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nlmixr2auto (version 1.0.0)

Automated Population Pharmacokinetic Modeling

Description

Automated population pharmacokinetic modeling framework for data-driven initialisation, model evaluation, and metaheuristic optimization. Supports genetic algorithms, ant colony optimization, tabu search, and stepwise procedures for automated model selection and parameter estimation within the nlmixr2 ecosystem.

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Version

Install

install.packages('nlmixr2auto')

Version

1.0.0

License

GPL (>= 3)

Issues

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Repository

https://github.com/ucl-pharmacometrics/nlmixr2auto

Maintainer

Zhonghui Huang

Last Published

February 6th, 2026

Functions in nlmixr2auto (1.0.0)

Initialize node list for ACO search space

Define Parameter Bounds for PK Models

Run population pharmacokinetic model with pre-defined search space

generate_neighbors_df

Generate neighbor models

initialize_param

Initialize model parameters from parameter table

Calculate selection probabilities for each node

initialize_param_table

Generate initial parameter table for pharmacometric model estimation

Summarize parameter estimates and run information from an nlmixr2 fit

Generate omega block Code for nlmixr2 model

Check if a move is tabu

Update pheromone levels for each decision node

Apply 2-bit perturbation to escape local optimum

Parse string vector to model parameters

print.sfOperatorResult

Print method for sfOperatorResult objects

print.acoOperatorResult

Print method for ACO operator results

Configure penalty settings for model evaluation

Generate a Pharmacokinetic (PK) Model for nlmixr2

print.gaOperatorResult

Print method for gaOperatorResult objects

Parse model coding vector to model name

print.tabuOperatorResult

Print method for tabu operator results

Ranking with significance difference threshold

step_correlation

Evaluate inclusion of ETA correlation structure

step_elimination

Screen elimination type (linear vs Michaelis-Menten)

Stepwise model building operator for model selection

Get search space configuration

Perform 1-bit local search

step_compartments

Screen number of compartments

run_model_in_subprocess

Run an nlmixr2 model in an isolated subprocess

Evaluate inter-individual variability on Ka

Forward selection of IIV on structural parameters

validStringbinary

Validate and correct model string for GA

Tabu search operator for model selection

Evaluate inter-individual variability on Km

Control Parameters for Tabu Search

Validate and correct model string for ACO/TS

Evaluate residual error model structure

add_variability

Add inter-individual variability to a parameter

Create control parameters for the ACO algorithm

Build ODE model lines for pharmacokinetic modeling

Create a base model code for single-start model search algorithms

Add a covariate effect to a parameter model

Create ant population for ACO

Apply parameter dependency rules

ACO operator for model selection

auto_param_table

Automatically generate a parameter table with initial estimates

Create an initial GA population

Control parameters for genetic algorithm

Evaluate fitness of a population pharmacokinetic model

Crossover operator (one- or two-point) for binary chromosomes

ga.sel.tournament

Tournament selection

Genetic algorithm operator for model selection

Mutation operator for binary genetic algorithms

2-bit code helper

Encode categorical encoding to binary encoding

Detect the primary move between two model codes

Decode binary encoding to categorical encoding