bella-companion 0.0.30__py3-none-any.whl → 0.0.32__py3-none-any.whl

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  1. bella_companion-0.0.32.dist-info/METADATA +11 -0
  2. bella_companion-0.0.32.dist-info/RECORD +41 -0
  3. {bella_companion-0.0.30.dist-info → bella_companion-0.0.32.dist-info}/WHEEL +2 -1
  4. bella_companion-0.0.32.dist-info/entry_points.txt +2 -0
  5. bella_companion-0.0.32.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/eucovid/data/predictors/changetimes_all_7e.tsv DELETED
@@ -1,6 +0,0 @@
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- 0.019125683060110532
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- 0.057377049180331596
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- 0.0983606557379062
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- 0.12295081967226906
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- 0.1420765027323796
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- 0.18306010928972682
bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv DELETED
@@ -1,3 +0,0 @@
1
- 0.019125683060110532
2
- 0.0983606557379062
3
- 0.18306010928972682
bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv DELETED
@@ -1,20 +0,0 @@
1
- -1.3405299471 -1.345806766 -1.3512072478 -1.3448952046
2
- -1.040355107 -0.0881656333 -0.4582081333 1.0712567879
3
- -1.0351370181 -0.2281786725 -0.4494345583 1.2186350836
4
- -1.3512072478 -0.3613020502 -0.2354915099 0.5261323835
5
- -1.2405584625 0.2198152275 0.5320931776 -0.3818162253
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- -1.3146740757 -1.3211624933 -1.3512072478 -1.3050486897
7
- -0.9401276287 0.4036780489 0.524890239 1.561202424
8
- -0.9527207215 0.2509108009 0.4583245048 1.7568044456
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- -1.3368793783 0.6153635605 0.676014604 1.6911556787
10
- -1.1536256133 0.6242106372 0.924551832 0.6534556808
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- -1.2293447841 -1.2183082911 -1.284435751 -1.0455195408
12
- -0.3334656741 0.4068453606 0.5550254535 1.5299700031
13
- -0.4472959305 0.2260837023 0.472758401 1.7126046255
14
- -0.5674230736 0.6579311005 0.7199273173 1.7312050096
15
- -0.5714216646 0.752964957 1.0273007955 0.8297001311
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- -1.2397477985 -1.2555826444 -1.3025435133 -1.1159647011
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- -0.2764997718 0.4125068998 0.6005798788 1.5818044584
18
- -0.3781670831 0.2838430455 0.553443893 1.8181907424
19
- -0.5085841919 0.6841126877 0.7369465342 1.7862369916
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- -0.499497862 0.6774213601 0.9790687736 0.7565746699
bella_companion/platyrrhine/beast_config.xml DELETED
@@ -1,117 +0,0 @@
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- <?xml version="1.0"?>
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- <beast
3
- namespace="
4
- :beast.base.evolution.operator.kernel
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- :beast.base.inference.parameter
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- :beast.base.inference.operator.kernel
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- :beast.base.inference
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- :beast.base.inference.distribution
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- :bdmmprime.distribution
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- :bdmmprime.parameterization
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- :feast.fileio
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- :feast.function
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- :feast.expressions"
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- version="2.5"
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- >
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- <map name="Uniform">beast.base.inference.distribution.Uniform</map>
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- <map name="Normal">beast.base.inference.distribution.Normal</map>
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-
19
- <map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
20
- <map name="TaxonSetFromTree">feast.fileio.TaxonSetFromTree</map>
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- <map name="TraitSetFromXSV">feast.fileio.TraitSetFromXSV</map>
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- <map name="RealParameterFromXSV">feast.fileio.RealParameterFromXSV</map>
23
- <map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
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-
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- <TreeFromNewickFile id="tree" fileName="$(treeFile)" treeIndex="$(treeIndex)" IsLabelledNewick="true" adjustTipHeights='false'/>
26
- <TaxonSetFromTree id="taxonSet" tree="@tree"/>
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- <TraitSetFromXSV id="typeTraitSet" traitname="type" fileName="$(traitsFile)" traitValueCol="$(traitValueCol)" skipFirstRow="true" taxa="@taxonSet"/>
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- <TypeSet id="typeSet" value="$(types)" typeTraitSet="@typeTraitSet"/>
29
-
30
- <Normal id="weightsPrior" mean="0" sigma="1"/>
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- <Uniform id="samplingRatePrior" upper="$(samplingRateUpper)"/>
32
- <Uniform id="migrationRatePrior" upper="$(migrationRateUpper)"/>
33
-
34
- <RealParameterFromXSV id="changeTimes" fileName="$(changeTimesFile)"/>
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-
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- <run spec="MCMC" chainLength="10000000">
37
- <state id="state">
38
- <plate var="n" range="$(layersRange)">
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- <stateNode spec="RealParameter" id="birthRateW$(n)" value="0"/>
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- <stateNode spec="RealParameter" id="deathRateW$(n)" value="0"/>
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- </plate>
42
- <stateNode spec="RealParameter" id="samplingRate" value="$(samplingRateInit)"/>
43
- <stateNode spec="RealParameter" id="migrationRate" value="$(migrationRateInit)"/>
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- </state>
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-
46
- <distribution id="posterior" spec="CompoundDistribution">
47
- <distribution id="likelihood" spec="CompoundDistribution">
48
- <distribution spec="BirthDeathMigrationDistribution" conditionOnRoot="true" tree="@tree" typeTraitSet="@typeTraitSet">
49
- <parameterization id="BDMMParameterization" spec="CanonicalParameterization" processLength="$(processLength)" typeSet="@typeSet">
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- <birthRate id="birthRateSP" spec="SkylineVectorParameter" changeTimes="@changeTimes" timesAreAges="true" processLength="$(processLength)" typeSet="@typeSet">
51
- <skylineValues id="birthRate" spec="bella.BayesMLP" nodes="$(nodes)">
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- <predictor spec="RealParameter" value="$(timePredictor)"/>
53
- <predictor spec="RealParameter" value="$(log10BMPredictor)"/>
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- <plate var="n" range="$(layersRange)">
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- <weights idref="birthRateW$(n)"/>
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- </plate>
57
- <activationFunctionsOutput spec="bella.Sigmoid" upper="$(birthRateUpper)"/>
58
- </skylineValues>
59
- </birthRate>
60
- <deathRate id="deathRateSP" spec="SkylineVectorParameter" changeTimes="@changeTimes" timesAreAges="true" processLength="$(processLength)" typeSet="@typeSet">
61
- <skylineValues id="deathRate" spec="bella.BayesMLP" nodes="$(nodes)">
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- <predictor spec="RealParameter" value="$(timePredictor)"/>
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- <predictor spec="RealParameter" value="$(log10BMPredictor)"/>
64
- <plate var="n" range="$(layersRange)">
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- <weights idref="deathRateW$(n)"/>
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- </plate>
67
- <activationFunctionsOutput spec="bella.Sigmoid" upper="$(deathRateUpper)"/>
68
- </skylineValues>
69
- </deathRate>
70
- <samplingRate id="samplingRateSP" spec="SkylineVectorParameter" skylineValues="@samplingRate" changeTimes="$(samplingChangeTimes)" timesAreAges="true" processLength="$(processLength)" typeSet="@typeSet"/>
71
- <migrationRate id="migrationRateSP" spec="SkylineMatrixParameter" skylineValues="@migrationRate" typeSet="@typeSet"/>
72
- <removalProb spec="SkylineVectorParameter" skylineValues="0.0" typeSet="@typeSet"/>
73
- <rhoSampling spec="TimedParameter" values="0.44" times="$(processLength)" typeSet="@typeSet"/>
74
- </parameterization>
75
- <startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
76
- </distribution>
77
- </distribution>
78
-
79
- <distribution id="prior" spec="CompoundDistribution">
80
- <plate var="n" range="$(layersRange)">
81
- <distribution spec="Prior" x="@birthRateW$(n)" distr="@weightsPrior"/>
82
- <distribution spec="Prior" x="@deathRateW$(n)" distr="@weightsPrior"/>
83
- </plate>
84
- <distribution spec="Prior" x="@samplingRate" distr="@samplingRatePrior"/>
85
- <distribution spec="Prior" x="@migrationRate" distr="@migrationRatePrior"/>
86
- </distribution>
87
- </distribution>
88
-
89
- <plate var="n" range="$(layersRange)">
90
- <operator spec="BactrianRandomWalkOperator" parameter="@birthRateW$(n)" weight="30.0"/>
91
- <operator spec="BactrianRandomWalkOperator" parameter="@deathRateW$(n)" weight="30.0"/>
92
- </plate>
93
- <operator spec="BactrianScaleOperator" parameter="@samplingRate" weight="30.0"/>
94
- <operator spec="BactrianScaleOperator" parameter="@migrationRate" weight="30.0"/>
95
-
96
- <logger spec="Logger" fileName="$(treeIndex).log" logEvery="1000" model="@posterior">
97
- <log idref="posterior"/>
98
- <log idref="prior"/>
99
- <log idref="likelihood"/>
100
- <log idref="birthRateSP"/>
101
- <log idref="deathRateSP"/>
102
- <log idref="samplingRateSP"/>
103
- <log idref="migrationRateSP"/>
104
- <log idref="birthRate"/>
105
- <log idref="deathRate"/>
106
- </logger>
107
-
108
- <logger fileName="$(treeIndex).trees" logEvery="100000" mode="tree">
109
- <log spec="bella.SkylineNodeTreeLogger" parameterization="@BDMMParameterization" precision="4">
110
- <typedTree spec="bdmmprime.mapping.TypeMappedTree" parameterization="@BDMMParameterization" startTypePriorProbs="$(startTypePriorProbs)" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@tree"/>
111
- <skylineParameter idref="birthRateSP"/>
112
- <skylineParameter idref="deathRateSP"/>
113
- </log>
114
- </logger>
115
- </run>
116
-
117
- </beast>
bella_companion/platyrrhine/data/change_times.csv DELETED
@@ -1,12 +0,0 @@
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- 0.126
2
- 0.781
3
- 1.80
4
- 2.58
5
- 3.6
6
- 5.333
7
- 7.246
8
- 11.63
9
- 13.82
10
- 15.97
11
- 20.44
12
- 23.03
bella_companion/platyrrhine/data/traits.csv DELETED
@@ -1,122 +0,0 @@
1
- species BM log10BM log10BM-cat
2
- Acrecebus_fraileyi 12000.0 4.08 3
3
- Alouatta_belzebul 6395.0 3.81 3
4
- Alouatta_caraya 5375.0 3.73 3
5
- Alouatta_coibensis ? ? ?
6
- Alouatta_guariba 5362.5 3.73 3
7
- Alouatta_macconnelli 6292.5 3.8 3
8
- Alouatta_nigerrima ? ? ?
9
- Alouatta_palliata 6250.0 3.8 3
10
- Alouatta_pigra 8915.0 3.95 3
11
- Alouatta_sara 6123.0 3.79 3
12
- Alouatta_seniculus 5950.0 3.77 3
13
- Antillothrix_bernensis 1500.0 3.18 2
14
- Aotus_azarae 1205.0 3.08 2
15
- Aotus_dindensis 1054.0 3.02 2
16
- Aotus_griseimembra 966.0 2.98 1
17
- Aotus_infulatus ? ? ?
18
- Aotus_lemurinus 896.0 2.95 1
19
- Aotus_nancymaae 787.0 2.9 1
20
- Aotus_nigriceps 957.5 2.98 1
21
- Aotus_trivirgatus 774.5 2.89 1
22
- Aotus_vociferans 703.0 2.85 1
23
- Ateles_belzebuth 7770.0 3.89 3
24
- Ateles_chamek 9370.0 3.97 3
25
- Ateles_fusciceps 9025.0 3.96 3
26
- Ateles_geoffroyi 7535.0 3.88 3
27
- Ateles_hybridus 8700.5 3.94 3
28
- Ateles_paniscus 8775.0 3.94 3
29
- Brachyteles_arachnoides 8840.0 3.95 3
30
- Brachyteles_hypoxanthus 8874.5 3.95 3
31
- Branisella_boliviana 1000.0 3.0 2
32
- Cacajao_ayresi ? ? ?
33
- Cacajao_calvus 3165.0 3.5 3
34
- Cacajao_hosomi 3800.0 3.58 3
35
- Cacajao_melanocephalus 2935.0 3.47 2
36
- Caipora_bambuiorum 24000.0 4.38 3
37
- Callicebus_brunneus 829.5 2.92 1
38
- Callicebus_caligatus 880.0 2.94 1
39
- Callicebus_coimbrai ? ? ?
40
- Callicebus_cupreus 1070.0 3.03 2
41
- Callicebus_donacophilus 950.0 2.98 1
42
- Callicebus_hoffmansi 1060.0 3.03 2
43
- Callicebus_lugens 1090.0 3.04 2
44
- Callicebus_moloch 988.0 2.99 1
45
- Callicebus_nigrifrons ? ? ?
46
- Callicebus_personatus 1245.0 3.1 2
47
- Callicebus_torquatus 1245.0 3.1 2
48
- Callimico_goeldii 483.5 2.68 0
49
- Callithrix_aurita 429.0 2.63 0
50
- Callithrix_geoffroyi 359.0 2.56 0
51
- Callithrix_jacchus 320.5 2.51 0
52
- Callithrix_kuhlii 375.0 2.57 0
53
- Callithrix_penicillata 325.5 2.51 0
54
- Canaanimico 2000.0 3.3 2
55
- Carlocebus_carmenensis 3500.0 3.54 3
56
- Cartelles_coimbrafilhoi 23500.0 4.37 3
57
- Cebuella_pygmaea 116.0 2.06 0
58
- Cebupithecia_sarmientoi 1602.0 3.2 2
59
- Cebus_albifrons 2735.0 3.44 2
60
- Cebus_capucinus 3110.0 3.49 3
61
- Cebus_olivaceus 2905.0 3.46 2
62
- Chilecebus_carrascoensis 1000.0 3.0 2
63
- Chiropotes_chiropotes 2740.0 3.44 2
64
- Chiropotes_israelita ? ? ?
65
- Chiropotes_utahicki 2740.0 3.44 2
66
- Dolichocebus_gaimanensis 2700.0 3.43 2
67
- Homunculus_patagonicus 2700.0 3.43 2
68
- Insulacebus_toussentiana 4805.0 3.68 3
69
- Killikaike_blakei 2000.0 3.3 2
70
- Lagonimico_conclucatus 595.0 2.77 1
71
- Lagothrix_cana 8571.5 3.93 3
72
- Lagothrix_lagotricha 7150.0 3.85 3
73
- Laventiana_annectens 605.0 2.78 1
74
- Leontopithecus_chrysomelas 577.5 2.76 1
75
- Leontopithecus_chrysopygus 577.5 2.76 1
76
- Leontopithecus_rosalia 609.0 2.78 1
77
- Mazzonicebus_almendrae 1602.0 3.2 2
78
- Mico_argentatus 346.5 2.54 0
79
- Mico_emiliae 321.5 2.51 0
80
- Mico_humeralifer 473.5 2.68 0
81
- Mico_mauesi 371.5 2.57 0
82
- Micodon_kyotensis 400.0 2.6 0
83
- Miocallicebus_villaviejai 1500.0 3.18 2
84
- Mohanamico_hershkovitzi 1000.0 3.0 2
85
- Neosaimiri_fieldsi 768.0 2.89 1
86
- Nuciruptor_rubricae 2000.0 3.3 2
87
- Panamacebus_transitus 2700.0 3.43 2
88
- Paralouatta_varonai 8444.0 3.93 3
89
- Patasola_magdalenae 480.0 2.68 0
90
- Perupithecus_ucayaliensis 400.0 2.6 0
91
- Pithecia_irrorata 2160.0 3.33 2
92
- Pithecia_monachus 2360.0 3.37 2
93
- Pithecia_pithecia 1760.0 3.25 2
94
- Proteropithecia_neuquenensis 1600.0 3.2 2
95
- Saguinus_bicolor 429.0 2.63 0
96
- Saguinus_fuscicollis 350.5 2.54 0
97
- Saguinus_geoffroyi 492.0 2.69 0
98
- Saguinus_graellsi 474.5 2.68 0
99
- Saguinus_imperator 585.0 2.77 1
100
- Saguinus_labiatus 514.5 2.71 1
101
- Saguinus_martinsi 492.0 2.69 0
102
- Saguinus_melanoleucus ? ? ?
103
- Saguinus_midas 545.0 2.74 1
104
- Saguinus_mystax 524.5 2.72 1
105
- Saguinus_nigricollis 476.0 2.68 0
106
- Saguinus_oedipus 411.0 2.61 0
107
- Saguinus_tripartitus 871.5 2.94 1
108
- Saimiri_boliviensis 788.5 2.9 1
109
- Saimiri_oerstedii 767.25 2.88 1
110
- Saimiri_sciureus 852.5 2.93 1
111
- Saimiri_ustus 800.0 2.9 1
112
- Sapajus_apella 3085.0 3.49 3
113
- Sapajus_libidinosus 2509.779135 3.4 2
114
- Sapajus_robustus 2730.833333 3.44 2
115
- Sapajus_xanthosternos 2440.47619 3.39 2
116
- Solimoea_acrensis 8000.0 3.9 3
117
- Soriacebus_ameghinorum 1483.0 3.17 2
118
- Stirtonia_tatacoensis 5513.0 3.74 3
119
- Stirtonia_victoriae 10000.0 4.0 3
120
- Szalatavus_attricuspis 550.0 2.74 1
121
- Tremacebus_harringtoni 1800.0 3.26 2
122
- Xenothrix_mcgregori 5720.0 3.76 3