API reference¶
The API reference is generated from the docstrings of the package.
pkpdsim¶
| module | description |
|---|---|
| pkpdsim | the package and its version |
| templates | creators and terms_of_use of a model, see Templates and annotations |
| annotations | compartments, the annotations of the recurring compartments, see Templates and annotations |
| data | studies_dir, collect_tsv_files: the study data of a model from the study folders of PK-DB, see Study data |
| initial_values | init_concentrations_changes, init_amounts_changes, get_species_keys: the initial values of a substance in every tissue, see Initial values |
| licenses | License, license_text, write_license: the texts of CC BY-SA 4.0 and MIT, see Licenses |
| model | PKPDModel, SimulatorSettings, FigureSettings, CheckSettings, ExtraAction, resolve: the description of a model, see Models and their commands |
| run | run_experiments, run_simulation_experiments: the run of the simulation experiments of a model |
| cli | run_command, fit_command, report_command, identifiability_command: the commands of a model |
| fit | default_fit_settings, mapping_metadata, observable_id, metadata_filter, observable_filter, select_mappings: the shared fit settings, the filters and the selection of the mappings of a fit, see Experiments and their metadata |
| metadata | Tissue, Route, Dosing, Fasting, ApplicationForm, DataType, PKPDData, PKPDMappingMetaData: the vocabulary of the metadata of a fit mapping, see Experiments and their metadata |
| experiment | PKPDSimulationExperiment, to_sid, define_unit, rename_units: the base of the simulation experiments of a model, the SIds of its keys and the units of its data, see Experiments and their metadata |
| impairment | the presets of the renal function, the cirrhosis and the cardiac function with their colors |
| pk | PK_LABELS, PK_UNITS: the labels and units of the pharmacokinetic parameters |
| scan | single_dimension, point_timecourse: the dimension of a scan and the timecourse of a point of its result, see Scans and sensitivity analyses |
| sensitivity | parameters_from_sbml, set_bounds, parameters_to_df, write_parameters, distributions, sample_size: the parameters of the sensitivity analyses of a model, see Scans and sensitivity analyses |
| testing | check_model, check_registry, initialize_experiments, run_all_experiments, start_fits: the tests of a model as functions |
| verify | pkpdsim-verify: the verification of a change of a model |