bella-companion 0.0.28__py3-none-any.whl → 0.0.29__py3-none-any.whl

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Files changed (13) hide show
  1. bella_companion/eucovid/beast_configs/GLM.xml +126 -407
  2. bella_companion/eucovid/beast_configs/MLP.xml +108 -288
  3. bella_companion/eucovid/run_beast.py +6 -6
  4. bella_companion/platyrrhine/beast_config.xml +2 -2
  5. bella_companion/platyrrhine/run_beast.py +3 -1
  6. bella_companion/simulations/beast_configs/epi-multitype/MLP.xml +1 -1
  7. bella_companion/simulations/beast_configs/epi-skyline/MLP.xml +1 -1
  8. bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml +2 -2
  9. bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml +2 -2
  10. {bella_companion-0.0.28.dist-info → bella_companion-0.0.29.dist-info}/METADATA +1 -1
  11. {bella_companion-0.0.28.dist-info → bella_companion-0.0.29.dist-info}/RECORD +13 -13
  12. {bella_companion-0.0.28.dist-info → bella_companion-0.0.29.dist-info}/WHEEL +0 -0
  13. {bella_companion-0.0.28.dist-info → bella_companion-0.0.29.dist-info}/entry_points.txt +0 -0
bella_companion/eucovid/beast_configs/GLM.xml CHANGED
@@ -1,450 +1,169 @@
1
- <?xml version="1.0" encoding="UTF-8" standalone="no"?>
2
- <beast namespace="beast.base.inference
3
- :beast.base.inference.parameter
4
- :beast.base.evolution.branchratemodel
5
- :beast.base.evolution.substitutionmodel
6
- :beast.base.evolution.sitemodel
7
- :beast.base.evolution.tree.coalescent
8
- :beast.base.evolution.tree
9
- :beast.base.evolution.likelihood
10
- :beast.base.evolution.alignment
11
- :beast.base.evolution.operator
12
- :beast.base.evolution.operator.kernel
13
- :beast.base.inference.operator.kernel
14
- :beast.base.inference.operator
15
- :beast.base.math.distributions
16
- :beast.base.evolution
17
- :bdmmprime.util.operators
18
- :bdmmprime.util.priors
19
- :bdmmprime.distribution
20
- :bdmmprime.parameterization
21
- :bdmmprime.mapping
22
- :bdmmprime.util
23
- :bdmmprime.trajectories
24
- :feast
25
- :feast.parameter
26
- :feast.fileio
27
- :feast.function
28
- :feast.expressions
29
- :glmprior.util"
30
- required="BEAST.base v2.7.7:BDMM-Prime v2.2.2" version="2.7">
31
-
32
-
33
- <!-- Map elements -->
34
- <map name="Uniform" >beast.base.inference.distribution.Uniform</map>
35
- <map name="Exponential" >beast.base.inference.distribution.Exponential</map>
36
- <map name="LogNormal" >beast.base.inference.distribution.LogNormalDistributionModel</map>
37
- <map name="Normal" >beast.base.inference.distribution.Normal</map>
38
- <map name="Poisson" >beast.base.inference.distribution.Poisson</map>
39
- <map name="prior" >beast.base.inference.distribution.Prior</map>
40
-
41
- <!-- Adapted from https://github.com/SarahNadeau/cov-europe-bdmm/blob/master/analyses/with_hubei_migration_decrease/with_hubei_migration_decrease_scrubbed.xml -->
42
- <!-- Sequence data loaded from GISAID with the gisaid EPI ISLs -->
43
-
44
- <!-- Alignment -->
45
- <alignment id="alignment" spec= "AlignmentFromFasta"
46
- fileName = "$(aligned_fasta)"/>
47
-
48
- <typeSet id="typeSetBDMMPrime" spec="TypeSet">
49
- <typeTraitSet id="typeTraitSet" spec="TraitSetFromTaxonSet"
50
- traitname="type"
51
- delimiter="|"
52
- takeGroup="1">
53
- <taxa spec="TaxonSet" alignment="@alignment"/>
54
- </typeTraitSet>
55
- </typeSet>
56
-
57
- <trait id="dateTrait" spec="TraitSetFromTaxonSet"
58
- traitname="date"
59
- dateFormat="yyyy-M-dd"
60
- delimiter= "|"
61
- everythingAfterLast="true">
62
- <taxa spec="TaxonSet" alignment="@alignment"/>
63
- </trait>
64
-
65
- <!-- BDMMPrime Population Model -->
66
-
67
- <processLength id="originBDMMPrime" spec="RealParameter">10.0</processLength>
68
-
69
- <Re id="ReSV" spec="SkylineVectorParameter"
70
- timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
71
- <skylineValues id="ReValues" spec="RealParameter">1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4</skylineValues>
72
- <changeTimes id="ReRateChangeTimes" spec="RealParameter">0.123</changeTimes>
73
- </Re>
74
-
75
- <samplingProportion id="samplingProportionSV" spec="SkylineVectorParameter"
76
- timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
77
- <skylineValues id="samplingProportionValues" spec="RealParameter" dimension="15" lower="0.0" upper="1.0">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</skylineValues>
78
-
79
-
80
- <changeTimes id="samplingProportionChangeTimes" spec="RealParameter">0.123 0.205</changeTimes>
81
- </samplingProportion>
82
-
83
-
84
- <becomeUninfectiousRate id="becomeUninfectiousRateSV" spec="SkylineVectorParameter"
85
- typeSet="@typeSetBDMMPrime">
86
- <skylineValues id="becomeUninfectiousValues" spec="RealParameter">36.5</skylineValues>
87
- </becomeUninfectiousRate>
88
-
89
-
90
- <migrationRate id="migrationRateSM" spec="SkylineMatrixParameter"
91
- timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
92
-
93
- <skylineValues id="migrationRateValues" spec="glmprior.util.GLMLogLinear" transform="false">
94
- <plate var="predictor" range="$(GLMpredictor_files)">
95
- <predictor spec="RealParameterFromXSV" id="$(predictor)" fileName="$(predictor)"/>
96
- </plate>
97
-
98
- <parameter id="coefficientsGLM" spec="RealParameter" name="coefficients" value="0.1"/>
99
- <parameter id="scaleFactorGLM" spec="RealParameter" name="scaleFactor" value="1"/>
100
- <parameter id="indicatorGLM" spec="BooleanParameter" name="indicators" value="1"/>
101
- <!-- <parameter id="errorTermGLM" spec="RealParameter" name="error" value="0.01" dimension="30"/> -->
102
-
103
- </skylineValues>
104
-
105
- <changeTimes id="migrationRateChangeTimes" spec="RealParameterFromXSV"
106
- fileName="$(GLMpredictor_changetimes)"/>
107
- </migrationRate>
108
-
109
-
110
-
111
- <removalProb id="removalProbSV" spec="SkylineVectorParameter" skylineValues="1.0"
112
- processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime"/>
113
-
114
- <startTypePriorProbs id="typeFrequencies" spec="RealParameter"
115
- estimate="false" lower="0.0" upper="1.0">1.0 0.0 0.0 0.0 0.0</startTypePriorProbs>
116
-
117
-
118
- <!-- Site Model -->
119
- <siteModel id="siteModel" spec="SiteModel" gammaCategoryCount="4">
120
- <parameter id="gammaShape" name="shape" value="1.0"/>
121
- <parameter name="mutationRate" estimate="false" value="1.0"/>
122
- <parameter name="proportionInvariant" estimate="false" value="0.0"/>
123
-
124
- <substModel spec="HKY">
125
- <kappa id="kappa" spec="RealParameter" value="2.0"/>
126
- <frequencies id="empiricalFreqs" spec="Frequencies" data="@alignment"/>
127
- </substModel>
128
- </siteModel>
129
-
130
-
131
- <!-- Branch rate Model -->
132
- <branchRateModel id="branchRateModel" spec="StrictClockModel">
133
- <parameter id="clockRate" name="clock.rate" estimate="false">8.0E-4</parameter>
134
- </branchRateModel>
135
-
136
-
137
- <!-- Population Model for Tree initialiser -->
138
- <popFunc id="popFunc" spec="ConstantPopulation">
139
- <popSize spec="RealParameter" value="0.1"/>
140
- </popFunc>
141
-
142
-
143
- <!-- MCMC -->
144
- <run id="mcmc" spec="MCMC" chainLength="10000000" numInitializationAttempts="100">
145
-
146
- <!-- State -->
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">
147
46
  <state id="state" spec="State">
148
-
149
- <stateNode id="treeBDMMPrime" spec="RandomTree"
150
- taxa="@alignment"
151
- populationModel="@popFunc"
152
- trait="@dateTrait">
47
+ <stateNode id="tree" spec="RandomTree" taxa="@alignment" trait="@dateTrait">
48
+ <populationModel spec="ConstantPopulation" popSize="0.1"/>
153
49
  </stateNode>
154
-
155
- <stateNode idref="originBDMMPrime"/>
156
- <stateNode idref="ReValues"/>
157
- <stateNode idref="samplingProportionValues"/>
158
- <stateNode idref="coefficientsGLM"/>
159
- <stateNode idref="scaleFactorGLM"/>
160
- <stateNode idref="indicatorGLM"/>
161
-
162
- <stateNode idref="kappa"/>
163
- <stateNode idref="gammaShape"/>
164
-
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"/>
165
57
  </state>
166
58
 
167
-
168
- <!-- Posterior Distribution -->
169
59
  <distribution id="posterior" spec="CompoundDistribution">
170
-
171
- <!-- Tree Likelihood -->
172
60
  <distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
173
-
174
- <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood"
175
- data="@alignment"
176
- tree="@treeBDMMPrime"
177
- siteModel="@siteModel"
178
- branchRateModel="@branchRateModel"/>
179
-
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>
180
69
  </distribution>
181
70
 
182
- <!-- Prior distribution -->
183
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>
184
90
 
185
- <!-- BDMM-Prime tree prior distribution -->
186
- <distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution"
187
- tree="@treeBDMMPrime"
188
- conditionOnSurvival="true"
189
- finalSampleOffset="0.0"
190
- typeTraitSet="@typeTraitSet"
191
- startTypePriorProbs="@typeFrequencies">
192
-
193
- <!-- Parameterization BDMM-Prime -->
194
- <parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization"
195
- processLength="@originBDMMPrime"
196
- Re="@ReSV"
197
- samplingProportion="@samplingProportionSV"
198
- becomeUninfectiousRate="@becomeUninfectiousRateSV"
199
- migrationRate="@migrationRateSM"
200
- removalProb="@removalProbSV"
201
- typeSet="@typeSetBDMMPrime"/>
202
-
203
- </distribution>
204
-
205
-
206
- <!-- Priors on parameters -->
207
- <!-- BDMMPrime parameters priors -->
208
-
209
- <prior id="originBDMMPrimePrior" name="distribution" x="@originBDMMPrime">
91
+ <prior name="distribution" x="@processLength">
210
92
  <LogNormal name="distr" M="-1.0" S="0.2"/>
211
93
  </prior>
212
-
213
- <!-- Reproductive number Prior -->
214
- <distribution id="RePrior" spec="SmartZeroExcludingPrior" x="@ReValues">
94
+ <distribution spec="SmartZeroExcludingPrior" x="@Re">
215
95
  <LogNormal name="distr" M="0.8" S="0.5"/>
216
96
  </distribution>
217
-
218
- <!-- Prior for sampling proportion for China -->
219
- <distribution id="spChinaE2Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
220
- classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
97
+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
221
98
  <Uniform name="distr" lower="0" upper="0.15"/>
222
99
  </distribution>
223
- <!-- Prior for sampling proportion for France -->
224
- <distribution id="spFranceE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
225
- classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
100
+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
226
101
  <Uniform name="distr" lower="0" upper="0.093"/>
227
102
  </distribution>
228
- <!-- Prior for sampling proportion for Germany Epoch -->
229
- <distribution id="spGermanyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
230
- classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
103
+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
231
104
  <Uniform name="distr" lower="0" upper="0.10"/>
232
105
  </distribution>
233
- <!-- Prior for sampling proportion for Italy -->
234
- <distribution id="spItalyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
235
- classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
106
+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
236
107
  <Uniform name="distr" lower="0" upper="0.005"/>
237
108
  </distribution>
238
- <!-- Prior for sampling proportion for OtherEuropean -->
239
- <distribution id="spOEE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
240
- classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
109
+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
241
110
  <Uniform name="distr" lower="0" upper="0.057"/>
242
111
  </distribution>
243
-
244
-
245
- <!-- Migration rate GLM Prior -->
246
- <!-- <prior id="migRatePrior" name="distribution" x="@migrationRateValues">
247
- <Uniform id="Uniform.migRate" name="distr" lower="0.0" upper="50.0"/>
248
- </prior> -->
249
-
250
- <!-- <prior id="migRatePrior" name="distribution" x="@migrationRateValues">
251
- <LogNormal name="distr" M="0" S="1.5"/>
252
- </prior> -->
253
-
254
- <prior id="coefficientsPrior" name="distribution" x="@coefficientsGLM">
255
- <Normal name="distr">
256
- <parameter spec="RealParameter" estimate="false" name="mean">0.0</parameter>
257
- <parameter spec="RealParameter" estimate="false" name="sigma">1.0</parameter>
258
- </Normal>
259
- </prior>
260
-
261
- <prior id="scaleFactorPrior" name="distribution" x="@scaleFactorGLM">
262
- <LogNormal name="distr">
263
- <parameter spec="RealParameter" estimate="false" name="M">0.0</parameter>
264
- <parameter spec="RealParameter" estimate="false" name="S">0.8</parameter>
265
- </LogNormal>
112
+ <plate var="n" range="$(layersRange)">
113
+ <prior name="distribution" x="@migrationW$(n)">
114
+ <Normal name="distr" mean="0.0" sigma="1.0"/>
115
+ </prior>
116
+ </plate>
117
+ <prior name="distribution" x="@gammaShape">
118
+ <Exponential name="distr" mean="0.5"/>
266
119
  </prior>
267
-
268
- <!-- <prior id="nonZeroIndicatorGLMPrior" name="distribution">
269
- <x id="indicatorSumGLM" spec="Sum" arg="@indicatorGLM"/>
270
- <Poisson name="distr" lambda='0.693'/>
271
- </prior> -->
272
-
273
- <!-- Substitution model parameter priors -->
274
- <prior id="GammaShapePrior" name="distribution" x="@gammaShape">
275
- <Exponential name="distr">
276
- <parameter spec="RealParameter" estimate="false" name="mean">0.5</parameter>
277
- </Exponential>
278
- </prior>
279
-
280
120
  <prior id="KappaPrior" name="distribution" x="@kappa">
281
- <LogNormal name="distr">
282
- <parameter spec="RealParameter" estimate="false" name="M">1.0</parameter>
283
- <parameter spec="RealParameter" estimate="false" name="S">1.25</parameter>
284
- </LogNormal>
121
+ <LogNormal name="distr" M="1.0" S="1.25"/>
285
122
  </prior>
286
-
287
123
  </distribution>
288
124
  </distribution>
289
125
 
290
-
291
- <!-- Operators -->
292
- <!-- Tree operators -->
293
- <operator id="BDMMPrimeTreeRootScaler" spec="BactrianScaleOperator" tree="@treeBDMMPrime"
294
- rootOnly="true" scaleFactor="0.25" weight="5.0"/>
295
-
296
- <operator id="BDMMPrimeUniformOperator" spec="BactrianNodeOperator" tree="@treeBDMMPrime"
297
- weight="30.0"/>
298
-
299
- <operator id="BDMMPrimeSubtreeSlideScaler" spec="BactrianSubtreeSlide" tree="@treeBDMMPrime"
300
- weight="15.0"/>
301
-
302
- <operator id="BDMMPrimeNarrow" spec="Exchange" tree="@treeBDMMPrime"
303
- weight="15.0"/>
304
-
305
- <operator id="BDMMPrimeWide" spec="Exchange" tree="@treeBDMMPrime"
306
- isNarrow="false" weight="3.0"/>
307
-
308
- <operator id="BDMMPrimeWilsonBalding" spec="WilsonBalding" tree="@treeBDMMPrime"
309
- weight="3.0"/>
310
-
311
- <operator id="BDMMPrimeBICEPSEpochTop" spec="EpochFlexOperator" tree="@treeBDMMPrime"
312
- scaleFactor="0.1" weight="2.0"/>
313
-
314
- <operator id="BDMMPrimeBICEPSEpochAll" spec="EpochFlexOperator" tree="@treeBDMMPrime"
315
- fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
316
-
317
- <operator id="BDMMPrimeBICEPSTreeFlex" spec="TreeStretchOperator" tree="@treeBDMMPrime"
318
- scaleFactor="0.01" weight="2.0"/>
319
-
320
-
321
- <!-- Population model operators -->
322
-
323
- <operator id="originBDMMPrimeScaler" spec="BactrianScaleOperator" parameter="@originBDMMPrime"
324
- scaleFactor="0.25" weight="3.0" />
325
-
326
- <operator id="ReScaler" spec="SmartScaleOperator" parameter="@ReValues" scaleFactor="0.25"
327
- weight="10.0" />
328
- <!-- <operator id="ReScalerAll" spec="BactrianScaleOperator" parameter="@ReValues" scaleFactor="0.25"
329
- weight="3.0" scaleAll="true" /> -->
330
-
331
- <operator id="samplingProportionScaler" spec="SmartScaleOperator" parameter="@samplingProportionValues"
332
- weight="3.0" />
333
-
334
- <!-- <operator id="scaleFactorGLMScaler" spec="BactrianScaleOperator" parameter="@scaleFactorGLM" scaleFactor="0.25" weight="3.0" /> -->
335
-
336
- <operator id="coefficientsGLMScaler" spec="BactrianRandomWalkOperator" parameter="@coefficientsGLM"
337
- weight="5.0" scaleFactor="0.1"/>
338
-
339
- <operator id="AVNMOperator" spec="beast.base.evolution.operator.kernel.AdaptableVarianceMultivariateNormalOperator" weight="5.0"
340
- coefficient="1.0"
341
- scaleFactor="0.5"
342
- beta="0.05"
343
- initial="800"
344
- burnin="400"
345
- every="1">
346
- <transformations spec="beast.base.inference.operator.kernel.Transform$NoTransform">
347
- <f idref="coefficientsGLM"/>
348
- </transformations>
126
+ <operator spec="BactrianScaleOperator" tree="@tree" rootOnly="true" scaleFactor="0.25" weight="5.0"/>
127
+ <operator spec="BactrianNodeOperator" tree="@tree" weight="30.0"/>
128
+ <operator spec="BactrianSubtreeSlide" tree="@tree" weight="15.0"/>
129
+ <operator spec="Exchange" tree="@tree" weight="15.0"/>
130
+ <operator spec="Exchange" tree="@tree" isNarrow="false" weight="3.0"/>
131
+ <operator spec="WilsonBalding" tree="@tree" weight="3.0"/>
132
+ <operator spec="EpochFlexOperator" tree="@tree" scaleFactor="0.1" weight="2.0"/>
133
+ <operator spec="EpochFlexOperator" tree="@tree" fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
134
+ <operator spec="TreeStretchOperator" tree="@tree" scaleFactor="0.01" weight="2.0"/>
135
+ <operator spec="BactrianScaleOperator" parameter="@processLength" scaleFactor="0.25" weight="3.0"/>
136
+ <operator spec="SmartScaleOperator" parameter="@Re" scaleFactor="0.25" weight="10.0"/>
137
+ <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0"/>
138
+ <operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW" weight="5.0" scaleFactor="0.1"/>
139
+ <operator spec="AdaptableVarianceMultivariateNormalOperator" weight="5.0" coefficient="1.0" scaleFactor="0.5" beta="0.05" initial="800" burnin="400" every="1">
140
+ <transformations spec="Transform$NoTransform" f="@migrationRateW"/>
349
141
  </operator>
142
+ <operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
143
+ <operator spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
350
144
 
351
- <!-- <operator id="indicatorParamGLMFlip" spec="BitFlipOperator" parameter="@indicatorGLM"
352
- weight="10.0" uniform="false" />
353
-
354
- <operator id="indicatorSwap" spec="glmprior.operator.ExtendedSwapOperator" boolparameter="@indicatorGLM" weight="5.0" />
355
-
356
- <operator id="indicatorParamGLMPick" spec="glmprior.operator.PickIndicatorOperator"
357
- parameter="@indicatorGLM" weight="3.0" />
358
-
359
- <operator id="BSSVSGLMoperator" spec="glmprior.operator.BitFlipBSSVSOperator" indicator="@indicatorGLM" mu="@scaleFactorGLM" weight="10"/>
360
-
361
- <operator id="multiSwapOperator" spec="glmprior.operator.MultiSwapOperator" boolparameter="@indicatorGLM" parameter="@coefficientsGLM" weight="10.0" />
362
-
363
- <operator id="JointSwapGLM1" spec="JointOperator" weight="3.0">
364
- <operator idref="indicatorSwap"/>
365
- <operator idref="AVNMOperator"/>
366
- </operator>
367
-
368
- <operator id="JointSwapGLM2" spec="JointOperator" weight="3.0">
369
- <operator idref="coefficientsGLMScaler"/>
370
- <operator idref="scaleFactorGLMScaler"/>
371
- </operator>
372
- -->
373
- <!-- <operator id="errorTermGLMScaler" spec="BactrianScaleOperator" parameter="@errorTermGLM"
374
- weight="5.0" upper="20.0"/> -->
375
-
376
-
377
- <!-- Substitution model operators -->
378
- <operator id="gammaShapeScaler" spec="BactrianScaleOperator" parameter="@gammaShape"
379
- weight="1.0"/>
380
-
381
- <operator id="KappaScaler" spec="BactrianScaleOperator" parameter="@kappa"
382
- weight="1.0"/>
383
-
384
-
385
- <!-- Loggers -->
386
- <logger id="tracelog" spec="Logger" fileName="$(filebase).log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
145
+ <logger spec="Logger" fileName="MCMC.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
387
146
  <log idref="posterior"/>
388
147
  <log idref="likelihood"/>
389
148
  <log idref="prior"/>
390
- <log idref="treeLikelihood"/>
391
- <log idref="gammaShape"/>
392
- <log idref="kappa"/>
393
- <log id="TreeHeight" spec="TreeStatLogger" tree="@treeBDMMPrime"/>
394
- <log id="typedTreeStats" spec="TypedTreeStatsLogger" includeRootEdge="true"
395
- typeLabel="type" typeSet="@typeSetBDMMPrime">
396
- <typedTree id="typeMappedTree" spec="TypeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@typeFrequencies" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@treeBDMMPrime"/>
397
- </log>
398
- <log idref="originBDMMPrime"/>
399
- <log idref="ReSV"/>
400
- <log idref="becomeUninfectiousRateSV"/>
401
- <log idref="samplingProportionSV"/>
402
- <log idref="migrationRateSM"/>
403
- <log idref="coefficientsGLM"/>
404
- <log idref="scaleFactorGLM"/>
405
- <log idref="indicatorGLM"/>
406
- <log id="coefbyindGLM" spec="ExpCalculator" value="coefficientsGLM*indicatorGLM" useCaching="false">
407
- <arg idref="coefficientsGLM"/>
408
- <arg idref="indicatorGLM"/>
409
- </log>
410
- <plate var="predictor" range="$(GLMpredictor_files)">
411
- <log idref="$(predictor)"/>
412
- </plate>
413
- <!-- <log idref="errorTermGLM"/> -->
414
- <log idref="removalProbSV"/>
415
- <log idref="typeFrequencies"/>
416
- </logger>
417
-
418
- <logger id="screenlog" spec="Logger" logEvery="1000">
419
- <log idref="posterior"/>
420
- <log arg="@posterior" id="ESS_posterior" spec="util.ESS"/>
421
- <log idref="likelihood"/>
422
- <log arg="@likelihood" id="ESS_likelihood" spec="util.ESS"/>
423
- <log idref="prior"/>
424
- <log arg="@prior" id="ESS_prior" spec="util.ESS"/>
425
149
  <log idref="BDMMPrime"/>
426
- <log arg="@BDMMPrime" id="ESS_BDMMPrime" spec="util.ESS"/>
427
- </logger>
428
-
429
- <logger id="treelog" spec="Logger" fileName="$(filebase).trees" logEvery="1000" mode="tree">
430
- <log id="TreeWithMetaDataLogger" spec="TreeWithMetaDataLogger" tree="@treeBDMMPrime"/>
150
+ <log idref="gammaShape"/>
151
+ <log idref="kappa"/>
152
+ <log idref="processLength"/>
153
+ <log idref="ReSP"/>
154
+ <log idref="samplingProportionSP"/>
155
+ <log idref="migrationRateSP"/>
156
+ <log idref="migrationRateW"/>
157
+ <log idref="migrationRateScaler"/>
431
158
  </logger>
432
-
433
- <logger id="typedTreeLogger" spec="OptionalLogger" enableLogger="true"
434
- fileName="$(filebase).typed.trees" logEvery="10000" mode="tree">
159
+ <logger spec="Logger" fileName="typedTrees.trees" logEvery="10000" mode="tree">
435
160
  <log idref="typeMappedTree"/>
436
161
  </logger>
437
- <logger id="nodeTypedTreeLogger.t:eubdmm_alignment" spec="OptionalLogger" enableLogger="true"
438
- fileName="$(filebase).typed.node.trees" logEvery="10000" mode="tree">
439
- <log id="nodeTypedTree" spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
162
+ <logger spec="Logger" fileName="TypedNodeTrees.trees" logEvery="10000" mode="tree">
163
+ <log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
440
164
  </logger>
441
- <logger id="trajLogger" spec="OptionalLogger" enableLogger="true" fileName="$(filebase).traj" logEvery="10000">
442
- <log id="typedTraj" spec="SampledTrajectory" bdmmDistrib="@BDMMPrime"
443
- startTypePriorProbs="@typeFrequencies" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
165
+ <logger spec="Logger" fileName="trajectories.csv" logEvery="10000">
166
+ <log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
444
167
  </logger>
445
-
446
- <operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/>
447
-
448
168
  </run>
449
-
450
169
  </beast>
bella_companion/eucovid/beast_configs/MLP.xml CHANGED
@@ -1,350 +1,170 @@
1
- <?xml version="1.0" encoding="UTF-8" standalone="no"?>
1
+ <?xml version="1.0"?>
2
2
  <beast
3
3
  namespace="
4
- :beast.base.inference
5
- :beast.base.inference.parameter
4
+ :beast.base.evolution
5
+ :beast.base.evolution.alignment
6
6
  :beast.base.evolution.branchratemodel
7
- :beast.base.evolution.substitutionmodel
8
- :beast.base.evolution.sitemodel
9
- :beast.base.evolution.tree.coalescent
10
- :beast.base.evolution.tree
11
7
  :beast.base.evolution.likelihood
12
- :beast.base.evolution.alignment
13
8
  :beast.base.evolution.operator
14
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
15
16
  :beast.base.inference.operator.kernel
16
- :beast.base.inference.operator
17
- :beast.base.math.distributions
18
- :beast.base.evolution
19
- :bdmmprime.util.operators
20
- :bdmmprime.util.priors
21
17
  :bdmmprime.distribution
22
- :bdmmprime.parameterization
23
18
  :bdmmprime.mapping
24
- :bdmmprime.util
25
19
  :bdmmprime.trajectories
26
- :feast
27
- :feast.parameter
28
- :feast.fileio
29
- :feast.function
30
- :feast.expressions
31
- :glmprior.util"
32
- required="BEAST.base v2.7.7:BDMM-Prime v2.2.2"
20
+ :bdmmprime.parameterization
21
+ :bdmmprime.util
22
+ :bdmmprime.util.operators
23
+ :bdmmprime.util.priors
24
+ :feast.fileio"
33
25
  version="2.7"
34
26
  >
35
- <map name="Uniform" >beast.base.inference.distribution.Uniform</map>
36
- <map name="Exponential" >beast.base.inference.distribution.Exponential</map>
37
- <map name="LogNormal" >beast.base.inference.distribution.LogNormalDistributionModel</map>
38
- <map name="Normal" >beast.base.inference.distribution.Normal</map>
39
- <map name="Poisson" >beast.base.inference.distribution.Poisson</map>
40
- <map name="prior" >beast.base.inference.distribution.Prior</map>
41
-
42
- <alignment id="alignment" spec= "AlignmentFromFasta" fileName = "$(aligned_fasta)"/>
43
-
44
- <typeSet id="typeSetBDMMPrime" spec="TypeSet">
45
- <typeTraitSet id="typeTraitSet" spec="TraitSetFromTaxonSet" traitname="type" delimiter="|" takeGroup="1">
46
- <taxa spec="TaxonSet" alignment="@alignment"/>
47
- </typeTraitSet>
48
- </typeSet>
49
-
50
- <trait id="dateTrait" spec="TraitSetFromTaxonSet" traitname="date" dateFormat="yyyy-M-dd" delimiter= "|" everythingAfterLast="true">
51
- <taxa spec="TaxonSet" alignment="@alignment"/>
52
- </trait>
53
-
54
- <processLength id="originBDMMPrime" spec="RealParameter">10.0</processLength>
55
-
56
- <Re id="ReSV" spec="SkylineVectorParameter" timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
57
- <skylineValues id="ReValues" spec="RealParameter">1.0 1.1 1.2 1.3 1.4 1.01 1.1 1.2 1.3 1.4</skylineValues>
58
- <changeTimes id="ReRateChangeTimes" spec="RealParameter">0.123</changeTimes>
59
- </Re>
60
-
61
- <samplingProportion id="samplingProportionSV" spec="SkylineVectorParameter"
62
- timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
63
- <skylineValues id="samplingProportionValues" spec="RealParameter" dimension="15" lower="0.0" upper="1.0">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</skylineValues>
64
- <changeTimes id="samplingProportionChangeTimes" spec="RealParameter">0.123 0.205</changeTimes>
65
- </samplingProportion>
66
-
67
- <becomeUninfectiousRate id="becomeUninfectiousRateSV" spec="SkylineVectorParameter"
68
- typeSet="@typeSetBDMMPrime">
69
- <skylineValues id="becomeUninfectiousValues" spec="RealParameter">36.5</skylineValues>
70
- </becomeUninfectiousRate>
71
-
72
- <migrationRate id="migrationRateSM" spec="SkylineMatrixParameter"
73
- timesAreAges="true" processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime">
74
-
75
- <skylineValues id="migrationRateValues" spec="bella.BayesMLP" nodes="$(nodes)">
76
- <plate var="predictor" range="$(GLMpredictor_files)">
77
- <predictor spec="RealParameterFromXSV" id="$(predictor)" fileName="$(predictor)"/>
78
- </plate>
79
-
80
- <plate var="n" range="$(layersRange)">
81
- <weights idref="migrationW$(n)"/>
82
- </plate>
83
-
84
- </skylineValues>
85
-
86
- <changeTimes id="migrationRateChangeTimes" spec="RealParameterFromXSV"
87
- fileName="$(GLMpredictor_changetimes)"/>
88
- </migrationRate>
89
-
90
-
91
-
92
- <removalProb id="removalProbSV" spec="SkylineVectorParameter" skylineValues="1.0"
93
- processLength="@originBDMMPrime" typeSet="@typeSetBDMMPrime"/>
94
-
95
- <startTypePriorProbs id="typeFrequencies" spec="RealParameter"
96
- estimate="false" lower="0.0" upper="1.0">1.0 0.0 0.0 0.0 0.0</startTypePriorProbs>
97
-
98
-
99
- <!-- Site Model -->
100
- <siteModel id="siteModel" spec="SiteModel" gammaCategoryCount="4">
101
- <parameter id="gammaShape" name="shape" value="1.0"/>
102
- <parameter name="mutationRate" estimate="false" value="1.0"/>
103
- <parameter name="proportionInvariant" estimate="false" value="0.0"/>
104
-
105
- <substModel spec="HKY">
106
- <kappa id="kappa" spec="RealParameter" value="2.0"/>
107
- <frequencies id="empiricalFreqs" spec="Frequencies" data="@alignment"/>
108
- </substModel>
109
- </siteModel>
110
-
111
-
112
- <!-- Branch rate Model -->
113
- <branchRateModel id="branchRateModel" spec="StrictClockModel">
114
- <parameter id="clockRate" name="clock.rate" estimate="false">8.0E-4</parameter>
115
- </branchRateModel>
116
-
117
-
118
- <!-- Population Model for Tree initialiser -->
119
- <popFunc id="popFunc" spec="ConstantPopulation">
120
- <popSize spec="RealParameter" value="0.1"/>
121
- </popFunc>
122
-
123
-
124
- <!-- MCMC -->
125
- <run id="mcmc" spec="MCMC" chainLength="10000000" numInitializationAttempts="100">
126
-
127
- <!-- State -->
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">
128
46
  <state id="state" spec="State">
129
-
130
- <stateNode id="treeBDMMPrime" spec="RandomTree"
131
- taxa="@alignment"
132
- populationModel="@popFunc"
133
- trait="@dateTrait">
47
+ <stateNode id="tree" spec="RandomTree" taxa="@alignment" trait="@dateTrait">
48
+ <populationModel spec="ConstantPopulation" popSize="0.1"/>
134
49
  </stateNode>
135
-
136
- <stateNode idref="originBDMMPrime"/>
137
- <stateNode idref="ReValues"/>
138
- <stateNode idref="samplingProportionValues"/>
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"/>
139
52
  <plate var="n" range="$(layersRange)">
140
- <stateNode spec="RealParameter" id="migrationW$(n)" value="0"/>
53
+ <stateNode spec="RealParameter" id="migrationRateW$(n)" value="0"/>
141
54
  </plate>
142
-
143
- <stateNode idref="kappa"/>
144
- <stateNode idref="gammaShape"/>
145
-
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"/>
146
58
  </state>
147
59
 
148
-
149
- <!-- Posterior Distribution -->
150
60
  <distribution id="posterior" spec="CompoundDistribution">
151
-
152
- <!-- Tree Likelihood -->
153
61
  <distribution id="likelihood" spec="CompoundDistribution" useThreads="true">
154
-
155
- <distribution id="treeLikelihood" spec="ThreadedTreeLikelihood"
156
- data="@alignment"
157
- tree="@treeBDMMPrime"
158
- siteModel="@siteModel"
159
- branchRateModel="@branchRateModel"/>
160
-
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>
161
70
  </distribution>
162
71
 
163
- <!-- Prior distribution -->
164
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>
165
93
 
166
- <!-- BDMM-Prime tree prior distribution -->
167
- <distribution id="BDMMPrime" spec="BirthDeathMigrationDistribution"
168
- tree="@treeBDMMPrime"
169
- conditionOnSurvival="true"
170
- finalSampleOffset="0.0"
171
- typeTraitSet="@typeTraitSet"
172
- startTypePriorProbs="@typeFrequencies">
173
-
174
- <!-- Parameterization BDMM-Prime -->
175
- <parameterization id="EpiBDMMPrimeParameterization" spec="EpiParameterization"
176
- processLength="@originBDMMPrime"
177
- Re="@ReSV"
178
- samplingProportion="@samplingProportionSV"
179
- becomeUninfectiousRate="@becomeUninfectiousRateSV"
180
- migrationRate="@migrationRateSM"
181
- removalProb="@removalProbSV"
182
- typeSet="@typeSetBDMMPrime"/>
183
-
184
- </distribution>
185
-
186
-
187
- <!-- Priors on parameters -->
188
- <!-- BDMMPrime parameters priors -->
189
-
190
- <prior id="originBDMMPrimePrior" name="distribution" x="@originBDMMPrime">
94
+ <prior name="distribution" x="@processLength">
191
95
  <LogNormal name="distr" M="-1.0" S="0.2"/>
192
96
  </prior>
193
-
194
- <!-- Reproductive number Prior -->
195
- <distribution id="RePrior" spec="SmartZeroExcludingPrior" x="@ReValues">
97
+ <distribution spec="SmartZeroExcludingPrior" x="@Re">
196
98
  <LogNormal name="distr" M="0.8" S="0.5"/>
197
99
  </distribution>
198
-
199
- <!-- Prior for sampling proportion for China -->
200
- <distribution id="spChinaE2Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
201
- classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
100
+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.2E-5 1.3E-5 1.4E-5 1.5E-5">
202
101
  <Uniform name="distr" lower="0" upper="0.15"/>
203
102
  </distribution>
204
- <!-- Prior for sampling proportion for France -->
205
- <distribution id="spFranceE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
206
- classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
103
+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.3E-5 1.4E-5 1.5E-5">
207
104
  <Uniform name="distr" lower="0" upper="0.093"/>
208
105
  </distribution>
209
- <!-- Prior for sampling proportion for Germany Epoch -->
210
- <distribution id="spGermanyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
211
- classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
106
+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.4E-5 1.5E-5">
212
107
  <Uniform name="distr" lower="0" upper="0.10"/>
213
108
  </distribution>
214
- <!-- Prior for sampling proportion for Italy -->
215
- <distribution id="spItalyE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
216
- classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
109
+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.5E-5">
217
110
  <Uniform name="distr" lower="0" upper="0.005"/>
218
111
  </distribution>
219
- <!-- Prior for sampling proportion for OtherEuropean -->
220
- <distribution id="spOEE1Prior" spec="SmartZeroExcludingPrior" x="@samplingProportionValues"
221
- classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
112
+ <distribution spec="SmartZeroExcludingPrior" x="@samplingProportion" classesToExclude="1.1E-5 1.2E-5 1.3E-5 1.4E-5">
222
113
  <Uniform name="distr" lower="0" upper="0.057"/>
223
114
  </distribution>
224
-
225
115
  <plate var="n" range="$(layersRange)">
226
- <prior name="distribution" x="@migrationW$(n)">
116
+ <prior name="distribution" x="@migrationRateW$(n)">
227
117
  <Normal name="distr" mean="0.0" sigma="1.0"/>
228
118
  </prior>
229
119
  </plate>
230
-
231
- <prior id="GammaShapePrior" name="distribution" x="@gammaShape">
232
- <Exponential name="distr">
233
- <parameter spec="RealParameter" estimate="false" name="mean">0.5</parameter>
234
- </Exponential>
120
+ <prior name="distribution" x="@gammaShape">
121
+ <Exponential name="distr" mean="0.5"/>
235
122
  </prior>
236
-
237
123
  <prior id="KappaPrior" name="distribution" x="@kappa">
238
- <LogNormal name="distr">
239
- <parameter spec="RealParameter" estimate="false" name="M">1.0</parameter>
240
- <parameter spec="RealParameter" estimate="false" name="S">1.25</parameter>
241
- </LogNormal>
124
+ <LogNormal name="distr" M="1.0" S="1.25"/>
242
125
  </prior>
243
-
244
126
  </distribution>
245
127
  </distribution>
246
128
 
247
-
248
- <operator id="BDMMPrimeTreeRootScaler" spec="BactrianScaleOperator" tree="@treeBDMMPrime"
249
- rootOnly="true" scaleFactor="0.25" weight="5.0"/>
250
-
251
- <operator id="BDMMPrimeUniformOperator" spec="BactrianNodeOperator" tree="@treeBDMMPrime"
252
- weight="30.0"/>
253
-
254
- <operator id="BDMMPrimeSubtreeSlideScaler" spec="BactrianSubtreeSlide" tree="@treeBDMMPrime"
255
- weight="15.0"/>
256
-
257
- <operator id="BDMMPrimeNarrow" spec="Exchange" tree="@treeBDMMPrime"
258
- weight="15.0"/>
259
-
260
- <operator id="BDMMPrimeWide" spec="Exchange" tree="@treeBDMMPrime"
261
- isNarrow="false" weight="3.0"/>
262
-
263
- <operator id="BDMMPrimeWilsonBalding" spec="WilsonBalding" tree="@treeBDMMPrime"
264
- weight="3.0"/>
265
-
266
- <operator id="BDMMPrimeBICEPSEpochTop" spec="EpochFlexOperator" tree="@treeBDMMPrime"
267
- scaleFactor="0.1" weight="2.0"/>
268
-
269
- <operator id="BDMMPrimeBICEPSEpochAll" spec="EpochFlexOperator" tree="@treeBDMMPrime"
270
- fromOldestTipOnly="false" scaleFactor="0.1" weight="2.0"/>
271
-
272
- <operator id="BDMMPrimeBICEPSTreeFlex" spec="TreeStretchOperator" tree="@treeBDMMPrime"
273
- scaleFactor="0.01" weight="2.0"/>
274
-
275
- <operator id="originBDMMPrimeScaler" spec="BactrianScaleOperator" parameter="@originBDMMPrime"
276
- scaleFactor="0.25" weight="3.0" />
277
-
278
- <operator id="ReScaler" spec="SmartScaleOperator" parameter="@ReValues" scaleFactor="0.25"
279
- weight="10.0" />
280
-
281
- <operator id="samplingProportionScaler" spec="SmartScaleOperator" parameter="@samplingProportionValues"
282
- weight="3.0" />
283
-
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"/>
284
141
  <plate var="n" range="$(layersRange)">
285
- <operator spec="BactrianRandomWalkOperator" parameter="@migrationW$(n)" weight="5.0"/>
142
+ <operator spec="BactrianRandomWalkOperator" parameter="@migrationRateW$(n)" weight="5.0"/>
286
143
  </plate>
144
+ <operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
145
+ <operator spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
287
146
 
288
- <operator id="gammaShapeScaler" spec="BactrianScaleOperator" parameter="@gammaShape"
289
- weight="1.0"/>
290
-
291
- <operator id="KappaScaler" spec="BactrianScaleOperator" parameter="@kappa"
292
- weight="1.0"/>
293
-
294
-
295
- <!-- Loggers -->
296
- <logger id="tracelog" spec="Logger" fileName="$(filebase).log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
297
- <log idref="posterior"/>
298
- <log idref="likelihood"/>
299
- <log idref="prior"/>
300
- <log idref="treeLikelihood"/>
301
- <log idref="gammaShape"/>
302
- <log idref="kappa"/>
303
- <log id="TreeHeight" spec="TreeStatLogger" tree="@treeBDMMPrime"/>
304
- <log id="typedTreeStats" spec="TypedTreeStatsLogger" includeRootEdge="true"
305
- typeLabel="type" typeSet="@typeSetBDMMPrime">
306
- <typedTree id="typeMappedTree" spec="TypeMappedTree" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@typeFrequencies" mapOnInit="false" remapOnLog="true" typeLabel="type" typeTraitSet="@typeTraitSet" untypedTree="@treeBDMMPrime"/>
307
- </log>
308
- <log idref="originBDMMPrime"/>
309
- <log idref="ReSV"/>
310
- <log idref="becomeUninfectiousRateSV"/>
311
- <log idref="samplingProportionSV"/>
312
- <log idref="migrationRateSM"/>
313
-
314
- <log idref="removalProbSV"/>
315
- <log idref="typeFrequencies"/>
316
- </logger>
317
-
318
- <logger id="screenlog" spec="Logger" logEvery="1000">
147
+ <logger spec="Logger" fileName="MCMC.log" logEvery="1000" model="@posterior" sanitiseHeaders="true" sort="smart">
319
148
  <log idref="posterior"/>
320
- <log arg="@posterior" id="ESS_posterior" spec="util.ESS"/>
321
149
  <log idref="likelihood"/>
322
- <log arg="@likelihood" id="ESS_likelihood" spec="util.ESS"/>
323
150
  <log idref="prior"/>
324
- <log arg="@prior" id="ESS_prior" spec="util.ESS"/>
325
151
  <log idref="BDMMPrime"/>
326
- <log arg="@BDMMPrime" id="ESS_BDMMPrime" spec="util.ESS"/>
327
- </logger>
328
-
329
- <logger id="treelog" spec="Logger" fileName="$(filebase).trees" logEvery="1000" mode="tree">
330
- <log id="TreeWithMetaDataLogger" spec="TreeWithMetaDataLogger" tree="@treeBDMMPrime"/>
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"/>
331
159
  </logger>
332
-
333
- <logger id="typedTreeLogger" spec="OptionalLogger" enableLogger="true"
334
- fileName="$(filebase).typed.trees" logEvery="10000" mode="tree">
160
+ <logger spec="Logger" fileName="typedTrees.trees" logEvery="100000" mode="tree">
335
161
  <log idref="typeMappedTree"/>
336
162
  </logger>
337
- <logger id="nodeTypedTreeLogger.t:eubdmm_alignment" spec="OptionalLogger" enableLogger="true"
338
- fileName="$(filebase).typed.node.trees" logEvery="10000" mode="tree">
339
- <log id="nodeTypedTree" spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
163
+ <logger spec="Logger" fileName="TypedNodeTrees.trees" logEvery="100000" mode="tree">
164
+ <log spec="TypedNodeTreeLogger" typedTree="@typeMappedTree"/>
340
165
  </logger>
341
- <logger id="trajLogger" spec="OptionalLogger" enableLogger="true" fileName="$(filebase).traj" logEvery="10000">
342
- <log id="typedTraj" spec="SampledTrajectory" bdmmDistrib="@BDMMPrime"
343
- startTypePriorProbs="@typeFrequencies" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
166
+ <logger spec="Logger" fileName="trajectories.csv" logEvery="100000">
167
+ <log spec="SampledTrajectory" bdmmDistrib="@BDMMPrime" startTypePriorProbs="@startTypePriorProbs" typeMappedTree="@typeMappedTree" useTauLeaping="true"/>
344
168
  </logger>
345
-
346
- <operatorschedule id="OperatorSchedule" spec="OperatorSchedule"/>
347
-
348
169
  </run>
349
-
350
170
  </beast>
bella_companion/eucovid/run_beast.py CHANGED
@@ -21,16 +21,16 @@ def run_beast():
21
21
  all_predictor_files = ",".join(glob(str(predictors_dir / "all" / "*.tsv")))
22
22
  all_predictors_data = " ".join(
23
23
  [
24
- f"-D aligned_fasta={msa_file}",
25
- f"-D GLMpredictor_changetimes={predictors_dir / 'changetimes_all_7e.tsv'}",
26
- f"-D GLMpredictor_files={all_predictor_files}",
24
+ f"-D msa_file={msa_file}",
25
+ f"-D changeTimesFile={predictors_dir / 'changetimes_all_7e.tsv'}",
26
+ f"-D predictorFiles={all_predictor_files}",
27
27
  ]
28
28
  )
29
29
  flight_predictor_data = " ".join(
30
30
  [
31
- f"-D aligned_fasta={msa_file}",
32
- f"-D GLMpredictor_changetimes={predictors_dir / 'changetimes_flights_4e.tsv'}",
33
- f"-D GLMpredictor_files={predictors_dir / 'flight_pop_x_4e_ls.tsv'}",
31
+ f"-D msa_file={msa_file}",
32
+ f"-D changeTimesFile={predictors_dir / 'changetimes_flights_4e.tsv'}",
33
+ f"-D predictorFiles={predictors_dir / 'flight_pop_x_4e_ls.tsv'}",
34
34
  ]
35
35
  )
36
36
 
bella_companion/platyrrhine/beast_config.xml CHANGED
@@ -36,8 +36,8 @@
36
36
  <run spec="MCMC" chainLength="10000000">
37
37
  <state id="state">
38
38
  <plate var="n" range="$(layersRange)">
39
- <stateNode spec="RealParameter" name="stateNode" id="birthRateW$(n)" value="0"/>
40
- <stateNode spec="RealParameter" name="stateNode" id="deathRateW$(n)" value="0"/>
39
+ <stateNode spec="RealParameter" id="birthRateW$(n)" value="0"/>
40
+ <stateNode spec="RealParameter" id="deathRateW$(n)" value="0"/>
41
41
  </plate>
42
42
  <stateNode spec="RealParameter" id="samplingRate" value="$(samplingRateInit)"/>
43
43
  <stateNode spec="RealParameter" id="migrationRate" value="$(migrationRateInit)"/>
bella_companion/platyrrhine/run_beast.py CHANGED
@@ -34,7 +34,9 @@ def run_beast():
34
34
  log10BM_predictor = " ".join(types * T)
35
35
 
36
36
  job_ids = {}
37
- for i, tree in enumerate(tqdm(trees)):
37
+ for i, tree in enumerate(
38
+ tqdm(trees, desc="Submitting BEAST jobs for platyrrhine datasets")
39
+ ):
38
40
  process_length = max(get_node_depths(tree).values())
39
41
  command = " ".join(
40
42
  [
bella_companion/simulations/beast_configs/epi-multitype/MLP.xml CHANGED
@@ -31,7 +31,7 @@
31
31
  <run spec="MCMC" chainLength="10000000">
32
32
  <state id="state">
33
33
  <plate var="n" range="$(layersRange)">
34
- <stateNode spec="RealParameter" name="stateNode" id="migrationRateW$(n)" value="0"/>
34
+ <stateNode spec="RealParameter" id="migrationRateW$(n)" value="0"/>
35
35
  </plate>
36
36
  </state>
37
37
 
bella_companion/simulations/beast_configs/epi-skyline/MLP.xml CHANGED
@@ -25,7 +25,7 @@
25
25
  <run spec="MCMC" chainLength="10000000">
26
26
  <state id="state">
27
27
  <plate var="n" range="$(layersRange)">
28
- <stateNode spec="RealParameter" name="stateNode" id="reproductionNumberW$(n)" value="0"/>
28
+ <stateNode spec="RealParameter" id="reproductionNumberW$(n)" value="0"/>
29
29
  </plate>
30
30
  </state>
31
31
 
bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml CHANGED
@@ -29,8 +29,8 @@
29
29
  <run spec="MCMC" chainLength="10000000">
30
30
  <state id="state">
31
31
  <plate var="n" range="$(layersRange)">
32
- <stateNode spec="RealParameter" name="stateNode" id="birthRateW$(n)" value="0"/>
33
- <stateNode spec="RealParameter" name="stateNode" id="deathRateW$(n)" value="0"/>
32
+ <stateNode spec="RealParameter" id="birthRateW$(n)" value="0"/>
33
+ <stateNode spec="RealParameter" id="deathRateW$(n)" value="0"/>
34
34
  </plate>
35
35
  </state>
36
36
 
bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml CHANGED
@@ -23,8 +23,8 @@
23
23
  <run spec="MCMC" chainLength="10000000">
24
24
  <state id="state">
25
25
  <plate var="n" range="$(layersRange)">
26
- <stateNode spec="RealParameter" name="stateNode" id="birthRateW$(n)" value="0"/>
27
- <stateNode spec="RealParameter" name="stateNode" id="deathRateW$(n)" value="0"/>
26
+ <stateNode spec="RealParameter" id="birthRateW$(n)" value="0"/>
27
+ <stateNode spec="RealParameter" id="deathRateW$(n)" value="0"/>
28
28
  </plate>
29
29
  </state>
30
30
 
{bella_companion-0.0.28.dist-info → bella_companion-0.0.29.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: bella-companion
3
- Version: 0.0.28
3
+ Version: 0.0.29
4
4
  Summary:
5
5
  Author: gabriele-marino
6
6
  Author-email: gabmarino.8601@gmail.com
{bella_companion-0.0.28.dist-info → bella_companion-0.0.29.dist-info}/RECORD RENAMED
@@ -1,8 +1,8 @@
1
1
  bella_companion/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
2
2
  bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
3
3
  bella_companion/eucovid/__init__.py,sha256=09Ld_G7fZvCDCgEWsmaOyLVQ8pFc9QHAGnXKJ9Zm2AM,81
4
- bella_companion/eucovid/beast_configs/GLM.xml,sha256=YMvcyeSRIGQOhSSoj7FV0R-5wZHcGWwf9bKxamJ0q9k,20739
5
- bella_companion/eucovid/beast_configs/MLP.xml,sha256=SGJVUYyi1ULU7zxx8xn9aiKZNQQ3D9ruyYRsDcFjPzo,16139
4
+ bella_companion/eucovid/beast_configs/GLM.xml,sha256=_pqs2-ADRGSmaBxCmMepuVMWiNEyce3azgE-qD6FNrs,10828
5
+ bella_companion/eucovid/beast_configs/MLP.xml,sha256=M0_B6t0bZpjCAQqAmjrFshW96pt9sNREcoLUjwchX6Q,10616
6
6
  bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=n-t4sUfDS9AzC02tbIk5mx_RDg2l62ELhdR3I3_jjHE,17783
7
7
  bella_companion/eucovid/data/case_data.tsv,sha256=XaSzZh5NcEMVt9d_XlQ19T8UuEkHGrjpSFXhe9IycNg,12412
8
8
  bella_companion/eucovid/data/change_dates.tsv,sha256=_pmVFYiL4X9Pd79uYVgyz3sKeRap7xVcXk0OjqVhuVQ,227
@@ -20,27 +20,27 @@ bella_companion/eucovid/data/predictors/all/sharedborders_7e_nt.tsv,sha256=pPVT5
20
20
  bella_companion/eucovid/data/predictors/changetimes_all_7e.tsv,sha256=hH0xXD2lr_8RPQRqvENv6clPHauAXH22SGQHb3hlfzs,120
21
21
  bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv,sha256=XEepIXKRwcKknJq4-ovKlorvCypGi67B8znuQ5f1LTg,60
22
22
  bella_companion/eucovid/data/predictors/flight_pop_x_4e_ls.tsv,sha256=tMR9-tuGtC3rVABXUtNdV9irUX-9aCCVb_fwksHTn8U,1068
23
- bella_companion/eucovid/run_beast.py,sha256=FYeqqG2_S3o_NrmYqyyll82CR0sbYtI7QuRv5MIrRVY,3748
23
+ bella_companion/eucovid/run_beast.py,sha256=DU3T0xVVQ6y0ZClyFyouMd939V7sf5KGfadEzTDQf6I,3712
24
24
  bella_companion/platyrrhine/__init__.py,sha256=dIx6exNz-vuKiG5FZumvq74QUWcIEFd3L6ErqnOa83c,274
25
- bella_companion/platyrrhine/beast_config.xml,sha256=8A6E5iPu9FqDL3UdlsqDbabLFlC6Qhfa4Ta47niRkVA,7090
25
+ bella_companion/platyrrhine/beast_config.xml,sha256=bLzavt-Zd8cmSgQQnlCBfZ9KyM7d1inOGx12VNjPFb4,7056
26
26
  bella_companion/platyrrhine/data/change_times.csv,sha256=tedobHbaY7-6M3V6F6HSqGAU9dpeeajR5mu1XGJfp6w,68
27
27
  bella_companion/platyrrhine/data/traits.csv,sha256=N_mCnaM9Gy0Qot7-l_mK0vMvr7e_5BZ4bgUHpcoG9UM,3949
28
28
  bella_companion/platyrrhine/data/trees.nwk,sha256=lpSiGUG5s3zE--IKPOyWrJ5vpJb_xAPnfxychs3YNIs,488232
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  bella_companion/platyrrhine/results.py,sha256=qosxqstTy7uadHARRt1WqmxZzxnQ3hiTjtw6V-YWKGA,2556
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- bella_companion/platyrrhine/run_beast.py,sha256=xYpK_QS5Qr-8jvq3_s-uXBW5yGsxE3c8AvHd12N6PFY,2552
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+ bella_companion/platyrrhine/run_beast.py,sha256=fnUmpJue3o0vZn9GWmwlmV0z2HIzXc4t_U2LFIKOq_I,2621
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  bella_companion/platyrrhine/summarize_logs.py,sha256=82N7rcmLthCyQqmP4Yub4KUsIjNzQl9vEuFLMvIv03o,951
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  bella_companion/simulations/__init__.py,sha256=ShYRdp1iSjnS_SzcsH-8jbqXz6P1nyRQZqAtPZJCMVE,454
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  bella_companion/simulations/beast_configs/epi-multitype/GLM.xml,sha256=VymAYsaZVuB3EPE0DCQSXpKepVq8pPjKaB5yhEpaVkE,4334
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- bella_companion/simulations/beast_configs/epi-multitype/MLP.xml,sha256=J-OVblMRmk4XRhz9DHhLpMwaIzqSqYZ7Yq7dTMvQW1s,4094
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+ bella_companion/simulations/beast_configs/epi-multitype/MLP.xml,sha256=AoJyjvVcwKtut64d7sB2gnnenx5sXyuTTNCivykUyqU,4077
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  bella_companion/simulations/beast_configs/epi-multitype/Nonparametric.xml,sha256=DfCMcLM53b-XP9oIiQ9wJWOVTEP3GnoZaL5BMzLLfIQ,3208
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  bella_companion/simulations/beast_configs/epi-skyline/GLM.xml,sha256=7LtJhU7o7aQsnWK7ZIKj-mzmHgCn_RjxvKKbLIlp1Go,3619
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- bella_companion/simulations/beast_configs/epi-skyline/MLP.xml,sha256=ovjFleUnTgyrT8T1uaKboUsL-ZFLCaQN5mk4HadFPU0,3443
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+ bella_companion/simulations/beast_configs/epi-skyline/MLP.xml,sha256=ptoLM0FLDp54bUSxPm12qIvOYWyBkWR1e9VWVWjgU8E,3426
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  bella_companion/simulations/beast_configs/epi-skyline/Nonparametric.xml,sha256=LTiatqeAMiFfdD1leQ5TrGaJhsYwlkbMDpxqhVFOgUQ,2561
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  bella_companion/simulations/beast_configs/fbd-2traits/GLM.xml,sha256=Iff0eAShKLeOnlTmNu6044Wljtla3yckqo2LZ7mP6LY,5897
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- bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml,sha256=E8sgfOAJI4rkbCVhGYa-HwM44ItwxVs4pIXkQOGNTtY,5462
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+ bella_companion/simulations/beast_configs/fbd-2traits/MLP.xml,sha256=RvF70fcnvoBcJxjyT4nELlFm94atSZpKm9d1aS-cJZ4,5428
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  bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml,sha256=ev6ZfMeCwMyK54G_4O8g-tbgoxoD3asxt71x91Cb1QY,3618
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  bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml,sha256=Caq7Gxqx-wYAu3_YkMikVqni3DjBv1Wt00sc1Upo1X8,4743
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- bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml,sha256=_EzDVPrU6Y5ZfzkVn---Sp62KeBZuRCZfoYqxblLq8I,4309
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+ bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml,sha256=JE_cGh2DW5yPAXyXXr0D3DlovmV-aIbze7qrhENHK3w,4275
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  bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml,sha256=m2xaHZwskCFInvVY1QH1fwQqH6p_fgESlPX2BbBeUhk,2822
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  bella_companion/simulations/features.py,sha256=DZOBpJGlQ0UinqUZYbEtoemZ2eQGVLV_i-DfpW31qJI,104
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  bella_companion/simulations/figures/__init__.py,sha256=aBYbJntH4egFmkSSWiVMYDEApXPYxJD7eA3TCPNNegM,658
@@ -69,7 +69,7 @@ bella_companion/utils/__init__.py,sha256=UtMwPK9dWf9NAl0ic8CSsgdW7aSm-5J49OqgvD7
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  bella_companion/utils/beast.py,sha256=TBa0cLklX1_tXqoQE4LRYvds7mLg_9fS2-6U6OHENHo,2184
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  bella_companion/utils/explain.py,sha256=uP7HPyn2YiykAI69BQV3RooDpC6qKoCLXfp3Uibp4zk,1475
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  bella_companion/utils/slurm.py,sha256=xEyf-Jxk8fy71t3fko_Ic9WtUFSdLFE3w4tR17gaBPw,1868
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- bella_companion-0.0.28.dist-info/METADATA,sha256=f_4at3vdN5Z4FMjq-1C71qUa1raHCBL4TaouU3S0TDw,576
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- bella_companion-0.0.28.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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- bella_companion-0.0.28.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
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- bella_companion-0.0.28.dist-info/RECORD,,
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+ bella_companion-0.0.29.dist-info/METADATA,sha256=GfkFvoMcKT2VpMWy3vrbyeKPMoR8xEo7UlZtLcVEon0,576
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+ bella_companion-0.0.29.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
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+ bella_companion-0.0.29.dist-info/entry_points.txt,sha256=rSeKoAhmjnQqAYFcXBv0gAM2ViJfJe0D8_dD-fWrXeg,50
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+ bella_companion-0.0.29.dist-info/RECORD,,