API Reference

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Every public name of commol, generated from the docstrings. The guide pages explain how to use them; these pages list every argument, attribute and error.

The table lists each name that the package root exports (commol.__all__), on the page that documents it. Import these names from the package root, as in from commol import Simulation.

Page	Names
ModelBuilder	ModelBuilder
Model	Model, Process, ModelStructure, Aggregate, Complete, Groups, SeriesValue, ModelDescription
AxisPattern	AxisPattern
AxisUnits	AxisUnits
Simulation	Simulation, SimulationResults, ReplicateRuns, SimulationReplicates, ODESolver, StochasticEventsSettings, StochasticStepsSettings, InfeasibleStateError, windowed_totals, sample
Plotting	plot_compared, PlotConfig; the methods SimulationResults.plot, SimulationReplicates.plot, Predictive.plot, PRCCResult.plot, MorrisResult.plot, SobolResult.plot, ChaosResult.plot, ProfileResult.plot
Calibration	Calibrator, CalibrationProblem, Quantile, ObservedDataPoint, CalibrationParameter, CalibrationConstraint, NelderMeadConfig, ParticleSwarmConfig, CalibrationResult, StartSummary, CalibrationHistory, CalibrationEvaluation
Observation models	ObservationModel, NormalObservations, LogNormalObservations, StudentTObservations, PoissonObservations, NegativeBinomialObservations, BinomialObservations
Reports	the methods Model.applied_parameters, SimulationResults.report, SimulationReplicates.report, Predictive.report, IdentifiabilityReport.report
Uncertainty	InferenceMethod, UncertaintyMethod, ParameterSample, SampleMethod, ParameterSummary, Predictive, PredictiveBand, SeriesBand, ObservationDraws, Scenarios, ScenarioSummary, NoNoise, ResidualNoise, DistributionNoise
Resampling	BayesianBootstrap, ResidualBootstrap, WildBootstrap, BlockJackknife, ParametricBootstrap, BootstrapResult, JackknifeResult, ResamplingDiagnostics, BoundError
Profile likelihood	ProfileLikelihood, PredictionProfile, PredictionSpec, Threshold, ProfileResult, Profile, ProfileInterval
Sequential Monte Carlo	Priors, Uniform, LogUniform, Beta, Normal, LogNormal, Gamma, GibbsPosterior, BayesianPosterior, InformationMatchingEta, BootstrapCoverageEta, ABCSMC, ABCRejection, LossDistance, SeriesDistance, SMCResult, GibbsResult, SMCDiagnostics
Local approximations	Laplace, Sandwich, LaplaceMixture, LikelihoodTarget, GibbsTarget, LocalResult, LaplaceResult, SandwichResult, DeltaBand, ImportanceResult, MixtureComponent
Conformal prediction	SplitConformal, RollingConformal, JackknifePlus, EnbPI, AdaptiveConformal, ConformalResult, PredictionIntervals, SeriesIntervals
Scores and intervals	weighted_quantiles, member_statistics, ci_percentiles
Identifiability	IdentifiabilityMethod, StructuralRank, Collinearity, SampleIdentifiability, StartsIdentifiability, IdentifiabilityReport
Sensitivity	SensitivityAnalysis, InputSpace, SensitivityMethod, Propagation, PropagationResult, QuantitySummary, PRCC, PRCCResult, Morris, MorrisResult, Sobol, SobolResult, PolynomialChaos, ChaosResult, Level, Increments, ValueAt, Gain, Peak, PeakPosition, Trajectory, Ratio, quantity_schedule
Parallelism	set_threads, threads, get_threads, get_levels
Package	__version__, build_info, BuildInfo

The pages also document names that are not in the package root:

• The scores are the module commol.scores (from commol import scores), on the Uncertainty page.
• LossFunction, the values of CalibrationProblem.loss_function, is in commol.context.constants.
• UnitConsistencyError is in commol.utils.equations.
• Some types are only read from what a method returns, and you do not import them: InitialCompartment (an entry of Aggregate.initial_state()), the blocks of a ModelDescription, the parts of an IdentifiabilityReport, and the types of a model in Model Structure.