evolution.sitemodel:beast.base.evolution.substitutionmodel:
+                     beast.base.evolution.likelihood:beast.base.util:
+                     beast.base.evolution.operator:beast.base.inference.operator:
+                     codonmodels.evolution.alignment:codonmodels.evolution.datatype:
+                     codonmodels.evolution.likelihood:codonmodels.evolution.operators:
+                     codonmodels.evolution.tree:codonmodels.evolution.operators:
+                     codonmodels:codonmodels.util">
     <!-- ntax=6 nchar=768                                                        -->
     <data id="alignment" dataType="nucleotide">
         <sequence taxon="Human_Horai">