Package: Certara.RDarwin 1.1.1

Certara.RDarwin: Interface for 'pyDarwin' Machine Learning Pharmacometric Model Development

Utilities that support the usage of 'pyDarwin' (<https://certara.github.io/pyDarwin/>) for ease of setup and execution of a machine learning based pharmacometric model search with Certara's Non-Linear Mixed Effects (NLME) modeling engine.

Authors:Michael Tomashevskiy [aut], James Craig [aut, cre], Certara USA, Inc [cph, fnd]

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Certara.RDarwin.pdf |Certara.RDarwin.html✨
Certara.RDarwin/json (API)

# Install 'Certara.RDarwin' in R:
install.packages('Certara.RDarwin', repos = c('https://certara-jcraig.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/certara/r-darwin/issues

Pkgdown site:https://certara.github.io

On CRAN:

Conda:

1.70 score 45 exports 2 dependencies

Last updated 16 days agofrom:7f36cc9121. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 26 2025
R-4.5-winOKFeb 26 2025
R-4.5-macOKFeb 26 2025
R-4.5-linuxOKFeb 26 2025
R-4.4-winOKFeb 26 2025
R-4.4-macOKFeb 26 2025
R-4.3-winOKFeb 26 2025
R-4.3-macOKFeb 26 2025

Exports:add_Covariateadd_CustomSpaceadd_StParmCovariatecreate_CustomSpacecreate_ModelEmaxcreate_ModelPDcreate_ModelPKcreate_pyDarwinOptionsDosepointget_ModelTermsToMapget_PMLParametersSetsInitialEstimatelist_Covariateslist_Dosepointslist_Observationslist_Omegaslist_StParmslist_Thetasmodify_Dosepointmodify_Observationmodify_Omegamodify_StParmmodify_StParmCustommodify_ThetaObservationOmegapyDarwinOptionsGApyDarwinOptionsGridAdapterpyDarwinOptionsPenaltypyDarwinOptionsPostprocesspyDarwinOptionsPSOremove_Covariateremove_Observationremove_StParmrun_pyDarwinSigmasspecify_EngineParamsspecify_SimParamsstop_pyDarwinStParmTableThetawrite_ModelTemplateTokenswrite_pyDarwinOptions

Dependencies:jsonlitemagrittr

Readme and manuals

Help Manual

Help pageTopics
Add Covariate into PML modelsadd_Covariate
Add a Custom Spaceadd_CustomSpace
Add Structural parameter into PML models Dosepointsadd_StParm
Create a new Covariate object and validate itCovariate
Create a Custom Spacecreate_CustomSpace
Get the list of objects describing the PML models by set of Emax parameterscreate_ModelEmax
Get the list of objects describing the PML models by set of PD parameterscreate_ModelPD
Get the list of objects describing the PML models by set of PK parameterscreate_ModelPK get_PMLParametersSets
Create pyDarwin Optionscreate_pyDarwinOptions
Create a new Dosepoint object and validate itDosepoint
Get Model Terms to Mapget_ModelTermsToMap
Create an object of class InitialEstimateInitialEstimate
List Covariates in the currrent PML setlist_Covariates
List Dosepoints in the current PML setlist_Dosepoints
List Observations in the current PML setlist_Observations
List Unique Omega Nameslist_Omegas
List Structural Parameters in the currrent PML setlist_StParms
List Unique Theta Nameslist_Thetas
Modify Dosepoint in PML modelsmodify_Dosepoint
Modify Observation class in PML modelsmodify_Observation
Modify Omega Parameters in PML Modelsmodify_Omega
Modify structural parameter in PML models setmodify_StParm
Modify custom structural parameter in PML spacesmodify_StParmCustom
Modify Theta Parameters in PML Modelsmodify_Theta
Create an instance of Observation class.Observation
Create an instance of custom Observation class.ObservationCustom
Create an Omega instance with validationOmega
Output a Custom Spaceoutput.CustomSpace
Create options for the Genetic Algorithm (GA) in pyDarwin.pyDarwinOptionsGA
Grid Adapter Options for pyDarwinpyDarwinOptionsGridAdapter
Create pyDarwin Penalty OptionspyDarwinOptionsPenalty
Create pyDarwin Postprocess OptionspyDarwinOptionsPostprocess
Create options for the Particle Swarm Optimization (PSO) in pyDarwin.pyDarwinOptionsPSO
Remove Covariate from PML modelsremove_Covariate
Remove Observation from PML modelsremove_Observation
Remove structural parameter from PML modelsremove_StParm
Run pyDarwin Model Searchrun_pyDarwin
Create an instance of Sigmas class.Sigmas
Specify engine parameters for model executionspecify_EngineParams
Specify engine parameters for model simulationspecify_SimParams
Stop pyDarwin Model Searchstop_pyDarwin
Create an instance of a Structural parameter.StParm
Class initializer for NLME tablesTable
Create a new Theta instance with validation.Theta
Prints NLME metamodel template file and token json file using given options, filepaths and datawrite_ModelTemplateTokens
Write pyDarwin options to a JSON file.write_pyDarwinOptions