Model Examples

Complete examples for all NeoPKPD PK and PK/PD models.

PK Models

Model	Description	Directory
OneCompIVBolus	One-compartment IV bolus	01_onecomp_iv_bolus
OneCompIVInfusion	One-compartment IV infusion	02_onecomp_iv_infusion
OneCompOralFirstOrder	One-compartment oral (first-order absorption)	03_onecomp_oral
TwoCompIVBolus	Two-compartment IV bolus	04_twocomp_iv
TwoCompOral	Two-compartment oral	05_twocomp_oral
ThreeCompIVBolus	Three-compartment IV bolus	06_threecomp_iv
TransitAbsorption	Transit compartment absorption	07_transit_absorption
MichaelisMentenElimination	Saturable (nonlinear) elimination	08_michaelis_menten

PK/PD Models

Model	Description	Directory
DirectEmax	Direct Emax response	01_direct_emax
SigmoidEmax	Sigmoidal Emax response	02_sigmoid_emax
BiophaseEquilibration	Effect compartment model	03_biophase_equilibration
IndirectResponse	Indirect response (turnover)	04_indirect_response

File Structure

Each model directory contains:

01_model_name/
├── README.md       # Model equations, parameters, typical values
├── julia.jl        # Julia implementation
├── python.py       # Python implementation
└── cli.json        # CLI specification

Running Examples

All Models (Julia)

julia --project=packages/core docs/examples/models/run_all.jl

Single Model

# Julia
julia --project=packages/core docs/examples/models/pk/01_onecomp_iv_bolus/julia.jl

# Python
python docs/examples/models/pk/01_onecomp_iv_bolus/python.py

# CLI
./bin/neopkpd simulate --spec docs/examples/models/pk/01_onecomp_iv_bolus/cli.json

Model Selection Guide

By Administration Route

Route	Single Compartment	Multi-Compartment
IV Bolus	OneCompIVBolus	TwoCompIVBolus, ThreeCompIVBolus
IV Infusion	OneCompIVInfusion	TwoCompIVInfusion
Oral	OneCompOralFirstOrder	TwoCompOral
Oral (complex)	TransitAbsorption	-

By Elimination Type

Elimination	Model
Linear (first-order)	OneCompIVBolus, TwoCompIVBolus, etc.
Nonlinear (saturable)	MichaelisMentenElimination

By PD Response

Response Type	Model	Use Case
Direct, hyperbolic	DirectEmax	Immediate response, receptor binding
Direct, sigmoidal	SigmoidEmax	Steep dose-response, threshold effects
Delayed	BiophaseEquilibration	Effect compartment, hysteresis
Indirect	IndirectResponse	Enzyme/receptor turnover, biomarkers

Parameter Conventions

PK Parameters

Parameter	Description	Typical Units
CL	Clearance	L/h
V, V1	Central volume	L
Q	Inter-compartmental clearance	L/h
V2, V3	Peripheral volumes	L
Ka	Absorption rate constant	1/h
Ktr	Transit rate constant	1/h
Vmax	Maximum elimination rate	mg/h
Km	Michaelis constant	mg/L

PD Parameters

Parameter	Description	Typical Units
E0	Baseline effect	varies
Emax	Maximum effect	varies
EC50	Concentration at 50% Emax	mg/L
gamma	Hill coefficient	dimensionless
Ke0	Effect compartment rate constant	1/h
Kin	Zero-order production rate	units/h
Kout	First-order elimination rate	1/h
IC50/SC50	Concentration for 50% inhibition/stimulation	mg/L