Unbounded priors

petabtests/cases/v2.0.0/sbml/0024/0024.py

@@ -85,7 +85,7 @@
 
 case = PetabV2TestCase.from_problem(
     id=24,
-    brief="Prior distributions.",
+    brief="Truncated prior distributions.",
     description=DESCRIPTION,
     model=sbml_file,
     problem=problem,

petabtests/cases/v2.0.0/sbml/0025/0025.py

@@ -0,0 +1,94 @@
+from inspect import cleandoc
+from numpy import inf
+
+from petab.v2.C import *
+from petab.v2 import Problem
+from petabtests import (
+    PetabV2TestCase,
+    antimony_to_sbml_str,
+)
+from pathlib import Path
+from petab.v2 import PriorDistribution
+
+DESCRIPTION = cleandoc(r"""
+## Objective
+
+This case tests different non-truncated prior distributions, as well as
+implicit uniform priors and fixed parameters.
+
+## Model
+
+A simple model with all constant parameters.
+""")
+
+# problem --------------------------------------------------------------------
+
+priors = [
+    (PriorDistribution.UNIFORM, (2, 8), 2, 8),
+    (PriorDistribution.NORMAL, (4, 2), -inf, inf),
+    (PriorDistribution.LOG_NORMAL, (5, 2), 0.0, inf),
+    (PriorDistribution.CAUCHY, (3, 5), -inf, inf),
+    (PriorDistribution.CHI_SQUARED, (4), 0.0, inf),
+    (PriorDistribution.EXPONENTIAL, (3), 0.0, inf),
+    (PriorDistribution.GAMMA, (3, 5), 0, inf),
+    (PriorDistribution.LAPLACE, (3, 5), -inf, inf),
+    (PriorDistribution.LOG_LAPLACE, (3, 5), 0, inf),
+    (PriorDistribution.LOG_UNIFORM, (3, 5), 3, 5),
+    (PriorDistribution.RAYLEIGH, (3), 0, inf),
+]
+
+tested_prior_distrs = {pd for pd, _, _, _ in priors}
+untested_distrs = [
+    pd.value for pd in PriorDistribution if pd not in tested_prior_distrs
+]
+if untested_distrs:
+    print("Untested prior distributions:", untested_distrs)
+
+sbml_file = Path(__file__).parent / "_model.xml"
+
+parameters = "\n".join(
+    f"p_{prior_type.value.replace('-', '_')} = 5;" for prior_type, _, _, _ in priors
+)
+ant_model = f"""
+model petab_test_0025
+    {parameters}
+end
+"""
+sbml_file.write_text(antimony_to_sbml_str(ant_model))
+
+problem = Problem()
+for prior_type, prior_pars, support_lb, support_ub in priors:
+    problem.add_parameter(
+        f"p_{prior_type.value.replace('-', '_')}",
+        estimate=True,
+        lb=support_lb,
+        ub=support_ub,
+        nominal_value=5,
+        prior_distribution=prior_type,
+        prior_parameters=prior_pars,
+    )
+# implicit uniform prior
+problem.add_parameter("p1", estimate=True, nominal_value=1, lb=0, ub=2)
+# fixed, i.e., no prior
+problem.add_parameter("p_fixed", estimate=False, nominal_value=1)
+# we need some observable and measurement
+problem.add_observable("obs_p1", "p1", noise_formula="p_fixed")
+problem.add_measurement("obs_p1", experiment_id="", time=0, measurement=1)
+
+# solutions ------------------------------------------------------------------
+
+simulation_df = problem.measurement_df.copy(deep=True).rename(
+    columns={MEASUREMENT: SIMULATION}
+)
+simulation_df[SIMULATION] = [
+    1,
+]
+
+case = PetabV2TestCase.from_problem(
+    id=25,
+    brief="Non-truncated prior distributions.",
+    description=DESCRIPTION,
+    model=sbml_file,
+    problem=problem,
+    simulation_df=simulation_df,
+)

petabtests/cases/v2.0.0/sbml/0025/README.md

@@ -0,0 +1,10 @@
+# PEtab test case 0025
+
+## Objective
+
+This case tests different non-truncated prior distributions, as well as
+implicit uniform priors and fixed parameters.
+
+## Model
+
+A simple model with all constant parameters.

petabtests/cases/v2.0.0/sbml/0025/_0025.yaml

@@ -0,0 +1,13 @@
+condition_files: []
+experiment_files: []
+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/0025/_0025_solution.yaml

@@ -0,0 +1,23 @@
+chi2: 0.0
+llh: -0.91893853320467
+log_prior:
+  p1: -0.69314718055995
+  p_cauchy: -2.90258780340177
+  p_chisquare: -2.27685644868579
+  p_exponential: -2.76527895533478
+  p_gamma: -3.30258509299405
+  p_laplace: -2.70258509299405
+  p_log_laplace: -4.19013542294133
+  p_log_normal: -4.65851253490362
+  p_log_uniform: -0.93771092034198
+  p_normal: -1.73708571376462
+  p_rayleigh: -1.97667555379101
+  p_uniform: -1.79175946922805
+simulation_files:
+- _simulations.tsv
+tol_chi2: 0.001
+tol_llh: 0.001
+tol_log_prior: 1.0e-14
+tol_simulations: 0.001
+tol_unnorm_log_posterior: 0.001
+unnorm_log_posterior: -30.85385872214566

petabtests/cases/v2.0.0/sbml/0025/_measurements.tsv

@@ -0,0 +1,2 @@
+modelId	observableId	experimentId	time	measurement	observableParameters	noiseParameters
+	obs_p1		0.0	1.0		

petabtests/cases/v2.0.0/sbml/0025/_model.xml

@@ -0,0 +1,19 @@
+<?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_0025" id="petab_test_0025">
+    <listOfParameters>
+      <parameter id="p_uniform" value="5" constant="true"/>
+      <parameter id="p_normal" value="5" constant="true"/>
+      <parameter id="p_log_normal" value="5" constant="true"/>
+      <parameter id="p_cauchy" value="5" constant="true"/>
+      <parameter id="p_chisquare" value="5" constant="true"/>
+      <parameter id="p_exponential" value="5" constant="true"/>
+      <parameter id="p_gamma" value="5" constant="true"/>
+      <parameter id="p_laplace" value="5" constant="true"/>
+      <parameter id="p_log_laplace" value="5" constant="true"/>
+      <parameter id="p_log_uniform" value="5" constant="true"/>
+      <parameter id="p_rayleigh" value="5" constant="true"/>
+    </listOfParameters>
+  </model>
+</sbml>

petabtests/cases/v2.0.0/sbml/0025/_observables.tsv

@@ -0,0 +1,2 @@
+observableId	observableName	observableFormula	noiseFormula	noiseDistribution	observablePlaceholders	noisePlaceholders
+obs_p1		p1	p_fixed	normal		

petabtests/cases/v2.0.0/sbml/0025/_parameters.tsv

@@ -0,0 +1,14 @@
+parameterId	lowerBound	upperBound	nominalValue	estimate	priorDistribution	priorParameters
+p_uniform	2.0	8.0	5.0	true	uniform	2.0;8.0
+p_normal	-inf	inf	5.0	true	normal	4.0;2.0
+p_log_normal	0.0	inf	5.0	true	log-normal	5.0;2.0
+p_cauchy	-inf	inf	5.0	true	cauchy	3.0;5.0
+p_chisquare	0.0	inf	5.0	true	chisquare	4.0
+p_exponential	0.0	inf	5.0	true	exponential	3.0
+p_gamma	0.0	inf	5.0	true	gamma	3.0;5.0
+p_laplace	-inf	inf	5.0	true	laplace	3.0;5.0
+p_log_laplace	0.0	inf	5.0	true	log-laplace	3.0;5.0
+p_log_uniform	3.0	5.0	5.0	true	log-uniform	3.0;5.0
+p_rayleigh	0.0	inf	5.0	true	rayleigh	3.0
+p1	0.0	2.0	1.0	true		
+p_fixed			1.0	false		

petabtests/cases/v2.0.0/sbml/0025/_simulations.tsv

@@ -0,0 +1,2 @@
+modelId	observableId	experimentId	time	simulation	observableParameters	noiseParameters
+	obs_p1		0.0	1		

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

@@ -88,5 +88,9 @@ Events during steady-state simulations.
 
 # [0024](0024/)
 
-Prior distributions.
+Truncated prior distributions.
+
+# [0025](0025/)
+
+Non-truncated prior distributions.