Tests with math expression condition table for initial assignments

petabtests/cases/v2.0.0/sbml/0026/0026.py

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+from inspect import cleandoc
+
+from petab.v2.C import *
+from petab.v2 import Problem
+
+from petabtests import (
+    PetabV2TestCase,
+    analytical_a,
+    analytical_b,
+    antimony_to_sbml_str,
+)
+from pathlib import Path
+
+DESCRIPTION = cleandoc("""
+## Objective
+
+This case tests the handling of initial concentrations that are specified
+via mathematical expressions (rather than a single value or parameter) in
+the conditions table. For species `A`, the initial concentration is given
+by an expression containing both parameters to be estimated and parameters
+that are not estimated. For species `B`, the initial concentration is
+specified via an expression involving only parameters that are not
+estimated.
+
+## Model
+
+A simple conversion reaction `A <=> B` in a single compartment, following
+mass action kinetics.
+""")
+
+# problem --------------------------------------------------------------------
+ant_model = """
+model *petab_test_0026()
+  compartment compartment_ = 1;
+  species A in compartment_, B in compartment_;
+
+  fwd: A => B; compartment_ * k1 * A;
+  rev: B => A; compartment_ * k2 * B;
+
+  A = a0;
+  B = 1;
+  a0 = 1;
+  k1 = 0;
+  k2 = 0;
+end
+"""
+model_file = Path(__file__).parent / "_model.xml"
+model_file.write_text(antimony_to_sbml_str(ant_model))
+
+problem = Problem()
+
+problem.add_condition("c0", A="initial_A1 + initial_A2", B="initial_B1 / initial_B2")
+problem.add_experiment("e1", 0, "c0")
+
+problem.add_observable("obs_a", "A", noise_formula="0.5")
+problem.add_observable("obs_b", "B", noise_formula="0.5")
+problem.add_measurement("obs_a", experiment_id="e1", time=0, measurement=0.7)
+problem.add_measurement("obs_a", experiment_id="e1", time=10, measurement=0.1)
+problem.add_measurement("obs_b", experiment_id="e1", time=0, measurement=0.7)
+problem.add_measurement("obs_b", experiment_id="e1", time=10, measurement=0.1)
+
+problem.add_parameter("k1", lb=0, ub=10, nominal_value=0.8, estimate=True)
+problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, estimate=True)
+problem.add_parameter("initial_A1", lb=1, ub=10, nominal_value=0.5, estimate=True)
+problem.add_parameter("initial_A2", lb=1, ub=10, nominal_value=1.5, estimate=False)
+problem.add_parameter("initial_B1", lb=0, ub=10, nominal_value=9, estimate=False)
+problem.add_parameter("initial_B2", lb=0, ub=10, nominal_value=3, estimate=False)
+
+
+# solutions ------------------------------------------------------------------
+
+simulation_df = problem.measurement_df.copy(deep=True).rename(
+    columns={MEASUREMENT: SIMULATION}
+)
+simulation_df[SIMULATION] = [
+    *(analytical_a(t, 2, 3, 0.8, 0.6) for t in (0, 10)),
+    *(analytical_b(t, 2, 3, 0.8, 0.6) for t in (0, 10)),
+]
+
+case = PetabV2TestCase.from_problem(
+    id=26,
+    brief="Simulation. Estimated initial value via math expressions in conditions table.",
+    description=DESCRIPTION,
+    model=model_file,
+    problem=problem,
+    simulation_df=simulation_df,
+)

petabtests/cases/v2.0.0/sbml/0026/README.md

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+# PEtab test case 0026
+
+## Objective
+
+This case tests the handling of initial concentrations that are specified
+via mathematical expressions (rather than a single value or parameter) in
+the conditions table. For species `A`, the initial concentration is given
+by an expression containing both parameters to be estimated and parameters
+that are not estimated. For species `B`, the initial concentration is
+specified via an expression involving only parameters that are not
+estimated.
+
+## Model
+
+A simple conversion reaction `A <=> B` in a single compartment, following
+mass action kinetics.

petabtests/cases/v2.0.0/sbml/0026/_0026.yaml

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+condition_files:
+- _conditions.tsv
+experiment_files:
+- _experiments.tsv
+format_version: 2.0.0
+measurement_files:
+- _measurements.tsv
+model_files:
+  model_0:
+    language: sbml
+    location: _model.xml
+observable_files:
+- _observables.tsv
+parameter_files:
+- _parameters.tsv

petabtests/cases/v2.0.0/sbml/0026/_0026_solution.yaml

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+chi2: 75.02040884206437
+llh: -38.41336983161109
+simulation_files:
+- _simulations.tsv
+tol_chi2: 0.001
+tol_llh: 0.001
+tol_simulations: 0.001

petabtests/cases/v2.0.0/sbml/0026/_conditions.tsv

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+conditionId	targetId	targetValue
+c0	A	initial_A1 + initial_A2
+c0	B	initial_B1/initial_B2

petabtests/cases/v2.0.0/sbml/0026/_experiments.tsv

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+experimentId	time	conditionId
+e1	0.0	c0

petabtests/cases/v2.0.0/sbml/0026/_measurements.tsv

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+modelId	observableId	experimentId	time	measurement	observableParameters	noiseParameters
+	obs_a	e1	0.0	0.7		
+	obs_a	e1	10.0	0.1		
+	obs_b	e1	0.0	0.7		
+	obs_b	e1	10.0	0.1		

petabtests/cases/v2.0.0/sbml/0026/_model.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Created by libAntimony version v3.1.1 with libSBML version 5.20.5. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
+  <model metaid="petab_test_0026" id="petab_test_0026">
+    <listOfCompartments>
+      <compartment id="compartment_" spatialDimensions="3" size="1" constant="true"/>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species id="A" compartment="compartment_" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+      <species id="B" compartment="compartment_" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
+    </listOfSpecies>
+    <listOfParameters>
+      <parameter id="k1" value="0" constant="true"/>
+      <parameter id="k2" value="0" constant="true"/>
+      <parameter id="a0" value="1" constant="true"/>
+    </listOfParameters>
+    <listOfInitialAssignments>
+      <initialAssignment symbol="A">
+        <math xmlns="http://www.w3.org/1998/Math/MathML">
+          <ci> a0 </ci>
+        </math>
+      </initialAssignment>
+    </listOfInitialAssignments>
+    <listOfReactions>
+      <reaction id="fwd" reversible="false">
+        <listOfReactants>
+          <speciesReference species="A" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="B" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment_ </ci>
+              <ci> k1 </ci>
+              <ci> A </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+      <reaction id="rev" reversible="false">
+        <listOfReactants>
+          <speciesReference species="B" stoichiometry="1" constant="true"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="A" stoichiometry="1" constant="true"/>
+        </listOfProducts>
+        <kineticLaw>
+          <math xmlns="http://www.w3.org/1998/Math/MathML">
+            <apply>
+              <times/>
+              <ci> compartment_ </ci>
+              <ci> k2 </ci>
+              <ci> B </ci>
+            </apply>
+          </math>
+        </kineticLaw>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>

petabtests/cases/v2.0.0/sbml/0026/_observables.tsv

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+observableId	observableName	observableFormula	noiseFormula	noiseDistribution	observablePlaceholders	noisePlaceholders
+obs_a		A	0.500000000000000	normal		
+obs_b		B	0.500000000000000	normal		

petabtests/cases/v2.0.0/sbml/0026/_parameters.tsv

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+parameterId	lowerBound	upperBound	nominalValue	estimate	priorDistribution	priorParameters
+k1	0.0	10.0	0.8	true		
+k2	0.0	10.0	0.6	true		
+initial_A1	1.0	10.0	0.5	true		
+initial_A2	1.0	10.0	1.5	false		
+initial_B1	0.0	10.0	9.0	false		
+initial_B2	0.0	10.0	3.0	false		

petabtests/cases/v2.0.0/sbml/0026/_simulations.tsv

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+modelId	observableId	experimentId	time	simulation	observableParameters	noiseParameters
+	obs_a	e1	0.0	2.0		
+	obs_a	e1	10.0	2.1428570240673257		
+	obs_b	e1	0.0	3.0		
+	obs_b	e1	10.0	2.8571429759326743		

petabtests/cases/v2.0.0/sbml/0027/0027.py

@@ -0,0 +1,86 @@
+from inspect import cleandoc
+from pathlib import Path
+
+from petab.v2.C import *
+from petab.v2 import Problem
+from petabtests import PetabV2TestCase, analytical_a, antimony_to_sbml_str
+
+DESCRIPTION = cleandoc("""
+## Objective
+
+This case tests support for parametric overrides from condition table
+via math expressions.
+
+The model is simulated for two different experimental conditions
+(here: different initial concentrations). The observable is offset via
+a parametric override in the condition table (i.e. the actual value
+has to be taken from the parameter table). The formulas in the
+condition table are mathematical expressions consisting of
+numerical values, parameters to be estimated, and parameters that
+are not to be estimated.
+
+## Model
+
+A simple conversion reaction `A <=> B` in a single compartment, following
+mass action kinetics.
+""")
+
+# problem --------------------------------------------------------------------
+ant_model = """
+model *petab_test_0027()
+  compartment compartment_ = 1;
+  species A in compartment_, B in compartment_;
+
+  fwd: A => B; compartment_ * k1 * A;
+  rev: B => A; compartment_ * k2 * B;
+
+  A = a0;
+  B = b0;
+  offset_A = 0;
+  a0 = 1;
+  b0 = 0;
+  k1 = 0;
+  k2 = 0;
+end
+"""
+model_file = Path(__file__).parent / "_model.xml"
+model_file.write_text(antimony_to_sbml_str(ant_model))
+
+problem = Problem()
+problem.add_condition("c0", offset_A="offset_A1_c0 + offset_A2_c0")
+problem.add_condition("c1", offset_A="offset_A1_c1 / 3.0")
+
+problem.add_experiment("e1", 0, "c0")
+problem.add_experiment("e2", 0, "c1")
+
+problem.add_observable("obs_a", "A + offset_A", noise_formula="1")
+
+problem.add_measurement("obs_a", experiment_id="e1", time=10, measurement=2.1)
+problem.add_measurement("obs_a", experiment_id="e2", time=10, measurement=3.2)
+
+problem.add_parameter("a0", lb=0, ub=10, nominal_value=1, estimate=True)
+problem.add_parameter("b0", lb=0, ub=10, nominal_value=0, estimate=True)
+problem.add_parameter("k1", lb=0, ub=10, nominal_value=0.8, estimate=True)
+problem.add_parameter("k2", lb=0, ub=10, nominal_value=0.6, estimate=True)
+problem.add_parameter("offset_A1_c0", lb=0, ub=10, nominal_value=0.5, estimate=True)
+problem.add_parameter("offset_A2_c0", lb=0, ub=10, nominal_value=1.5, estimate=False)
+problem.add_parameter("offset_A1_c1", lb=0, ub=10, nominal_value=9, estimate=True)
+
+# solutions ------------------------------------------------------------------
+
+simulation_df = problem.measurement_df.copy(deep=True).rename(
+    columns={MEASUREMENT: SIMULATION}
+)
+simulation_df[SIMULATION] = [
+    analytical_a(10, 1, 0, 0.8, 0.6) + offset for offset in [2, 3]
+]
+
+case = PetabV2TestCase.from_problem(
+    id=27,
+    brief="Simulation. Condition-specific parameters defined via "
+    "math expressions in the parameter table.",
+    description=DESCRIPTION,
+    model=model_file,
+    problem=problem,
+    simulation_df=simulation_df,
+)

petabtests/cases/v2.0.0/sbml/0027/README.md

@@ -0,0 +1,19 @@
+# PEtab test case 0027
+
+## Objective
+
+This case tests support for parametric overrides from condition table
+via math expressions.
+
+The model is simulated for two different experimental conditions
+(here: different initial concentrations). The observable is offset via
+a parametric override in the condition table (i.e. the actual value
+has to be taken from the parameter table). The formulas in the
+condition table are mathematical expressions consisting of
+numerical values, parameters to be estimated, and parameters that
+are not to be estimated.
+
+## Model
+
+A simple conversion reaction `A <=> B` in a single compartment, following
+mass action kinetics.

petabtests/cases/v2.0.0/sbml/0027/_0027.yaml

@@ -0,0 +1,15 @@
+condition_files:
+- _conditions.tsv
+experiment_files:
+- _experiments.tsv
+format_version: 2.0.0
+measurement_files:
+- _measurements.tsv
+model_files:
+  model_0:
+    language: sbml
+    location: _model.xml
+observable_files:
+- _observables.tsv
+parameter_files:
+- _parameters.tsv

petabtests/cases/v2.0.0/sbml/0027/_0027_solution.yaml

@@ -0,0 +1,7 @@
+chi2: 0.16020461109629
+llh: -1.91797937195749
+simulation_files:
+- _simulations.tsv
+tol_chi2: 0.001
+tol_llh: 0.001
+tol_simulations: 0.001

petabtests/cases/v2.0.0/sbml/0027/_conditions.tsv

@@ -0,0 +1,3 @@
+conditionId	targetId	targetValue
+c0	offset_A	offset_A1_c0 + offset_A2_c0
+c1	offset_A	0.333333333333333*offset_A1_c1

petabtests/cases/v2.0.0/sbml/0027/_experiments.tsv

@@ -0,0 +1,3 @@
+experimentId	time	conditionId
+e1	0.0	c0
+e2	0.0	c1

petabtests/cases/v2.0.0/sbml/0027/_measurements.tsv

@@ -0,0 +1,3 @@
+modelId	observableId	experimentId	time	measurement	observableParameters	noiseParameters
+	obs_a	e1	10.0	2.1		
+	obs_a	e2	10.0	3.2