ppkmodGen: Generate a Pharmacokinetic (PK) Model for nlmixr2

Description

Constructs a PK model based on specified parameters, absorption characteristics, variability components, and residual error models. The model is generated as a text file compatible with nlmixr syntax. The function handles various absorption types, multi-compartment models, Michaelis-Menten kinetics, and different residual variability structures.

Usage

ppkmodGen(
  modi = 1,
  route = "bolus",
  no.cmpt = 1,
  abs.bio = 0,
  abs.type = 1,
  abs.delay = 0,
  eta.ka = 0,
  eta.cl = 0,
  eta.vc = 0,
  eta.vp = 0,
  eta.vp2 = 0,
  eta.q = 0,
  eta.q2 = 0,
  mm = 0,
  eta.vmax = 0,
  eta.km = 0,
  eta.tlag = 0,
  eta.n = 0,
  eta.mtt = 0,
  eta.bio = 0,
  eta.D2 = 0,
  eta.F1 = 0,
  eta.Fr = 0,
  mcorr = 0,
  rv = 1,
  allometric_scaling = 0,
  param_table = NULL,
  return.func = FALSE,
  out.dir = NULL,
  verbose = TRUE
)

Value

Generates a text file ('modX.txt' where X = modi) containing the nlmixr-compatible model code. The file is written to the current working directory. No explicit return value. If return.func = TRUE, returns a compiled model function object.

Arguments

modi: Model identification number (default: 1). Used for generating unique model filenames.
route: Administration route. Valid options: "bolus", "oral", "mixed_iv_oral" (default: "bolus").
no.cmpt: Number of compartments in the model (1, 2, or 3) (default: 1).
abs.bio: Bioavailability flag (0 = no bioavailability, 1 = with bioavailability) (default: 0).
abs.type: Absorption type (1 = first-order, 2 = zero-order, 3 = sequential first-order and zero-order absorption, 4 = dual first-order and zero-order absorption) (default: 1).
abs.delay: Absorption delay type (0 = none, 1 = lag time, 2 = transit compartments) (default: 0).
eta.ka: Variability flag for absorption rate (ka) (0 = no variability, 1 = include variability).
eta.cl: Variability flag for clearance (CL) (0 = no variability, 1 = include variability).
eta.vc: Variability flag for central volume (Vc) (0 = no variability, 1 = include variability).
eta.vp: Variability flag for peripheral volume (Vp) in multi-compartment models.
eta.vp2: Variability flag for second peripheral volume (Vp2) in 3-compartment models.
eta.q: Variability flag for intercompartmental clearance (Q) in multi-compartment models.
eta.q2: Variability flag for second intercompartmental clearance (Q2) in 3-compartment models.
mm: Michaelis-Menten kinetics flag (0 = linear kinetics, 1 = Michaelis-Menten kinetics).
eta.vmax: Variability flag for Vmax when using Michaelis-Menten kinetics.
eta.km: Variability flag for Km when using Michaelis-Menten kinetics.
eta.tlag: Variability flag for lag time (tlag) when abs.delay=1.
eta.n: Variability flag for number of transit compartments when abs.delay=2.
eta.mtt: Variability flag for mean transit time when abs.delay=2.
eta.bio: Variability flag for bioavailability when abs.delay=2.
eta.D2: Variability flag for zero-order duration (D2) when abs.type=2 or 3.
eta.F1: Variability flag for bioavailability fraction (F1) when abs.bio=1.
eta.Fr: Variability flag for absorption fraction (Fr) when abs.type=4.
mcorr: Correlation flag for omega blocks (0 = no correlation, 1 = include correlations).
rv: Residual variability type (1 = additive, 2 = proportional, 3 = combined, 4 = log-normal).
allometric_scaling: Allometric scaling type (0 = none, 1 = weight, 2 = BMI, 3 = FFM).
param_table: Data frame containing parameter initial values and variability components. Should contain columns: Name (parameter name), init (initial value), eta (TRUE/FALSE for variability inclusion), cov (covariate relationships).
return.func: Logical, whether to return a compiled function (default FALSE returns model code as text).
out.dir: Directory where model files and results are written. Defaults to the current working directory when not provided.
verbose: Logical; if TRUE, progress messages are printed.

Author

Zhonghui Huang

Examples

Run this code

withr::with_dir(tempdir(), {
#' # Create a 1-compartment oral model with first-order absorption
 ppkmodGen( no.cmpt = 1, abs.type = 1,return.func = TRUE,param_table = initialize_param_table())
})

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