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

bella_companion/simulations/beast_configs/fbd-2traits/Nonparametric.xml

@@ -1,70 +0,0 @@
-<?xml version="1.0"?>
-<beast
-    namespace="
-        :beast.base.evolution.operator.kernel
-        :beast.base.inference.parameter
-        :beast.base.inference.operator.kernel
-        :beast.base.inference
-        :beast.base.inference.distribution
-        :bdmmprime.distribution
-        :bdmmprime.parameterization
-        :feast.fileio
-        :feast.function
-        :feast.expressions"
-    version="2.5"
->
-    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
-
-    <map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
-    <map name="TaxonSetFromTree">feast.fileio.TaxonSetFromTree</map>
-	<map name="TraitSetFromTaxonSet">feast.fileio.TraitSetFromTaxonSet</map>
-    <map name="TypeSet">bdmmprime.parameterization.TypeSet</map>
-
-    <TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
-    <TaxonSetFromTree id="taxonSet" tree="@tree"/>
-	<TraitSetFromTaxonSet id="typeTraitSet" traitname="type" delimiter="|" takeGroup="1" taxa="@taxonSet"/>
-	<TypeSet id="typeSet" value="$(types)" typeTraitSet="@typeTraitSet"/>
-
-    <Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
-    <Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
-
-    <run spec="MCMC" chainLength="10000000">
-        <state id="state">
-            <stateNode spec="RealParameter" id="birthRate" value="$(birthRateInit)"/>
-            <stateNode spec="RealParameter" id="deathRate" value="$(deathRateInit)"/>
-        </state>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution spec="BirthDeathMigrationDistribution" tree="@tree" typeTraitSet="@typeTraitSet">
-                    <parameterization spec="CanonicalParameterization" processLength="$(processLength)" typeSet="@typeSet">
-                        <birthRate id="birthRateSP" spec="SkylineVectorParameter" skylineValues="@birthRate" changeTimes="$(changeTimes)" typeSet="@typeSet"/>
-                        <deathRate id="deathRateSP" spec="SkylineVectorParameter" skylineValues="@deathRate" changeTimes="$(changeTimes)" typeSet="@typeSet"/>
-                        <migrationRate spec="SkylineMatrixParameter" skylineValues="$(migrationRate)" typeSet="@typeSet"/>
-                        <samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)" typeSet="@typeSet"/>
-                        <removalProb spec="SkylineVectorParameter" skylineValues="0.0" typeSet="@typeSet"/>
-                        <rhoSampling spec="TimedParameter" values="1" times="$(processLength)" typeSet="@typeSet"/>
-                    </parameterization>
-                    <startTypePriorProbs spec="RealParameter" value="$(startTypePriorProbs)"/>
-                </distribution>
-            </distribution>
-
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution spec="Prior" x="@deathRate" distr="@deathRatePrior"/>
-                <distribution spec="Prior" x="@birthRate" distr="@birthRatePrior"/>
-            </distribution>
-        </distribution>
-
-        <operator spec="BactrianScaleOperator" parameter="@birthRate" weight="30.0"/>
-        <operator spec="BactrianScaleOperator" parameter="@deathRate" weight="30.0"/>
-
-        <logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
-            <log idref="posterior"/>
-            <log idref="prior"/>
-            <log idref="likelihood"/>
-            <log idref="birthRateSP"/>
-            <log idref="deathRateSP"/>
-        </logger>
-    </run>
-
-</beast>

bella_companion/simulations/beast_configs/fbd-no-traits/GLM.xml

@@ -1,88 +0,0 @@
-<?xml version="1.0"?>
-<beast
-    namespace="
-        :beast.base.evolution.operator.kernel
-        :beast.base.inference.parameter
-        :beast.base.inference.operator.kernel
-        :beast.base.inference
-        :beast.base.inference.distribution
-        :bdmmprime.distribution
-        :bdmmprime.parameterization
-        :feast.fileio
-        :feast.function
-        :feast.expressions"
-    version="2.5"
->
-    <map name="Normal">beast.base.inference.distribution.Normal</map>
-    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
-
-    <map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
-
-    <TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
-
-    <Normal id="weightsPrior" mean="0" sigma="1"/>
-    <Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
-    <Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
-
-    <run spec="MCMC" chainLength="10000000">
-        <state id="state">
-            <stateNode spec="RealParameter" id="birthRateScaler" value="1"/>
-            <stateNode spec="RealParameter" id="deathRateScaler" value="1"/>
-            <stateNode spec="RealParameter" id="birthRateW" value="0"/>
-            <stateNode spec="RealParameter" id="deathRateW" value="0"/>
-        </state>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution spec="BirthDeathMigrationDistribution" tree="@tree">
-                    <parameterization spec="CanonicalParameterization" processLength="$(processLength)">
-                        <birthRate id="birthRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
-                            <skylineValues id="birthRate" spec="glmprior.util.GLMLogLinear" coefficients="@birthRateW" scaleFactor="@birthRateScaler" transform="false">
-                                <predictor spec="RealParameter" value="$(timePredictor)"/>
-                                <predictor spec="RealParameter" value="$(randomPredictor)"/>
-                                <indicators spec="BooleanParameter" value="1"/>
-                            </skylineValues>
-                        </birthRate>
-                        <deathRate id="deathRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
-                            <skylineValues id="deathRate" spec="glmprior.util.GLMLogLinear" coefficients="@deathRateW" scaleFactor="@deathRateScaler" transform="false">
-                                <predictor spec="RealParameter" value="$(timePredictor)"/>
-                                <predictor spec="RealParameter" value="$(randomPredictor)"/>
-                                <indicators spec="BooleanParameter" value="1"/>
-                            </skylineValues>
-                        </deathRate>
-                        <samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)"/>
-                        <removalProb spec="SkylineVectorParameter" skylineValues="0.0"/>
-                        <rhoSampling spec="TimedParameter" values="1" times="$(processLength)"/>
-                    </parameterization>
-                </distribution>
-            </distribution>
-
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution spec="Prior" x="@birthRateScaler" distr="@weightsPrior"/>
-                <distribution spec="Prior" x="@deathRateScaler" distr="@weightsPrior"/>
-                <distribution spec="Prior" x="@birthRateW" distr="@weightsPrior"/>
-                <distribution spec="Prior" x="@deathRateW" distr="@weightsPrior"/>
-                <distribution spec="Prior" x="@birthRate" distr="@birthRatePrior"/>
-                <distribution spec="Prior" x="@deathRate" distr="@deathRatePrior"/>
-            </distribution>
-        </distribution>
-
-        <operator spec="BactrianScaleOperator" parameter="@birthRateScaler" weight="30.0"/>
-        <operator spec="BactrianScaleOperator" parameter="@deathRateScaler" weight="30.0"/>
-        <operator spec="BactrianRandomWalkOperator" parameter="@birthRateW" weight="30.0"/>
-        <operator spec="BactrianRandomWalkOperator" parameter="@deathRateW" weight="30.0"/>
-
-        <logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
-            <log idref="posterior"/>
-            <log idref="prior"/>
-            <log idref="likelihood"/>
-            <log idref="birthRateSP"/>
-            <log idref="deathRateSP"/>
-            <log idref="birthRateW"/>
-            <log idref="deathRateW"/>
-            <log idref="birthRateScaler"/>
-            <log idref="deathRateScaler"/>
-        </logger>
-    </run>
-
-</beast>

bella_companion/simulations/beast_configs/fbd-no-traits/MLP.xml

@@ -1,86 +0,0 @@
-<?xml version="1.0"?>
-<beast
-    namespace="
-        :beast.base.inference.parameter
-        :beast.base.inference.operator.kernel
-        :beast.base.inference
-        :beast.base.inference.distribution
-        :bdmmprime.distribution
-        :bdmmprime.parameterization
-        :feast.fileio
-        :feast.function
-        :feast.expressions"
-    version="2.5"
->
-    <map name="Normal">beast.base.inference.distribution.Normal</map>
-
-    <map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
-
-    <TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
-
-    <Normal id="weightsPrior" mean="0" sigma="1"/>
-
-    <run spec="MCMC" chainLength="10000000">
-        <state id="state">
-            <plate var="n" range="$(layersRange)">
-                <stateNode spec="RealParameter" id="birthRateW$(n)" value="0"/>
-                <stateNode spec="RealParameter" id="deathRateW$(n)" value="0"/>
-            </plate>
-        </state>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution spec="BirthDeathMigrationDistribution" tree="@tree">
-                    <parameterization spec="CanonicalParameterization" processLength="$(processLength)">
-                        <birthRate id="birthRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
-                            <skylineValues id="birthRate" spec="bella.BayesMLP" nodes="$(nodes)">
-                                <predictor spec="RealParameter" value="$(timePredictor)"/>
-                                <predictor spec="RealParameter" value="$(randomPredictor)"/>
-                                <plate var="n" range="$(layersRange)">
-                                    <weights idref="birthRateW$(n)"/>
-                                </plate>
-                                <activationFunctionsOutput spec="bella.Sigmoid" upper="$(birthRateUpper)"/>
-                            </skylineValues>
-                        </birthRate>
-                        <deathRate id="deathRateSP" spec="SkylineVectorParameter" changeTimes="$(changeTimes)">
-                            <skylineValues id="deathRate" spec="bella.BayesMLP" nodes="$(nodes)">
-                                <predictor spec="RealParameter" value="$(timePredictor)"/>
-                                <predictor spec="RealParameter" value="$(randomPredictor)"/>
-                                <plate var="n" range="$(layersRange)">
-                                    <weights idref="deathRateW$(n)"/>
-                                </plate>
-                                <activationFunctionsOutput spec="bella.Sigmoid" upper="$(deathRateUpper)"/>
-                            </skylineValues>
-                        </deathRate>
-                        <samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)"/>
-                        <removalProb spec="SkylineVectorParameter" skylineValues="0.0"/>
-                        <rhoSampling spec="TimedParameter" values="1" times="$(processLength)"/>
-                    </parameterization>
-                </distribution>
-            </distribution>
-
-            <distribution id="prior" spec="CompoundDistribution">
-                <plate var="n" range="$(layersRange)">
-                    <distribution spec="Prior" x="@birthRateW$(n)" distr="@weightsPrior"/>
-                    <distribution spec="Prior" x="@deathRateW$(n)" distr="@weightsPrior"/>
-                </plate>
-            </distribution>
-        </distribution>
-
-        <plate var="n" range="$(layersRange)">
-            <operator spec="BactrianRandomWalkOperator" parameter="@birthRateW$(n)" weight="30.0"/>
-            <operator spec="BactrianRandomWalkOperator" parameter="@deathRateW$(n)" weight="30.0"/>
-        </plate>
-
-        <logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
-            <log idref="posterior"/>
-            <log idref="prior"/>
-            <log idref="likelihood"/>
-            <log idref="birthRateSP"/>
-            <log idref="deathRateSP"/>
-            <log idref="birthRate"/>
-            <log idref="deathRate"/>
-        </logger>
-    </run>
-
-</beast>

bella_companion/simulations/beast_configs/fbd-no-traits/Nonparametric.xml

@@ -1,62 +0,0 @@
-<?xml version="1.0"?>
-<beast
-    namespace="
-        :beast.base.evolution.operator.kernel
-        :beast.base.inference.parameter
-        :beast.base.inference.operator.kernel
-        :beast.base.inference
-        :beast.base.inference.distribution
-        :bdmmprime.distribution
-        :bdmmprime.parameterization
-        :feast.fileio
-        :feast.function
-        :feast.expressions"
-    version="2.5"
->
-    <map name="Uniform">beast.base.inference.distribution.Uniform</map>
-
-    <map name="TreeFromNewickFile">feast.fileio.TreeFromNewickFile</map>
-
-    <TreeFromNewickFile id="tree" fileName="$(treeFile)" IsLabelledNewick="true" adjustTipHeights='false'/>
-
-    <Uniform id="birthRatePrior" upper="$(birthRateUpper)"/>
-    <Uniform id="deathRatePrior" upper="$(deathRateUpper)"/>
-
-    <run spec="MCMC" chainLength="10000000">
-        <state id="state">
-            <stateNode spec="RealParameter" id="birthRate" value="$(birthRateInit)"/>
-            <stateNode spec="RealParameter" id="deathRate" value="$(deathRateInit)"/>
-        </state>
-
-        <distribution id="posterior" spec="CompoundDistribution">
-            <distribution id="likelihood" spec="CompoundDistribution">
-                <distribution spec="BirthDeathMigrationDistribution" tree="@tree">
-                    <parameterization spec="CanonicalParameterization" processLength="$(processLength)">
-                        <birthRate id="birthRateSP" spec="SkylineVectorParameter" skylineValues="@birthRate" changeTimes="$(changeTimes)"/>
-                        <deathRate id="deathRateSP" spec="SkylineVectorParameter" skylineValues="@deathRate" changeTimes="$(changeTimes)"/>
-                        <samplingRate spec="SkylineVectorParameter" skylineValues="$(samplingRate)"/>
-                        <removalProb spec="SkylineVectorParameter" skylineValues="0.0"/>
-                        <rhoSampling spec="TimedParameter" values="1" times="$(processLength)"/>
-                    </parameterization>
-                </distribution>
-            </distribution>
-
-            <distribution id="prior" spec="CompoundDistribution">
-                <distribution spec="Prior" x="@birthRate" distr="@birthRatePrior"/>
-                <distribution spec="Prior" x="@deathRate" distr="@deathRatePrior"/>
-            </distribution>
-        </distribution>
-
-        <operator spec="BactrianScaleOperator" parameter="@birthRate" weight="30.0"/>
-        <operator spec="BactrianScaleOperator" parameter="@deathRate" weight="30.0"/>
-
-        <logger spec="Logger" fileName="$(treeID).log" logEvery="1000" model="@posterior">
-            <log idref="posterior"/>
-            <log idref="prior"/>
-            <log idref="likelihood"/>
-            <log idref="birthRateSP"/>
-            <log idref="deathRateSP"/>
-        </logger>
-    </run>
-
-</beast>

bella_companion-0.0.30.dist-info/METADATA

@@ -1,16 +0,0 @@
-Metadata-Version: 2.1
-Name: bella-companion
-Version: 0.0.30
-Summary: 
-Author: gabriele-marino
-Author-email: gabmarino.8601@gmail.com
-Requires-Python: >=3.10,<4.0
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Requires-Dist: arviz (>=0.22.0,<0.23.0)
-Requires-Dist: bella-lumiere (>=0.0.14,<0.0.15)
-Requires-Dist: dotenv (>=0.9.9,<0.10.0)
-Requires-Dist: phylogenie (>=3.1.2,<4.0.0)
-Requires-Dist: seaborn (>=0.13.2,<0.14.0)

bella_companion-0.0.30.dist-info/RECORD

@@ -1,75 +0,0 @@
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-bella_companion/cli.py,sha256=0SwDxkDPqvsp36kGnrBMLPIhAQM8PIpNXrztZayqmDc,2409
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-bella_companion/eucovid/beast_configs/MLP.xml,sha256=M0_B6t0bZpjCAQqAmjrFshW96pt9sNREcoLUjwchX6Q,10616
-bella_companion/eucovid/beast_configs/Nonparametric.xml,sha256=n-t4sUfDS9AzC02tbIk5mx_RDg2l62ELhdR3I3_jjHE,17783
-bella_companion/eucovid/data/case_data.tsv,sha256=XaSzZh5NcEMVt9d_XlQ19T8UuEkHGrjpSFXhe9IycNg,12412
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-bella_companion/eucovid/data/predictors/changetimes_flights_4e.tsv,sha256=XEepIXKRwcKknJq4-ovKlorvCypGi67B8znuQ5f1LTg,60
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bella_companion-0.0.30.dist-info/entry_points.txt

@@ -1,3 +0,0 @@
-[console_scripts]
-bella=bella_companion.cli:main
-