bella-companion 0.0.18__tar.gz → 0.0.19__tar.gz

{bella_companion-0.0.18 → bella_companion-0.0.19}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: bella-companion
-Version: 0.0.18
+Version: 0.0.19
 Summary: 
 Author: gabriele-marino
 Author-email: gabmarino.8601@gmail.com

{bella_companion-0.0.18 → bella_companion-0.0.19}/bella_companion/eucovid/beast_configs/GLM.xml

@@ -68,6 +68,7 @@
             </plate>
             <coefficients id="coefficientsGLM" spec="RealParameter" value="0.1"/>
             <scaleFactor id="scaleFactorGLM" spec="RealParameter" value="1"/>
+            <indicators spec="BooleanParameter"  value="1"/>
         </skylineValues>
         <changeTimes spec="RealParameterFromXSV" fileName="$(changeTimesFile)"/>
     </migrationRate> 

{bella_companion-0.0.18 → bella_companion-0.0.19}/bella_companion/eucovid/beast_configs/Nonparametric.xml

@@ -88,7 +88,7 @@
                 0.0 0.12 0.16      0.25 
                 0.0 0.13 0.17 0.21
             </arg>
-            <arg id="migrationRateScaler" spec="RealParameter" value="0.5"/>
+            <arg id="f" spec="RealParameter" value="0.5"/>
         </skylineValues>
     </migrationRate> 
 
@@ -116,7 +116,7 @@
             <stateNode idref="Re"/>
             <stateNode idref="samplingProportion"/>
             <stateNode idref="migrationRate"/>
-            <stateNode idref="migrationRateScaler"/>
+            <stateNode idref="f"/>
             <stateNode idref="kappa"/>
             <stateNode idref="gammaShape"/>
         </state>
@@ -155,7 +155,7 @@
                 <distribution spec="SmartZeroExcludingPrior" x="@migrationRate">
                     <LogNormal name="distr" M="0.0" S="1.0"/>
                 </distribution> 
-                <distribution spec="ZeroExcludingPrior" x="@migrationRateScaler">
+                <distribution spec="ZeroExcludingPrior" x="@f">
                     <Uniform name="distr" lower="0.0" upper="1.0"/>
                 </distribution>
                 <prior name="distribution" x="@gammaShape">
@@ -180,7 +180,7 @@
         <operator spec="BactrianScaleOperator" parameter="@Re" weight="5.0" />
         <operator spec="SmartScaleOperator" parameter="@samplingProportion" weight="3.0" />
         <operator spec="SmartScaleOperator" parameter="@migrationRate" weight="5.0" />
-        <operator spec="BactrianScaleOperator" parameter="@migrationRateScaler" weight="5.0"/>
+        <operator spec="BactrianScaleOperator" parameter="@f" weight="5.0"/>
         <operator spec="BactrianScaleOperator" parameter="@gammaShape" weight="1.0"/>
         <operator spec="BactrianScaleOperator" parameter="@kappa" weight="1.0"/>
 

{bella_companion-0.0.18 → bella_companion-0.0.19}/bella_companion/eucovid/run_beast.py

@@ -22,14 +22,14 @@ def run_beast():
     all_predictors_data = " ".join(
         [
             f"-D msa_file={msa_file}",
-            f"-D changeTimes={predictors_dir / 'changetimes_all_7e.tsv'}",
+            f"-D changeTimesFile={predictors_dir / 'changetimes_all_7e.tsv'}",
             f"-D predictorFiles={all_predictor_files}",
         ]
     )
     flight_predictor_data = " ".join(
         [
             f"-D msa_file={msa_file}",
-            f"-D changeTimes={predictors_dir / 'changetimes_flights_4e.tsv'}",
+            f"-D changeTimesFile={predictors_dir / 'changetimes_flights_4e.tsv'}",
             f"-D predictorFiles={predictors_dir / 'flight_pop_x_4e_ls.tsv'}",
         ]
     )

{bella_companion-0.0.18 → bella_companion-0.0.19}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "bella-companion"
-version = "0.0.18"
+version = "0.0.19"
 description = ""
 authors = ["gabriele-marino <gabmarino.8601@gmail.com>"]