Automated Population Pharmacokinetic Modeling

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Documentation for package ‘nlmixr2auto’ version 1.0.0

• DESCRIPTION file

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.twoBitCode	2-bit code helper
aco.operator	ACO operator for model selection
acoControl	Create control parameters for the ACO algorithm
add_covariate	Add a covariate effect to a parameter model
add_variability	Add inter-individual variability to a parameter
applyParamDeps	Apply parameter dependency rules
auto_param_table	Automatically generate a parameter table with initial estimates
base_model	Create a base model code for single-start model search algorithms
build_odeline	Build ODE model lines for pharmacokinetic modeling
create.pop	Create an initial GA population
createAnts	Create ant population for ACO
decodeBinary	Decode binary encoding to categorical encoding
detect_move	Detect the primary move between two model codes
encodeBinary	Encode categorical encoding to binary encoding
fitness	Evaluate fitness of a population pharmacokinetic model
ga.crossover	Crossover operator (one- or two-point) for binary chromosomes
ga.mutation	Mutation operator for binary genetic algorithms
ga.operator	Genetic algorithm operator for model selection
ga.sel.tournament	Tournament selection
gaControl	Control parameters for genetic algorithm
generate_neighbors_df	Generate neighbor models
get.mod.lst	Summarize parameter estimates and run information from an nlmixr2 fit
initialize_param	Initialize model parameters from parameter table
initialize_param_table	Generate initial parameter table for pharmacometric model estimation
initNodeList	Initialize node list for ACO search space
is_move_tabu	Check if a move is tabu
mod.run	Run population pharmacokinetic model with pre-defined search space
omega_block	Generate omega block Code for nlmixr2 model
p.calculation	Calculate selection probabilities for each node
param.bounds	Define Parameter Bounds for PK Models
parseName	Parse model coding vector to model name
parseParams	Parse string vector to model parameters
penaltyControl	Configure penalty settings for model evaluation
perturb_2bit	Apply 2-bit perturbation to escape local optimum
phi.calculate	Update pheromone levels for each decision node
ppkmodGen	Generate a Pharmacokinetic (PK) Model for nlmixr2
print.acoOperatorResult	Print method for ACO operator results
print.gaOperatorResult	Print method for gaOperatorResult objects
print.sfOperatorResult	Print method for sfOperatorResult objects
print.tabuOperatorResult	Print method for tabu operator results
rank_new	Ranking with significance difference threshold
runlocal	Perform 1-bit local search
run_model_in_subprocess	Run an nlmixr2 model in an isolated subprocess
sf.operator	Stepwise model building operator for model selection
spaceConfig	Get search space configuration
step_compartments	Screen number of compartments
step_correlation	Evaluate inclusion of ETA correlation structure
step_elimination	Screen elimination type (linear vs Michaelis-Menten)
step_iiv_f	Forward selection of IIV on structural parameters
step_iiv_ka	Evaluate inter-individual variability on Ka
step_iiv_km	Evaluate inter-individual variability on Km
step_rv	Evaluate residual error model structure
tabu.operator	Tabu search operator for model selection
tabuControl	Control Parameters for Tabu Search
validStringbinary	Validate and correct model string for GA
validStringcat	Validate and correct model string for ACO/TS