bella-companion 0.0.30__py3-none-any.whl → 0.0.33__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.

Files changed (43) hide show
  1. bella_companion-0.0.33.dist-info/METADATA +12 -0
  2. bella_companion-0.0.33.dist-info/RECORD +41 -0
  3. {bella_companion-0.0.30.dist-info → bella_companion-0.0.33.dist-info}/WHEEL +2 -1
  4. bella_companion-0.0.33.dist-info/entry_points.txt +2 -0
  5. bella_companion-0.0.33.dist-info/top_level.txt +1 -0
  6. bella_companion/eucovid/beast_configs/GLM.xml +0 -170
  7. bella_companion/eucovid/beast_configs/MLP.xml +0 -170
  8. bella_companion/eucovid/beast_configs/Nonparametric.xml +0 -399
  9. bella_companion/eucovid/data/case_data.tsv +0 -346
  10. bella_companion/eucovid/data/change_dates.tsv +0 -8
  11. bella_companion/eucovid/data/msa.fasta +0 -79500
  12. bella_companion/eucovid/data/osi.tsv +0 -376
  13. bella_companion/eucovid/data/predictors/all/closedborders_7e_nt.tsv +0 -35
  14. bella_companion/eucovid/data/predictors/all/dist_7e_ls.tsv +0 -35
  15. bella_companion/eucovid/data/predictors/all/flight_7e_ls.tsv +0 -35
  16. bella_companion/eucovid/data/predictors/all/flight_pop_x_7e_ls.tsv +0 -35
  17. bella_companion/eucovid/data/predictors/all/osi_x_7e_ls.tsv +0 -35
  18. bella_companion/eucovid/data/predictors/all/osi_y_7e_ls.tsv +0 -35
  19. bella_companion/eucovid/data/predictors/all/pop_x_7e_ls.tsv +0 -35
  20. bella_companion/eucovid/data/predictors/all/pop_y_7e_ls.tsv +0 -35
  21. bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv +0 -35
  22. bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv +0 -6
  23. bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv +0 -3
  24. bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv +0 -20
  25. bella_companion/platyrrhine/beast_config.xml +0 -117
  26. bella_companion/platyrrhine/data/change_times.csv +0 -12
  27. bella_companion/platyrrhine/data/traits.csv +0 -122
  28. bella_companion/platyrrhine/data/trees.nwk +0 -100
  29. bella_companion/simulations/beast_configs/epi-multitype/GLM.xml +0 -81
  30. bella_companion/simulations/beast_configs/epi-multitype/MLP.xml +0 -81
  31. bella_companion/simulations/beast_configs/epi-multitype/Nonparametric.xml +0 -65
  32. bella_companion/simulations/beast_configs/epi-skyline/GLM.xml +0 -71
  33. bella_companion/simulations/beast_configs/epi-skyline/MLP.xml +0 -73
  34. bella_companion/simulations/beast_configs/epi-skyline/Nonparametric.xml +0 -57
  35. bella_companion/simulations/beast_configs/fbd-2traits/GLM.xml +0 -101
  36. bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml +0 -98
  37. bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml +0 -70
  38. bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml +0 -88
  39. bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml +0 -86
  40. bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml +0 -62
  41. bella_companion-0.0.30.dist-info/METADATA +0 -16
  42. bella_companion-0.0.30.dist-info/RECORD +0 -75
  43. bella_companion-0.0.30.dist-info/entry_points.txt +0 -3
bella_companion-0.0.33.dist-info/METADATA ADDED
@@ -0,0 +1,12 @@
1
+ Metadata-Version: 2.4
2
+ Name: bella-companion
3
+ Version: 0.0.33
4
+ Summary: Add your description here
5
+ Requires-Python: >=3.10
6
+ Description-Content-Type: text/markdown
7
+ Requires-Dist: arviz>=0.22.0
8
+ Requires-Dist: bella-lumiere>=0.0.14
9
+ Requires-Dist: dotenv>=0.9.9
10
+ Requires-Dist: phylogenie>=3.1.2
11
+ Requires-Dist: poetry>=2.2.1
12
+ Requires-Dist: seaborn>=0.13.2
bella_companion-0.0.33.dist-info/RECORD ADDED
@@ -0,0 +1,41 @@
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/platyrrhine/__init__.py,sha256=dIx6exNz-vuKiG5FZumvq74QUWcIEFd3L6ErqnOa83c,274
6
+ bella_companion/platyrrhine/results.py,sha256=qosxqstTy7uadHARRt1WqmxZzxnQ3hiTjtw6V-YWKGA,2556
7
+ bella_companion/platyrrhine/run_beast.py,sha256=_9Ex2B65zu6I68uY6s3_dohPYPaFP3E7u-uyWuDLAJc,2477
8
+ bella_companion/platyrrhine/summarize_logs.py,sha256=82N7rcmLthCyQqmP4Yub4KUsIjNzQl9vEuFLMvIv03o,951
9
+ bella_companion/simulations/__init__.py,sha256=ShYRdp1iSjnS_SzcsH-8jbqXz6P1nyRQZqAtPZJCMVE,454
10
+ bella_companion/simulations/features.py,sha256=DZOBpJGlQ0UinqUZYbEtoemZ2eQGVLV_i-DfpW31qJI,104
11
+ bella_companion/simulations/generate_data.py,sha256=edfhXrs76hl30i_xizup4z6qgzXZyaDzX_PVC62Ytpw,849
12
+ bella_companion/simulations/generate_figures.py,sha256=layMgoj3Bfl78Ceb1oE7YirAQ8zhjDyD9IrxDRXf6go,657
13
+ bella_companion/simulations/metrics.py,sha256=duIkPb8cCXmIzjKA2yk9HLf4Y9eFIB_hRWaH05uIDws,1876
14
+ bella_companion/simulations/run_beast.py,sha256=qniy326i-vDCeHzzHpQRrSnY2ULqNNrO0z3GEsWx4Mc,3208
15
+ bella_companion/simulations/summarize_logs.py,sha256=Shf3Dx9k4lTbmO__MSLw-aIA8a8kTCXhbctBcV6Izug,1216
16
+ bella_companion/simulations/figures/__init__.py,sha256=aBYbJntH4egFmkSSWiVMYDEApXPYxJD7eA3TCPNNegM,658
17
+ bella_companion/simulations/figures/epi_multitype_results.py,sha256=j85WgvN5AyAtX-CalMegr2lwlAZBmzyJxkikBPXRjCc,2629
18
+ bella_companion/simulations/figures/epi_skyline_results.py,sha256=gI5Ha-OIEShcZLmqVuy0W8hJzkrsydQE-Coa65_BFCo,1667
19
+ bella_companion/simulations/figures/fbd_2traits_results.py,sha256=JiXrbYkH1HwdJQhTHXj6KhMEXYgQmQ6LmDboAIO1CPA,2728
20
+ bella_companion/simulations/figures/fbd_no_traits_results.py,sha256=fLsgpV3IbLLtxQEFNOL9K4jEEJrG324ziUM0rxIv7_k,1962
21
+ bella_companion/simulations/figures/scenarios.py,sha256=gbMz1TUxxT2RSIq2kQlFioNdgSHk-gQY2OQuf6-7Fww,2817
22
+ bella_companion/simulations/figures/utils.py,sha256=0M5OrxaEuqcj9rR2uAc_O7utQvhEceZGH0sKrGRWaWs,3129
23
+ bella_companion/simulations/figures/explain/__init__.py,sha256=DnmVIWO65nTT5VsWnbS7NyYgKEY_eo4oMCtCY_ML2Vk,260
24
+ bella_companion/simulations/figures/explain/pdp.py,sha256=3n3ssgufW_43pn2hO5V5J_jgcJH3Fpb8stIRtTnlQ8w,3801
25
+ bella_companion/simulations/figures/explain/shap.py,sha256=qRfOMNwkU-hsBy5MHMTfVFAszaPESVOugCKQTVY8Q4Y,1940
26
+ bella_companion/simulations/scenarios/__init__.py,sha256=3Kl1lKcFpfb3vLX64DmSW4XCF5kXU1ZoHtstFH-ZIzU,876
27
+ bella_companion/simulations/scenarios/common.py,sha256=_ddaSuTvEVdttGkXB4HPc2B7IB1F_GBOCW3cVOPZ-ZM,807
28
+ bella_companion/simulations/scenarios/epi_multitype.py,sha256=fTkFeGHxyV_1f2nX3g_Oyr_e6wkorhXEicJjIAgeZKA,2439
29
+ bella_companion/simulations/scenarios/epi_skyline.py,sha256=JqnOVATECxBUqEbkR5lBlMI2O8k4hO6ipR8k9cHUsm0,2365
30
+ bella_companion/simulations/scenarios/fbd_2traits.py,sha256=-amB3NX0GsVgYbFuHH71t93FuXUEnRUyhWf2Qpcpia4,3541
31
+ bella_companion/simulations/scenarios/fbd_no_traits.py,sha256=R6CH0fVeQg-Iesl39pq2uY8ICVEO4VZbvUVUCGwauJU,2520
32
+ bella_companion/simulations/scenarios/scenario.py,sha256=_FRWAyOFbw94lAzd3zCD-1ek4TrssoiXfXRQPShLiIA,620
33
+ bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7UpYw,480
34
+ bella_companion/utils/beast.py,sha256=TBa0cLklX1_tXqoQE4LRYvds7mLg_9fS2-6U6OHENHo,2184
35
+ bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
36
+ bella_companion/utils/slurm.py,sha256=xEyf-Jxk8fy71t3fko_Ic9WtUFSdLFE3w4tR17gaBPw,1868
37
+ bella_companion-0.0.33.dist-info/METADATA,sha256=R9jDiQK4X7l_yZMmMHo_vtkqts6xpfL5J3ij2UYMd4k,347
38
+ bella_companion-0.0.33.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
39
+ bella_companion-0.0.33.dist-info/entry_points.txt,sha256=SVEYDBrkBWPrOGwnEH2aO5TSVIAvfKE37sqm-9ut9jg,51
40
+ bella_companion-0.0.33.dist-info/top_level.txt,sha256=q0loZYv4vf3zF_tOATyAJqeyLOEuPyLbObNqIGP7Fmc,16
41
+ bella_companion-0.0.33.dist-info/RECORD,,
{bella_companion-0.0.30.dist-info → bella_companion-0.0.33.dist-info}/WHEEL RENAMED
@@ -1,4 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: poetry-core 1.9.0
2
+ Generator: setuptools (80.9.0)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py3-none-any
5
+
bella_companion-0.0.33.dist-info/entry_points.txt ADDED
@@ -0,0 +1,2 @@
1
+ [console_scripts]
2
+ bella = bella_companion.cli:main
bella_companion-0.0.33.dist-info/top_level.txt ADDED
@@ -0,0 +1 @@
1
+ bella_companion
bella_companion/eucovid/beast_configs/GLM.xml DELETED
@@ -1,170 +0,0 @@
1
- <?xml version="1.0"?>
2
- <beast
3
- namespace="
4
- :beast.base.evolution
5
- :beast.base.evolution.alignment
6
- :beast.base.evolution.branchratemodel
7
- :beast.base.evolution.likelihood
8
- :beast.base.evolution.operator
9
- :beast.base.evolution.operator.kernel
10
- :beast.base.evolution.sitemodel
11
- :beast.base.evolution.substitutionmodel
12
- :beast.base.evolution.tree
13
- :beast.base.evolution.tree.coalescent
14
- :beast.base.inference
15
- :beast.base.inference.parameter
16
- :beast.base.inference.operator.kernel
17
- :bdmmprime.distribution
18
- :bdmmprime.mapping
19
- :bdmmprime.trajectories
20
- :bdmmprime.parameterization
21
- :bdmmprime.util
22
- :bdmmprime.util.operators
23
- :bdmmprime.util.priors
24
- :feast.fileio"
25
- version="2.7"
26
- >
27
- <map name="Uniform">beast.base.inference.distribution.Uniform</map>
28
- <map name="Exponential">beast.base.inference.distribution.Exponential</map>
29
- <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
30
- <map name="Normal">beast.base.inference.distribution.Normal</map>
31
- <map name="prior">beast.base.inference.distribution.Prior</map>
32
- <map name="AlignmentFromFasta">feast.fileio.AlignmentFromFasta</map>
33
- <map name="TaxonSet">beast.base.evolution.alignment.TaxonSet</map>
34
- <map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
35
- <map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
36
- <map name="TypeMappedTree">bdmmprime.mapping.TypeMappedTree</map>
37
-
38
- <AlignmentFromFasta id="alignment" fileName="$(msa_file)"/>
39
- <TaxonSet id="taxonSet" alignment="@alignment"/>
40
- <TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
41
- <TypeSet id="typeSet" typeTraitSet="@typeTraitSet"/>
42
- <TraitSetFromTaxonSet id="dateTrait" traitname="date" dateFormat="yyyy-M-dd" delimiter="|" everythingAfterLast="true" taxa="@taxonSet"/>
43
- <TypeMappedTree id="typeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@tree"/>
44
-
45
- <run spec="MCMC" chainLength="10000000">
46
- <state id="state" spec="State">
47
- <stateNode id="tree" spec="RandomTree" taxa="@alignment" trait="@dateTrait">
48
- <populationModel spec="ConstantPopulation" popSize="0.1"/>
49
- </stateNode>
50
- <stateNode id="Re" spec="RealParameter" value="1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4"/>
51
- <stateNode id="samplingProportion" spec="RealParameter" value="1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0"/>
52
- <stateNode id="migrationRateW" spec="RealParameter" value="0"/>
53
- <stateNode id="migrationRateScaler" spec="RealParameter" value="0.1"/>
54
- <stateNode id="processLength" spec="RealParameter" value="10.0"/>
55
- <stateNode id="gammaShape" spec="RealParameter" value="1.0"/>
56
- <stateNode id="kappa" spec="RealParameter" value="2.0"/>
57
- </state>
58
-
59
- <distribution id="posterior" spec="CompoundDistribution">
60
- <distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
61
- <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood" data="@alignment" tree="@tree">
62
- <siteModel spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape" mutationRate="1.0">
63
- <substModel spec="HKY" kappa="@kappa">
64
- <frequencies spec="Frequencies" data="@alignment"/>
65
- </substModel>
66
- </siteModel>
67
- <branchRateModel spec="StrictClockModel" clock.rate="8.0E-4"/>
68
- </distribution>
69
- </distribution>
70
-
71
- <distribution id="prior" spec="CompoundDistribution">
72
- <distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution" tree="@tree" conditionOnSurvival="true" typeTraitSet="@typeTraitSet">
73
- <parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization" processLength="@processLength" typeSet="@typeSet">
74
- <Re id="ReSP" spec="SkylineVectorParameter" skylineValues="@Re" changeTimes="0.123" timesAreAges="true" processLength="@processLength" typeSet="@typeSet"/>
75
- <samplingProportion id="samplingProportionSP" spec="SkylineVectorParameter" skylineValues="@samplingProportion" changeTimes="0.123 0.205" timesAreAges="true" processLength="@processLength" typeSet="@typeSet"/>
76
- <becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="36.5" typeSet="@typeSet"/>
77
- <migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
78
- <skylineValues spec="glmprior.util.GLMLogLinear" coefficients="@migrationRateW" scaleFactor="@migrationRateScaler" transform="false">
79
- <plate var="predictorFile" range="$(predictorFiles)">
80
- <predictor spec="RealParameterFromXSV" fileName="$(predictorFile)"/>
81
- </plate>
82
- <indicators spec="BooleanParameter" value="1"/>
83
- </skylineValues>
84
- <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
85
- </migrationRate>
86
- <removalProb spec="SkylineVectorParameter" skylineValues="1.0" typeSet="@typeSet"/>
87
- </parameterization>
88
- <startTypePriorProbs id="startTypePriorProbs" spec="RealParameter" value="1.0 0.0 0.0 0.0 0.0"/>
89
- </distribution>
90
-
91
- <prior name="distribution" x="@processLength">
92
- <LogNormal name="distr" M="-1.0" S="0.2"/>
93
- </prior>
94
- <distribution spec="SmartZeroExcludingPrior" x="@Re">
95
- <LogNormal name="distr" M="0.8" S="0.5"/>
96
- </distribution>
97
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
98
- <Uniform name="distr" lower="0" upper="0.15"/>
99
- </distribution>
100
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
101
- <Uniform name="distr" lower="0" upper="0.093"/>
102
- </distribution>
103
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
104
- <Uniform name="distr" lower="0" upper="0.10"/>
105
- </distribution>
106
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
107
- <Uniform name="distr" lower="0" upper="0.005"/>
108
- </distribution>
109
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
110
- <Uniform name="distr" lower="0" upper="0.057"/>
111
- </distribution>
112
- <prior name="distribution" x="@migrationRateW">
113
- <Normal name="distr" mean="0.0" sigma="1.0"/>
114
- </prior>
115
- <prior name="distribution" x="@migrationRateScaler">
116
- <LogNormal name="distr" M="0.0" S="0.8"/>
117
- </prior>
118
- <prior name="distribution" x="@gammaShape">
119
- <Exponential name="distr" mean="0.5"/>
120
- </prior>
121
- <prior id="KappaPrior" name="distribution" x="@kappa">
122
- <LogNormal name="distr" M="1.0" S="1.25"/>
123
- </prior>
124
- </distribution>
125
- </distribution>
126
-
127
- <operator spec="BactrianScaleOperator" tree="@tree" rootOnly="true" scaleFactor="0.25" weight="5.0"/>
128
- <operator spec="BactrianNodeOperator" tree="@tree" weight="30.0"/>
129
- <operator spec="BactrianSubtreeSlide" tree="@tree" weight="15.0"/>
130
- <operator spec="Exchange" tree="@tree" weight="15.0"/>
131
- <operator spec="Exchange" tree="@tree" isNarrow="false" weight="3.0"/>
132
- <operator spec="WilsonBalding" tree="@tree" weight="3.0"/>
133
- <operator spec="EpochFlexOperator" tree="@tree" scaleFactor="0.1" weight="2.0"/>
134
- <operator spec="EpochFlexOperator" tree="@tree" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
135
- <operator spec="TreeStretchOperator" tree="@tree" scaleFactor="0.01" weight="2.0"/>
136
- <operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0"/>
137
- <operator spec="SmartScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
138
- <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0"/>
139
- <operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW" weight="5.0" scaleFactor="0.1"/>
140
- <operator spec="AdaptableVarianceMultivariateNormalOperator" weight="5.0" coefficient="1.0" scaleFactor="0.5" beta="0.05" initial="800" burnin="400" every="1">
141
- <transformations spec="Transform$NoTransform" f="@migrationRateW"/>
142
- </operator>
143
- <operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
144
- <operator spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
145
-
146
- <logger spec="Logger" fileName="MCMC.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
147
- <log idref="posterior"/>
148
- <log idref="likelihood"/>
149
- <log idref="prior"/>
150
- <log idref="BDMMPrime"/>
151
- <log idref="gammaShape"/>
152
- <log idref="kappa"/>
153
- <log idref="processLength"/>
154
- <log idref="ReSP"/>
155
- <log idref="samplingProportionSP"/>
156
- <log idref="migrationRateSP"/>
157
- <log idref="migrationRateW"/>
158
- <log idref="migrationRateScaler"/>
159
- </logger>
160
- <logger spec="Logger" fileName="typedTrees.trees" logEvery="10000" mode="tree">
161
- <log idref="typeMappedTree"/>
162
- </logger>
163
- <logger spec="Logger" fileName="TypedNodeTrees.trees" logEvery="10000" mode="tree">
164
- <log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
165
- </logger>
166
- <logger spec="Logger" fileName="trajectories.csv" logEvery="10000">
167
- <log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
168
- </logger>
169
- </run>
170
- </beast>
bella_companion/eucovid/beast_configs/MLP.xml DELETED
@@ -1,170 +0,0 @@
1
- <?xml version="1.0"?>
2
- <beast
3
- namespace="
4
- :beast.base.evolution
5
- :beast.base.evolution.alignment
6
- :beast.base.evolution.branchratemodel
7
- :beast.base.evolution.likelihood
8
- :beast.base.evolution.operator
9
- :beast.base.evolution.operator.kernel
10
- :beast.base.evolution.sitemodel
11
- :beast.base.evolution.substitutionmodel
12
- :beast.base.evolution.tree
13
- :beast.base.evolution.tree.coalescent
14
- :beast.base.inference
15
- :beast.base.inference.parameter
16
- :beast.base.inference.operator.kernel
17
- :bdmmprime.distribution
18
- :bdmmprime.mapping
19
- :bdmmprime.trajectories
20
- :bdmmprime.parameterization
21
- :bdmmprime.util
22
- :bdmmprime.util.operators
23
- :bdmmprime.util.priors
24
- :feast.fileio"
25
- version="2.7"
26
- >
27
- <map name="Uniform">beast.base.inference.distribution.Uniform</map>
28
- <map name="Exponential">beast.base.inference.distribution.Exponential</map>
29
- <map name="LogNormal">beast.base.inference.distribution.LogNormalDistributionModel</map>
30
- <map name="Normal">beast.base.inference.distribution.Normal</map>
31
- <map name="prior">beast.base.inference.distribution.Prior</map>
32
- <map name="AlignmentFromFasta">feast.fileio.AlignmentFromFasta</map>
33
- <map name="TaxonSet">beast.base.evolution.alignment.TaxonSet</map>
34
- <map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
35
- <map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
36
- <map name="TypeMappedTree">bdmmprime.mapping.TypeMappedTree</map>
37
-
38
- <AlignmentFromFasta id="alignment" fileName="$(msa_file)"/>
39
- <TaxonSet id="taxonSet" alignment="@alignment"/>
40
- <TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
41
- <TypeSet id="typeSet" typeTraitSet="@typeTraitSet"/>
42
- <TraitSetFromTaxonSet id="dateTrait" traitname="date" dateFormat="yyyy-M-dd" delimiter="|" everythingAfterLast="true" taxa="@taxonSet"/>
43
- <TypeMappedTree id="typeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@tree"/>
44
-
45
- <run spec="MCMC" chainLength="10000000">
46
- <state id="state" spec="State">
47
- <stateNode id="tree" spec="RandomTree" taxa="@alignment" trait="@dateTrait">
48
- <populationModel spec="ConstantPopulation" popSize="0.1"/>
49
- </stateNode>
50
- <stateNode id="Re" spec="RealParameter" value="1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4"/>
51
- <stateNode id="samplingProportion" spec="RealParameter" value="1.11E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 1.1E-5 1.2E-5 1.3E-5 1.4E-5 1.5E-5 0.0 0.0 0.0 0.0 0.0"/>
52
- <plate var="n" range="$(layersRange)">
53
- <stateNode spec="RealParameter" id="migrationRateW$(n)" value="0"/>
54
- </plate>
55
- <stateNode id="processLength" spec="RealParameter" value="10.0"/>
56
- <stateNode id="gammaShape" spec="RealParameter" value="1.0"/>
57
- <stateNode id="kappa" spec="RealParameter" value="2.0"/>
58
- </state>
59
-
60
- <distribution id="posterior" spec="CompoundDistribution">
61
- <distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
62
- <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood" data="@alignment" tree="@tree">
63
- <siteModel spec="SiteModel" gammaCategoryCount="4" shape="@gammaShape" mutationRate="1.0">
64
- <substModel spec="HKY" kappa="@kappa">
65
- <frequencies spec="Frequencies" data="@alignment"/>
66
- </substModel>
67
- </siteModel>
68
- <branchRateModel spec="StrictClockModel" clock.rate="8.0E-4"/>
69
- </distribution>
70
- </distribution>
71
-
72
- <distribution id="prior" spec="CompoundDistribution">
73
- <distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution" tree="@tree" conditionOnSurvival="true" typeTraitSet="@typeTraitSet">
74
- <parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization" processLength="@processLength" typeSet="@typeSet">
75
- <Re id="ReSP" spec="SkylineVectorParameter" skylineValues="@Re" changeTimes="0.123" timesAreAges="true" processLength="@processLength" typeSet="@typeSet" />
76
- <samplingProportion id="samplingProportionSP" spec="SkylineVectorParameter" skylineValues="@samplingProportion" changeTimes="0.123 0.205" timesAreAges="true" processLength="@processLength" typeSet="@typeSet"/>
77
- <becomeUninfectiousRate spec="SkylineVectorParameter" skylineValues="36.5" typeSet="@typeSet"/>
78
- <migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" timesAreAges="true" processLength="@processLength" typeSet="@typeSet">
79
- <skylineValues id="migrationRate" spec="bella.BayesMLP" nodes="$(nodes)">
80
- <plate var="predictorFile" range="$(predictorFiles)">
81
- <predictor spec="RealParameterFromXSV" fileName="$(predictorFile)"/>
82
- </plate>
83
- <plate var="n" range="$(layersRange)">
84
- <weights idref="migrationRateW$(n)"/>
85
- </plate>
86
- </skylineValues>
87
- <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
88
- </migrationRate>
89
- <removalProb spec="SkylineVectorParameter" skylineValues="1.0" typeSet="@typeSet"/>
90
- </parameterization>
91
- <startTypePriorProbs id="startTypePriorProbs" spec="RealParameter" value="1.0 0.0 0.0 0.0 0.0"/>
92
- </distribution>
93
-
94
- <prior name="distribution" x="@processLength">
95
- <LogNormal name="distr" M="-1.0" S="0.2"/>
96
- </prior>
97
- <distribution spec="SmartZeroExcludingPrior" x="@Re">
98
- <LogNormal name="distr" M="0.8" S="0.5"/>
99
- </distribution>
100
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
101
- <Uniform name="distr" lower="0" upper="0.15"/>
102
- </distribution>
103
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
104
- <Uniform name="distr" lower="0" upper="0.093"/>
105
- </distribution>
106
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
107
- <Uniform name="distr" lower="0" upper="0.10"/>
108
- </distribution>
109
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
110
- <Uniform name="distr" lower="0" upper="0.005"/>
111
- </distribution>
112
- <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
113
- <Uniform name="distr" lower="0" upper="0.057"/>
114
- </distribution>
115
- <plate var="n" range="$(layersRange)">
116
- <prior name="distribution" x="@migrationRateW$(n)">
117
- <Normal name="distr" mean="0.0" sigma="1.0"/>
118
- </prior>
119
- </plate>
120
- <prior name="distribution" x="@gammaShape">
121
- <Exponential name="distr" mean="0.5"/>
122
- </prior>
123
- <prior id="KappaPrior" name="distribution" x="@kappa">
124
- <LogNormal name="distr" M="1.0" S="1.25"/>
125
- </prior>
126
- </distribution>
127
- </distribution>
128
-
129
- <operator spec="BactrianScaleOperator" tree="@tree" rootOnly="true" scaleFactor="0.25" weight="5.0"/>
130
- <operator spec="BactrianNodeOperator" tree="@tree" weight="30.0"/>
131
- <operator spec="BactrianSubtreeSlide" tree="@tree" weight="15.0"/>
132
- <operator spec="Exchange" tree="@tree" weight="15.0"/>
133
- <operator spec="Exchange" tree="@tree" isNarrow="false" weight="3.0"/>
134
- <operator spec="WilsonBalding" tree="@tree" weight="3.0"/>
135
- <operator spec="EpochFlexOperator" tree="@tree" scaleFactor="0.1" weight="2.0"/>
136
- <operator spec="EpochFlexOperator" tree="@tree" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
137
- <operator spec="TreeStretchOperator" tree="@tree" scaleFactor="0.01" weight="2.0"/>
138
- <operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0"/>
139
- <operator spec="SmartScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
140
- <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0"/>
141
- <plate var="n" range="$(layersRange)">
142
- <operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW$(n)" weight="5.0"/>
143
- </plate>
144
- <operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
145
- <operator spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
146
-
147
- <logger spec="Logger" fileName="MCMC.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
148
- <log idref="posterior"/>
149
- <log idref="likelihood"/>
150
- <log idref="prior"/>
151
- <log idref="BDMMPrime"/>
152
- <log idref="gammaShape"/>
153
- <log idref="kappa"/>
154
- <log idref="processLength"/>
155
- <log idref="ReSP"/>
156
- <log idref="samplingProportionSP"/>
157
- <log idref="migrationRateSP"/>
158
- <log idref="migrationRate"/>
159
- </logger>
160
- <logger spec="Logger" fileName="typedTrees.trees" logEvery="100000" mode="tree">
161
- <log idref="typeMappedTree"/>
162
- </logger>
163
- <logger spec="Logger" fileName="TypedNodeTrees.trees" logEvery="100000" mode="tree">
164
- <log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
165
- </logger>
166
- <logger spec="Logger" fileName="trajectories.csv" logEvery="100000">
167
- <log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
168
- </logger>
169
- </run>
170
- </beast>