pyPESTO - Parameter EStimation TOolbox for python
Version: 0.2.16
Source code: https://github.com/icb-dcm/pypesto
User's guide
- Install and upgrade
- Examples
- Storage
- API reference
- Engines
EngineMultiProcessEngineMultiThreadEngineSingleCoreEngineTask- Ensemble
EnsembleEnsemblePredictionget_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()- History
CountHistoryCountHistoryBaseCsvHistoryCsvHistoryTemplateErrorHdf5HistoryHistoryBaseHistoryOptionsHistoryTypeErrorMemoryHistoryNoHistoryOptimizerHistorycreate_history()- Logging
log()log_level_active()log_to_console()log_to_file()- Objective
AggregatedObjectiveAmiciObjectiveFDFDDeltaNegLogParameterPriorsNegLogPriorsObjectiveObjectiveBaseget_parameter_prior_dict()- Julia objective
JuliaObjectivedisplay_source_ipython()- Optimize
CESSOptimizerCmaesOptimizerDlibOptimizerESSOptimizerFidesOptimizerIpoptOptimizerNLoptOptimizerOptimizeOptionsOptimizerPyswarmOptimizerPyswarmsOptimizerSacessOptimizerScipyDifferentialEvolutionOptimizerScipyOptimizerfill_result_from_history()minimize()optimization_result_from_history()read_result_from_file()read_results_from_file()- PEtab
PetabImporterPetabImporterPysb- Prediction
AmiciPredictorPredictorTask- Problem
Problem- Profile
ProfileOptionsapproximate_parameter_profile()calculate_approximate_ci()chi2_quantile_to_ratio()parameter_profile()validation_profile_significance()- Result
McmcPtResultOptimizeResultOptimizerResultPredictionConditionResultPredictionResultProfileResultProfilerResultResultSampleResult- Sample
AdaptiveMetropolisSamplerAdaptiveParallelTemperingSamplerDynestySamplerEmceeSamplerInternalSamplerMetropolisSamplerParallelTemperingSamplerSamplerauto_correlation()calculate_ci_mcmc_sample()calculate_ci_mcmc_sample_prediction()effective_sample_size()geweke_test()sample()- Model Selection
Problemmodel_to_pypesto_problem()- Startpoint
CheckedStartpointsFunctionStartpointsLatinHypercubeStartpointsNoStartpointsStartpointMethodUniformStartpointslatin_hypercube()to_startpoint_method()uniform()- Storage
OptimizationResultHDF5ReaderOptimizationResultHDF5WriterProblemHDF5ReaderProblemHDF5WriterProfileResultHDF5ReaderProfileResultHDF5WriterSamplingResultHDF5ReaderSamplingResultHDF5Writerautosave()load_objective_config()read_result()write_array()write_result()- Visualize
ReferencePointassign_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_lowlevel()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