Examples

Selected documentation pages for the example suite. The repository currently ships 34 self-contained example scripts covering common population PK/PD workflows, while the docs below cover a curated subset of those scripts in worked-example form. All shipped scripts can be run directly:

python examples/01_theophylline_fo.py

Set OPENPKPD_EXAMPLE_OUTPUT=/tmp/figs to save figures to disk instead of displaying them interactively.

Basic PK modelling

Script	Topic
01_theophylline_fo.py	One-compartment oral model, FO estimation
02_warfarin_foce.py	Warfarin FOCE with interaction
03_two_compartment_iv.py	Two-compartment IV bolus, ADVAN3
09_three_compartment.py	Three-compartment IV with ADVAN11

PD and PKPD models

Script	Topic
04_emax_pd_model.py	Direct Emax PD effect
05_indirect_response.py	Indirect-response simulation with an approximate direct-effect fit
19_count_categorical_models.py	Poisson/NegBin/ZIP count models; proportional odds, Markov state models
24_advanced_pd_models.py	Effect compartment, turnover, TGI (Simeoni), placebo response

Special features

Script	Topic
06_from_control_stream.py	Parse and run an existing NONMEM .ctl file
08_ode_transit_absorption.py	ODE-based transit absorption
10_blq_handling.py	Below-limit-of-quantification (M1/M3/M5)
11_tte_model.py	Time-to-event survival model
16_dde_model.py	Delay differential equation (DDE) PK model
17_sbml_import.py	SBML/QSP model import
22_pbpk_model.py	5-organ physiologically-based PK (PBPK) model
23_iov_model.py	Inter-occasion variability (IOV) modelling
25_focei_optimizer_controls.py	FOCEI optimizer robustness controls from the Python API
26_control_stream_optimizer_extensions.py	Inspect FOCEI optimizer extensions from a control stream
27_phenobarbital_population_pk.py	Neonatal phenobarbital population PK with weight scaling
28_indometh_nca.py	NCA on the public Indometh WinNonlin-backed dataset
29_optimal_design.py	PFIM-backed sampling-time optimization
30_four_compartment_advan5.py	Four-compartment ADVAN5 example with ADVAN11 consistency check
31_impmap_warm_start.py	Short IMPMAP warm-start diagnostics on warfarin PK
32_nonparametric_support_points.py	Synthetic nonparametric support-point estimation demo
33_tmdd_model.py	Full TMDD / QSSA / Michaelis-Menten approximation comparison
34_multidose_ss_nca.py	Multi-dose steady-state NCA (AUCtau, Ctrough, accumulation ratio)

Estimation methods

Script	Topic
01_theophylline_fo.py	FO estimation
02_warfarin_foce.py	FOCE with interaction
15_bayes_laplace.py	Bayesian Laplace approximation (PyMC optional)
20_saem_estimation.py	SAEM (stochastic EM) with convergence history
21_laplacian_prior.py	Laplacian estimation + prior augmentation (MAP)

Analysis workflows

Script	Topic
07_diagnostic_plots.py	GOF, spaghetti, ETA diagnostic panels
12_nca.py	Non-compartmental analysis (NCA)
13_covariate_search.py	Stepwise covariate modelling (SCM)
14_simulation_vpc.py	Visual Predictive Check (VPC)
18_parallel_bootstrap.py	Parallel bootstrap resampling

• Example 1 — Theophylline (FO)
• Example 2 — Warfarin (FOCE)
• Example 3 — Two-Compartment IV (ADVAN3)
• Example 4 — Emax PD Model
• Example 5 — Indirect Response Model
• Example 6 — Running a Control Stream File
• Example 7 — Full Diagnostic Plot Gallery
• Example 8 — FOCEI Optimizer Controls from Python
• Example 9 — FOCEI Optimizer Controls from a Control Stream
• Example 29 — Optimal Design with PFIM
• Example 16: Delay Differential Equation (DDE) PK model
• Example 20 — SAEM Estimation
• Example 22 — PBPK Modelling
• Example 31 — IMPMAP Warm-Start Diagnostics
• Example 32 — Nonparametric Support Points
• Example 33 — TMDD Model Comparison
• Example 34 — Multi-Dose Steady-State NCA