Index

A

add_condition() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.core.Problem method) (petab.v2.Problem method) add_dataplot() (petab.v1.visualize.plotting.Subplot method) add_experiment() (petab.v2.core.Problem method) (petab.v2.Problem method) add_mapping() (petab.v2.core.Problem method) (petab.v2.Problem method) add_measurement() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.core.Problem method) (petab.v2.Problem method) add_noise() (petab.v1.simulate.Simulator method) (petab.v1.Simulator method) add_observable() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.core.Problem method) (petab.v2.Problem method) add_offsets() (petab.v1.visualize.plotting.DataSeries method) add_parameter() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.core.Problem method) (petab.v2.Problem method) add_subplot() (petab.v1.visualize.Figure method) (petab.v1.visualize.plotting.Figure method) add_x_offset() (petab.v1.visualize.plotting.DataSeries method) add_y_offset() (petab.v1.visualize.plotting.DataSeries method) assert_all_parameters_present_in_parameter_df() (in module petab.v1) (in module petab.v1.lint) assert_measured_observables_defined() (in module petab.v1) (in module petab.v1.lint) assert_measurement_conditions_present_in_condition_table() (in module petab.v1) (in module petab.v1.lint)

assert_measurements_not_null() (in module petab.v1) (in module petab.v1.lint) assert_measurements_numeric() (in module petab.v1) (in module petab.v1.lint) assert_model_parameters_in_condition_or_parameter_table() (in module petab.v1) (in module petab.v1.lint) assert_no_leading_trailing_whitespace() (in module petab.v1) (in module petab.v1.lint) assert_noise_distributions_valid() (in module petab.v1) (in module petab.v1.lint) assert_overrides_match_parameter_count() (in module petab.v1) (in module petab.v1.measurements) assert_parameter_bounds_are_numeric() (in module petab.v1) (in module petab.v1.lint) assert_parameter_estimate_is_boolean() (in module petab.v1) (in module petab.v1.lint) assert_parameter_id_is_string() (in module petab.v1) (in module petab.v1.lint) assert_parameter_prior_parameters_are_valid() (in module petab.v1) (in module petab.v1.lint) assert_parameter_prior_type_is_valid() (in module petab.v1) (in module petab.v1.lint) assert_parameter_scale_is_valid() (in module petab.v1) (in module petab.v1.lint) assert_single_condition_and_sbml_file() (in module petab.v1) (in module petab.v1.yaml) assert_unique_observable_ids() (in module petab.v1) (in module petab.v1.lint) assert_unique_parameter_ids() (in module petab.v1) (in module petab.v1.lint) assert_valid() (petab.v2.core.Problem method) (petab.v2.Problem method)

B

BAR_PLOT (in module petab.v1.C)

base_path (petab.v2.core.ProblemConfig attribute) (petab.v2.ProblemConfig attribute)

C

calculate_chi2() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2.calculate) calculate_chi2_for_table_from_residuals() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2.calculate) calculate_llh() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2.calculate) calculate_llh_for_table() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2.calculate) calculate_residuals() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2.calculate) calculate_residuals_for_table() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2.calculate) calculate_single_llh() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2.calculate) Cauchy (class in petab.v1.distributions) (class in petab.v2) CAUCHY (in module petab.v2.C) (petab.v2.core.PriorDistribution attribute) (petab.v2.PriorDistribution attribute) cdf() (petab.v1.distributions.Distribution method) (petab.v2.Distribution method) Change (class in petab.v2) (class in petab.v2.core) changes (petab.v2.Condition attribute) (petab.v2.core.Condition attribute) check_condition_df() (in module petab.v1) (in module petab.v1.lint) check_ids() (in module petab.v1) (in module petab.v1.lint) check_mapping_df() (in module petab.v1) (in module petab.v1.mapping) check_measurement_df() (in module petab.v1) (in module petab.v1.lint) check_observable_df() (in module petab.v1) (in module petab.v1.lint) check_parameter_bounds() (in module petab.v1) (in module petab.v1.lint) check_parameter_df() (in module petab.v1) (in module petab.v1.lint) CheckAllParametersPresentInParameterTable (class in petab.v2.lint) CheckExperimentConditionsExist (class in petab.v2.lint) CheckExperimentTable (class in petab.v2.lint) CheckInitialChangeSymbols (class in petab.v2.lint) CheckMeasuredExperimentsDefined (class in petab.v2.lint) CheckMeasuredObservablesDefined (class in petab.v2.lint) CheckMeasurementModelId (class in petab.v2.lint) CheckModel (class in petab.v2.lint) CheckObservablesDoNotShadowModelEntities (class in petab.v2.lint) CheckOverridesMatchPlaceholders (class in petab.v2.lint) CheckPosLogMeasurements (class in petab.v2.lint) CheckPriorDistribution (class in petab.v2.lint) CheckProblemConfig (class in petab.v2.lint)

CheckUndefinedExperiments (class in petab.v2.lint) CheckUniquePrimaryKeys (class in petab.v2.lint) CheckUnusedConditions (class in petab.v2.lint) CheckUnusedExperiments (class in petab.v2.lint) CheckValidConditionTargets (class in petab.v2.lint) CheckValidParameterInConditionOrParameterTable (class in petab.v2.lint) CHI_SQUARED (petab.v2.core.PriorDistribution attribute) (petab.v2.PriorDistribution attribute) ChiSquare (class in petab.v1.distributions) (class in petab.v2) CompositeProblem (class in petab.v1) (class in petab.v1.composite_problem) concat_tables() (in module petab.v1) (in module petab.v1.core) Condition (class in petab.v2) (class in petab.v2.core) condition_df (petab.v2.core.Problem property) (petab.v2.Problem property) CONDITION_FILES (in module petab.v1.C) (in module petab.v2.C) condition_files (petab.v2.core.ProblemConfig attribute) (petab.v2.ProblemConfig attribute) CONDITION_ID (in module petab.v1.C) (in module petab.v2.C) CONDITION_ID_PREEQ_OFF (petab.v2.converters.ExperimentsToSbmlConverter attribute) CONDITION_ID_PREEQ_ON (petab.v2.converters.ExperimentsToSbmlConverter attribute) condition_ids (petab.v2.core.ExperimentPeriod attribute) (petab.v2.ExperimentPeriod attribute) CONDITION_NAME (in module petab.v1.C) condition_parameters_to_parameter_table() (in module petab.v1.simplify) condition_table_is_parameter_free() (in module petab.v1) (in module petab.v1.lint) conditions (petab.v2.ConditionTable property) (petab.v2.core.ConditionTable property) (petab.v2.core.Problem property) (petab.v2.Problem property) ConditionTable (class in petab.v2) (class in petab.v2.core) convert() (petab.v2.converters.ExperimentsToSbmlConverter method) convert_nan_to_none() (petab.v2.core.Measurement class method) (petab.v2.Measurement class method) create_combine_archive() (in module petab.v1) (in module petab.v1.core) create_condition_df() (in module petab.v1) (in module petab.v1.conditions) create_dataset_id_list_new() (in module petab.v1.visualize.helper_functions) create_measurement_df() (in module petab.v1) (in module petab.v1.measurements) create_observable_df() (in module petab.v1) (in module petab.v1.observables) create_parameter_df() (in module petab.v1) (in module petab.v1.parameters) (petab.v1.Problem method) (petab.v1.problem.Problem method) create_problem_yaml() (in module petab.v1) (in module petab.v1.yaml) create_report() (in module petab.v1.visualize.data_overview) create_subplot() (petab.v1.visualize.plotting.VisSpecParser static method) CRITICAL (petab.v2.lint.ValidationIssueSeverity attribute)

D

data_provider (petab.v1.visualize.plotter.Plotter attribute) DataPlot (class in petab.v1.visualize.plotting) DataProvider (class in petab.v1.visualize) (class in petab.v1.visualize.plotting) DataSeries (class in petab.v1.visualize.plotting) DATASET_ID (in module petab.v1.C) (in module petab.v2.C)

default_validation_tasks (in module petab.v2.lint) Distribution (class in petab.v1.distributions) (class in petab.v2) dof (petab.v1.distributions.ChiSquare property) (petab.v2.ChiSquare property)

E

ENV_NUM_THREADS (in module petab) ERROR (petab.v2.lint.ValidationIssueSeverity attribute) ESTIMATE (in module petab.v1.C) (in module petab.v2.C) estimate (petab.v2.core.Parameter attribute) (petab.v2.Parameter attribute) evaluate_noise_formula() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2.calculate) Experiment (class in petab.v2) (class in petab.v2.core) experiment_df (petab.v2.core.Problem property) (petab.v2.Problem property) EXPERIMENT_FILES (in module petab.v2.C) experiment_files (petab.v2.core.ProblemConfig attribute) (petab.v2.ProblemConfig attribute) EXPERIMENT_ID (in module petab.v2.C) experiment_id (petab.v2.core.Measurement attribute) (petab.v2.Measurement attribute)

ExperimentPeriod (class in petab.v2) (class in petab.v2.core) experiments (petab.v2.core.ExperimentTable property) (petab.v2.core.Problem property) (petab.v2.ExperimentTable property) (petab.v2.Problem property) ExperimentsToSbmlConverter (class in petab.v2.converters) ExperimentTable (class in petab.v2) (class in petab.v2.core) Exponential (class in petab.v1.distributions) (class in petab.v2) EXPONENTIAL (in module petab.v2.C) (petab.v2.core.PriorDistribution attribute) (petab.v2.PriorDistribution attribute) EXTENSIONS (in module petab.v2.C) extensions (petab.v2.core.ProblemConfig attribute) (petab.v2.ProblemConfig attribute)

F

Figure (class in petab.v1.visualize) (class in petab.v1.visualize.plotting) figure (petab.v1.visualize.plotter.Plotter attribute) filepath (petab.v2.core.ProblemConfig attribute) (petab.v2.ProblemConfig attribute) flatten_timepoint_specific_output_overrides() (in module petab.v1) (in module petab.v1.core) format() (petab.petablint.LintFormatter method) FORMAT_VERSION (in module petab.v1.C) (in module petab.v2.C) format_version (petab.v2.core.ProblemConfig attribute) (petab.v2.ProblemConfig attribute) format_version_tuple (petab.v2.core.ProblemConfig property) (petab.v2.ProblemConfig property) formats (petab.petablint.LintFormatter attribute) formula (petab.v2.core.Observable attribute) (petab.v2.Observable attribute) free_symbols (petab.v2.ConditionTable property) (petab.v2.core.ConditionTable property) from_antimony() (petab.v1.models.sbml_model.SbmlModel static method) (petab.v2.models.sbml_model.SbmlModel static method) from_combine() (petab.v1.Problem static method) (petab.v1.problem.Problem static method) (petab.v2.core.Problem static method) (petab.v2.Problem static method) from_df() (petab.v1.visualize.plotting.DataPlot class method) (petab.v1.visualize.plotting.Subplot class method) (petab.v2.ConditionTable class method) (petab.v2.core.ConditionTable class method) (petab.v2.core.ExperimentTable class method) (petab.v2.core.MappingTable class method) (petab.v2.core.MeasurementTable class method) (petab.v2.core.ObservableTable class method) (petab.v2.core.ParameterTable class method) (petab.v2.ExperimentTable class method) (petab.v2.MappingTable class method) (petab.v2.MeasurementTable class method) (petab.v2.ObservableTable class method) (petab.v2.ParameterTable class method)

from_file() (petab.v1.Model static method) (petab.v1.models.Model static method) (petab.v1.models.model.Model static method) (petab.v1.models.pysb_model.PySBModel static method) (petab.v1.models.sbml_model.SbmlModel static method) (petab.v2.Model static method) (petab.v2.models.Model static method) (petab.v2.models.model.Model static method) (petab.v2.models.pysb_model.PySBModel static method) (petab.v2.models.sbml_model.SbmlModel static method) from_files() (petab.v1.Problem static method) (petab.v1.problem.Problem static method) from_problem() (petab.v1.visualize.plotting.VisSpecParser class method) from_string() (petab.v1.models.sbml_model.SbmlModel static method) (petab.v2.models.sbml_model.SbmlModel static method) from_yaml() (petab.v1.composite_problem.CompositeProblem static method) (petab.v1.CompositeProblem static method) (petab.v1.Problem static method) (petab.v1.problem.Problem static method) (petab.v2.core.Problem static method) (petab.v2.Problem static method)

G

Gamma (class in petab.v1.distributions) (class in petab.v2) GAMMA (in module petab.v2.C) (petab.v2.core.PriorDistribution attribute) (petab.v2.PriorDistribution attribute) generate_barplot() (petab.v1.visualize.MPLPlotter method) (petab.v1.visualize.plotter.MPLPlotter method) generate_dataset_id_col() (in module petab.v1.visualize.helper_functions) generate_figure() (petab.v1.visualize.MPLPlotter method) (petab.v1.visualize.plotter.MPLPlotter method) (petab.v1.visualize.plotter.Plotter method) (petab.v1.visualize.plotter.SeabornPlotter method) generate_lineplot() (petab.v1.visualize.MPLPlotter method) (petab.v1.visualize.plotter.MPLPlotter method) generate_scatterplot() (petab.v1.visualize.MPLPlotter method) (petab.v1.visualize.plotter.MPLPlotter method) generate_subplot() (petab.v1.visualize.MPLPlotter method) (petab.v1.visualize.plotter.MPLPlotter method) get() (petab.v2.core.MappingTable method) (petab.v2.MappingTable method) get_changes_for_period() (petab.v2.core.Problem method) (petab.v2.Problem method) get_compartment_ids() (petab.v1.models.pysb_model.PySBModel method) (petab.v2.models.pysb_model.PySBModel method) get_condition_df() (in module petab.v1) (in module petab.v1.conditions) (in module petab.v2) (in module petab.v2.conditions) get_data_series() (petab.v1.visualize.DataProvider method) (petab.v1.visualize.plotting.DataProvider method) get_data_to_plot() (petab.v1.visualize.DataProvider method) (petab.v1.visualize.plotting.DataProvider method) get_experiment_df() (in module petab.v2) (in module petab.v2.experiments) get_experiment_indicator() (petab.v2.converters.ExperimentsToSbmlConverter static method) get_formula_placeholders() (in module petab.v1) (in module petab.v1.observables) get_free_parameter_ids_with_values() (petab.v1.Model method) (petab.v1.models.Model method) (petab.v1.models.model.Model method) (petab.v1.models.pysb_model.PySBModel method) (petab.v1.models.sbml_model.SbmlModel method) (petab.v2.Model method) (petab.v2.models.Model method) (petab.v2.models.model.Model method) (petab.v2.models.pysb_model.PySBModel method) (petab.v2.models.sbml_model.SbmlModel method) get_lb() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.core.Problem method) (petab.v2.Problem method) get_major_version() (in module petab.petablint) (in module petab.versions) get_mapping_df() (in module petab.v1) (in module petab.v1.mapping) (in module petab.v2) get_measurement_df() (in module petab.v1) (in module petab.v1.measurements) (in module petab.v2) get_measurement_parameter_ids() (in module petab.v1) (in module petab.v1.measurements) get_measurements_for_experiment() (petab.v2.core.Problem method) (petab.v2.Problem method) get_model_for_condition() (in module petab.v1) (in module petab.v1.sbml) get_model_parameters() (in module petab.v1) (in module petab.v1.sbml) (petab.v1.Problem method) (petab.v1.problem.Problem method) get_non_unique() (in module petab.v1) (in module petab.v1.lint) get_notnull_columns() (in module petab.v1) (in module petab.v1.core) get_observable_df() (in module petab.v1) (in module petab.v1.observables) (in module petab.v2) get_observable_ids() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.core.Problem method) (petab.v2.Problem method) get_optimization_parameter_scales() (petab.v1.Problem method) (petab.v1.problem.Problem method) get_optimization_parameter_scaling() (in module petab.v1) (in module petab.v1.parameters) get_optimization_parameters() (in module petab.v1) (in module petab.v1.parameters) (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.core.Problem method) (petab.v2.Problem method) get_optimization_to_simulation_parameter_mapping() (in module petab.v1) (in module petab.v1.parameter_mapping) (petab.v1.Problem method) (petab.v1.problem.Problem method) get_output_parameters() (in module petab.v1) (in module petab.v1.observables) (petab.v2.core.Problem method) (petab.v2.Problem method)

get_parameter_df() (in module petab.v1) (in module petab.v1.parameters) (in module petab.v2) get_parameter_ids() (petab.v1.Model method) (petab.v1.models.Model method) (petab.v1.models.model.Model method) (petab.v1.models.pysb_model.PySBModel method) (petab.v1.models.sbml_model.SbmlModel method) (petab.v2.Model method) (petab.v2.models.Model method) (petab.v2.models.model.Model method) (petab.v2.models.pysb_model.PySBModel method) (petab.v2.models.sbml_model.SbmlModel method) get_parameter_ids_with_values() (petab.v1.models.sbml_model.SbmlModel method) (petab.v2.models.sbml_model.SbmlModel method) get_parameter_mapping_for_condition() (in module petab.v1) (in module petab.v1.parameter_mapping) get_parameter_value() (petab.v1.Model method) (petab.v1.models.Model method) (petab.v1.models.model.Model method) (petab.v1.models.pysb_model.PySBModel method) (petab.v1.models.sbml_model.SbmlModel method) (petab.v2.Model method) (petab.v2.models.Model method) (petab.v2.models.model.Model method) (petab.v2.models.pysb_model.PySBModel method) (petab.v2.models.sbml_model.SbmlModel method) get_parametric_overrides() (in module petab.v1) (in module petab.v1.conditions) get_path_prefix() (in module petab.v1) (in module petab.v1.yaml) get_placeholders() (in module petab.v1) (in module petab.v1.observables) get_priors() (petab.v2.core.Problem method) (petab.v2.Problem method) get_priors_from_df() (in module petab.v1) (in module petab.v1.parameters) get_problem() (petab.v2.core.Problem static method) (petab.v2.Problem static method) get_rows_for_condition() (in module petab.v1) (in module petab.v1.measurements) get_sbml_model() (in module petab.v1) (in module petab.v1.sbml) get_simulation_conditions() (in module petab.v1) (in module petab.v1.measurements) get_simulation_conditions_from_measurement_df() (petab.v1.Problem method) (petab.v1.problem.Problem method) get_simulation_df() (in module petab.v1) (in module petab.v1.core) get_startpoint_distributions() (petab.v2.core.Problem method) (petab.v2.Problem method) get_symbolic_noise_formulas() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2.calculate) get_ub() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.core.Problem method) (petab.v2.Problem method) get_valid_ids_for_condition_table() (petab.v1.Model method) (petab.v1.models.Model method) (petab.v1.models.model.Model method) (petab.v1.models.pysb_model.PySBModel method) (petab.v1.models.sbml_model.SbmlModel method) (petab.v2.Model method) (petab.v2.models.Model method) (petab.v2.models.model.Model method) (petab.v2.models.pysb_model.PySBModel method) (petab.v2.models.sbml_model.SbmlModel method) get_valid_parameters_for_parameter_table() (in module petab.v1) (in module petab.v1.parameters) (petab.v1.Model method) (petab.v1.models.Model method) (petab.v1.models.model.Model method) (petab.v1.models.pysb_model.PySBModel method) (petab.v1.models.sbml_model.SbmlModel method) (petab.v2.Model method) (petab.v2.models.Model method) (petab.v2.models.model.Model method) (petab.v2.models.pysb_model.PySBModel method) (petab.v2.models.sbml_model.SbmlModel method) get_visualization_df() (in module petab.v1) (in module petab.v1.core) get_x_ids() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.core.Problem method) (petab.v2.Problem method) get_x_nominal() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.core.Problem method) (petab.v2.Problem method) get_x_nominal_dict() (petab.v2.core.Problem method) (petab.v2.Problem method) globalize_parameters() (in module petab.v1) (in module petab.v1.sbml)

H

handle_missing_overrides() (in module petab.v1) (in module petab.v1.parameter_mapping) has_entity_with_id() (petab.v1.Model method) (petab.v1.models.Model method) (petab.v1.models.model.Model method) (petab.v1.models.pysb_model.PySBModel method) (petab.v1.models.sbml_model.SbmlModel method) (petab.v2.Model method) (petab.v2.models.Model method) (petab.v2.models.model.Model method) (petab.v2.models.pysb_model.PySBModel method) (petab.v2.models.sbml_model.SbmlModel method)

has_errors() (petab.v2.lint.ValidationResultList method) has_map_objective (petab.v2.core.Problem property) (petab.v2.Problem property) has_ml_objective (petab.v2.core.Problem property) (petab.v2.Problem property) has_preequilibration (petab.v2.core.Experiment property) (petab.v2.Experiment property)

I

id (petab.v2.Condition attribute) (petab.v2.core.Condition attribute) (petab.v2.core.Experiment attribute) (petab.v2.core.Observable attribute) (petab.v2.core.Parameter attribute) (petab.v2.core.Problem property) (petab.v2.core.ProblemConfig attribute) (petab.v2.Experiment attribute) (petab.v2.Observable attribute) (petab.v2.Parameter attribute) (petab.v2.Problem property) (petab.v2.ProblemConfig attribute) INFO (petab.v2.lint.ValidationIssueSeverity attribute) init_colorama() (in module petab.petablint) INITIALIZATION (in module petab.v1.C) (in module petab.v2.C) INITIALIZATION_PRIOR_PARAMETERS (in module petab.v1.C) INITIALIZATION_PRIOR_TYPE (in module petab.v1.C) is_composite_problem() (in module petab.v1) (in module petab.v1.yaml) is_empty() (in module petab.v1) (in module petab.v1.core) is_preequilibration (petab.v2.core.ExperimentPeriod property) (petab.v2.ExperimentPeriod property) is_sbml_consistent() (in module petab.v1) (in module petab.v1.sbml)

is_scalar_float() (in module petab.v1) (in module petab.v1.lint) is_state_variable() (petab.v1.Model method) (petab.v1.models.Model method) (petab.v1.models.model.Model method) (petab.v1.models.pysb_model.PySBModel method) (petab.v1.models.sbml_model.SbmlModel method) (petab.v2.Model method) (petab.v2.models.Model method) (petab.v2.models.model.Model method) (petab.v2.models.pysb_model.PySBModel method) (petab.v2.models.sbml_model.SbmlModel method) is_valid() (petab.v1.Model method) (petab.v1.models.Model method) (petab.v1.models.model.Model method) (petab.v1.models.pysb_model.PySBModel method) (petab.v1.models.sbml_model.SbmlModel method) (petab.v2.Model method) (petab.v2.models.Model method) (petab.v2.models.model.Model method) (petab.v2.models.pysb_model.PySBModel method) (petab.v2.models.sbml_model.SbmlModel method) is_valid_identifier() (in module petab.v1) (in module petab.v1.lint)

L

Laplace (class in petab.v1.distributions) (class in petab.v2) LAPLACE (in module petab.v1.C) (in module petab.v2.C) (petab.v2.core.NoiseDistribution attribute) (petab.v2.core.PriorDistribution attribute) (petab.v2.NoiseDistribution attribute) (petab.v2.PriorDistribution attribute) lb (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.core.Parameter attribute) (petab.v2.core.Problem property) (petab.v2.Parameter attribute) (petab.v2.Problem property) lb_scaled (petab.v1.Problem property) (petab.v1.problem.Problem property) LEGEND_ENTRY (in module petab.v1.C) level (petab.v2.lint.ValidationError attribute) (petab.v2.lint.ValidationIssue attribute), [1] LIN (in module petab.v1.C) (in module petab.v2.C) (petab.v2.core.ParameterScale attribute) (petab.v2.ParameterScale attribute) LINE_PLOT (in module petab.v1.C) lint_problem() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) (in module petab.v2.lint) LintFormatter (class in petab.petablint) load_sbml_from_file() (in module petab.v1) (in module petab.v1.sbml) load_sbml_from_string() (in module petab.v1) (in module petab.v1.sbml) load_yaml() (in module petab.v1) (in module petab.v1.yaml) (in module petab.v2) loc (petab.v1.distributions.Cauchy property) (petab.v1.distributions.Laplace property) (petab.v1.distributions.Normal property) (petab.v2.Cauchy property) (petab.v2.Laplace property) (petab.v2.Normal property)

LOG (in module petab.v1.C) (in module petab.v2.C) (petab.v2.core.ParameterScale attribute) (petab.v2.ParameterScale attribute) log() (petab.v2.lint.ValidationResultList method) LOG10 (in module petab.v1.C) (in module petab.v2.C) (petab.v2.core.ParameterScale attribute) (petab.v2.ParameterScale attribute) LOG_LAPLACE (in module petab.v1.C) (in module petab.v2.C) (petab.v2.core.NoiseDistribution attribute) (petab.v2.core.PriorDistribution attribute) (petab.v2.NoiseDistribution attribute) (petab.v2.PriorDistribution attribute) LOG_NORMAL (in module petab.v1.C) (in module petab.v2.C) (petab.v2.core.NoiseDistribution attribute) (petab.v2.core.PriorDistribution attribute) (petab.v2.NoiseDistribution attribute) (petab.v2.PriorDistribution attribute) log_sbml_errors() (in module petab.v1) (in module petab.v1.sbml) LOG_UNIFORM (in module petab.v2.C) (petab.v2.core.PriorDistribution attribute) (petab.v2.PriorDistribution attribute) logbase (petab.v1.distributions.Distribution property) (petab.v2.Distribution property) LogUniform (class in petab.v1.distributions) (class in petab.v2) LOWER_BOUND (in module petab.v1.C) (in module petab.v2.C)

M

main() (in module petab.petablint) map_scale() (in module petab.v1) (in module petab.v1.parameters) map_unscale() (in module petab.v1) (in module petab.v1.parameters) Mapping (class in petab.v2) (class in petab.v2.core) mapping_df (petab.v2.core.Problem property) (petab.v2.Problem property) MAPPING_DF_REQUIRED_COLS (in module petab.v2.C) MAPPING_FILES (in module petab.v2.C) mapping_files (petab.v2.core.ProblemConfig attribute) (petab.v2.ProblemConfig attribute) mappings (petab.v2.core.MappingTable property) (petab.v2.core.Problem property) (petab.v2.MappingTable property) (petab.v2.Problem property) MappingTable (class in petab.v2) (class in petab.v2.core) MathVisitorSympy (class in petab.v1.math.SympyVisitor) Measurement (class in petab.v2) (class in petab.v2.core) MEASUREMENT (in module petab.v1.C) (in module petab.v2.C) measurement (petab.v2.core.Measurement attribute) (petab.v2.Measurement attribute) measurement_df (petab.v2.core.Problem property) (petab.v2.Problem property) MEASUREMENT_DF_COLS (in module petab.v1.C) (in module petab.v2.C) MEASUREMENT_DF_OPTIONAL_COLS (in module petab.v1.C) (in module petab.v2.C) MEASUREMENT_DF_REQUIRED_COLS (in module petab.v1.C) (in module petab.v2.C) MEASUREMENT_FILES (in module petab.v1.C) (in module petab.v2.C) measurement_files (petab.v2.core.ProblemConfig attribute) (petab.v2.ProblemConfig attribute) measurement_is_at_steady_state() (in module petab.v1) (in module petab.v1.measurements) measurement_table_has_observable_parameter_numeric_overrides() (in module petab.v1) (in module petab.v1.lint) measurement_table_has_timepoint_specific_mappings() (in module petab.v1) (in module petab.v1.lint) measurements (petab.v2.core.MeasurementTable property) (petab.v2.core.Problem property) (petab.v2.MeasurementTable property) (petab.v2.Problem property) measurements_have_replicates() (in module petab.v1) (in module petab.v1.measurements) MeasurementTable (class in petab.v2) (class in petab.v2.core) merge_preeq_and_sim_pars() (in module petab.v1) (in module petab.v1.parameter_mapping) merge_preeq_and_sim_pars_condition() (in module petab.v1) (in module petab.v1.parameter_mapping) message (petab.v2.lint.ValidationIssue attribute), [1] Model (class in petab.v1) (class in petab.v1.models) (class in petab.v1.models.model) (class in petab.v2) (class in petab.v2.models) (class in petab.v2.models.model) model (petab.v2.core.Problem property) (petab.v2.Problem property) model_config (petab.v2.ConditionTable attribute) (petab.v2.core.ConditionTable attribute) (petab.v2.core.ExperimentTable attribute) (petab.v2.core.MappingTable attribute) (petab.v2.core.MeasurementTable attribute) (petab.v2.core.ObservableTable attribute) (petab.v2.core.ParameterTable attribute) (petab.v2.core.ProblemConfig attribute) (petab.v2.ExperimentTable attribute) (petab.v2.MappingTable attribute) (petab.v2.MeasurementTable attribute) (petab.v2.ObservableTable attribute) (petab.v2.ParameterTable attribute) (petab.v2.ProblemConfig attribute) model_dump() (petab.v2.core.Problem method) (petab.v2.Problem method) MODEL_ENTITY_ID (in module petab.v2.C) model_factory() (in module petab.v1.models.model) (in module petab.v2.models.model)

MODEL_FILES (in module petab.v2.C) model_files (petab.v2.core.ProblemConfig attribute) (petab.v2.ProblemConfig attribute) MODEL_ID (in module petab.v2.C) model_id (petab.v1.Model property) (petab.v1.models.Model property) (petab.v1.models.model.Model property) (petab.v1.models.pysb_model.PySBModel property) (petab.v1.models.sbml_model.SbmlModel property) (petab.v2.core.Mapping attribute) (petab.v2.core.Measurement attribute) (petab.v2.Mapping attribute) (petab.v2.Measurement attribute) (petab.v2.Model property) (petab.v2.models.Model property) (petab.v2.models.model.Model property) (petab.v2.models.pysb_model.PySBModel property) (petab.v2.models.sbml_model.SbmlModel property) MODEL_LANGUAGE (in module petab.v2.C) MODEL_LOCATION (in module petab.v2.C) MODEL_TYPE_PYSB (in module petab.v1.models) MODEL_TYPE_SBML (in module petab.v1.models) models (petab.v2.core.Problem attribute) (petab.v2.Problem attribute) module petab petab.petablint petab.v1 petab.v1.C petab.v1.calculate petab.v1.composite_problem petab.v1.conditions petab.v1.core petab.v1.distributions petab.v1.format_version petab.v1.lint petab.v1.mapping petab.v1.math petab.v1.math.printer petab.v1.math.sympify petab.v1.math.SympyVisitor petab.v1.measurements petab.v1.models petab.v1.models.model petab.v1.models.pysb_model petab.v1.models.sbml_model petab.v1.observables petab.v1.parameter_mapping petab.v1.parameters petab.v1.priors petab.v1.problem petab.v1.sampling petab.v1.sbml petab.v1.simplify petab.v1.simulate petab.v1.visualize petab.v1.visualize.cli petab.v1.visualize.data_overview petab.v1.visualize.helper_functions petab.v1.visualize.lint petab.v1.visualize.plot_data_and_simulation petab.v1.visualize.plot_residuals petab.v1.visualize.plotter petab.v1.visualize.plotting petab.v1.yaml petab.v2 petab.v2.C petab.v2.calculate petab.v2.conditions petab.v2.converters petab.v2.core petab.v2.experiments petab.v2.lint petab.v2.math petab.v2.models petab.v2.models.model petab.v2.models.pysb_model petab.v2.models.sbml_model petab.v2.petab1to2 petab.version petab.versions MPLPlotter (class in petab.v1.visualize) (class in petab.v1.visualize.plotter)

N

n_estimated (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.core.ParameterTable property) (petab.v2.core.Problem property) (petab.v2.ParameterTable property) (petab.v2.Problem property) n_measurements (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.core.Problem property) (petab.v2.Problem property) n_priors (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.core.Problem property) (petab.v2.Problem property) NAME (in module petab.v2.C) name (petab.v2.core.Mapping attribute) (petab.v2.core.Observable attribute) (petab.v2.Mapping attribute) (petab.v2.Observable attribute) NOISE_DISTRIBUTION (in module petab.v1.C) (in module petab.v2.C) noise_distribution (petab.v2.core.Observable attribute) (petab.v2.Observable attribute) NOISE_DISTRIBUTIONS (in module petab.v2.C) NOISE_FORMULA (in module petab.v1.C) (in module petab.v2.C) noise_formula (petab.v2.core.Observable attribute) (petab.v2.Observable attribute)

noise_formulas (petab.v1.simulate.Simulator attribute) (petab.v1.Simulator attribute) NOISE_MODELS (in module petab.v1.C) NOISE_PARAMETERS (in module petab.v1.C) (in module petab.v2.C) noise_parameters (petab.v2.core.Measurement attribute) (petab.v2.Measurement attribute) NOISE_PLACEHOLDERS (in module petab.v2.C) noise_placeholders (petab.v2.core.Observable attribute) (petab.v2.Observable attribute) NOISE_VALUE (in module petab.v1.C) NoiseDistribution (class in petab.v2) (class in petab.v2.core) NOMINAL_VALUE (in module petab.v1.C) (in module petab.v2.C) nominal_value (petab.v2.core.Parameter attribute) (petab.v2.Parameter attribute) Normal (class in petab.v1.distributions) (class in petab.v2) NORMAL (in module petab.v1.C) (in module petab.v2.C) (petab.v2.core.NoiseDistribution attribute) (petab.v2.core.PriorDistribution attribute) (petab.v2.NoiseDistribution attribute) (petab.v2.PriorDistribution attribute) normalize_parameter_df() (in module petab.v1) (in module petab.v1.parameters) num_subplots (petab.v1.visualize.Figure property) (petab.v1.visualize.plotting.Figure property)

O

OBJECTIVE (in module petab.v1.C) (in module petab.v2.C) OBJECTIVE_PRIOR_PARAMETERS (in module petab.v1.C) OBJECTIVE_PRIOR_TYPE (in module petab.v1.C) Observable (class in petab.v2) (class in petab.v2.core) observable_df (petab.v2.core.Problem property) (petab.v2.Problem property) OBSERVABLE_DF_COLS (in module petab.v1.C) (in module petab.v2.C) OBSERVABLE_DF_OPTIONAL_COLS (in module petab.v1.C) (in module petab.v2.C) OBSERVABLE_DF_REQUIRED_COLS (in module petab.v1.C) (in module petab.v2.C) OBSERVABLE_FILES (in module petab.v1.C) (in module petab.v2.C) observable_files (petab.v2.core.ProblemConfig attribute) (petab.v2.ProblemConfig attribute) OBSERVABLE_FORMULA (in module petab.v1.C) (in module petab.v2.C) OBSERVABLE_ID (in module petab.v1.C) (in module petab.v2.C)

observable_id (petab.v2.core.Measurement attribute) (petab.v2.Measurement attribute) OBSERVABLE_NAME (in module petab.v1.C) (in module petab.v2.C) OBSERVABLE_PARAMETERS (in module petab.v1.C) (in module petab.v2.C) observable_parameters (petab.v2.core.Measurement attribute) (petab.v2.Measurement attribute) OBSERVABLE_PLACEHOLDERS (in module petab.v2.C) observable_placeholders (petab.v2.core.Observable attribute) (petab.v2.Observable attribute) observable_table_has_nontrivial_noise_formula() (in module petab.v1) (in module petab.v1.lint) OBSERVABLE_TRANSFORMATION (in module petab.v1.C) OBSERVABLE_TRANSFORMATIONS (in module petab.v1.C) observables (petab.v2.core.ObservableTable property) (petab.v2.core.Problem property) (petab.v2.ObservableTable property) (petab.v2.Problem property) ObservableTable (class in petab.v2) (class in petab.v2.core)

P

Parameter (class in petab.v2) (class in petab.v2.core) parameter_df (petab.v1.composite_problem.CompositeProblem attribute) (petab.v1.CompositeProblem attribute) (petab.v2.core.Problem property) (petab.v2.Problem property) PARAMETER_DF_COLS (in module petab.v1.C) (in module petab.v2.C) PARAMETER_DF_OPTIONAL_COLS (in module petab.v1.C) (in module petab.v2.C) PARAMETER_DF_REQUIRED_COLS (in module petab.v1.C) (in module petab.v2.C) PARAMETER_FILE (in module petab.v1.C) PARAMETER_FILES (in module petab.v2.C) parameter_files (petab.v2.core.ProblemConfig attribute) (petab.v2.ProblemConfig attribute) PARAMETER_ID (in module petab.v1.C) (in module petab.v2.C) PARAMETER_NAME (in module petab.v1.C) (in module petab.v2.C) PARAMETER_SCALE (in module petab.v1.C) PARAMETER_SCALE_LAPLACE (in module petab.v1.C) PARAMETER_SCALE_NORMAL (in module petab.v1.C) PARAMETER_SCALE_PRIOR_TYPES (in module petab.v1.C) PARAMETER_SCALE_UNIFORM (in module petab.v1.C) PARAMETER_SCALES (in module petab.v1.C) PARAMETER_SEPARATOR (in module petab.v1.C) (in module petab.v2.C) parameters (petab.v2.core.ParameterTable property) (petab.v2.core.Problem property) (petab.v2.ParameterTable property) (petab.v2.Problem property) ParameterScale (class in petab.v2) (class in petab.v2.core) ParameterTable (class in petab.v2) (class in petab.v2.core) parse_cli_args() (in module petab.petablint) parse_from_id_list() (petab.v1.visualize.plotting.VisSpecParser method) parse_from_vis_spec() (petab.v1.visualize.plotting.VisSpecParser method) parse_species_name() (in module petab.v1.models.pysb_model) (in module petab.v2.models.pysb_model) parse_version() (in module petab.versions) pattern_from_string() (in module petab.v1.models.pysb_model) (in module petab.v2.models.pysb_model) pdf() (petab.v1.distributions.Distribution method) (petab.v2.Distribution method) periods (petab.v2.core.Experiment attribute) (petab.v2.Experiment attribute) petab module petab.petablint module petab.v1 module petab.v1.C module petab.v1.calculate module petab.v1.composite_problem module petab.v1.conditions module petab.v1.core module petab.v1.distributions module petab.v1.format_version module petab.v1.lint module petab.v1.mapping module petab.v1.math module petab.v1.math.printer module petab.v1.math.sympify module petab.v1.math.SympyVisitor module petab.v1.measurements module petab.v1.models module petab.v1.models.model module petab.v1.models.pysb_model module petab.v1.models.sbml_model module petab.v1.observables module petab.v1.parameter_mapping module petab.v1.parameters module petab.v1.priors module petab.v1.problem module petab.v1.sampling module petab.v1.sbml module petab.v1.simplify module petab.v1.simulate module petab.v1.visualize module

petab.v1.visualize.cli module petab.v1.visualize.data_overview module petab.v1.visualize.helper_functions module petab.v1.visualize.lint module petab.v1.visualize.plot_data_and_simulation module petab.v1.visualize.plot_residuals module petab.v1.visualize.plotter module petab.v1.visualize.plotting module petab.v1.yaml module petab.v2 module petab.v2.C module petab.v2.calculate module petab.v2.conditions module petab.v2.converters module petab.v2.core module petab.v2.experiments module petab.v2.lint module petab.v2.math module petab.v2.models module petab.v2.models.model module petab.v2.models.pysb_model module petab.v2.models.sbml_model module petab.v2.petab1to2 module petab.version module petab.versions module petab1to2() (in module petab.v2.petab1to2) PETAB_ENTITY_ID (in module petab.v2.C) petab_id (petab.v2.core.Mapping attribute) (petab.v2.Mapping attribute) petab_math_str() (in module petab.v1.math) (in module petab.v1.math.printer) (in module petab.v2.math) petab_problem (petab.v1.simulate.Simulator attribute) (petab.v1.Simulator attribute) PetabStrPrinter (class in petab.v1.math) (class in petab.v1.math.printer) (class in petab.v2.math) plot_goodness_of_fit() (in module petab.v1.visualize) (in module petab.v1.visualize.plot_residuals) PLOT_ID (in module petab.v1.C) PLOT_NAME (in module petab.v1.C) plot_problem() (in module petab.v1.visualize) (in module petab.v1.visualize.plot_data_and_simulation) plot_residuals_vs_simulation() (in module petab.v1.visualize) (in module petab.v1.visualize.plot_residuals) PLOT_TYPE_DATA (in module petab.v1.C) PLOT_TYPE_SIMULATION (in module petab.v1.C) PLOT_TYPES_DATA (in module petab.v1.C) PLOT_TYPES_SIMULATION (in module petab.v1.C) plot_with_vis_spec() (in module petab.v1.visualize) (in module petab.v1.visualize.plot_data_and_simulation) plot_without_vis_spec() (in module petab.v1.visualize) (in module petab.v1.visualize.plot_data_and_simulation) Plotter (class in petab.v1.visualize.plotter) ppf() (petab.v1.distributions.Distribution method) (petab.v2.Distribution method) PREEQ_INDICATOR (petab.v2.converters.ExperimentsToSbmlConverter attribute) PREEQUILIBRATION_CONDITION_ID (in module petab.v1.C) prior_dist (petab.v2.core.Parameter property) (petab.v2.Parameter property) PRIOR_DISTRIBUTION (in module petab.v2.C) prior_distribution (petab.v2.core.Parameter attribute) (petab.v2.Parameter attribute) PRIOR_DISTRIBUTIONS (in module petab.v2.C) PRIOR_PARAMETERS (in module petab.v2.C) prior_parameters (petab.v2.core.Parameter attribute) (petab.v2.Parameter attribute) PRIOR_TYPES (in module petab.v1.C) PriorDistribution (class in petab.v2) (class in petab.v2.core) priors_to_measurements() (in module petab.v1.priors) Problem (class in petab.v1) (class in petab.v1.problem) (class in petab.v2) (class in petab.v2.core) ProblemConfig (class in petab.v2) (class in petab.v2.core) PROBLEMS (in module petab.v1.C) (in module petab.v2.C) problems (petab.v1.composite_problem.CompositeProblem attribute) (petab.v1.CompositeProblem attribute) PROVIDED (in module petab.v1.C) PySBModel (class in petab.v1.models.pysb_model) (class in petab.v2.models.pysb_model)

R

Rayleigh (class in petab.v1.distributions) (class in petab.v2) RAYLEIGH (in module petab.v2.C) (petab.v2.core.PriorDistribution attribute) (petab.v2.PriorDistribution attribute) remove_nan_measurements() (in module petab.v1.simplify) remove_unused_conditions() (in module petab.v1.simplify) remove_unused_observables() (in module petab.v1.simplify) remove_working_dir() (petab.v1.simulate.Simulator method) (petab.v1.Simulator method) REPLICATE (in module petab.v1.C) REPLICATE_ID (in module petab.v1.C) (in module petab.v2.C) RESIDUAL (in module petab.v1.C) (in module petab.v2.C) resolve_mapping() (in module petab.v1) (in module petab.v1.mapping) rng (petab.v1.simulate.Simulator attribute) (petab.v1.Simulator attribute)

run() (petab.v2.lint.CheckAllParametersPresentInParameterTable method) (petab.v2.lint.CheckExperimentConditionsExist method) (petab.v2.lint.CheckExperimentTable method) (petab.v2.lint.CheckInitialChangeSymbols method) (petab.v2.lint.CheckMeasuredExperimentsDefined method) (petab.v2.lint.CheckMeasuredObservablesDefined method) (petab.v2.lint.CheckMeasurementModelId method) (petab.v2.lint.CheckModel method) (petab.v2.lint.CheckObservablesDoNotShadowModelEntities method) (petab.v2.lint.CheckOverridesMatchPlaceholders method) (petab.v2.lint.CheckPosLogMeasurements method) (petab.v2.lint.CheckPriorDistribution method) (petab.v2.lint.CheckProblemConfig method) (petab.v2.lint.CheckUndefinedExperiments method) (petab.v2.lint.CheckUniquePrimaryKeys method) (petab.v2.lint.CheckUnusedConditions method) (petab.v2.lint.CheckUnusedExperiments method) (petab.v2.lint.CheckValidConditionTargets method) (petab.v2.lint.CheckValidParameterInConditionOrParameterTable method) (petab.v2.lint.ValidationTask method)

S

sample() (petab.v1.distributions.Distribution method) (petab.v2.Distribution method) sample_from_prior() (in module petab.v1) (in module petab.v1.sampling) sample_noise() (in module petab.v1) (in module petab.v1.simulate) sample_parameter_startpoints() (in module petab.v1) (in module petab.v1.sampling) (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.core.Problem method) (petab.v2.Problem method) sample_parameter_startpoints_dict() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.core.Problem method) (petab.v2.Problem method) save_to_tsv() (petab.v1.visualize.Figure method) (petab.v1.visualize.plotting.Figure method) sbml_document (petab.v2.models.sbml_model.SbmlModel attribute) SBML_FILES (in module petab.v1.C) sbml_model (petab.v2.models.sbml_model.SbmlModel attribute) sbml_reader (petab.v2.models.sbml_model.SbmlModel attribute) SbmlModel (class in petab.v1.models.sbml_model) (class in petab.v2.models.sbml_model) scale (petab.v1.distributions.Cauchy property) (petab.v1.distributions.Exponential property) (petab.v1.distributions.Gamma property) (petab.v1.distributions.Laplace property) (petab.v1.distributions.Normal property) (petab.v1.distributions.Rayleigh property) (petab.v2.Cauchy property) (petab.v2.Exponential property) (petab.v2.Gamma property) (petab.v2.Laplace property) (petab.v2.Normal property) (petab.v2.Rayleigh property) scale() (in module petab.v1) (in module petab.v1.parameters) scale_parameters() (petab.v1.Problem method) (petab.v1.problem.Problem method)

SCATTER_PLOT (in module petab.v1.C) SchemaValidationError (in module petab.petablint) SeabornPlotter (class in petab.v1.visualize.plotter) set_axes_limits() (petab.v1.visualize.Figure method) (petab.v1.visualize.plotting.Figure method) (petab.v1.visualize.plotting.Subplot method) shape (petab.v1.distributions.Gamma property) (petab.v2.Gamma property) simplify_problem() (in module petab.v1.simplify) simulate() (petab.v1.simulate.Simulator method) (petab.v1.Simulator method) simulate_without_noise() (petab.v1.simulate.Simulator method) (petab.v1.Simulator method) SIMULATION (in module petab.v1.C) (in module petab.v2.C) SIMULATION_CONDITION_ID (in module petab.v1.C) Simulator (class in petab.v1) (class in petab.v1.simulate) sort_periods() (petab.v2.core.Experiment method) (petab.v2.Experiment method) sorted_periods (petab.v2.core.Experiment property) (petab.v2.Experiment property) split_parameter_replacement_list() (in module petab.v1) (in module petab.v1.measurements) Subplot (class in petab.v1.visualize.plotting) symbol_allowed_in_observable_formula() (petab.v1.Model method) (petab.v1.models.Model method) (petab.v1.models.model.Model method) (petab.v1.models.pysb_model.PySBModel method) (petab.v1.models.sbml_model.SbmlModel method) (petab.v2.Model method) (petab.v2.models.Model method) (petab.v2.models.model.Model method) (petab.v2.models.pysb_model.PySBModel method) (petab.v2.models.sbml_model.SbmlModel method) sympify_petab() (in module petab.v1.math) (in module petab.v1.math.sympify) (in module petab.v2.math)

T

TARGET_ID (in module petab.v2.C) target_id (petab.v2.Change attribute) (petab.v2.core.Change attribute) TARGET_VALUE (in module petab.v2.C) target_value (petab.v2.Change attribute) (petab.v2.core.Change attribute) task (petab.v2.lint.ValidationIssue attribute) temporary_working_dir (petab.v1.simulate.Simulator attribute) (petab.v1.Simulator attribute) TIME (in module petab.v1.C) (in module petab.v2.C) time (petab.v2.core.ExperimentPeriod attribute) (petab.v2.core.Measurement attribute) (petab.v2.ExperimentPeriod attribute) (petab.v2.Measurement attribute) TIME_PREEQUILIBRATION (in module petab.v2.C) TIME_STEADY_STATE (in module petab.v1.C) (in module petab.v2.C) TIME_SYMBOL (in module petab.v2.C) to_antimony() (petab.v1.models.sbml_model.SbmlModel method) (petab.v2.models.sbml_model.SbmlModel method) to_df() (petab.v2.ConditionTable method) (petab.v2.core.ConditionTable method) (petab.v2.core.ExperimentTable method) (petab.v2.core.MappingTable method) (petab.v2.core.MeasurementTable method) (petab.v2.core.ObservableTable method) (petab.v2.core.ParameterTable method) (petab.v2.ExperimentTable method) (petab.v2.MappingTable method) (petab.v2.MeasurementTable method) (petab.v2.ObservableTable method) (petab.v2.ParameterTable method) to_file() (petab.v1.Model method) (petab.v1.models.Model method) (petab.v1.models.model.Model method) (petab.v1.models.pysb_model.PySBModel method) (petab.v1.models.sbml_model.SbmlModel method) (petab.v2.Model method) (petab.v2.models.Model method) (petab.v2.models.model.Model method) (petab.v2.models.pysb_model.PySBModel method) (petab.v2.models.sbml_model.SbmlModel method)

to_files() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.core.Problem method) (petab.v2.Problem method) to_files_generic() (petab.v1.Problem method) (petab.v1.problem.Problem method) to_float_if_float() (in module petab.v1) (in module petab.v1.core) to_sbml_str() (petab.v1.models.sbml_model.SbmlModel method) (petab.v2.models.sbml_model.SbmlModel method) to_str() (petab.v1.models.pysb_model.PySBModel method) (petab.v2.models.pysb_model.PySBModel method) to_yaml() (petab.v2.core.ProblemConfig method) (petab.v2.ProblemConfig method) trunc_high (petab.v1.distributions.Distribution property) (petab.v2.Distribution property) trunc_low (petab.v1.distributions.Distribution property) (petab.v2.Distribution property) type_id (petab.v1.Model property) (petab.v1.models.Model property) (petab.v1.models.model.Model property) (petab.v1.models.pysb_model.PySBModel attribute) (petab.v1.models.sbml_model.SbmlModel attribute) (petab.v2.Model property) (petab.v2.models.Model property) (petab.v2.models.model.Model property) (petab.v2.models.pysb_model.PySBModel attribute) (petab.v2.models.sbml_model.SbmlModel attribute)

U

ub (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.core.Parameter attribute) (petab.v2.core.Problem property) (petab.v2.Parameter attribute) (petab.v2.Problem property) ub_scaled (petab.v1.Problem property) (petab.v1.problem.Problem property) unflatten_simulation_df() (in module petab.v1) (in module petab.v1.core) Uniform (class in petab.v1.distributions) (class in petab.v2)

UNIFORM (in module petab.v1.C) (in module petab.v2.C) (petab.v2.core.PriorDistribution attribute) (petab.v2.PriorDistribution attribute) unique_preserve_order() (in module petab.v1) (in module petab.v1.core) unscale() (in module petab.v1) (in module petab.v1.parameters) unscale_parameters() (petab.v1.Problem method) (petab.v1.problem.Problem method) UPPER_BOUND (in module petab.v1.C) (in module petab.v2.C)

V

validate() (in module petab.v1) (in module petab.v1.yaml) (petab.v2.core.Problem method) (petab.v2.Problem method) validate_visualization_df() (in module petab.v1.visualize.lint) validate_yaml_semantics() (in module petab.petablint) (in module petab.v1) (in module petab.v1.yaml) validate_yaml_syntax() (in module petab.petablint) (in module petab.v1) (in module petab.v1.yaml) validation_tasks (petab.v2.core.Problem attribute) (petab.v2.Problem attribute) ValidationError (class in petab.v2.lint) ValidationIssue (class in petab.v2.lint) ValidationIssueSeverity (class in petab.v2.lint) ValidationResultList (class in petab.v2.lint) ValidationTask (class in petab.v2.lint) visitAddExpr() (petab.v1.math.SympyVisitor.MathVisitorSympy method) visitArgumentList() (petab.v1.math.SympyVisitor.MathVisitorSympy method)

visitBooleanAndOrExpr() (petab.v1.math.SympyVisitor.MathVisitorSympy method) visitBooleanLiteral() (petab.v1.math.SympyVisitor.MathVisitorSympy method) visitBooleanNotExpr() (petab.v1.math.SympyVisitor.MathVisitorSympy method) visitComparisonExpr() (petab.v1.math.SympyVisitor.MathVisitorSympy method) visitFunctionCall() (petab.v1.math.SympyVisitor.MathVisitorSympy method) visitMultExpr() (petab.v1.math.SympyVisitor.MathVisitorSympy method) visitNumber() (petab.v1.math.SympyVisitor.MathVisitorSympy method) visitParenExpr() (petab.v1.math.SympyVisitor.MathVisitorSympy method) visitPetabExpression() (petab.v1.math.SympyVisitor.MathVisitorSympy method) visitPowerExpr() (petab.v1.math.SympyVisitor.MathVisitorSympy method) visitUnaryExpr() (petab.v1.math.SympyVisitor.MathVisitorSympy method) visitVar() (petab.v1.math.SympyVisitor.MathVisitorSympy method) VisSpecParser (class in petab.v1.visualize.plotting) VISUALIZATION_DF_COLS (in module petab.v1.C) VISUALIZATION_DF_OPTIONAL_COLS (in module petab.v1.C) VISUALIZATION_DF_REQUIRED_COLS (in module petab.v1.C) VISUALIZATION_DF_SINGLE_PLOT_LEVEL_COLS (in module petab.v1.C) VISUALIZATION_DF_SUBPLOT_LEVEL_COLS (in module petab.v1.C) VISUALIZATION_FILES (in module petab.v1.C) (in module petab.v2.C)

W

WARNING (petab.v2.lint.ValidationIssueSeverity attribute) working_dir (petab.v1.simulate.Simulator attribute) (petab.v1.Simulator attribute) write_condition_df() (in module petab.v1) (in module petab.v1.conditions) (in module petab.v2) (in module petab.v2.conditions) write_experiment_df() (in module petab.v2) (in module petab.v2.experiments) write_mapping_df() (in module petab.v1) (in module petab.v1.mapping) (in module petab.v2) write_measurement_df() (in module petab.v1) (in module petab.v1.measurements) (in module petab.v2)

write_observable_df() (in module petab.v1) (in module petab.v1.observables) (in module petab.v2) write_parameter_df() (in module petab.v1) (in module petab.v1.parameters) (in module petab.v2) write_sbml() (in module petab.v1) (in module petab.v1.sbml) write_simulation_df() (in module petab.v1) (in module petab.v1.core) write_visualization_df() (in module petab.v1) (in module petab.v1.core) write_yaml() (in module petab.v1) (in module petab.v1.yaml)

X

x_fixed_ids (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.core.Problem property) (petab.v2.Problem property) x_fixed_indices (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.core.Problem property) (petab.v2.Problem property) x_free_ids (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.core.Problem property) (petab.v2.Problem property) x_free_indices (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.core.Problem property) (petab.v2.Problem property) x_ids (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.core.Problem property) (petab.v2.Problem property) X_LABEL (in module petab.v1.C)

x_nominal (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.core.Problem property) (petab.v2.Problem property) x_nominal_fixed (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.core.Problem property) (petab.v2.Problem property) x_nominal_fixed_scaled (petab.v1.Problem property) (petab.v1.problem.Problem property) x_nominal_free (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.core.Problem property) (petab.v2.Problem property) x_nominal_free_scaled (petab.v1.Problem property) (petab.v1.problem.Problem property) x_nominal_scaled (petab.v1.Problem property) (petab.v1.problem.Problem property) X_OFFSET (in module petab.v1.C) X_SCALE (in module petab.v1.C) X_SCALES (in module petab.v1.C) X_VALUES (in module petab.v1.C)

Y

Y_LABEL (in module petab.v1.C) Y_OFFSET (in module petab.v1.C)

Y_SCALE (in module petab.v1.C) Y_SCALES (in module petab.v1.C) Y_VALUES (in module petab.v1.C)