User Guide
This guide documents the current end-user surface of OpenPKPD: the Python API, the NONMEM-style control-stream workflow, the CLI, and the desktop GUI.
The pages below reflect the current source tree as of the 2026-03 documentation
audit. Some advanced capabilities are still covered more deeply in examples/
and API docstrings than in narrative documentation, especially for PBPK, DDE,
Bayesian workflows, bootstrap, and IOV-heavy models.
Use the guide with the validation matrix in mind:
the Python API is the broadest surface,
the CLI/control-stream workflow tracks a large subset of that surface,
the desktop GUI intentionally fronts a narrower, more curated workflow layer,
the examples directory is larger than the annotated worked-example section.
What this guide covers
dataset expectations and NONMEM-style inputs
programmatic modelling with
ModelBuildercontrol-stream parsing and execution
currently implemented PK subroutines and estimation methods
covariance/output/reporting workflows
the current GUI shell, menus, and workflow map
comparison and functionality-gap tables updated to match the codebase
- Desktop GUI
- Data Format
- ModelBuilder API
- Control Streams
- PK Subroutines
- Estimation Methods
- Covariance Step
- Output Files
- Diagnostic Plots
- Coverage and Validation Map
- How to read this page
- Estimation methods
- PK subroutines and solver surfaces
- Diagnostics, simulation, and NCA
- Analysis and model families
- Workflow, parsing, outputs, and GUI
- Dedicated release lanes
- External anchors and citations
- Current strongest areas
- Current thinner areas
- Recommended maintenance rule
- Analysis validation gaps and next tests
- Validation notes
- Validation matrix
- Test suite
- Advanced PK Features
- Non-Compartmental Analysis (NCA)
- Migrating from Monolix
- Comparison with Other PK/PD Software
- External validation benchmarks
- Validated estimator envelope
- Monolix: theophylline SAEM
- Advanced estimators: empirical benchmark notes
- PKNCA / Phoenix-style NCA: theophylline
- WinNonlin-backed NCA: Indometh
- WinNonlin status
- nlmixr2 FOCEI: theophylline and warfarin
- NONMEM 7.x: multi-compartment and covariate models
- Phenobarbital — Neonatal Population PK (1-Compartment FO)
- New Example Control Streams
- Priority Improvement Areas
- Current conclusions
- References
- Algorithm and Method Citations
- Estimation methods
- Covariance step
- PK structural models (ADVAN subroutines)
- Pharmacodynamic models
- Covariate modelling
- Non-compartmental analysis (NCA)
- Simulation and diagnostics
- Optimal design
- Prior distributions (MAP / NWPRI)
- Software and numerical tools
- Validation datasets
- Validation reference outputs