bella-companion 0.0.38__py3-none-any.whl → 0.0.42__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Potentially problematic release.
This version of bella-companion might be problematic. Click here for more details.
- bella_companion/eucovid/beast_configs/GLM.xml +170 -0
- bella_companion/eucovid/beast_configs/MLP.xml +170 -0
- bella_companion/eucovid/beast_configs/Nonparametric.xml +399 -0
- bella_companion/eucovid/data/case_data.tsv +346 -0
- bella_companion/eucovid/data/change_dates.tsv +8 -0
- bella_companion/eucovid/data/msa.fasta +79500 -0
- bella_companion/eucovid/data/osi.tsv +376 -0
- bella_companion/eucovid/data/predictors/all/closedborders_7e_nt.tsv +35 -0
- bella_companion/eucovid/data/predictors/all/dist_7e_ls.tsv +35 -0
- bella_companion/eucovid/data/predictors/all/flight_7e_ls.tsv +35 -0
- bella_companion/eucovid/data/predictors/all/flight_pop_x_7e_ls.tsv +35 -0
- bella_companion/eucovid/data/predictors/all/osi_x_7e_ls.tsv +35 -0
- bella_companion/eucovid/data/predictors/all/osi_y_7e_ls.tsv +35 -0
- bella_companion/eucovid/data/predictors/all/pop_x_7e_ls.tsv +35 -0
- bella_companion/eucovid/data/predictors/all/pop_y_7e_ls.tsv +35 -0
- bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv +35 -0
- bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv +6 -0
- bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv +3 -0
- bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv +20 -0
- bella_companion/platyrrhine/beast_config.xml +117 -0
- bella_companion/platyrrhine/data/change_times.csv +12 -0
- bella_companion/platyrrhine/data/traits.csv +122 -0
- bella_companion/platyrrhine/data/trees.nwk +100 -0
- bella_companion/simulations/beast_configs/epi-multitype/GLM.xml +81 -0
- bella_companion/simulations/beast_configs/epi-multitype/MLP.xml +81 -0
- bella_companion/simulations/beast_configs/epi-multitype/Nonparametric.xml +65 -0
- bella_companion/simulations/beast_configs/epi-skyline/GLM.xml +71 -0
- bella_companion/simulations/beast_configs/epi-skyline/MLP.xml +73 -0
- bella_companion/simulations/beast_configs/epi-skyline/Nonparametric.xml +57 -0
- bella_companion/simulations/beast_configs/fbd-2traits/GLM.xml +101 -0
- bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml +98 -0
- bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml +70 -0
- bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml +88 -0
- bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml +86 -0
- bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml +62 -0
- {bella_companion-0.0.38.dist-info → bella_companion-0.0.42.dist-info}/METADATA +1 -1
- bella_companion-0.0.42.dist-info/RECORD +76 -0
- bella_companion-0.0.38.dist-info/RECORD +0 -41
- {bella_companion-0.0.38.dist-info → bella_companion-0.0.42.dist-info}/WHEEL +0 -0
- {bella_companion-0.0.38.dist-info → bella_companion-0.0.42.dist-info}/entry_points.txt +0 -0
- {bella_companion-0.0.38.dist-info → bella_companion-0.0.42.dist-info}/top_level.txt +0 -0
|
@@ -0,0 +1,81 @@
|
|
|
1
|
+
<?xml version="1.0"?>
|
|
2
|
+
<beast
|
|
3
|
+
namespace="
|
|
4
|
+
:beast.base.evolution.operator.kernel
|
|
5
|
+
:beast.base.inference.parameter
|
|
6
|
+
:beast.base.inference.operator.kernel
|
|
7
|
+
:beast.base.inference
|
|
8
|
+
:beast.base.inference.distribution
|
|
9
|
+
:bdmmprime.distribution
|
|
10
|
+
:bdmmprime.parameterization
|
|
11
|
+
:feast.fileio
|
|
12
|
+
:feast.function
|
|
13
|
+
:feast.expressions"
|
|
14
|
+
version="2.5"
|
|
15
|
+
>
|
|
16
|
+
<map name="Normal">beast.base.inference.distribution.Normal</map>
|
|
17
|
+
<map name="Uniform">beast.base.inference.distribution.Uniform</map>
|
|
18
|
+
|
|
19
|
+
<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
|
|
20
|
+
<map name="TaxonSetFromTree">feast.fileio.TaxonSetFromTree</map>
|
|
21
|
+
<map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
|
|
22
|
+
<map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
|
|
23
|
+
|
|
24
|
+
<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
|
|
25
|
+
<TaxonSetFromTree id="taxonSet" tree="@tree"/>
|
|
26
|
+
<TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
|
|
27
|
+
<TypeSet id="typeSet" value="$(types)" typeTraitSet="@typeTraitSet"/>
|
|
28
|
+
|
|
29
|
+
<parameter id="finalSampleOffset" spec="ExpCalculator" value="$(processLength)-$(lastSampleTime)"/>
|
|
30
|
+
|
|
31
|
+
<Normal id="weightsPrior" mean="0" sigma="1"/>
|
|
32
|
+
<Uniform id="migrationRatePrior" upper="$(migrationRateUpper)"/>
|
|
33
|
+
|
|
34
|
+
<run spec="MCMC" chainLength="10000000">
|
|
35
|
+
<state id="state">
|
|
36
|
+
<stateNode spec="RealParameter" id="migrationRateScaler" value="0.01"/>
|
|
37
|
+
<stateNode spec="RealParameter" id="migrationRateW" value="0"/>
|
|
38
|
+
</state>
|
|
39
|
+
|
|
40
|
+
<distribution id="posterior" spec="CompoundDistribution">
|
|
41
|
+
<distribution id="likelihood" spec="CompoundDistribution">
|
|
42
|
+
<distribution spec="BirthDeathMigrationDistribution" tree="@tree" finalSampleOffset="@finalSampleOffset" typeTraitSet="@typeTraitSet">
|
|
43
|
+
<parameterization spec="EpiParameterization" processLength="$(processLength)" typeSet="@typeSet">
|
|
44
|
+
<Re spec="SkylineVectorParameter" skylineValues="$(reproductionNumber)" typeSet="@typeSet"/>
|
|
45
|
+
<becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="$(becomeUninfectiousRate)" typeSet="@typeSet"/>
|
|
46
|
+
<samplingProportion spec="SkylineVectorParameter" skylineValues="$(samplingProportion)" typeSet="@typeSet"/>
|
|
47
|
+
<migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" typeSet="@typeSet">
|
|
48
|
+
<skylineValues id="migrationRate" spec="glmprior.util.GLMLogLinear" coefficients="@migrationRateW" scaleFactor="@migrationRateScaler" transform="false">
|
|
49
|
+
<predictor spec="RealParameter" value="$(migrationPredictor)"/>
|
|
50
|
+
<predictor spec="RealParameter" value="$(randomPredictor)"/>
|
|
51
|
+
<indicators spec="BooleanParameter" value="1"/>
|
|
52
|
+
</skylineValues>
|
|
53
|
+
</migrationRate>
|
|
54
|
+
<removalProb spec="SkylineVectorParameter" skylineValues="1.0" typeSet="@typeSet"/>
|
|
55
|
+
</parameterization>
|
|
56
|
+
<startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
|
|
57
|
+
</distribution>
|
|
58
|
+
</distribution>
|
|
59
|
+
|
|
60
|
+
<distribution id="prior" spec="CompoundDistribution">
|
|
61
|
+
<distribution spec="Prior" x="@migrationRateScaler" distr="@weightsPrior"/>
|
|
62
|
+
<distribution spec="Prior" x="@migrationRateW" distr="@weightsPrior"/>
|
|
63
|
+
<distribution spec="Prior" x="@migrationRate" distr="@migrationRatePrior"/>
|
|
64
|
+
</distribution>
|
|
65
|
+
|
|
66
|
+
</distribution>
|
|
67
|
+
|
|
68
|
+
<operator spec="BactrianScaleOperator" parameter="@migrationRateScaler" weight="30.0"/>
|
|
69
|
+
<operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW" weight="30.0"/>
|
|
70
|
+
|
|
71
|
+
<logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
|
|
72
|
+
<log idref="posterior"/>
|
|
73
|
+
<log idref="prior"/>
|
|
74
|
+
<log idref="likelihood"/>
|
|
75
|
+
<log idref="migrationRateSP"/>
|
|
76
|
+
<log idref="migrationRateW"/>
|
|
77
|
+
<log idref="migrationRateScaler"/>
|
|
78
|
+
</logger>
|
|
79
|
+
</run>
|
|
80
|
+
|
|
81
|
+
</beast>
|
|
@@ -0,0 +1,81 @@
|
|
|
1
|
+
<?xml version="1.0"?>
|
|
2
|
+
<beast
|
|
3
|
+
namespace="
|
|
4
|
+
:beast.base.inference.parameter
|
|
5
|
+
:beast.base.inference.operator.kernel
|
|
6
|
+
:beast.base.inference
|
|
7
|
+
:beast.base.inference.distribution
|
|
8
|
+
:bdmmprime.distribution
|
|
9
|
+
:bdmmprime.parameterization
|
|
10
|
+
:feast.fileio
|
|
11
|
+
:feast.function
|
|
12
|
+
:feast.expressions"
|
|
13
|
+
version="2.5"
|
|
14
|
+
>
|
|
15
|
+
<map name="Normal">beast.base.inference.distribution.Normal</map>
|
|
16
|
+
|
|
17
|
+
<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
|
|
18
|
+
<map name="TaxonSetFromTree">feast.fileio.TaxonSetFromTree</map>
|
|
19
|
+
<map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
|
|
20
|
+
<map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
|
|
21
|
+
|
|
22
|
+
<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
|
|
23
|
+
<TaxonSetFromTree id="taxonSet" tree="@tree"/>
|
|
24
|
+
<TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
|
|
25
|
+
<TypeSet id="typeSet" value="$(types)" typeTraitSet="@typeTraitSet"/>
|
|
26
|
+
|
|
27
|
+
<parameter id="finalSampleOffset" spec="ExpCalculator" value="$(processLength)-$(lastSampleTime)"/>
|
|
28
|
+
|
|
29
|
+
<Normal id="weightsPrior" mean="0" sigma="1"/>
|
|
30
|
+
|
|
31
|
+
<run spec="MCMC" chainLength="10000000">
|
|
32
|
+
<state id="state">
|
|
33
|
+
<plate var="n" range="$(layersRange)">
|
|
34
|
+
<stateNode spec="RealParameter" id="migrationRateW$(n)" value="0"/>
|
|
35
|
+
</plate>
|
|
36
|
+
</state>
|
|
37
|
+
|
|
38
|
+
<distribution id="posterior" spec="CompoundDistribution">
|
|
39
|
+
<distribution id="likelihood" spec="CompoundDistribution">
|
|
40
|
+
<distribution spec="BirthDeathMigrationDistribution" tree="@tree" finalSampleOffset="@finalSampleOffset" typeTraitSet="@typeTraitSet">
|
|
41
|
+
<parameterization spec="EpiParameterization" processLength="$(processLength)" typeSet="@typeSet">
|
|
42
|
+
<Re spec="SkylineVectorParameter" skylineValues="$(reproductionNumber)" typeSet="@typeSet"/>
|
|
43
|
+
<becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="$(becomeUninfectiousRate)" typeSet="@typeSet"/>
|
|
44
|
+
<samplingProportion spec="SkylineVectorParameter" skylineValues="$(samplingProportion)" typeSet="@typeSet"/>
|
|
45
|
+
<migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" typeSet="@typeSet">
|
|
46
|
+
<skylineValues id="migrationRate" spec="bella.BayesMLP" nodes="$(nodes)">
|
|
47
|
+
<predictor spec="RealParameter" value="$(migrationPredictor)"/>
|
|
48
|
+
<predictor spec="RealParameter" value="$(randomPredictor)"/>
|
|
49
|
+
<plate var="n" range="$(layersRange)">
|
|
50
|
+
<weights idref="migrationRateW$(n)"/>
|
|
51
|
+
</plate>
|
|
52
|
+
<activationFunctionsOutput spec="bella.Sigmoid" upper="$(migrationRateUpper)"/>
|
|
53
|
+
</skylineValues>
|
|
54
|
+
</migrationRate>
|
|
55
|
+
<removalProb spec="SkylineVectorParameter" skylineValues="1.0" typeSet="@typeSet"/>
|
|
56
|
+
</parameterization>
|
|
57
|
+
<startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
|
|
58
|
+
</distribution>
|
|
59
|
+
</distribution>
|
|
60
|
+
|
|
61
|
+
<distribution id="prior" spec="CompoundDistribution">
|
|
62
|
+
<plate var="n" range="$(layersRange)">
|
|
63
|
+
<distribution spec="Prior" x="@migrationRateW$(n)" distr="@weightsPrior"/>
|
|
64
|
+
</plate>
|
|
65
|
+
</distribution>
|
|
66
|
+
</distribution>
|
|
67
|
+
|
|
68
|
+
<plate var="n" range="$(layersRange)">
|
|
69
|
+
<operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW$(n)" weight="30.0"/>
|
|
70
|
+
</plate>
|
|
71
|
+
|
|
72
|
+
<logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
|
|
73
|
+
<log idref="posterior"/>
|
|
74
|
+
<log idref="prior"/>
|
|
75
|
+
<log idref="likelihood"/>
|
|
76
|
+
<log idref="migrationRateSP"/>
|
|
77
|
+
<log idref="migrationRate"/>
|
|
78
|
+
</logger>
|
|
79
|
+
</run>
|
|
80
|
+
|
|
81
|
+
</beast>
|
|
@@ -0,0 +1,65 @@
|
|
|
1
|
+
<?xml version="1.0"?>
|
|
2
|
+
<beast
|
|
3
|
+
namespace="
|
|
4
|
+
:beast.base.evolution.operator.kernel
|
|
5
|
+
:beast.base.inference.parameter
|
|
6
|
+
:beast.base.inference
|
|
7
|
+
:beast.base.inference.distribution
|
|
8
|
+
:bdmmprime.distribution
|
|
9
|
+
:bdmmprime.parameterization
|
|
10
|
+
:feast.fileio
|
|
11
|
+
:feast.function
|
|
12
|
+
:feast.expressions"
|
|
13
|
+
version="2.5"
|
|
14
|
+
>
|
|
15
|
+
<map name="Uniform">beast.base.inference.distribution.Uniform</map>
|
|
16
|
+
|
|
17
|
+
<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
|
|
18
|
+
<map name="TaxonSetFromTree">feast.fileio.TaxonSetFromTree</map>
|
|
19
|
+
<map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
|
|
20
|
+
<map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
|
|
21
|
+
|
|
22
|
+
<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
|
|
23
|
+
<TaxonSetFromTree id="taxonSet" tree="@tree"/>
|
|
24
|
+
<TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
|
|
25
|
+
<TypeSet id="typeSet" value="$(types)" typeTraitSet="@typeTraitSet"/>
|
|
26
|
+
|
|
27
|
+
<parameter id="finalSampleOffset" spec="ExpCalculator" value="$(processLength)-$(lastSampleTime)"/>
|
|
28
|
+
|
|
29
|
+
<Uniform id="migrationRatePrior" upper="$(migrationRateUpper)"/>
|
|
30
|
+
|
|
31
|
+
<run spec="MCMC" chainLength="10000000">
|
|
32
|
+
<state id="state">
|
|
33
|
+
<stateNode id="migrationRate" spec="RealParameter" value="$(migrationRateInit)"/>
|
|
34
|
+
</state>
|
|
35
|
+
|
|
36
|
+
<distribution id="posterior" spec="CompoundDistribution">
|
|
37
|
+
<distribution id="likelihood" spec="CompoundDistribution">
|
|
38
|
+
<distribution spec="BirthDeathMigrationDistribution" tree="@tree" finalSampleOffset="@finalSampleOffset" typeTraitSet="@typeTraitSet">
|
|
39
|
+
<parameterization spec="EpiParameterization" processLength="$(processLength)" typeSet="@typeSet">
|
|
40
|
+
<Re spec="SkylineVectorParameter" skylineValues="$(reproductionNumber)" typeSet="@typeSet"/>
|
|
41
|
+
<becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="$(becomeUninfectiousRate)" typeSet="@typeSet"/>
|
|
42
|
+
<samplingProportion spec="SkylineVectorParameter" skylineValues="$(samplingProportion)" typeSet="@typeSet"/>
|
|
43
|
+
<migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" skylineValues="@migrationRate" typeSet="@typeSet"/>
|
|
44
|
+
<removalProb spec="SkylineVectorParameter" skylineValues="1.0" typeSet="@typeSet"/>
|
|
45
|
+
</parameterization>
|
|
46
|
+
<startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
|
|
47
|
+
</distribution>
|
|
48
|
+
</distribution>
|
|
49
|
+
|
|
50
|
+
<distribution id="prior" spec="CompoundDistribution">
|
|
51
|
+
<distribution spec="Prior" x="@migrationRate" distr="@migrationRatePrior"/>
|
|
52
|
+
</distribution>
|
|
53
|
+
</distribution>
|
|
54
|
+
|
|
55
|
+
<operator spec="BactrianScaleOperator" parameter="@migrationRate" weight="30.0"/>
|
|
56
|
+
|
|
57
|
+
<logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
|
|
58
|
+
<log idref="posterior"/>
|
|
59
|
+
<log idref="prior"/>
|
|
60
|
+
<log idref="likelihood"/>
|
|
61
|
+
<log idref="migrationRateSP"/>
|
|
62
|
+
</logger>
|
|
63
|
+
</run>
|
|
64
|
+
|
|
65
|
+
</beast>
|
|
@@ -0,0 +1,71 @@
|
|
|
1
|
+
<?xml version="1.0"?>
|
|
2
|
+
<beast
|
|
3
|
+
namespace="
|
|
4
|
+
:beast.base.evolution.operator.kernel
|
|
5
|
+
:beast.base.inference.parameter
|
|
6
|
+
:beast.base.inference.operator.kernel
|
|
7
|
+
:beast.base.inference
|
|
8
|
+
:beast.base.inference.distribution
|
|
9
|
+
:bdmmprime.distribution
|
|
10
|
+
:bdmmprime.parameterization
|
|
11
|
+
:feast.fileio
|
|
12
|
+
:feast.expressions"
|
|
13
|
+
version="2.5"
|
|
14
|
+
>
|
|
15
|
+
<map name="Normal">beast.base.inference.distribution.Normal</map>
|
|
16
|
+
<map name="Uniform">beast.base.inference.distribution.Uniform</map>
|
|
17
|
+
|
|
18
|
+
<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
|
|
19
|
+
|
|
20
|
+
<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
|
|
21
|
+
|
|
22
|
+
<parameter id="finalSampleOffset" spec="ExpCalculator" value="$(processLength)-$(lastSampleTime)"/>
|
|
23
|
+
|
|
24
|
+
<Normal id="weightsPrior" mean="0" sigma="1"/>
|
|
25
|
+
<Uniform id="reproductionNumberPrior" upper="$(reproductionNumberUpper)"/>
|
|
26
|
+
|
|
27
|
+
<run spec="MCMC" chainLength="10000000">
|
|
28
|
+
<state id="state">
|
|
29
|
+
<stateNode spec="RealParameter" id="reproductionNumberScaler" value="1"/>
|
|
30
|
+
<stateNode spec="RealParameter" id="reproductionNumberW" value="0"/>
|
|
31
|
+
</state>
|
|
32
|
+
|
|
33
|
+
<distribution id="posterior" spec="CompoundDistribution">
|
|
34
|
+
<distribution id="likelihood" spec="CompoundDistribution">
|
|
35
|
+
<distribution spec="BirthDeathMigrationDistribution" tree="@tree" finalSampleOffset="@finalSampleOffset">
|
|
36
|
+
<parameterization spec="EpiParameterization" processLength="$(processLength)">
|
|
37
|
+
<Re id="reproductionNumberSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
|
|
38
|
+
<skylineValues id="reproductionNumber" spec="glmprior.util.GLMLogLinear" coefficients="@reproductionNumberW" scaleFactor="@reproductionNumberScaler" transform="false">
|
|
39
|
+
<predictor spec="RealParameter" value="$(timePredictor)"/>
|
|
40
|
+
<predictor spec="RealParameter" value="$(randomPredictor)"/>
|
|
41
|
+
<indicators spec="BooleanParameter" value="1"/>
|
|
42
|
+
</skylineValues>
|
|
43
|
+
</Re>
|
|
44
|
+
<becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="$(becomeUninfectiousRate)"/>
|
|
45
|
+
<samplingProportion spec="SkylineVectorParameter" skylineValues="$(samplingProportion)"/>
|
|
46
|
+
<removalProb spec="SkylineVectorParameter" skylineValues="1.0"/>
|
|
47
|
+
</parameterization>
|
|
48
|
+
</distribution>
|
|
49
|
+
</distribution>
|
|
50
|
+
|
|
51
|
+
<distribution id="prior" spec="CompoundDistribution">
|
|
52
|
+
<distribution spec="Prior" x="@reproductionNumber" distr="@reproductionNumberPrior"/>
|
|
53
|
+
<distribution spec="Prior" x="@reproductionNumberScaler" distr="@weightsPrior"/>
|
|
54
|
+
<distribution spec="Prior" x="@reproductionNumberW" distr="@weightsPrior"/>
|
|
55
|
+
</distribution>
|
|
56
|
+
</distribution>
|
|
57
|
+
|
|
58
|
+
<operator spec="BactrianScaleOperator" parameter="@reproductionNumberScaler" weight="30.0"/>
|
|
59
|
+
<operator spec="BactrianRandomWalkOperator" parameter="@reproductionNumberW" weight="30.0"/>
|
|
60
|
+
|
|
61
|
+
<logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
|
|
62
|
+
<log idref="posterior"/>
|
|
63
|
+
<log idref="prior"/>
|
|
64
|
+
<log idref="likelihood"/>
|
|
65
|
+
<log idref="reproductionNumberSP"/>
|
|
66
|
+
<log idref="reproductionNumberW"/>
|
|
67
|
+
<log idref="reproductionNumberScaler"/>
|
|
68
|
+
</logger>
|
|
69
|
+
</run>
|
|
70
|
+
|
|
71
|
+
</beast>
|
|
@@ -0,0 +1,73 @@
|
|
|
1
|
+
<?xml version="1.0"?>
|
|
2
|
+
<beast
|
|
3
|
+
namespace="
|
|
4
|
+
:beast.base.evolution.operator.kernel
|
|
5
|
+
:beast.base.inference.parameter
|
|
6
|
+
:beast.base.inference.operator.kernel
|
|
7
|
+
:beast.base.inference
|
|
8
|
+
:beast.base.inference.distribution
|
|
9
|
+
:bdmmprime.distribution
|
|
10
|
+
:bdmmprime.parameterization
|
|
11
|
+
:feast.fileio
|
|
12
|
+
:feast.expressions"
|
|
13
|
+
version="2.5"
|
|
14
|
+
>
|
|
15
|
+
<map name="Normal">beast.base.inference.distribution.Normal</map>
|
|
16
|
+
|
|
17
|
+
<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
|
|
18
|
+
|
|
19
|
+
<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
|
|
20
|
+
|
|
21
|
+
<parameter id="finalSampleOffset" spec="ExpCalculator" value="$(processLength)-$(lastSampleTime)"/>
|
|
22
|
+
|
|
23
|
+
<Normal id="weightsPrior" mean="0" sigma="1"/>
|
|
24
|
+
|
|
25
|
+
<run spec="MCMC" chainLength="10000000">
|
|
26
|
+
<state id="state">
|
|
27
|
+
<plate var="n" range="$(layersRange)">
|
|
28
|
+
<stateNode spec="RealParameter" id="reproductionNumberW$(n)" value="0"/>
|
|
29
|
+
</plate>
|
|
30
|
+
</state>
|
|
31
|
+
|
|
32
|
+
<distribution id="posterior" spec="CompoundDistribution">
|
|
33
|
+
<distribution id="likelihood" spec="CompoundDistribution">
|
|
34
|
+
<distribution spec="BirthDeathMigrationDistribution" tree="@tree" finalSampleOffset="@finalSampleOffset">
|
|
35
|
+
<parameterization spec="EpiParameterization" processLength="$(processLength)">
|
|
36
|
+
<Re id="reproductionNumberSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
|
|
37
|
+
<skylineValues id="reproductionNumber" spec="bella.BayesMLP" nodes="$(nodes)">
|
|
38
|
+
<predictor spec="RealParameter" value="$(timePredictor)"/>
|
|
39
|
+
<predictor spec="RealParameter" value="$(randomPredictor)"/>
|
|
40
|
+
<plate var="n" range="$(layersRange)">
|
|
41
|
+
<weights idref="reproductionNumberW$(n)"/>
|
|
42
|
+
</plate>
|
|
43
|
+
<activationFunctionsOutput spec="bella.Sigmoid" upper="$(reproductionNumberUpper)"/>
|
|
44
|
+
</skylineValues>
|
|
45
|
+
</Re>
|
|
46
|
+
<becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="$(becomeUninfectiousRate)"/>
|
|
47
|
+
<samplingProportion spec="SkylineVectorParameter" skylineValues="$(samplingProportion)"/>
|
|
48
|
+
<removalProb spec="SkylineVectorParameter" skylineValues="1.0"/>
|
|
49
|
+
</parameterization>
|
|
50
|
+
</distribution>
|
|
51
|
+
</distribution>
|
|
52
|
+
|
|
53
|
+
<distribution id="prior" spec="CompoundDistribution">
|
|
54
|
+
<plate var="n" range="$(layersRange)">
|
|
55
|
+
<distribution spec="Prior" x="@reproductionNumberW$(n)" distr="@weightsPrior"/>
|
|
56
|
+
</plate>
|
|
57
|
+
</distribution>
|
|
58
|
+
</distribution>
|
|
59
|
+
|
|
60
|
+
<plate var="n" range="$(layersRange)">
|
|
61
|
+
<operator spec="BactrianRandomWalkOperator" parameter="@reproductionNumberW$(n)" weight="30.0"/>
|
|
62
|
+
</plate>
|
|
63
|
+
|
|
64
|
+
<logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
|
|
65
|
+
<log idref="posterior"/>
|
|
66
|
+
<log idref="prior"/>
|
|
67
|
+
<log idref="likelihood"/>
|
|
68
|
+
<log idref="reproductionNumberSP"/>
|
|
69
|
+
<log idref="reproductionNumber"/>
|
|
70
|
+
</logger>
|
|
71
|
+
</run>
|
|
72
|
+
|
|
73
|
+
</beast>
|
|
@@ -0,0 +1,57 @@
|
|
|
1
|
+
<?xml version="1.0"?>
|
|
2
|
+
<beast
|
|
3
|
+
namespace="
|
|
4
|
+
:beast.base.evolution.operator.kernel
|
|
5
|
+
:beast.base.inference.parameter
|
|
6
|
+
:beast.base.inference.operator.kernel
|
|
7
|
+
:beast.base.inference
|
|
8
|
+
:beast.base.inference.distribution
|
|
9
|
+
:bdmmprime.distribution
|
|
10
|
+
:bdmmprime.parameterization
|
|
11
|
+
:feast.fileio
|
|
12
|
+
:feast.expressions"
|
|
13
|
+
version="2.5"
|
|
14
|
+
>
|
|
15
|
+
<map name="Uniform">beast.base.inference.distribution.Uniform</map>
|
|
16
|
+
|
|
17
|
+
<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
|
|
18
|
+
|
|
19
|
+
<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
|
|
20
|
+
|
|
21
|
+
<parameter id="finalSampleOffset" spec="ExpCalculator" value="$(processLength)-$(lastSampleTime)"/>
|
|
22
|
+
|
|
23
|
+
<Uniform id="reproductionNumberPrior" upper="$(reproductionNumberUpper)"/>
|
|
24
|
+
|
|
25
|
+
<run spec="MCMC" chainLength="10000000">
|
|
26
|
+
<state id="state">
|
|
27
|
+
<stateNode id="reproductionNumber" spec="RealParameter" value="$(reproductionNumberInit)"/>
|
|
28
|
+
</state>
|
|
29
|
+
|
|
30
|
+
<distribution id="posterior" spec="CompoundDistribution">
|
|
31
|
+
<distribution id="likelihood" spec="CompoundDistribution">
|
|
32
|
+
<distribution spec="BirthDeathMigrationDistribution" tree="@tree" finalSampleOffset="@finalSampleOffset">
|
|
33
|
+
<parameterization spec="EpiParameterization" processLength="$(processLength)">
|
|
34
|
+
<Re id="reproductionNumberSP" spec="SkylineVectorParameter" skylineValues="@reproductionNumber" changeTimes="$(changeTimes)"/>
|
|
35
|
+
<becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="$(becomeUninfectiousRate)"/>
|
|
36
|
+
<samplingProportion spec="SkylineVectorParameter" skylineValues="$(samplingProportion)"/>
|
|
37
|
+
<removalProb spec="SkylineVectorParameter" skylineValues="1.0"/>
|
|
38
|
+
</parameterization>
|
|
39
|
+
</distribution>
|
|
40
|
+
</distribution>
|
|
41
|
+
|
|
42
|
+
<distribution id="prior" spec="CompoundDistribution">
|
|
43
|
+
<distribution spec="Prior" x="@reproductionNumber" distr="@reproductionNumberPrior"/>
|
|
44
|
+
</distribution>
|
|
45
|
+
</distribution>
|
|
46
|
+
|
|
47
|
+
<operator spec="BactrianScaleOperator" parameter="@reproductionNumber" weight="30.0" scaleFactor="0.75"/>
|
|
48
|
+
|
|
49
|
+
<logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
|
|
50
|
+
<log idref="posterior"/>
|
|
51
|
+
<log idref="prior"/>
|
|
52
|
+
<log idref="likelihood"/>
|
|
53
|
+
<log idref="reproductionNumberSP"/>
|
|
54
|
+
</logger>
|
|
55
|
+
</run>
|
|
56
|
+
|
|
57
|
+
</beast>
|
|
@@ -0,0 +1,101 @@
|
|
|
1
|
+
<?xml version="1.0"?>
|
|
2
|
+
<beast
|
|
3
|
+
namespace="
|
|
4
|
+
:beast.base.evolution.operator.kernel
|
|
5
|
+
:beast.base.inference.parameter
|
|
6
|
+
:beast.base.inference.operator.kernel
|
|
7
|
+
:beast.base.inference
|
|
8
|
+
:beast.base.inference.distribution
|
|
9
|
+
:bdmmprime.distribution
|
|
10
|
+
:bdmmprime.parameterization
|
|
11
|
+
:feast.fileio
|
|
12
|
+
:feast.function
|
|
13
|
+
:feast.expressions"
|
|
14
|
+
version="2.5"
|
|
15
|
+
>
|
|
16
|
+
<map name="Normal">beast.base.inference.distribution.Normal</map>
|
|
17
|
+
<map name="Uniform">beast.base.inference.distribution.Uniform</map>
|
|
18
|
+
|
|
19
|
+
<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
|
|
20
|
+
<map name="TaxonSetFromTree">feast.fileio.TaxonSetFromTree</map>
|
|
21
|
+
<map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
|
|
22
|
+
<map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
|
|
23
|
+
|
|
24
|
+
<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
|
|
25
|
+
<TaxonSetFromTree id="taxonSet" tree="@tree"/>
|
|
26
|
+
<TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
|
|
27
|
+
<TypeSet id="typeSet" value="$(types)" typeTraitSet="@typeTraitSet"/>
|
|
28
|
+
|
|
29
|
+
<Normal id="weightsPrior" mean="0" sigma="1"/>
|
|
30
|
+
<Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
|
|
31
|
+
<Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
|
|
32
|
+
|
|
33
|
+
<run spec="MCMC" chainLength="10000000">
|
|
34
|
+
<state id="state">
|
|
35
|
+
<stateNode spec="RealParameter" id="birthRateScaler" value="1"/>
|
|
36
|
+
<stateNode spec="RealParameter" id="deathRateScaler" value="1"/>
|
|
37
|
+
<stateNode spec="RealParameter" id="birthRateW" value="0"/>
|
|
38
|
+
<stateNode spec="RealParameter" id="deathRateW" value="0"/>
|
|
39
|
+
</state>
|
|
40
|
+
|
|
41
|
+
<distribution id="posterior" spec="CompoundDistribution">
|
|
42
|
+
<distribution id="likelihood" spec="CompoundDistribution">
|
|
43
|
+
<distribution spec="BirthDeathMigrationDistribution" tree="@tree" typeTraitSet="@typeTraitSet">
|
|
44
|
+
<parameterization spec="CanonicalParameterization" processLength="$(processLength)" typeSet="@typeSet">
|
|
45
|
+
<birthRate id="birthRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)" typeSet="@typeSet">
|
|
46
|
+
<skylineValues id="birthRate" spec="glmprior.util.GLMLogLinear" coefficients="@birthRateW" scaleFactor="@birthRateScaler" transform="false">
|
|
47
|
+
<predictor spec="RealParameter" value="$(timePredictor)"/>
|
|
48
|
+
<predictor spec="RealParameter" value="$(trait1Predictor)"/>
|
|
49
|
+
<predictor spec="RealParameter" value="$(trait2Predictor)"/>
|
|
50
|
+
<predictor spec="RealParameter" value="$(randomPredictor)"/>
|
|
51
|
+
<indicators spec="BooleanParameter" value="1"/>
|
|
52
|
+
</skylineValues>
|
|
53
|
+
</birthRate>
|
|
54
|
+
<deathRate id="deathRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)" typeSet="@typeSet">
|
|
55
|
+
<skylineValues id="deathRate" spec="glmprior.util.GLMLogLinear" coefficients="@deathRateW" scaleFactor="@deathRateScaler" transform="false">
|
|
56
|
+
<predictor spec="RealParameter" value="$(timePredictor)"/>
|
|
57
|
+
<predictor spec="RealParameter" value="$(trait1Predictor)"/>
|
|
58
|
+
<predictor spec="RealParameter" value="$(trait2Predictor)"/>
|
|
59
|
+
<predictor spec="RealParameter" value="$(randomPredictor)"/>
|
|
60
|
+
<indicators spec="BooleanParameter" value="1"/>
|
|
61
|
+
</skylineValues>
|
|
62
|
+
</deathRate>
|
|
63
|
+
<migrationRate spec="SkylineMatrixParameter" skylineValues="$(migrationRate)" typeSet="@typeSet"/>
|
|
64
|
+
<samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)" typeSet="@typeSet"/>
|
|
65
|
+
<removalProb spec="SkylineVectorParameter" skylineValues="0.0" typeSet="@typeSet"/>
|
|
66
|
+
<rhoSampling spec="TimedParameter" values="1" times="$(processLength)" typeSet="@typeSet"/>
|
|
67
|
+
</parameterization>
|
|
68
|
+
<startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
|
|
69
|
+
</distribution>
|
|
70
|
+
</distribution>
|
|
71
|
+
|
|
72
|
+
<distribution id="prior" spec="CompoundDistribution">
|
|
73
|
+
<distribution spec="Prior" x="@birthRateScaler" distr="@weightsPrior"/>
|
|
74
|
+
<distribution spec="Prior" x="@deathRateScaler" distr="@weightsPrior"/>
|
|
75
|
+
<distribution spec="Prior" x="@birthRateW" distr="@weightsPrior"/>
|
|
76
|
+
<distribution spec="Prior" x="@deathRateW" distr="@weightsPrior"/>
|
|
77
|
+
<distribution spec="Prior" x="@birthRate" distr="@birthRatePrior"/>
|
|
78
|
+
<distribution spec="Prior" x="@deathRate" distr="@deathRatePrior"/>
|
|
79
|
+
</distribution>
|
|
80
|
+
|
|
81
|
+
</distribution>
|
|
82
|
+
|
|
83
|
+
<operator spec="BactrianScaleOperator" parameter="@birthRateScaler" weight="30.0"/>
|
|
84
|
+
<operator spec="BactrianScaleOperator" parameter="@deathRateScaler" weight="30.0"/>
|
|
85
|
+
<operator spec="BactrianRandomWalkOperator" parameter="@birthRateW" weight="30.0"/>
|
|
86
|
+
<operator spec="BactrianRandomWalkOperator" parameter="@deathRateW" weight="30.0"/>
|
|
87
|
+
|
|
88
|
+
<logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
|
|
89
|
+
<log idref="posterior"/>
|
|
90
|
+
<log idref="prior"/>
|
|
91
|
+
<log idref="likelihood"/>
|
|
92
|
+
<log idref="birthRateSP"/>
|
|
93
|
+
<log idref="deathRateSP"/>
|
|
94
|
+
<log idref="birthRateW"/>
|
|
95
|
+
<log idref="deathRateW"/>
|
|
96
|
+
<log idref="birthRateScaler"/>
|
|
97
|
+
<log idref="deathRateScaler"/>
|
|
98
|
+
</logger>
|
|
99
|
+
</run>
|
|
100
|
+
|
|
101
|
+
</beast>
|
|
@@ -0,0 +1,98 @@
|
|
|
1
|
+
<?xml version="1.0"?>
|
|
2
|
+
<beast
|
|
3
|
+
namespace="
|
|
4
|
+
:beast.base.inference.parameter
|
|
5
|
+
:beast.base.inference.operator.kernel
|
|
6
|
+
:beast.base.inference
|
|
7
|
+
:beast.base.inference.distribution
|
|
8
|
+
:bdmmprime.distribution
|
|
9
|
+
:bdmmprime.parameterization
|
|
10
|
+
:feast.fileio
|
|
11
|
+
:feast.function
|
|
12
|
+
:feast.expressions"
|
|
13
|
+
version="2.5"
|
|
14
|
+
>
|
|
15
|
+
<map name="Normal">beast.base.inference.distribution.Normal</map>
|
|
16
|
+
|
|
17
|
+
<map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
|
|
18
|
+
<map name="TaxonSetFromTree">feast.fileio.TaxonSetFromTree</map>
|
|
19
|
+
<map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
|
|
20
|
+
<map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
|
|
21
|
+
|
|
22
|
+
<TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
|
|
23
|
+
<TaxonSetFromTree id="taxonSet" tree="@tree"/>
|
|
24
|
+
<TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
|
|
25
|
+
<TypeSet id="typeSet" value="$(types)" typeTraitSet="@typeTraitSet"/>
|
|
26
|
+
|
|
27
|
+
<Normal id="weightsPrior" mean="0" sigma="1"/>
|
|
28
|
+
|
|
29
|
+
<run spec="MCMC" chainLength="10000000">
|
|
30
|
+
<state id="state">
|
|
31
|
+
<plate var="n" range="$(layersRange)">
|
|
32
|
+
<stateNode spec="RealParameter" id="birthRateW$(n)" value="0"/>
|
|
33
|
+
<stateNode spec="RealParameter" id="deathRateW$(n)" value="0"/>
|
|
34
|
+
</plate>
|
|
35
|
+
</state>
|
|
36
|
+
|
|
37
|
+
<distribution id="posterior" spec="CompoundDistribution">
|
|
38
|
+
<distribution id="likelihood" spec="CompoundDistribution">
|
|
39
|
+
<distribution spec="BirthDeathMigrationDistribution" tree="@tree" typeTraitSet="@typeTraitSet">
|
|
40
|
+
<parameterization spec="CanonicalParameterization" processLength="$(processLength)" typeSet="@typeSet">
|
|
41
|
+
<birthRate id="birthRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)" typeSet="@typeSet">
|
|
42
|
+
<skylineValues id="birthRate" spec="bella.BayesMLP" nodes="$(nodes)">
|
|
43
|
+
<predictor spec="RealParameter" value="$(timePredictor)"/>
|
|
44
|
+
<predictor spec="RealParameter" value="$(trait1Predictor)"/>
|
|
45
|
+
<predictor spec="RealParameter" value="$(trait2Predictor)"/>
|
|
46
|
+
<predictor spec="RealParameter" value="$(randomPredictor)"/>
|
|
47
|
+
<plate var="n" range="$(layersRange)">
|
|
48
|
+
<weights idref="birthRateW$(n)"/>
|
|
49
|
+
</plate>
|
|
50
|
+
<activationFunctionsOutput spec="bella.Sigmoid" upper="$(birthRateUpper)"/>
|
|
51
|
+
</skylineValues>
|
|
52
|
+
</birthRate>
|
|
53
|
+
<deathRate id="deathRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)" typeSet="@typeSet">
|
|
54
|
+
<skylineValues id="deathRate" spec="bella.BayesMLP" nodes="$(nodes)">
|
|
55
|
+
<predictor spec="RealParameter" value="$(timePredictor)"/>
|
|
56
|
+
<predictor spec="RealParameter" value="$(trait1Predictor)"/>
|
|
57
|
+
<predictor spec="RealParameter" value="$(trait2Predictor)"/>
|
|
58
|
+
<predictor spec="RealParameter" value="$(randomPredictor)"/>
|
|
59
|
+
<plate var="n" range="$(layersRange)">
|
|
60
|
+
<weights idref="deathRateW$(n)"/>
|
|
61
|
+
</plate>
|
|
62
|
+
<activationFunctionsOutput spec="bella.Sigmoid" upper="$(deathRateUpper)"/>
|
|
63
|
+
</skylineValues>
|
|
64
|
+
</deathRate>
|
|
65
|
+
<migrationRate spec="SkylineMatrixParameter" skylineValues="$(migrationRate)" typeSet="@typeSet"/>
|
|
66
|
+
<samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)" typeSet="@typeSet"/>
|
|
67
|
+
<removalProb spec="SkylineVectorParameter" skylineValues="0.0" typeSet="@typeSet"/>
|
|
68
|
+
<rhoSampling spec="TimedParameter" values="1" times="$(processLength)" typeSet="@typeSet"/>
|
|
69
|
+
</parameterization>
|
|
70
|
+
<startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
|
|
71
|
+
</distribution>
|
|
72
|
+
</distribution>
|
|
73
|
+
|
|
74
|
+
<distribution id="prior" spec="CompoundDistribution">
|
|
75
|
+
<plate var="n" range="$(layersRange)">
|
|
76
|
+
<distribution spec="Prior" x="@birthRateW$(n)" distr="@weightsPrior"/>
|
|
77
|
+
<distribution spec="Prior" x="@deathRateW$(n)" distr="@weightsPrior"/>
|
|
78
|
+
</plate>
|
|
79
|
+
</distribution>
|
|
80
|
+
</distribution>
|
|
81
|
+
|
|
82
|
+
<plate var="n" range="$(layersRange)">
|
|
83
|
+
<operator spec="BactrianRandomWalkOperator" parameter="@birthRateW$(n)" weight="30.0"/>
|
|
84
|
+
<operator spec="BactrianRandomWalkOperator" parameter="@deathRateW$(n)" weight="30.0"/>
|
|
85
|
+
</plate>
|
|
86
|
+
|
|
87
|
+
<logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
|
|
88
|
+
<log idref="posterior"/>
|
|
89
|
+
<log idref="prior"/>
|
|
90
|
+
<log idref="likelihood"/>
|
|
91
|
+
<log idref="birthRateSP"/>
|
|
92
|
+
<log idref="deathRateSP"/>
|
|
93
|
+
<log idref="birthRate"/>
|
|
94
|
+
<log idref="deathRate"/>
|
|
95
|
+
</logger>
|
|
96
|
+
</run>
|
|
97
|
+
|
|
98
|
+
</beast>
|