Generate initial parameter table for pharmacometric model estimation
Source:R/modelGen.R
initialize_param_table.RdCreates a structured parameter table containing initial estimates with constraints for base parameters, inter-individual variability (ETA), residual errors (SIGMA), and correlation terms (OMEGA) to initialize nonlinear mixed-effects model fitting.
Value
A data.frame with 29 columns containing parameter specifications. The structure includes:
- Name
Parameter name (e.g., "lcl", "eta.vc", "cor.eta_cl_vc")
- init
Numeric initial value for parameter estimation
- lb
Lower bound constraint (use -Inf for unconstrained)
- ub
Upper bound constraint (use Inf for unconstrained)
- fixed
Integer flag indicating whether parameter should be fixed (1) or estimated (0)
- Description
Text description of parameter's biological/pharmacometric meaning
Details
This table includes:
Base PK parameters (absorption, clearance, volumes, etc.) in log-scale
Michaelis-Menten kinetics parameters (vmax, km)
Absorption parameters including zero-order, mixed-order, and transit compartment models
Residual variability components (additive and proportional error)
Inter-individual variability (ETA) terms with variance parameters
Correlation parameters between ETA terms in two blocks:
Block 1: vmax and km parameters
Block 2: clearance, volumes, and inter-compartmental clearance
Parameters are organized with:
Name: Parameter name following standard nomenclature
init: Initial estimate for model fitting
lb/ub: Lower/upper bounds for parameter estimation
fixed: Flag indicating fixed parameters (1) vs estimated (0)
Description: Plain-text explanation of parameter meaning
Examples
# Generate default parameter table
initialize_param_table()
#> Name init lb ub fixed
#> 1 lka 1.00 -Inf Inf 0
#> 2 lcl 1.00 -Inf Inf 0
#> 3 lvc1cmpt 1.00 -Inf Inf 0
#> 4 lvc2cmpt 1.00 -Inf Inf 0
#> 5 lvc3cmpt 1.00 -Inf Inf 0
#> 6 lvp2cmpt 1.00 -Inf Inf 0
#> 7 lvp3cmpt 1.00 -Inf Inf 0
#> 8 lq2cmpt 1.00 -Inf Inf 0
#> 9 lq3cmpt 1.00 -Inf Inf 0
#> 10 lvp2 1.00 -Inf Inf 0
#> 11 lq2 1.00 -Inf Inf 0
#> 12 lvmax 1.00 -Inf Inf 0
#> 13 lkm 1.00 -Inf Inf 0
#> 14 lD2 1.00 -Inf Inf 0
#> 15 lF1 0.01 -Inf Inf 0
#> 16 lFr 0.01 -Inf Inf 0
#> 17 ltlag 1.00 -Inf Inf 0
#> 18 lmtt 1.00 -Inf Inf 0
#> 19 ln 0.01 -Inf Inf 0
#> 20 lbio 0.01 -Inf Inf 0
#> 21 sigma_add 1.00 0 Inf 0
#> 22 sigma_prop 0.10 0 1 0
#> 23 eta.ka 0.10 0 1 0
#> 24 eta.cl 0.10 0 1 0
#> 25 eta.vc 0.10 0 1 0
#> 26 eta.vp 0.10 0 1 0
#> 27 eta.q 0.10 0 1 0
#> 28 eta.vp2 0.10 0 1 0
#> 29 eta.q2 0.10 0 1 0
#> 30 eta.vmax 0.10 0 1 0
#> 31 eta.km 0.10 0 1 0
#> 32 eta.tlag 0.10 0 1 0
#> 33 eta.D2 0.10 0 1 0
#> 34 eta.mtt 0.10 0 1 0
#> 35 eta.n 0.10 0 1 0
#> 36 eta.bio 0.10 0 1 0
#> 37 eta.F1 0.10 0 1 0
#> 38 eta.Fr 0.10 0 1 0
#> 39 cor.eta_vmax_km 0.10 0 1 0
#> 40 cor.eta_cl_vc 0.10 0 1 0
#> 41 cor.eta_cl_vp 0.10 0 1 0
#> 42 cor.eta_cl_vp2 0.10 0 1 0
#> 43 cor.eta_cl_q 0.10 0 1 0
#> 44 cor.eta_cl_q2 0.10 0 1 0
#> 45 cor.eta_vc_vp 0.10 0 1 0
#> 46 cor.eta_vc_vp2 0.10 0 1 0
#> 47 cor.eta_vc_q 0.10 0 1 0
#> 48 cor.eta_vc_q2 0.10 0 1 0
#> 49 cor.eta_vp_vp2 0.10 0 1 0
#> 50 cor.eta_vp_q 0.10 0 1 0
#> 51 cor.eta_vp_q2 0.10 0 1 0
#> 52 cor.eta_vp2_q 0.10 0 1 0
#> 53 cor.eta_vp2_q2 0.10 0 1 0
#> 54 cor.eta_q_q2 0.10 0 1 0
#> Description
#> 1 Log of the absorption rate constant
#> 2 Log of clearance
#> 3 Log of central volume of distribution for 1-compartment model
#> 4 Log of central volume of distribution for 2-compartment model
#> 5 Log of central volume of distribution for 3-compartment model
#> 6 Log of peripheral volume for 2-compartment model
#> 7 Log of peripheral volume for 3-compartment model
#> 8 Log of intercompartmental clearance between central and first peripheral compartments for 2-compartment model
#> 9 Log of intercompartmental clearance between central and first peripheral compartments for 3-compartment model
#> 10 Log of volume for the second peripheral compartment
#> 11 Log of intercompartmental clearance between central and second peripheral compartments
#> 12 Log of the maximum elimination rate
#> 13 Log of the concentration at which the rate is half of Vmax
#> 14 Log of zero-order absorption duration
#> 15 Log of absolute bioavailability, typically used in IV and oral mixed dosing
#> 16 Log of the fraction absorbed through first-order kinetics in a mixed absorption model
#> 17 Log of lag time before absorption begins
#> 18 Log of mean transit time
#> 19 Log of the number of transit compartments
#> 20 Log of the bioavailability of transit compartment model
#> 21 Additive residual error component, constant across all concentrations.
#> 22 Proportional residual error component, scales with drug concentration.
#> 23 Inter-individual variability inka, modeled with variance as the initial estimate
#> 24 Inter-individual variability incl, modeled with variance as the initial estimate
#> 25 Inter-individual variability invc, modeled with variance as the initial estimate
#> 26 Inter-individual variability invp, modeled with variance as the initial estimate
#> 27 Inter-individual variability inq, modeled with variance as the initial estimate
#> 28 Inter-individual variability invp2, modeled with variance as the initial estimate
#> 29 Inter-individual variability inq2, modeled with variance as the initial estimate
#> 30 Inter-individual variability invmax, modeled with variance as the initial estimate
#> 31 Inter-individual variability inkm, modeled with variance as the initial estimate
#> 32 Inter-individual variability intlag, modeled with variance as the initial estimate
#> 33 Inter-individual variability inD2, modeled with variance as the initial estimate
#> 34 Inter-individual variability inmtt, modeled with variance as the initial estimate
#> 35 Inter-individual variability inn, modeled with variance as the initial estimate
#> 36 Inter-individual variability inbio, modeled with variance as the initial estimate
#> 37 Inter-individual variability inF1, modeled with variance as the initial estimate
#> 38 Inter-individual variability inFr, modeled with variance as the initial estimate
#> 39 Correlation between eta.vmax and eta.km
#> 40 Correlation between eta.cl and eta.vc
#> 41 Correlation between eta.cl and eta.vp
#> 42 Correlation between eta.cl and eta.vp2
#> 43 Correlation between eta.cl and eta.q
#> 44 Correlation between eta.cl and eta.q2
#> 45 Correlation between eta.vc and eta.vp
#> 46 Correlation between eta.vc and eta.vp2
#> 47 Correlation between eta.vc and eta.q
#> 48 Correlation between eta.vc and eta.q2
#> 49 Correlation between eta.vp and eta.vp2
#> 50 Correlation between eta.vp and eta.q
#> 51 Correlation between eta.vp and eta.q2
#> 52 Correlation between eta.vp2 and eta.q
#> 53 Correlation between eta.vp2 and eta.q2
#> 54 Correlation between eta.q and eta.q2