Index

A

add_dataplot() (petab.v1.visualize.plotting.Subplot method) add_noise() (petab.v1.simulate.Simulator method) (petab.v1.Simulator method) (petab.v2.Simulator method) add_offsets() (petab.v1.visualize.plotting.DataSeries method) add_subplot() (petab.v1.visualize.Figure method) (petab.v1.visualize.plotting.Figure method) add_x_offset() (petab.v1.visualize.plotting.DataSeries method) append() (petab.v2.lint.ValidationResultList method) as_integer_ratio() (petab.v2.lint.ValidationIssueSeverity method) assert_all_parameters_present_in_parameter_df() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_measured_observables_defined() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_measurement_conditions_present_in_condition_table() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_measurements_not_null() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_measurements_numeric() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_model_parameters_in_condition_or_parameter_table() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_no_leading_trailing_whitespace() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_noise_distributions_valid() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2)

assert_overrides_match_parameter_count() (in module petab.v1) (in module petab.v1.measurements) (in module petab.v2) assert_parameter_bounds_are_numeric() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_parameter_estimate_is_boolean() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_parameter_id_is_string() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_parameter_prior_parameters_are_valid() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_parameter_prior_type_is_valid() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_parameter_scale_is_valid() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_single_condition_and_sbml_file() (in module petab.v1) (in module petab.v1.yaml) (in module petab.v2) assert_unique_observable_ids() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) assert_unique_parameter_ids() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2)

B

BAR_PLOT (in module petab.v1.C) (in module petab.v2.C)

bit_count() (petab.v2.lint.ValidationIssueSeverity method) bit_length() (petab.v2.lint.ValidationIssueSeverity method)

C

calculate_chi2() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2) calculate_chi2_for_table_from_residuals() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2) calculate_llh() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2) calculate_llh_for_table() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2) calculate_residuals() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2) calculate_residuals_for_table() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2) calculate_single_llh() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2) check_condition_df() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) check_ids() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) check_mapping_df() (in module petab.v1) (in module petab.v1.mapping) (in module petab.v2) check_measurement_df() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) check_observable_df() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) check_parameter_bounds() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) check_parameter_df() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) CheckAllParametersPresentInParameterTable (class in petab.v2.lint) CheckConditionTable (class in petab.v2.lint) CheckMeasurementTable (class in petab.v2.lint) CheckModel (class in petab.v2.lint) CheckObservableTable (class in petab.v2.lint) CheckParameterTable (class in petab.v2.lint)

CheckTableExists (class in petab.v2.lint) CheckValidParameterInConditionOrParameterTable (class in petab.v2.lint) CheckVisualizationTable (class in petab.v2.lint) clear() (petab.v2.lint.ValidationResultList method) CompositeProblem (class in petab.v1) (class in petab.v1.composite_problem) (class in petab.v2) concat_tables() (in module petab.v1) (in module petab.v1.core) (in module petab.v2) CONDITION_FILES (in module petab.v1.C) (in module petab.v2.C) CONDITION_ID (in module petab.v1.C) (in module petab.v2.C) CONDITION_NAME (in module petab.v1.C) (in module petab.v2.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) (in module petab.v2) conjugate() (petab.v2.lint.ValidationIssueSeverity method) converter() (petab.petablint.LintFormatter method) copy() (petab.v2.lint.ValidationResultList method) count() (petab.v2.lint.ValidationResultList method) create_combine_archive() (in module petab.v1) (in module petab.v1.core) (in module petab.v2) create_condition_df() (in module petab.v1) (in module petab.v1.conditions) (in module petab.v2) create_dataset_id_list_new() (in module petab.v1.visualize.helper_functions) create_measurement_df() (in module petab.v1) (in module petab.v1.measurements) (in module petab.v2) create_observable_df() (in module petab.v1) (in module petab.v1.observables) (in module petab.v2) create_parameter_df() (in module petab.v1) (in module petab.v1.parameters) (in module petab.v2) (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.Problem method) (petab.v2.problem.Problem method) create_problem_yaml() (in module petab.v1) (in module petab.v1.yaml) (in module petab.v2) create_report() (in module petab.v1.visualize.data_overview) create_subplot() (petab.v1.visualize.plotting.VisSpecParser static method)

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) denominator (petab.v2.lint.ValidationIssueSeverity attribute)

E

ENV_NUM_THREADS (in module petab) ESTIMATE (in module petab.v1.C) (in module petab.v2.C) evaluate_noise_formula() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2)

extend() (petab.v2.lint.ValidationResultList method) EXTENSIONS (in module petab.v2.C)

F

Figure (class in petab.v1.visualize) (class in petab.v1.visualize.plotting) figure (petab.v1.visualize.plotter.Plotter attribute) flatten_timepoint_specific_output_overrides() (in module petab.v1) (in module petab.v1.core) (in module petab.v2) format() (petab.petablint.LintFormatter method) FORMAT_VERSION (in module petab.v1.C) (in module petab.v2.C) formatException() (petab.petablint.LintFormatter method) formatStack() (petab.petablint.LintFormatter method) formatTime() (petab.petablint.LintFormatter method) from_bytes() (petab.v2.lint.ValidationIssueSeverity method) from_combine() (petab.v1.Problem static method) (petab.v1.problem.Problem static method) (petab.v2.Problem static method) (petab.v2.problem.Problem static method)

from_file() (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.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_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.CompositeProblem static method) (petab.v2.Problem static method) (petab.v2.problem.Problem static method)

G

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) 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_condition_df() (in module petab.v1) (in module petab.v1.conditions) (in module petab.v2) 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_formula_placeholders() (in module petab.v1) (in module petab.v1.observables) (in module petab.v2) get_free_parameter_ids_with_values() (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.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.Problem method) (petab.v2.problem.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) (in module petab.v2) get_model_for_condition() (in module petab.v1) (in module petab.v1.sbml) (in module petab.v2) get_model_parameters() (in module petab.v1) (in module petab.v1.sbml) (in module petab.v2) (petab.v1.Problem method) (petab.v1.problem.Problem method) get_notnull_columns() (in module petab.v1) (in module petab.v1.core) (in module petab.v2) 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.Problem method) (petab.v2.problem.Problem method) get_optimization_parameter_scales() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.Problem method) (petab.v2.problem.Problem method) get_optimization_parameter_scaling() (in module petab.v1) (in module petab.v1.parameters) (in module petab.v2) get_optimization_parameters() (in module petab.v1) (in module petab.v1.parameters) (in module petab.v2) (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.Problem method) (petab.v2.problem.Problem method) get_optimization_to_simulation_parameter_mapping() (in module petab.v1) (in module petab.v1.parameter_mapping) (in module petab.v2) (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.Problem method) (petab.v2.problem.Problem method) get_output_parameters() (in module petab.v1) (in module petab.v1.observables) (in module petab.v2) get_parameter_df() (in module petab.v1) (in module petab.v1.parameters) (in module petab.v2)

get_parameter_ids() (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.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_mapping_for_condition() (in module petab.v1) (in module petab.v1.parameter_mapping) (in module petab.v2) get_parameter_value() (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.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) (in module petab.v2) get_path_prefix() (in module petab.v1) (in module petab.v1.yaml) (in module petab.v2) get_placeholders() (in module petab.v1) (in module petab.v1.observables) (in module petab.v2) get_priors_from_df() (in module petab.v1) (in module petab.v1.parameters) (in module petab.v2) get_problem() (petab.v2.Problem static method) (petab.v2.problem.Problem static method) get_rows_for_condition() (in module petab.v1) (in module petab.v1.measurements) (in module petab.v2) get_sbml_model() (in module petab.v1) (in module petab.v1.sbml) (in module petab.v2) get_simulation_conditions() (in module petab.v1) (in module petab.v1.measurements) (in module petab.v2) get_simulation_conditions_from_measurement_df() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.Problem method) (petab.v2.problem.Problem method) get_simulation_df() (in module petab.v1) (in module petab.v1.core) (in module petab.v2) get_symbolic_noise_formulas() (in module petab.v1) (in module petab.v1.calculate) (in module petab.v2) get_ub() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.Problem method) (petab.v2.problem.Problem method) get_valid_ids_for_condition_table() (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.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) (in module petab.v2) (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.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) (in module petab.v2) get_x_ids() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.Problem method) (petab.v2.problem.Problem method) get_x_nominal() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.Problem method) (petab.v2.problem.Problem method) globalize_parameters() (in module petab.v1) (in module petab.v1.sbml) (in module petab.v2)

H

handle_missing_overrides() (in module petab.v1) (in module petab.v1.parameter_mapping) (in module petab.v2) has_entity_with_id() (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.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)

I

imag (petab.v2.lint.ValidationIssueSeverity attribute) index() (petab.v2.lint.ValidationResultList method) INITIALIZATION (in module petab.v1.C) (in module petab.v2.C) INITIALIZATION_PRIOR_PARAMETERS (in module petab.v1.C) (in module petab.v2.C) INITIALIZATION_PRIOR_TYPE (in module petab.v1.C) (in module petab.v2.C) insert() (petab.v2.lint.ValidationResultList method) is_composite_problem() (in module petab.v1) (in module petab.v1.yaml) (in module petab.v2) is_empty() (in module petab.v1) (in module petab.v1.core) (in module petab.v2) is_sbml_consistent() (in module petab.v1) (in module petab.v1.sbml) (in module petab.v2) is_scalar_float() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2)

is_state_variable() (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.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.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.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) (in module petab.v2)

L

LAPLACE (in module petab.v1.C) (in module petab.v2.C) lb (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.Problem property) (petab.v2.problem.Problem property) lb_scaled (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.Problem property) (petab.v2.problem.Problem property) LEGEND_ENTRY (in module petab.v1.C) (in module petab.v2.C) level (petab.v2.lint.ValidationIssue attribute) LIN (in module petab.v1.C) (in module petab.v2.C) LINE_PLOT (in module petab.v1.C) (in module petab.v2.C) lint_problem() (in module petab.petablint) (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) (in module petab.v2) load_sbml_from_string() (in module petab.v1) (in module petab.v1.sbml) (in module petab.v2) load_yaml() (in module petab.v1) (in module petab.v1.yaml) (in module petab.v2) LOG (in module petab.v1.C) (in module petab.v2.C) log() (petab.v2.lint.ValidationResultList method) LOG10 (in module petab.v1.C) (in module petab.v2.C) LOG_LAPLACE (in module petab.v1.C) (in module petab.v2.C) LOG_NORMAL (in module petab.v1.C) (in module petab.v2.C) log_sbml_errors() (in module petab.v1) (in module petab.v1.sbml) (in module 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) (in module petab.v2) map_unscale() (in module petab.v1) (in module petab.v1.parameters) (in module petab.v2) MAPPING_DF_REQUIRED_COLS (in module petab.v2.C) MAPPING_FILES (in module petab.v2.C) MathVisitorSympy (class in petab.v1.math.SympyVisitor) MEASUREMENT (in module petab.v1.C) (in module petab.v2.C) 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_is_at_steady_state() (in module petab.v1) (in module petab.v1.measurements) (in module petab.v2) measurement_table_has_observable_parameter_numeric_overrides() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) measurement_table_has_timepoint_specific_mappings() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) measurements_have_replicates() (in module petab.v1) (in module petab.v1.measurements) (in module petab.v2) merge_preeq_and_sim_pars() (in module petab.v1) (in module petab.v1.parameter_mapping) (in module petab.v2) merge_preeq_and_sim_pars_condition() (in module petab.v1) (in module petab.v1.parameter_mapping) (in module petab.v2) message (petab.v2.lint.ValidationIssue attribute) Model (class in petab.v1.models) (class in petab.v1.models.model) (class in petab.v2.models) (class in petab.v2.models.model) 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_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)

module petab petab.petablint petab.v1 petab.v1.C petab.v1.calculate petab.v1.composite_problem petab.v1.conditions petab.v1.core petab.v1.format_version petab.v1.lint petab.v1.mapping petab.v1.math 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.lint petab.v2.models petab.v2.models.model petab.v2.models.pysb_model petab.v2.models.sbml_model petab.v2.petab1to2 petab.v2.problem 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.Problem property) (petab.v2.problem.Problem property) n_measurements (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.Problem property) (petab.v2.problem.Problem property) n_priors (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.Problem property) (petab.v2.problem.Problem property) NOISE_DISTRIBUTION (in module petab.v1.C) (in module petab.v2.C) NOISE_FORMULA (in module petab.v1.C) (in module petab.v2.C)

noise_formulas (petab.v1.simulate.Simulator attribute) (petab.v1.Simulator attribute) (petab.v2.Simulator attribute) NOISE_MODELS (in module petab.v1.C) (in module petab.v2.C) NOISE_PARAMETERS (in module petab.v1.C) (in module petab.v2.C) NOISE_VALUE (in module petab.v1.C) (in module petab.v2.C) NOMINAL_VALUE (in module petab.v1.C) (in module petab.v2.C) NORMAL (in module petab.v1.C) (in module petab.v2.C) normalize_parameter_df() (in module petab.v1) (in module petab.v1.parameters) (in module petab.v2) numerator (petab.v2.lint.ValidationIssueSeverity attribute)

O

OBJECTIVE (in module petab.v1.C) (in module petab.v2.C) OBJECTIVE_PRIOR_PARAMETERS (in module petab.v1.C) (in module petab.v2.C) OBJECTIVE_PRIOR_TYPE (in module petab.v1.C) (in module petab.v2.C) 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_FORMULA (in module petab.v1.C) (in module petab.v2.C) OBSERVABLE_ID (in module petab.v1.C) (in module petab.v2.C) 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_table_has_nontrivial_noise_formula() (in module petab.v1) (in module petab.v1.lint) (in module petab.v2) OBSERVABLE_TRANSFORMATION (in module petab.v1.C) (in module petab.v2.C) OBSERVABLE_TRANSFORMATIONS (in module petab.v1.C) (in module petab.v2.C)

P

parameter_df (petab.v1.composite_problem.CompositeProblem attribute) (petab.v1.CompositeProblem attribute) (petab.v2.CompositeProblem attribute) 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) (in module petab.v2.C) 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) (in module petab.v2.C) PARAMETER_SCALE_LAPLACE (in module petab.v1.C) (in module petab.v2.C) PARAMETER_SCALE_NORMAL (in module petab.v1.C) (in module petab.v2.C) PARAMETER_SCALE_UNIFORM (in module petab.v1.C) (in module petab.v2.C) PARAMETER_SEPARATOR (in module petab.v1.C) (in module petab.v2.C) ParMappingDict (in module petab.v1) (in module petab.v1.parameter_mapping) (in module petab.v2) ParMappingDictQuadruple (in module petab.v1) (in module petab.v1.parameter_mapping) (in module petab.v2) ParMappingDictTuple (in module petab.v1) (in module petab.v1.parameter_mapping) (in module petab.v2) 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) pattern_from_string() (in module petab.v1.models.pysb_model) (in module petab.v2.models.pysb_model) 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.format_version module petab.v1.lint module petab.v1.mapping module petab.v1.math 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.lint 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.v2.problem module petab.version module petab.versions module petab1to2() (in module petab.v2.petab1to2) PETAB_ENTITY_ID (in module petab.v2.C) petab_problem (petab.v1.simulate.Simulator attribute) (petab.v1.Simulator attribute) (petab.v2.Simulator attribute) plot_goodness_of_fit() (in module petab.v1.visualize) (in module petab.v1.visualize.plot_residuals) PLOT_ID (in module petab.v1.C) (in module petab.v2.C) PLOT_NAME (in module petab.v1.C) (in module petab.v2.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) (in module petab.v2.C) PLOT_TYPE_SIMULATION (in module petab.v1.C) (in module petab.v2.C) PLOT_TYPES_DATA (in module petab.v1.C) (in module petab.v2.C) PLOT_TYPES_SIMULATION (in module petab.v1.C) (in module petab.v2.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) pop() (petab.v2.lint.ValidationResultList method) PREEQUILIBRATION_CONDITION_ID (in module petab.v1.C) (in module petab.v2.C) PRIOR_TYPES (in module petab.v1.C) (in module petab.v2.C) 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.problem) PROBLEMS (in module petab.v1.C) (in module petab.v2.C) problems (petab.v1.composite_problem.CompositeProblem attribute) (petab.v1.CompositeProblem attribute) (petab.v2.CompositeProblem attribute) PROVIDED (in module petab.v1.C) (in module petab.v2.C) PySBModel (class in petab.v1.models.pysb_model) (class in petab.v2.models.pysb_model)

R

real (petab.v2.lint.ValidationIssueSeverity attribute) remove() (petab.v2.lint.ValidationResultList method) 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) (petab.v2.Simulator method) REPLICATE (in module petab.v1.C) (in module petab.v2.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) (in module petab.v2)

reverse() (petab.v2.lint.ValidationResultList method) rng (petab.v1.simulate.Simulator attribute) (petab.v1.Simulator attribute) (petab.v2.Simulator attribute) run() (petab.v2.lint.CheckAllParametersPresentInParameterTable method) (petab.v2.lint.CheckConditionTable method) (petab.v2.lint.CheckMeasurementTable method) (petab.v2.lint.CheckModel method) (petab.v2.lint.CheckObservableTable method) (petab.v2.lint.CheckParameterTable method) (petab.v2.lint.CheckTableExists method) (petab.v2.lint.CheckValidParameterInConditionOrParameterTable method) (petab.v2.lint.CheckVisualizationTable method) (petab.v2.lint.ValidationTask method)

S

sample_from_prior() (in module petab.v1) (in module petab.v1.sampling) (in module petab.v2) sample_noise() (in module petab.v1) (in module petab.v1.simulate) (in module petab.v2) sample_parameter_startpoints() (in module petab.v1) (in module petab.v1.sampling) (in module petab.v2) (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.Problem method) (petab.v2.problem.Problem method) sample_parameter_startpoints_dict() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.Problem method) (petab.v2.problem.Problem method) save_to_tsv() (petab.v1.visualize.Figure method) (petab.v1.visualize.plotting.Figure method) SBML_FILES (in module petab.v1.C) SbmlModel (class in petab.v1.models.sbml_model) (class in petab.v2.models.sbml_model) scale() (in module petab.v1) (in module petab.v1.parameters) (in module petab.v2) scale_parameters() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.Problem method) (petab.v2.problem.Problem method) ScaleMappingDict (in module petab.v1) (in module petab.v1.parameter_mapping) (in module petab.v2) ScaleMappingDictTuple (in module petab.v1) (in module petab.v1.parameter_mapping) (in module petab.v2)

SCATTER_PLOT (in module petab.v1.C) (in module petab.v2.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) simulate() (petab.v1.simulate.Simulator method) (petab.v1.Simulator method) (petab.v2.Simulator method) simulate_without_noise() (petab.v1.simulate.Simulator method) (petab.v1.Simulator method) (petab.v2.Simulator method) SIMULATION (in module petab.v1.C) (in module petab.v2.C) SIMULATION_CONDITION_ID (in module petab.v1.C) (in module petab.v2.C) Simulator (class in petab.v1) (class in petab.v1.simulate) (class in petab.v2) sort() (petab.v2.lint.ValidationResultList method) split_parameter_replacement_list() (in module petab.v1) (in module petab.v1.measurements) (in module petab.v2) Subplot (class in petab.v1.visualize.plotting) symbol_allowed_in_observable_formula() (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.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)

T

temporary_working_dir (petab.v1.simulate.Simulator attribute) (petab.v1.Simulator attribute) (petab.v2.Simulator attribute) TIME (in module petab.v1.C) (in module petab.v2.C) TIME_STEADY_STATE (in module petab.v1.C) (in module petab.v2.C) to_bytes() (petab.v2.lint.ValidationIssueSeverity method) to_file() (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.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) 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) (in module petab.v2)

U

ub (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.Problem property) (petab.v2.problem.Problem property) ub_scaled (petab.v1.Problem property) (petab.v1.problem.Problem property) (petab.v2.Problem property) (petab.v2.problem.Problem property) unflatten_simulation_df() (in module petab.v1) (in module petab.v1.core) (in module petab.v2) UNIFORM (in module petab.v1.C) (in module petab.v2.C)

unique_preserve_order() (in module petab.v1) (in module petab.v1.core) (in module petab.v2) unscale() (in module petab.v1) (in module petab.v1.parameters) (in module petab.v2) unscale_parameters() (petab.v1.Problem method) (petab.v1.problem.Problem method) (petab.v2.Problem method) (petab.v2.problem.Problem method) UPPER_BOUND (in module petab.v1.C) (in module petab.v2.C) usesTime() (petab.petablint.LintFormatter method)

V

validate() (in module petab.petablint) (in module petab.v1) (in module petab.v1.yaml) (in module petab.v2) (petab.v2.Problem method) (petab.v2.problem.Problem method) validate_visualization_df() (in module petab.v1.visualize.lint) validate_yaml_semantics() (in module petab.v1) (in module petab.v1.yaml) (in module petab.v2) validate_yaml_syntax() (in module petab.v1) (in module petab.v1.yaml) (in module petab.v2) 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) (in module petab.v2.C) VISUALIZATION_DF_OPTIONAL_COLS (in module petab.v1.C) (in module petab.v2.C) VISUALIZATION_DF_REQUIRED_COLS (in module petab.v1.C) (in module petab.v2.C) VISUALIZATION_DF_SINGLE_PLOT_LEVEL_COLS (in module petab.v1.C) (in module petab.v2.C) VISUALIZATION_DF_SUBPLOT_LEVEL_COLS (in module petab.v1.C) (in module petab.v2.C) VISUALIZATION_FILES (in module petab.v1.C) (in module petab.v2.C)

W

warn() (in module petab.v2) working_dir (petab.v1.simulate.Simulator attribute) (petab.v1.Simulator attribute) (petab.v2.Simulator attribute) write_condition_df() (in module petab.v1) (in module petab.v1.conditions) (in module petab.v2) 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) (in module petab.v2) write_simulation_df() (in module petab.v1) (in module petab.v1.core) (in module petab.v2) write_visualization_df() (in module petab.v1) (in module petab.v1.core) (in module petab.v2) write_yaml() (in module petab.v1) (in module petab.v1.yaml) (in module petab.v2)

X

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

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

Y

Y_LABEL (in module petab.v1.C) (in module petab.v2.C) Y_OFFSET (in module petab.v1.C) (in module petab.v2.C) Y_SCALE (in module petab.v1.C) (in module petab.v2.C)

Y_SCALES (in module petab.v1.C) (in module petab.v2.C) Y_VALUES (in module petab.v1.C) (in module petab.v2.C)