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 |
| timecourse | SimPart, Simulation, run_simulation: the timecourse of a roadrunner model which is simulated in parts, see Timecourses in parts |
| 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; Sex (pkpdsim.sex): the sex of a build, 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 |
| profiling | run_profiled, profiler_available, profile_dir: a command under the sampling profiler of python 3.15 (--profile), see Commands |
| fit | default_fit_settings, mapping_metadata, observable_id, check_sampling_sites, metadata_filter, observable_filter, select_mappings: the shared fit settings, the filters and the selection of the mappings of a fit; fit_subset, current_fixed_fits, recorded_fixed_fits, report_context, records_context: the subset of a fit id and the context of the report of a fit, see Experiments and their metadata |
| metadata | Tissue, Route, Dosing, Fasting, ApplicationForm, Health, Coadministration, Genotype, Phenotype, AdministrationSite, DataType, PKPDData, SamplingSite, 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 | scan_nca, nca_frame: the non-compartmental analysis of a timecourse at every point of a scan, vectorized, and its rows; PK_LABELS, PK_UNITS: the labels and units of the pharmacokinetic parameters |
| scan | single_dimension, scan_dimensions, point_timecourse, point_band, start_values, end_values: the dimensions of a scan, the timecourse of a point of its result and the band of its draws, see Scans and sensitivity analyses |
| sensitivity | parameters_from_sbml, set_bounds, parameters_to_df, write_parameters, distributions, free_parameters, sample_size: the parameters of the sensitivity analyses of a model; build_values, design_factors, relative_design: a global design around the values of another build; SensitivityRunner (run, parse_command_line, main), run_subfolders with LocalAnalysis, SamplingAnalysis, FastAnalysis, SobolAnalysis, SensitivityGroup, SensitivityOutput, CommandLine: the analyses of its script, see Scans and sensitivity analyses |
| uncertainty | adopt_fit, FitRecord, FitRecords, ParameterUncertainty: the adopted fits of a model and the distrib uncertainty of its fitted parameters; parameter_distributions, uncertainty_dimension, UncertaintySettings, UncertaintyRun, apply_uncertainty, check_fit_parameters: the run of the experiments over draws of the fitted parameters, see Uncertainty of the fitted parameters |
| distrib | parse, support, DistribFormula: the grammar of the distrib formulas of the draws of a fitted parameter, without a simulator, read by uncertainty and the PBPK library |
| reports | adopted_record, adopted_reports: the reports of the adopted fits of a model, each written from its record, see Commands |
| release | ReleaseSettings, Author: the release metadata of a model (PKPDModel.release); release, main: the release of a model repository, the command pkpd_release, see Release of a model repository |
| 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 |
| pbpk | PBPKDefinition, Substance, Binding, Erythrocytes, Kp, KpMethod, Excretion, Metabolism, Transport, CustomReaction, Route, Variants, PDComponent, SlowPool, build, compose, create_archive, sex_definition, model_figure: the PBPK model library and its modules, see PBPK library |
| pbpk organs | Organ, Part, Pool, parts_for, StandardOrgan, OrganComponent, GutComponent, Boundary, OrganContext, ZonatedLiver, NephronKidney, SegmentedIntestine, SingleLumen, LumenConversion, RegionalAbsorption, the segments and builders of the intestine, steady_state, stationary: the standard organ, its placement of the chemistry, the Kp methods, the organ variants, the steady state of the organs as formulas and the generated steady state, see Standard organ |
| pbpk physiology | physiology_objects, the populations, the impairment, the observers and the sinks, see Physiology |
| pbpk experiment | PBPKSimulationExperiment, ScaledRenalMap, healthy_gfr, REFERENCE_GFR: the base of the experiments of a model built on the library, the healthy GFR, the renal function of a measured clearance and the classes of impairment as the severities of the library, see Impairment |
| pbpk equilibration | equilibrated_simulation, Equilibration, drug_free_zeros, accumulating_states, growing_states, EQUILIBRATION_TOLERANCES: the drug-free equilibration of a condition, which the experiments and the groups of a sensitivity analysis share (SensitivityGroup(prepare=Equilibration(...))); flat_model, loaded_model: a flat model file parsed and compiled once for the equilibration and the validity of the kidney outflow, see Impairment |
| pbpk regional absorption | derive_regional_absorption, release_auc_ratios, regional_key: the factors of a regional absorption profile derived with the model from a release study, see Intestine and routes |
| pbpk kidney validity | kidney_outflow, KidneyOutflow, simulated_individuals, individual_values: the simulated individual and the validity of the kidney outflow, which the experiments check, see Standard organ |
| pbpk ids and data | ids, annotate, Value, fitted, load, cite, U: the id scheme, the annotation, the values with provenance and the data files, see Annotation |