Package: nlmixr2auto 1.0.0

Zhonghui Huang

nlmixr2auto: Automated Population Pharmacokinetic Modeling

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.

Authors:Zhonghui Huang [aut, cre], Joseph Standing [ctb], Matthew Fidler [ctb], Frank Kloprogge [ctb]

nlmixr2auto_1.0.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
nlmixr2auto/json (API)

# Install 'nlmixr2auto' in R:
install.packages('nlmixr2auto', repos = c('https://ucl-pharmacometrics.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ucl-pharmacometrics/nlmixr2auto/issues

On CRAN:

Conda:

3.60 score 1 stars 510 downloads 52 exports 158 dependencies

Last updated from:f361ec7c97. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK201
source / vignettesOK221
linux-releaseOK195
macos-releaseOK170
macos-oldrelOK401
windows-develOK818
windows-releaseOK852
windows-oldrelOK644
wasm-releaseOK165

Exports:.twoBitCodeaco.operatoracoControladd_covariateadd_variabilityapplyParamDepsauto_param_tablebase_modelbuild_odelinecreate.popcreateAntsdecodeBinarydetect_moveencodeBinaryfitnessga.crossoverga.mutationga.operatorga.sel.tournamentgaControlgenerate_neighbors_dfget.mod.lstinitialize_paraminitialize_param_tableinitNodeListis_move_tabumod.runomega_blockp.calculationparam.boundsparseNameparseParamspenaltyControlperturb_2bitphi.calculateppkmodGenrank_newrun_model_in_subprocessrunlocalsf.operatorspaceConfigstep_compartmentsstep_correlationstep_eliminationstep_iiv_fstep_iiv_kastep_iiv_kmstep_rvtabu.operatortabuControlvalidStringbinaryvalidStringcat

Dependencies:armadillo4raskpassassertthatbackportsbase64encBHbinombitbit64bitopsbootbslibcachemcellrangercheckmateclassclassIntclicliprclisymbolsclustercolorspacecpp11cpp4rcrayoncurldata.tableDerivDescToolsdigestdparserdplyre1071evaluateExactexpmfarverfastmapfontawesomeforcatsforeignFormulafsgenericsggforceggplot2ggtibblegldgluegridExtragtablehavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrinlineisobandjquerylibjsonliteKernSmoothknitrL0Learnlabelinglatticelbfgsb3clifecyclelmomlotrimagrittrMASSMatrixmemoisemimeminpack.lmminqamiraimvtnormn1qn1nanonextnlmenlmixr2nlmixr2autoinitnlmixr2datanlmixr2estnlmixr2extranlmixr2plotnlmixr2savennetnumDerivopensslpanderpillarpkgconfigplyrpngpolyclipPreciseSumsprettyunitsprocessxprogressprogressrproxypspurrrqs2R6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRcppTrustRCurlreadrreadxlrematchreshape2rexrlangrmarkdownrootSolverpartrstudioapirxode2rxode2llS7sassscalessitmoStanHeadersstringfishstringistringrsurvivalsymenginesyssystemfontstibbletidyrtidyselecttinytextweenrtzdbutf8vctrsviridisLitevpcvroomwithrxfunxgxryamlzip

Readme and manuals

Help Manual

Help pageTopics
2-bit code helper.twoBitCode
ACO operator for model selectionaco.operator
Create control parameters for the ACO algorithmacoControl
Add a covariate effect to a parameter modeladd_covariate
Add inter-individual variability to a parameteradd_variability
Apply parameter dependency rulesapplyParamDeps
Automatically generate a parameter table with initial estimatesauto_param_table
Create a base model code for single-start model search algorithmsbase_model
Build ODE model lines for pharmacokinetic modelingbuild_odeline
Create an initial GA populationcreate.pop
Create ant population for ACOcreateAnts
Decode binary encoding to categorical encodingdecodeBinary
Detect the primary move between two model codesdetect_move
Encode categorical encoding to binary encodingencodeBinary
Evaluate fitness of a population pharmacokinetic modelfitness
Crossover operator (one- or two-point) for binary chromosomesga.crossover
Mutation operator for binary genetic algorithmsga.mutation
Genetic algorithm operator for model selectionga.operator
Tournament selectionga.sel.tournament
Control parameters for genetic algorithmgaControl
Generate neighbor modelsgenerate_neighbors_df
Summarize parameter estimates and run information from an nlmixr2 fitget.mod.lst
Initialize model parameters from parameter tableinitialize_param
Generate initial parameter table for pharmacometric model estimationinitialize_param_table
Initialize node list for ACO search spaceinitNodeList
Check if a move is tabuis_move_tabu
Run population pharmacokinetic model with pre-defined search spacemod.run
Generate omega block Code for nlmixr2 modelomega_block
Calculate selection probabilities for each nodep.calculation
Define Parameter Bounds for PK Modelsparam.bounds
Parse model coding vector to model nameparseName
Parse string vector to model parametersparseParams
Configure penalty settings for model evaluationpenaltyControl
Apply 2-bit perturbation to escape local optimumperturb_2bit
Update pheromone levels for each decision nodephi.calculate
Generate a Pharmacokinetic (PK) Model for nlmixr2ppkmodGen
Print method for ACO operator resultsprint.acoOperatorResult
Print method for gaOperatorResult objectsprint.gaOperatorResult
Print method for sfOperatorResult objectsprint.sfOperatorResult
Print method for tabu operator resultsprint.tabuOperatorResult
Ranking with significance difference thresholdrank_new
Run an nlmixr2 model in an isolated subprocessrun_model_in_subprocess
Perform 1-bit local searchrunlocal
Stepwise model building operator for model selectionsf.operator
Get search space configurationspaceConfig
Screen number of compartmentsstep_compartments
Evaluate inclusion of ETA correlation structurestep_correlation
Screen elimination type (linear vs Michaelis-Menten)step_elimination
Forward selection of IIV on structural parametersstep_iiv_f
Evaluate inter-individual variability on Kastep_iiv_ka
Evaluate inter-individual variability on Kmstep_iiv_km
Evaluate residual error model structurestep_rv
Tabu search operator for model selectiontabu.operator
Control Parameters for Tabu SearchtabuControl
Validate and correct model string for GAvalidStringbinary
Validate and correct model string for ACO/TSvalidStringcat