bella-companion 0.0.38__py3-none-any.whl → 0.0.42__py3-none-any.whl

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Files changed (41) hide show
  1. bella_companion/eucovid/beast_configs/GLM.xml +170 -0
  2. bella_companion/eucovid/beast_configs/MLP.xml +170 -0
  3. bella_companion/eucovid/beast_configs/Nonparametric.xml +399 -0
  4. bella_companion/eucovid/data/case_data.tsv +346 -0
  5. bella_companion/eucovid/data/change_dates.tsv +8 -0
  6. bella_companion/eucovid/data/msa.fasta +79500 -0
  7. bella_companion/eucovid/data/osi.tsv +376 -0
  8. bella_companion/eucovid/data/predictors/all/closedborders_7e_nt.tsv +35 -0
  9. bella_companion/eucovid/data/predictors/all/dist_7e_ls.tsv +35 -0
  10. bella_companion/eucovid/data/predictors/all/flight_7e_ls.tsv +35 -0
  11. bella_companion/eucovid/data/predictors/all/flight_pop_x_7e_ls.tsv +35 -0
  12. bella_companion/eucovid/data/predictors/all/osi_x_7e_ls.tsv +35 -0
  13. bella_companion/eucovid/data/predictors/all/osi_y_7e_ls.tsv +35 -0
  14. bella_companion/eucovid/data/predictors/all/pop_x_7e_ls.tsv +35 -0
  15. bella_companion/eucovid/data/predictors/all/pop_y_7e_ls.tsv +35 -0
  16. bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv +35 -0
  17. bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv +6 -0
  18. bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv +3 -0
  19. bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv +20 -0
  20. bella_companion/platyrrhine/beast_config.xml +117 -0
  21. bella_companion/platyrrhine/data/change_times.csv +12 -0
  22. bella_companion/platyrrhine/data/traits.csv +122 -0
  23. bella_companion/platyrrhine/data/trees.nwk +100 -0
  24. bella_companion/simulations/beast_configs/epi-multitype/GLM.xml +81 -0
  25. bella_companion/simulations/beast_configs/epi-multitype/MLP.xml +81 -0
  26. bella_companion/simulations/beast_configs/epi-multitype/Nonparametric.xml +65 -0
  27. bella_companion/simulations/beast_configs/epi-skyline/GLM.xml +71 -0
  28. bella_companion/simulations/beast_configs/epi-skyline/MLP.xml +73 -0
  29. bella_companion/simulations/beast_configs/epi-skyline/Nonparametric.xml +57 -0
  30. bella_companion/simulations/beast_configs/fbd-2traits/GLM.xml +101 -0
  31. bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml +98 -0
  32. bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml +70 -0
  33. bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml +88 -0
  34. bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml +86 -0
  35. bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml +62 -0
  36. {bella_companion-0.0.38.dist-info → bella_companion-0.0.42.dist-info}/METADATA +1 -1
  37. bella_companion-0.0.42.dist-info/RECORD +76 -0
  38. bella_companion-0.0.38.dist-info/RECORD +0 -41
  39. {bella_companion-0.0.38.dist-info → bella_companion-0.0.42.dist-info}/WHEEL +0 -0
  40. {bella_companion-0.0.38.dist-info → bella_companion-0.0.42.dist-info}/entry_points.txt +0 -0
  41. {bella_companion-0.0.38.dist-info → bella_companion-0.0.42.dist-info}/top_level.txt +0 -0
bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml ADDED
@@ -0,0 +1,70 @@
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+ <?xml version="1.0"?>
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+ <beast
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+ 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="Uniform">beast.base.inference.distribution.Uniform</map>
17
+
18
+ <map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
19
+ <map name="TaxonSetFromTree">feast.fileio.TaxonSetFromTree</map>
20
+ <map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
21
+ <map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
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+
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+ <TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
24
+ <TaxonSetFromTree id="taxonSet" tree="@tree"/>
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+ <TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
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+ <TypeSet id="typeSet" value="$(types)" typeTraitSet="@typeTraitSet"/>
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+
28
+ <Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
29
+ <Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
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+
31
+ <run spec="MCMC" chainLength="10000000">
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+ <state id="state">
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+ <stateNode spec="RealParameter" id="birthRate" value="$(birthRateInit)"/>
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+ <stateNode spec="RealParameter" id="deathRate" value="$(deathRateInit)"/>
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+ </state>
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+
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="$(processLength)" typeSet="@typeSet">
41
+ <birthRate id="birthRateSP" spec="SkylineVectorParameter" skylineValues="@birthRate" changeTimes="$(changeTimes)" typeSet="@typeSet"/>
42
+ <deathRate id="deathRateSP" spec="SkylineVectorParameter" skylineValues="@deathRate" changeTimes="$(changeTimes)" typeSet="@typeSet"/>
43
+ <migrationRate spec="SkylineMatrixParameter" skylineValues="$(migrationRate)" typeSet="@typeSet"/>
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+ <samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)" typeSet="@typeSet"/>
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+ <removalProb spec="SkylineVectorParameter" skylineValues="0.0" typeSet="@typeSet"/>
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+ <rhoSampling spec="TimedParameter" values="1" times="$(processLength)" typeSet="@typeSet"/>
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+ </parameterization>
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+ <startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
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+ </distribution>
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+ </distribution>
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+
52
+ <distribution id="prior" spec="CompoundDistribution">
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+ <distribution spec="Prior" x="@deathRate" distr="@deathRatePrior"/>
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+ <distribution spec="Prior" x="@birthRate" distr="@birthRatePrior"/>
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+ </distribution>
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+ </distribution>
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+
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+ <operator spec="BactrianScaleOperator" parameter="@birthRate" weight="30.0"/>
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+ <operator spec="BactrianScaleOperator" parameter="@deathRate" weight="30.0"/>
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+
61
+ <logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
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+ <log idref="posterior"/>
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+ <log idref="prior"/>
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+ <log idref="likelihood"/>
65
+ <log idref="birthRateSP"/>
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+ <log idref="deathRateSP"/>
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+ </logger>
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+ </run>
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+
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+ </beast>
bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml ADDED
@@ -0,0 +1,88 @@
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+ <?xml version="1.0"?>
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+ <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
+
21
+ <TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
22
+
23
+ <Normal id="weightsPrior" mean="0" sigma="1"/>
24
+ <Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
25
+ <Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
26
+
27
+ <run spec="MCMC" chainLength="10000000">
28
+ <state id="state">
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+ <stateNode spec="RealParameter" id="birthRateScaler" value="1"/>
30
+ <stateNode spec="RealParameter" id="deathRateScaler" value="1"/>
31
+ <stateNode spec="RealParameter" id="birthRateW" value="0"/>
32
+ <stateNode spec="RealParameter" id="deathRateW" value="0"/>
33
+ </state>
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+
35
+ <distribution id="posterior" spec="CompoundDistribution">
36
+ <distribution id="likelihood" spec="CompoundDistribution">
37
+ <distribution spec="BirthDeathMigrationDistribution" tree="@tree">
38
+ <parameterization spec="CanonicalParameterization" processLength="$(processLength)">
39
+ <birthRate id="birthRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
40
+ <skylineValues id="birthRate" spec="glmprior.util.GLMLogLinear" coefficients="@birthRateW" scaleFactor="@birthRateScaler" transform="false">
41
+ <predictor spec="RealParameter" value="$(timePredictor)"/>
42
+ <predictor spec="RealParameter" value="$(randomPredictor)"/>
43
+ <indicators spec="BooleanParameter" value="1"/>
44
+ </skylineValues>
45
+ </birthRate>
46
+ <deathRate id="deathRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
47
+ <skylineValues id="deathRate" spec="glmprior.util.GLMLogLinear" coefficients="@deathRateW" scaleFactor="@deathRateScaler" transform="false">
48
+ <predictor spec="RealParameter" value="$(timePredictor)"/>
49
+ <predictor spec="RealParameter" value="$(randomPredictor)"/>
50
+ <indicators spec="BooleanParameter" value="1"/>
51
+ </skylineValues>
52
+ </deathRate>
53
+ <samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)"/>
54
+ <removalProb spec="SkylineVectorParameter" skylineValues="0.0"/>
55
+ <rhoSampling spec="TimedParameter" values="1" times="$(processLength)"/>
56
+ </parameterization>
57
+ </distribution>
58
+ </distribution>
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+
60
+ <distribution id="prior" spec="CompoundDistribution">
61
+ <distribution spec="Prior" x="@birthRateScaler" distr="@weightsPrior"/>
62
+ <distribution spec="Prior" x="@deathRateScaler" distr="@weightsPrior"/>
63
+ <distribution spec="Prior" x="@birthRateW" distr="@weightsPrior"/>
64
+ <distribution spec="Prior" x="@deathRateW" distr="@weightsPrior"/>
65
+ <distribution spec="Prior" x="@birthRate" distr="@birthRatePrior"/>
66
+ <distribution spec="Prior" x="@deathRate" distr="@deathRatePrior"/>
67
+ </distribution>
68
+ </distribution>
69
+
70
+ <operator spec="BactrianScaleOperator" parameter="@birthRateScaler" weight="30.0"/>
71
+ <operator spec="BactrianScaleOperator" parameter="@deathRateScaler" weight="30.0"/>
72
+ <operator spec="BactrianRandomWalkOperator" parameter="@birthRateW" weight="30.0"/>
73
+ <operator spec="BactrianRandomWalkOperator" parameter="@deathRateW" weight="30.0"/>
74
+
75
+ <logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
76
+ <log idref="posterior"/>
77
+ <log idref="prior"/>
78
+ <log idref="likelihood"/>
79
+ <log idref="birthRateSP"/>
80
+ <log idref="deathRateSP"/>
81
+ <log idref="birthRateW"/>
82
+ <log idref="deathRateW"/>
83
+ <log idref="birthRateScaler"/>
84
+ <log idref="deathRateScaler"/>
85
+ </logger>
86
+ </run>
87
+
88
+ </beast>
bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml ADDED
@@ -0,0 +1,86 @@
1
+ <?xml version="1.0"?>
2
+ <beast
3
+ namespace="
4
+ :beast.base.inference.parameter
5
+ :beast.base.inference.operator.kernel
6
+ :beast.base.inference
7
+ :beast.base.inference.distribution
8
+ :bdmmprime.distribution
9
+ :bdmmprime.parameterization
10
+ :feast.fileio
11
+ :feast.function
12
+ :feast.expressions"
13
+ version="2.5"
14
+ >
15
+ <map name="Normal">beast.base.inference.distribution.Normal</map>
16
+
17
+ <map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
18
+
19
+ <TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
20
+
21
+ <Normal id="weightsPrior" mean="0" sigma="1"/>
22
+
23
+ <run spec="MCMC" chainLength="10000000">
24
+ <state id="state">
25
+ <plate var="n" range="$(layersRange)">
26
+ <stateNode spec="RealParameter" id="birthRateW$(n)" value="0"/>
27
+ <stateNode spec="RealParameter" id="deathRateW$(n)" value="0"/>
28
+ </plate>
29
+ </state>
30
+
31
+ <distribution id="posterior" spec="CompoundDistribution">
32
+ <distribution id="likelihood" spec="CompoundDistribution">
33
+ <distribution spec="BirthDeathMigrationDistribution" tree="@tree">
34
+ <parameterization spec="CanonicalParameterization" processLength="$(processLength)">
35
+ <birthRate id="birthRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
36
+ <skylineValues id="birthRate" spec="bella.BayesMLP" nodes="$(nodes)">
37
+ <predictor spec="RealParameter" value="$(timePredictor)"/>
38
+ <predictor spec="RealParameter" value="$(randomPredictor)"/>
39
+ <plate var="n" range="$(layersRange)">
40
+ <weights idref="birthRateW$(n)"/>
41
+ </plate>
42
+ <activationFunctionsOutput spec="bella.Sigmoid" upper="$(birthRateUpper)"/>
43
+ </skylineValues>
44
+ </birthRate>
45
+ <deathRate id="deathRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
46
+ <skylineValues id="deathRate" spec="bella.BayesMLP" nodes="$(nodes)">
47
+ <predictor spec="RealParameter" value="$(timePredictor)"/>
48
+ <predictor spec="RealParameter" value="$(randomPredictor)"/>
49
+ <plate var="n" range="$(layersRange)">
50
+ <weights idref="deathRateW$(n)"/>
51
+ </plate>
52
+ <activationFunctionsOutput spec="bella.Sigmoid" upper="$(deathRateUpper)"/>
53
+ </skylineValues>
54
+ </deathRate>
55
+ <samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)"/>
56
+ <removalProb spec="SkylineVectorParameter" skylineValues="0.0"/>
57
+ <rhoSampling spec="TimedParameter" values="1" times="$(processLength)"/>
58
+ </parameterization>
59
+ </distribution>
60
+ </distribution>
61
+
62
+ <distribution id="prior" spec="CompoundDistribution">
63
+ <plate var="n" range="$(layersRange)">
64
+ <distribution spec="Prior" x="@birthRateW$(n)" distr="@weightsPrior"/>
65
+ <distribution spec="Prior" x="@deathRateW$(n)" distr="@weightsPrior"/>
66
+ </plate>
67
+ </distribution>
68
+ </distribution>
69
+
70
+ <plate var="n" range="$(layersRange)">
71
+ <operator spec="BactrianRandomWalkOperator" parameter="@birthRateW$(n)" weight="30.0"/>
72
+ <operator spec="BactrianRandomWalkOperator" parameter="@deathRateW$(n)" weight="30.0"/>
73
+ </plate>
74
+
75
+ <logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
76
+ <log idref="posterior"/>
77
+ <log idref="prior"/>
78
+ <log idref="likelihood"/>
79
+ <log idref="birthRateSP"/>
80
+ <log idref="deathRateSP"/>
81
+ <log idref="birthRate"/>
82
+ <log idref="deathRate"/>
83
+ </logger>
84
+ </run>
85
+
86
+ </beast>
bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml ADDED
@@ -0,0 +1,62 @@
1
+ <?xml version="1.0"?>
2
+ <beast
3
+ namespace="
4
+ :beast.base.evolution.operator.kernel
5
+ :beast.base.inference.parameter
6
+ :beast.base.inference.operator.kernel
7
+ :beast.base.inference
8
+ :beast.base.inference.distribution
9
+ :bdmmprime.distribution
10
+ :bdmmprime.parameterization
11
+ :feast.fileio
12
+ :feast.function
13
+ :feast.expressions"
14
+ version="2.5"
15
+ >
16
+ <map name="Uniform">beast.base.inference.distribution.Uniform</map>
17
+
18
+ <map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
19
+
20
+ <TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
21
+
22
+ <Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
23
+ <Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
24
+
25
+ <run spec="MCMC" chainLength="10000000">
26
+ <state id="state">
27
+ <stateNode spec="RealParameter" id="birthRate" value="$(birthRateInit)"/>
28
+ <stateNode spec="RealParameter" id="deathRate" value="$(deathRateInit)"/>
29
+ </state>
30
+
31
+ <distribution id="posterior" spec="CompoundDistribution">
32
+ <distribution id="likelihood" spec="CompoundDistribution">
33
+ <distribution spec="BirthDeathMigrationDistribution" tree="@tree">
34
+ <parameterization spec="CanonicalParameterization" processLength="$(processLength)">
35
+ <birthRate id="birthRateSP" spec="SkylineVectorParameter" skylineValues="@birthRate" changeTimes="$(changeTimes)"/>
36
+ <deathRate id="deathRateSP" spec="SkylineVectorParameter" skylineValues="@deathRate" changeTimes="$(changeTimes)"/>
37
+ <samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)"/>
38
+ <removalProb spec="SkylineVectorParameter" skylineValues="0.0"/>
39
+ <rhoSampling spec="TimedParameter" values="1" times="$(processLength)"/>
40
+ </parameterization>
41
+ </distribution>
42
+ </distribution>
43
+
44
+ <distribution id="prior" spec="CompoundDistribution">
45
+ <distribution spec="Prior" x="@birthRate" distr="@birthRatePrior"/>
46
+ <distribution spec="Prior" x="@deathRate" distr="@deathRatePrior"/>
47
+ </distribution>
48
+ </distribution>
49
+
50
+ <operator spec="BactrianScaleOperator" parameter="@birthRate" weight="30.0"/>
51
+ <operator spec="BactrianScaleOperator" parameter="@deathRate" weight="30.0"/>
52
+
53
+ <logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
54
+ <log idref="posterior"/>
55
+ <log idref="prior"/>
56
+ <log idref="likelihood"/>
57
+ <log idref="birthRateSP"/>
58
+ <log idref="deathRateSP"/>
59
+ </logger>
60
+ </run>
61
+
62
+ </beast>
{bella_companion-0.0.38.dist-info → bella_companion-0.0.42.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: bella-companion
3
- Version: 0.0.38
3
+ Version: 0.0.42
4
4
  Summary: Add your description here
5
5
  Requires-Python: >=3.10
6
6
  Description-Content-Type: text/markdown
bella_companion-0.0.42.dist-info/RECORD ADDED
@@ -0,0 +1,76 @@
1
+ bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
2
+ bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
3
+ bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
4
+ bella_companion/eucovid/run_beast.py,sha256=etaD_4SVdy_Pmz5s4jvDLzp2K_QV8leEY8Pe3xySBsk,3443
5
+ bella_companion/eucovid/beast_configs/GLM.xml,sha256=b5rAeKVEam3u2AGSJsm7EHB6LcC0l9bp1SyZT2QyjpI,10892
6
+ bella_companion/eucovid/beast_configs/MLP.xml,sha256=M0_B6t0bZpjCAQqAmjrFshW96pt9sNREcoLUjwchX6Q,10616
7
+ bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=n-t4sUfDS9AzC02tbIk5mx_RDg2l62ELhdR3I3_jjHE,17783
8
+ bella_companion/eucovid/data/case_data.tsv,sha256=XaSzZh5NcEMVt9d_XlQ19T8UuEkHGrjpSFXhe9IycNg,12412
9
+ bella_companion/eucovid/data/change_dates.tsv,sha256=_pmVFYiL4X9Pd79uYVgyz3sKeRap7xVcXk0OjqVhuVQ,227
10
+ bella_companion/eucovid/data/msa.fasta,sha256=sWaVSINSJDDLjmwlpl31JWM5VnKF7yViSpERI69glQc,4839354
11
+ bella_companion/eucovid/data/osi.tsv,sha256=iTDWL_-PnVQPg_-hWROXWKNFakDq_S1fEig1A_MqMVI,9228
12
+ bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv,sha256=hH0xXD2lr_8RPQRqvENv6clPHauAXH22SGQHb3hlfzs,120
13
+ bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv,sha256=XEepIXKRwcKknJq4-ovKlorvCypGi67B8znuQ5f1LTg,60
14
+ bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv,sha256=tMR9-tuGtC3rVABXUtNdV9irUX-9aCCVb_fwksHTn8U,1068
15
+ bella_companion/eucovid/data/predictors/all/closedborders_7e_nt.tsv,sha256=5gP-cEzgKSCvlK0_PlkrimYGEwOaLPO0GiiM4PIKU-M,280
16
+ bella_companion/eucovid/data/predictors/all/dist_7e_ls.tsv,sha256=rr71QPiJu35CYbySMJyH_GDX51D2iTIncZImwAXIvlo,1890
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