Examples

ferx-core includes several example models in the examples/ directory with corresponding datasets in data/.

Example	Model	Route	Features
One-Compartment Oral	1-cpt	Oral	Basic PopPK, FOCE and SAEM
Two-Compartment IV	2-cpt	IV bolus	Multi-compartment dynamics
Covariates	2-cpt	Oral	Weight and renal function effects
ODE Model	1-cpt	Oral	Michaelis-Menten elimination, ODE solver
BLOQ (M3 method)	1-cpt	Oral	Likelihood-based handling of censored observations
Inter-Occasion Variability	1-cpt	Oral	IOV with kappa parameters, FOCE
IOV with SAEM	1-cpt	Oral	IOV estimated by SAEM
Multiple Dosing (ADDL)	1-cpt	Oral	ADDL / II columns, TAD reset, derived NCA
Steady-State Dosing (SS)	1-cpt	Oral	SS=1 / II columns, analytical accumulation
Unit Scaling	1-cpt	Oral	obs_scale for AMT/DV unit conversion
Derived Columns and Output	1-cpt	Oral	[derived] and [output] blocks, NCA metrics
Data Selection	1-cpt	Oral	[data_selection] IGNORE/ACCEPT filter
ODE with Lag Time	1-cpt ODE	Oral	LAGTIME keyword, IIV on lag, obs_scale = V
Transit Absorption	2-cpt ODE	Oral	Transit chain, allometric scaling, FOCEI
Stochastic Differential Equations	1-cpt ODE	Oral	[diffusion] block, EKF process noise
Multi-start	1-cpt ODE	Oral	Multiple starting values to avoid local minima

Running Examples

# One-compartment oral (warfarin)
ferx examples/warfarin.ferx --data data/warfarin.csv

# Two-compartment IV
ferx examples/two_cpt_iv.ferx --data data/two_cpt_iv.csv

# Covariates model
ferx examples/two_cpt_oral_cov.ferx --data data/two_cpt_oral_cov.csv

# ODE model (Michaelis-Menten)
ferx examples/mm_oral.ferx --data data/mm_oral.csv

# SAEM estimation
ferx examples/warfarin_saem.ferx --data data/warfarin.csv

# BLOQ (M3 method)
ferx examples/warfarin_bloq.ferx --data data/warfarin_bloq.csv

# IOV (inter-occasion variability)
ferx examples/warfarin_iov.ferx --data data/warfarin_iov.csv

# IOV with SAEM
ferx examples/warfarin_iov_saem.ferx --data data/warfarin_iov_saem.csv

# Multiple dosing (ADDL/II columns)
ferx examples/warfarin_addl.ferx --data data/warfarin_addl.csv

# Steady-state dosing (SS/II columns)
ferx examples/warfarin_ss.ferx --data data/warfarin_ss.csv

# Unit scaling (AMT in µg, DV in mg/L)
ferx examples/warfarin_scaled.ferx --data data/warfarin_scaled.csv

# Derived columns and output (NCA metrics, [output] block)
ferx examples/warfarin_derived.ferx --data data/warfarin.csv

# Data selection (IGNORE filter)
ferx examples/warfarin_data_selection.ferx --data data/warfarin.csv

# ODE model with absorption lag time
ferx examples/warfarin_ode_lagtime.ferx --data data/warfarin_ode_lagtime.csv

# Transit-compartment absorption (2-cpt ODE, allometric scaling)
ferx examples/transit_2cpt.ferx --data data/transit_2cpt.csv

# Stochastic differential equations (EKF process noise)
ferx examples/warfarin_sde.ferx --data data/warfarin_sde.csv

# Multi-start (Michaelis-Menten)
ferx examples/mm_multistart.ferx --data data/mm_oral.csv