User's guide
Engine
Engine.__init__()
Engine.execute()
MultiProcessEngine
MultiProcessEngine.__init__()
MultiProcessEngine.execute()
MultiThreadEngine
MultiThreadEngine.__init__()
MultiThreadEngine.execute()
SingleCoreEngine
SingleCoreEngine.__init__()
SingleCoreEngine.execute()
Task
Task.__init__()
Task.execute()
Ensemble
Ensemble.__init__()
Ensemble.check_identifiability()
Ensemble.compute_summary()
Ensemble.from_optimization_endpoints()
Ensemble.from_optimization_history()
Ensemble.from_sample()
Ensemble.predict()
EnsemblePrediction
EnsemblePrediction.__init__()
EnsemblePrediction.compute_chi2()
EnsemblePrediction.compute_summary()
EnsemblePrediction.condense_to_arrays()
get_covariance_matrix_parameters()
get_covariance_matrix_predictions()
get_pca_representation_parameters()
get_pca_representation_predictions()
get_percentile_label()
get_spectral_decomposition_lowlevel()
get_spectral_decomposition_parameters()
get_spectral_decomposition_predictions()
get_umap_representation_parameters()
get_umap_representation_predictions()
read_ensemble_prediction_from_h5()
read_from_csv()
read_from_df()
write_ensemble_prediction_to_h5()
AnalyticalInnerSolver
AnalyticalInnerSolver.solve()
HierarchicalAmiciCalculator
HierarchicalAmiciCalculator.__call__()
HierarchicalAmiciCalculator.__init__()
HierarchicalAmiciCalculator.get_inner_parameter_ids()
HierarchicalAmiciCalculator.initialize()
InnerParameter
InnerParameter.coupled
InnerParameter.dummy_value
InnerParameter.inner_parameter_id
InnerParameter.inner_parameter_type
InnerParameter.ixs
InnerParameter.lb
InnerParameter.scale
InnerParameter.ub
InnerParameter.__init__()
InnerParameter.check_bounds()
InnerProblem
InnerProblem.xs
InnerProblem.data
InnerProblem.__init__()
InnerProblem.from_petab_amici()
InnerProblem.get_dummy_values()
InnerProblem.get_for_id()
InnerProblem.get_x_ids()
InnerProblem.get_xs_for_type()
InnerProblem.is_empty()
InnerSolver
InnerSolver.initialize()
InnerSolver.solve()
NumericalInnerSolver
NumericalInnerSolver.minimize_kwargs
NumericalInnerSolver.n_cached
NumericalInnerSolver.problem_kwargs
NumericalInnerSolver.x_guesses
NumericalInnerSolver.__init__()
NumericalInnerSolver.initialize()
NumericalInnerSolver.solve()
OptimalScalingAmiciCalculator
OptimalScalingAmiciCalculator.__call__()
OptimalScalingAmiciCalculator.__init__()
OptimalScalingAmiciCalculator.get_inner_parameter_ids()
OptimalScalingAmiciCalculator.initialize()
OptimalScalingInnerSolver
OptimalScalingInnerSolver.__init__()
OptimalScalingInnerSolver.calculate_gradients()
OptimalScalingInnerSolver.calculate_obj_function()
OptimalScalingInnerSolver.get_default_options()
OptimalScalingInnerSolver.solve()
OptimalScalingInnerSolver.validate_options()
OptimalScalingParameter
OptimalScalingParameter.dummy_value
OptimalScalingParameter.inner_parameter_id
OptimalScalingParameter.inner_parameter_type
OptimalScalingParameter.ixs
OptimalScalingParameter.lb
OptimalScalingParameter.scale
OptimalScalingParameter.ub
OptimalScalingParameter.observable_id
OptimalScalingParameter.category
OptimalScalingParameter.group
OptimalScalingParameter.value
OptimalScalingParameter.estimate
OptimalScalingParameter.censoring_type
OptimalScalingParameter.__init__()
OptimalScalingParameter.initialize()
OptimalScalingProblem
OptimalScalingProblem.xs
OptimalScalingProblem.data
OptimalScalingProblem.groups
OptimalScalingProblem.method
OptimalScalingProblem.__init__()
OptimalScalingProblem.from_petab_amici()
OptimalScalingProblem.get_cat_lb_parameters_for_group()
OptimalScalingProblem.get_cat_ub_parameters_for_group()
OptimalScalingProblem.get_censored_group_quantitative_ixs()
OptimalScalingProblem.get_d()
OptimalScalingProblem.get_dd_dtheta()
OptimalScalingProblem.get_fixed_xs_for_group()
OptimalScalingProblem.get_free_xs_for_group()
OptimalScalingProblem.get_groups_for_xs()
OptimalScalingProblem.get_inner_parameter_dictionary()
OptimalScalingProblem.get_w()
OptimalScalingProblem.get_wdot()
OptimalScalingProblem.get_xs_for_group()
OptimalScalingProblem.initialize()
OptimalScalingProblem.initialize_c()
OptimalScalingProblem.initialize_w()
SplineAmiciCalculator
SplineAmiciCalculator.__call__()
SplineAmiciCalculator.__init__()
SplineAmiciCalculator.get_inner_parameter_ids()
SplineAmiciCalculator.initialize()
SplineInnerParameter
SplineInnerParameter.observable_id
SplineInnerParameter.group
SplineInnerParameter.index
SplineInnerParameter.value
SplineInnerParameter.estimate
SplineInnerParameter.__init__()
SplineInnerParameter.initialize()
SplineInnerProblem
SplineInnerProblem.xs
SplineInnerProblem.data
SplineInnerProblem.groups
SplineInnerProblem.spline_ratio
SplineInnerProblem.__init__()
SplineInnerProblem.from_petab_amici()
SplineInnerProblem.get_fixed_xs_for_group()
SplineInnerProblem.get_free_xs_for_group()
SplineInnerProblem.get_groups_for_xs()
SplineInnerProblem.get_inner_noise_parameter_dictionary()
SplineInnerProblem.get_inner_parameter_dictionary()
SplineInnerProblem.get_measurements_for_group()
SplineInnerProblem.get_noise_dummy_values()
SplineInnerProblem.get_noise_parameters_for_group()
SplineInnerProblem.get_xs_for_group()
SplineInnerProblem.initialize()
SplineInnerSolver
SplineInnerSolver.__init__()
SplineInnerSolver.calculate_gradients()
SplineInnerSolver.calculate_obj_function()
SplineInnerSolver.get_default_options()
SplineInnerSolver.solve()
SplineInnerSolver.validate_options()
CountHistory
CountHistory.get_fval_trace()
CountHistory.get_grad_trace()
CountHistory.get_hess_trace()
CountHistory.get_res_trace()
CountHistory.get_sres_trace()
CountHistory.get_time_trace()
CountHistory.get_x_trace()
CountHistoryBase
CountHistoryBase.__init__()
CountHistoryBase.exitflag
CountHistoryBase.finalize()
CountHistoryBase.message
CountHistoryBase.n_fval
CountHistoryBase.n_grad
CountHistoryBase.n_hess
CountHistoryBase.n_res
CountHistoryBase.n_sres
CountHistoryBase.start_time
CountHistoryBase.update()
CsvHistory
CsvHistory.__init__()
CsvHistory.finalize()
CsvHistory.get_fval_trace()
CsvHistory.get_grad_trace()
CsvHistory.get_hess_trace()
CsvHistory.get_res_trace()
CsvHistory.get_sres_trace()
CsvHistory.get_time_trace()
CsvHistory.get_x_trace()
CsvHistory.update()
CsvHistoryTemplateError
CsvHistoryTemplateError.__init__()
Hdf5History
Hdf5History.__init__()
Hdf5History.exitflag
Hdf5History.finalize()
Hdf5History.get_fval_trace()
Hdf5History.get_grad_trace()
Hdf5History.get_hess_trace()
Hdf5History.get_res_trace()
Hdf5History.get_sres_trace()
Hdf5History.get_time_trace()
Hdf5History.get_x_trace()
Hdf5History.load()
Hdf5History.message
Hdf5History.n_fval
Hdf5History.n_grad
Hdf5History.n_hess
Hdf5History.n_res
Hdf5History.n_sres
Hdf5History.recover_options()
Hdf5History.start_time
Hdf5History.trace_save_iter
Hdf5History.update()
HistoryBase
HistoryBase.ALL_KEYS
HistoryBase.RESULT_KEYS
HistoryBase.__init__()
HistoryBase.exitflag
HistoryBase.finalize()
HistoryBase.get_chi2_trace()
HistoryBase.get_fval_trace()
HistoryBase.get_grad_trace()
HistoryBase.get_hess_trace()
HistoryBase.get_res_trace()
HistoryBase.get_schi2_trace()
HistoryBase.get_sres_trace()
HistoryBase.get_time_trace()
HistoryBase.get_trimmed_indices()
HistoryBase.get_x_trace()
HistoryBase.implements_trace()
HistoryBase.message
HistoryBase.n_fval
HistoryBase.n_grad
HistoryBase.n_hess
HistoryBase.n_res
HistoryBase.n_sres
HistoryBase.start_time
HistoryBase.update()
HistoryOptions
HistoryOptions.__init__()
HistoryOptions.assert_instance()
HistoryTypeError
HistoryTypeError.__init__()
MemoryHistory
MemoryHistory.__init__()
MemoryHistory.get_fval_trace()
MemoryHistory.get_grad_trace()
MemoryHistory.get_hess_trace()
MemoryHistory.get_res_trace()
MemoryHistory.get_sres_trace()
MemoryHistory.get_time_trace()
MemoryHistory.get_x_trace()
MemoryHistory.update()
NoHistory
NoHistory.exitflag
NoHistory.get_fval_trace()
NoHistory.get_grad_trace()
NoHistory.get_hess_trace()
NoHistory.get_res_trace()
NoHistory.get_sres_trace()
NoHistory.get_time_trace()
NoHistory.get_x_trace()
NoHistory.message
NoHistory.n_fval
NoHistory.n_grad
NoHistory.n_hess
NoHistory.n_res
NoHistory.n_sres
NoHistory.start_time
NoHistory.update()
OptimizerHistory
OptimizerHistory.grad_min
OptimizerHistory.hess_min
OptimizerHistory.res_min
OptimizerHistory.sres_min
OptimizerHistory.MIN_KEYS
OptimizerHistory.__init__()
OptimizerHistory.finalize()
OptimizerHistory.update()
create_history()
log()
log_level_active()
log_to_console()
log_to_file()
AggregatedObjective
AggregatedObjective.__init__()
AggregatedObjective.call_unprocessed()
AggregatedObjective.check_mode()
AggregatedObjective.check_sensi_orders()
AggregatedObjective.get_config()
AggregatedObjective.initialize()
AmiciObjective
AmiciObjective.__call__()
AmiciObjective.__init__()
AmiciObjective.apply_custom_timepoints()
AmiciObjective.apply_steadystate_guess()
AmiciObjective.call_unprocessed()
AmiciObjective.check_gradients_match_finite_differences()
AmiciObjective.check_mode()
AmiciObjective.check_sensi_orders()
AmiciObjective.get_config()
AmiciObjective.initialize()
AmiciObjective.par_arr_to_dct()
AmiciObjective.reset_steadystate_guesses()
AmiciObjective.set_custom_timepoints()
AmiciObjective.store_steadystate_guess()
FD
FD.BACKWARD
FD.CENTRAL
FD.FORWARD
FD.METHODS
FD.__init__()
FD.call_unprocessed()
FD.has_fun
FD.has_grad
FD.has_hess
FD.has_res
FD.has_sres
FDDelta
FDDelta.ALWAYS
FDDelta.CONSTANT
FDDelta.DISTANCE
FDDelta.STEPS
FDDelta.UPDATE_CONDITIONS
FDDelta.__init__()
FDDelta.get()
FDDelta.update()
NegLogParameterPriors
NegLogParameterPriors.__init__()
NegLogParameterPriors.call_unprocessed()
NegLogParameterPriors.check_mode()
NegLogParameterPriors.check_sensi_orders()
NegLogParameterPriors.gradient_neg_log_density()
NegLogParameterPriors.hessian_neg_log_density()
NegLogParameterPriors.hessian_vp_neg_log_density()
NegLogParameterPriors.neg_log_density()
NegLogParameterPriors.residual()
NegLogParameterPriors.residual_jacobian()
NegLogPriors
Objective
Objective.__init__()
Objective.call_unprocessed()
Objective.get_config()
Objective.has_fun
Objective.has_grad
Objective.has_hess
Objective.has_hessp
Objective.has_res
Objective.has_sres
ObjectiveBase
ObjectiveBase.history
ObjectiveBase.pre_post_processor
ObjectiveBase.__call__()
ObjectiveBase.__init__()
ObjectiveBase.call_unprocessed()
ObjectiveBase.check_grad()
ObjectiveBase.check_grad_multi_eps()
ObjectiveBase.check_gradients_match_finite_differences()
ObjectiveBase.check_mode()
ObjectiveBase.check_sensi_orders()
ObjectiveBase.get_config()
ObjectiveBase.get_fval()
ObjectiveBase.get_grad()
ObjectiveBase.get_hess()
ObjectiveBase.get_res()
ObjectiveBase.get_sres()
ObjectiveBase.has_fun
ObjectiveBase.has_grad
ObjectiveBase.has_hess
ObjectiveBase.has_hessp
ObjectiveBase.has_res
ObjectiveBase.has_sres
ObjectiveBase.initialize()
ObjectiveBase.output_to_tuple()
ObjectiveBase.update_from_problem()
ObjectiveBase.x_names
get_parameter_prior_dict()
AesaraObjective
AesaraObjective.__init__()
AesaraObjective.call_unprocessed()
AesaraObjective.check_mode()
AesaraObjective.check_sensi_orders()
JaxObjective
JaxObjective.__init__()
JaxObjective.cached_fval()
JaxObjective.cached_grad()
JaxObjective.cached_hess()
JaxObjective.call_unprocessed()
JaxObjective.check_mode()
JaxObjective.check_sensi_orders()
JuliaObjective
JuliaObjective.__init__()
JuliaObjective.get()
PEtabJlObjective
PEtabJlObjective.__init__()
PEtabJlObjective.precompile_model()
display_source_ipython()
CESSOptimizer
CESSOptimizer.ess_init_args
CESSOptimizer.max_iter
CESSOptimizer.max_walltime_s
CESSOptimizer.fx_best
CESSOptimizer.x_best
CESSOptimizer.starttime
CESSOptimizer.i_iter
CESSOptimizer.__init__()
CESSOptimizer.minimize()
CmaesOptimizer
CmaesOptimizer.__init__()
CmaesOptimizer.is_least_squares()
CmaesOptimizer.minimize()
DlibOptimizer
DlibOptimizer.__init__()
DlibOptimizer.check_x0_support()
DlibOptimizer.get_default_options()
DlibOptimizer.is_least_squares()
DlibOptimizer.minimize()
ESSOptimizer
ESSOptimizer.__init__()
ESSOptimizer.minimize()
FidesOptimizer
FidesOptimizer.__init__()
FidesOptimizer.is_least_squares()
FidesOptimizer.minimize()
IpoptOptimizer
IpoptOptimizer.__init__()
IpoptOptimizer.is_least_squares()
IpoptOptimizer.minimize()
NLoptOptimizer
NLoptOptimizer.__init__()
NLoptOptimizer.check_x0_support()
NLoptOptimizer.is_least_squares()
NLoptOptimizer.minimize()
OptimizeOptions
OptimizeOptions.__init__()
OptimizeOptions.assert_instance()
Optimizer
Optimizer.__init__()
Optimizer.check_x0_support()
Optimizer.get_default_options()
Optimizer.is_least_squares()
Optimizer.minimize()
PyswarmOptimizer
PyswarmOptimizer.__init__()
PyswarmOptimizer.check_x0_support()
PyswarmOptimizer.is_least_squares()
PyswarmOptimizer.minimize()
PyswarmsOptimizer
PyswarmsOptimizer.__init__()
PyswarmsOptimizer.check_x0_support()
PyswarmsOptimizer.is_least_squares()
PyswarmsOptimizer.minimize()
SacessOptimizer
SacessOptimizer.__init__()
SacessOptimizer.minimize()
ScipyDifferentialEvolutionOptimizer
ScipyDifferentialEvolutionOptimizer.__init__()
ScipyDifferentialEvolutionOptimizer.is_least_squares()
ScipyDifferentialEvolutionOptimizer.minimize()
ScipyOptimizer
ScipyOptimizer.__init__()
ScipyOptimizer.get_default_options()
ScipyOptimizer.is_least_squares()
ScipyOptimizer.minimize()
fill_result_from_history()
minimize()
optimization_result_from_history()
read_result_from_file()
read_results_from_file()
PetabImporter
PetabImporter.MODEL_BASE_DIR
PetabImporter.__init__()
PetabImporter.check_gradients()
PetabImporter.compile_model()
PetabImporter.create_edatas()
PetabImporter.create_model()
PetabImporter.create_objective()
PetabImporter.create_predictor()
PetabImporter.create_prior()
PetabImporter.create_problem()
PetabImporter.create_solver()
PetabImporter.create_startpoint_method()
PetabImporter.from_yaml()
PetabImporter.prediction_to_petab_measurement_df()
PetabImporter.prediction_to_petab_simulation_df()
PetabImporter.rdatas_to_measurement_df()
PetabImporter.rdatas_to_simulation_df()
PetabImporter.validate_inner_options()
AmiciPredictor
AmiciPredictor.__call__()
AmiciPredictor.__init__()
PredictorTask
PredictorTask.predictor
PredictorTask.x
PredictorTask.sensi_orders
PredictorTask.mode
PredictorTask.id
PredictorTask.__init__()
PredictorTask.execute()
Problem
Problem.__init__()
Problem.dim
Problem.fix_parameters()
Problem.full_index_to_free_index()
Problem.get_full_matrix()
Problem.get_full_vector()
Problem.get_reduced_matrix()
Problem.get_reduced_vector()
Problem.lb
Problem.lb_init
Problem.normalize()
Problem.print_parameter_summary()
Problem.set_x_guesses()
Problem.ub
Problem.ub_init
Problem.unfix_parameters()
Problem.x_free_indices
Problem.x_guesses
ProfileOptions
ProfileOptions.default_step_size
ProfileOptions.min_step_size
ProfileOptions.max_step_size
ProfileOptions.step_size_factor
ProfileOptions.delta_ratio_max
ProfileOptions.ratio_min
ProfileOptions.reg_points
ProfileOptions.reg_order
ProfileOptions.magic_factor_obj_value
ProfileOptions.whole_path
ProfileOptions.__init__()
ProfileOptions.create_instance()
ProfileOptions.validate()
approximate_parameter_profile()
calculate_approximate_ci()
chi2_quantile_to_ratio()
parameter_profile()
validation_profile_significance()
adaptive_step()
fixed_step()
next_guess()
McmcPtResult
McmcPtResult.__init__()
OptimizeResult
OptimizeResult.__init__()
OptimizeResult.append()
OptimizeResult.as_dataframe()
OptimizeResult.as_list()
OptimizeResult.get_by_id()
OptimizeResult.get_for_key()
OptimizeResult.sort()
OptimizeResult.summary()
OptimizerResult
OptimizerResult.id
OptimizerResult.x
OptimizerResult.fval
OptimizerResult.grad
OptimizerResult.hess
OptimizerResult.res
OptimizerResult.sres
OptimizerResult.n_fval
OptimizerResult.n_grad
OptimizerResult.n_hess
OptimizerResult.n_res
OptimizerResult.n_sres
OptimizerResult.x0
OptimizerResult.fval0
OptimizerResult.history
OptimizerResult.exitflag
OptimizerResult.time
OptimizerResult.message
OptimizerResult.optimizer
OptimizerResult.__init__()
OptimizerResult.summary()
OptimizerResult.update_to_full()
PredictionConditionResult
PredictionConditionResult.__init__()
PredictionResult
PredictionResult.__init__()
PredictionResult.write_to_csv()
PredictionResult.write_to_h5()
ProfileResult
ProfileResult.__init__()
ProfileResult.append_empty_profile_list()
ProfileResult.append_profiler_result()
ProfileResult.get_profiler_result()
ProfileResult.set_profiler_result()
ProfilerResult
ProfilerResult.x_path
ProfilerResult.fval_path
ProfilerResult.ratio_path
ProfilerResult.gradnorm_path
ProfilerResult.exitflag_path
ProfilerResult.time_path
ProfilerResult.time_total
ProfilerResult.n_fval
ProfilerResult.n_grad
ProfilerResult.n_hess
ProfilerResult.message
ProfilerResult.__init__()
ProfilerResult.append_profile_point()
ProfilerResult.flip_profile()
Result
Result.problem
Result.optimize_result
Result.profile_result
Result.sample_result
Result.__init__()
Result.summary()
SampleResult
SampleResult.__init__()
AdaptiveMetropolisSampler
AdaptiveMetropolisSampler.__init__()
AdaptiveMetropolisSampler.default_options()
AdaptiveMetropolisSampler.initialize()
AdaptiveParallelTemperingSampler
AdaptiveParallelTemperingSampler.adjust_betas()
AdaptiveParallelTemperingSampler.default_options()
DynestySampler
DynestySampler.__init__()
DynestySampler.get_original_samples()
DynestySampler.get_samples()
DynestySampler.initialize()
DynestySampler.loglikelihood()
DynestySampler.prior_transform()
DynestySampler.restore_internal_sampler()
DynestySampler.sample()
DynestySampler.save_internal_sampler()
EmceeSampler
EmceeSampler.__init__()
EmceeSampler.get_epsilon_ball_initial_state()
EmceeSampler.get_samples()
EmceeSampler.initialize()
EmceeSampler.sample()
InternalSampler
InternalSampler.get_last_sample()
InternalSampler.make_internal()
InternalSampler.set_last_sample()
MetropolisSampler
MetropolisSampler.__init__()
MetropolisSampler.default_options()
MetropolisSampler.get_last_sample()
MetropolisSampler.get_samples()
MetropolisSampler.initialize()
MetropolisSampler.make_internal()
MetropolisSampler.sample()
MetropolisSampler.set_last_sample()
ParallelTemperingSampler
ParallelTemperingSampler.__init__()
ParallelTemperingSampler.adjust_betas()
ParallelTemperingSampler.default_options()
ParallelTemperingSampler.get_samples()
ParallelTemperingSampler.initialize()
ParallelTemperingSampler.sample()
ParallelTemperingSampler.swap_samples()
Sampler
Sampler.__init__()
Sampler.default_options()
Sampler.get_samples()
Sampler.initialize()
Sampler.sample()
Sampler.translate_options()
auto_correlation()
calculate_ci_mcmc_sample()
calculate_ci_mcmc_sample_prediction()
effective_sample_size()
geweke_test()
sample()
Problem.calibrated_models
Problem.newly_calibrated_models
Problem.method_caller
Problem.model_postprocessor
Problem.petab_select_problem
Problem.create_method_caller()
Problem.handle_select_kwargs()
Problem.multistart_select()
Problem.select()
Problem.select_to_completion()
Problem.set_state()
Problem.update_with_newly_calibrated_models()
model_to_pypesto_problem()
model_id_binary_postprocessor()
multi_postprocessor()
report_postprocessor()
save_postprocessor()
waterfall_plot_postprocessor()
CheckedStartpoints
CheckedStartpoints.__call__()
CheckedStartpoints.__init__()
CheckedStartpoints.check_and_resample()
CheckedStartpoints.sample()
FunctionStartpoints
FunctionStartpoints.__init__()
FunctionStartpoints.sample()
LatinHypercubeStartpoints
LatinHypercubeStartpoints.__init__()
LatinHypercubeStartpoints.sample()
NoStartpoints
NoStartpoints.__call__()
StartpointMethod
StartpointMethod.__call__()
UniformStartpoints
UniformStartpoints.__init__()
latin_hypercube()
to_startpoint_method()
uniform()
OptimizationResultHDF5Reader
OptimizationResultHDF5Reader.storage_filename
OptimizationResultHDF5Reader.__init__()
OptimizationResultHDF5Reader.read()
OptimizationResultHDF5Writer
OptimizationResultHDF5Writer.storage_filename
OptimizationResultHDF5Writer.__init__()
OptimizationResultHDF5Writer.write()
ProblemHDF5Reader
ProblemHDF5Reader.storage_filename
ProblemHDF5Reader.__init__()
ProblemHDF5Reader.read()
ProblemHDF5Writer
ProblemHDF5Writer.storage_filename
ProblemHDF5Writer.__init__()
ProblemHDF5Writer.write()
ProfileResultHDF5Reader
ProfileResultHDF5Reader.storage_filename
ProfileResultHDF5Reader.__init__()
ProfileResultHDF5Reader.read()
ProfileResultHDF5Writer
ProfileResultHDF5Writer.storage_filename
ProfileResultHDF5Writer.__init__()
ProfileResultHDF5Writer.write()
SamplingResultHDF5Reader
SamplingResultHDF5Reader.storage_filename
SamplingResultHDF5Reader.__init__()
SamplingResultHDF5Reader.read()
SamplingResultHDF5Writer
SamplingResultHDF5Writer.storage_filename
SamplingResultHDF5Writer.__init__()
SamplingResultHDF5Writer.write()
autosave()
load_objective_config()
read_result()
write_array()
write_result()
ReferencePoint
ReferencePoint.x
ReferencePoint.fval
ReferencePoint.color
ReferencePoint.auto_color
ReferencePoint.legend
ReferencePoint.__init__()
assign_clustered_colors()
assign_clusters()
assign_colors()
create_references()
delete_nan_inf()
ensemble_crosstab_scatter_lowlevel()
ensemble_identifiability()
ensemble_scatter_lowlevel()
optimization_run_properties_one_plot()
optimization_run_properties_per_multistart()
optimization_run_property_per_multistart()
optimization_scatter()
optimizer_convergence()
optimizer_history()
optimizer_history_lowlevel()
parameter_hist()
parameters()
parameters_correlation_matrix()
parameters_lowlevel()
plot_categories_from_inner_result()
plot_categories_from_pypesto_result()
plot_splines_from_inner_result()
plot_splines_from_pypesto_result()
process_offset_y()
process_result_list()
process_y_limits()
profile_cis()
profile_lowlevel()
profiles()
profiles_lowlevel()
projection_scatter_pca()
projection_scatter_umap()
projection_scatter_umap_original()
sampling_1d_marginals()
sampling_fval_traces()
sampling_parameter_cis()
sampling_parameter_traces()
sampling_prediction_trajectories()
sampling_scatter()
waterfall()
waterfall_lowlevel()
time_trajectory_model()
visualize_optimized_model_fit()
Developer's guide
About
pypesto
pypesto.engine
pypesto.ensemble
pypesto.hierarchical
pypesto.hierarchical.optimal_scaling
pypesto.hierarchical.spline_approximation
pypesto.history
pypesto.logging
pypesto.objective
pypesto.objective.aesara
pypesto.objective.jax
pypesto.objective.julia
pypesto.optimize
pypesto.petab
pypesto.predict
pypesto.problem
pypesto.profile
pypesto.profile.profile_next_guess
pypesto.result
pypesto.sample
pypesto.select
pypesto.select.postprocessors
pypesto.startpoint
pypesto.store
pypesto.visualize
pypesto.visualize.model_fit
