R: Automated Population Pharmacokinetic Modeling

# Automated Population Pharmacokinetic Modeling

## Documentation for package ‘nlmixr2auto’ version 1.0.0

- DESCRIPTION file

## Help Pages

.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