Package: Certara.RDarwin 1.2.0

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]

Certara.RDarwin_1.2.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
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/docs site:https://certara.github.io

On CRAN:

Conda:

1.70 score 150 downloads 53 exports 8 dependencies

Last updated from:60e583b108. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK184
source / vignettesOK268
linux-release-x86_64OK170
macos-release-arm64OK125
macos-oldrel-arm64OK83
windows-develOK120
windows-releaseOK114
windows-oldrelOK115
wasm-releaseOK148

Exports:add_Covariateadd_CustomSpaceadd_Dosepointadd_Spacesadd_StParmCovariatecreate_CustomSpacecreate_ModelEmaxcreate_ModelPDcreate_ModelPKcreate_pyDarwinOptionsDosepointExpressionget_ModelTermsToMapget_PMLParametersSetsInitialEstimatelist_Covariateslist_Dosepointslist_Observationslist_Omegaslist_StParmslist_Thetasmodify_Dosepointmodify_Observationmodify_Omegamodify_StParmmodify_StParmCustommodify_ThetaObservationOmegaoutput_NLMETemplatepyDarwinOptionsGApyDarwinOptionsGridAdapterpyDarwinOptionsMOGApyDarwinOptionsPenaltypyDarwinOptionsPostprocesspyDarwinOptionsPSOreconnect_pyDarwinJobremove_Covariateremove_Observationremove_StParmrun_pyDarwinrun_pyDarwinRemoteSigmasspecify_EngineParamsspecify_SimParamsstop_pyDarwinstop_pyDarwinRemoteStParmTableThetawrite_ModelTemplateTokenswrite_pyDarwinOptions

Dependencies:askpasscredentialscurljsonlitemagrittropensslsshsys

Readme and manuals

Help Manual

Help pageTopics
Add Covariate into PML modelsadd_Covariate
Add a Custom Space to a PMLModels Objectadd_CustomSpace
Add Dosepoint in PML modelsadd_Dosepoint
Add Multiple Model Spaces to a PMLModels Objectadd_Spaces
Add Structural parameter into PML models Dosepointsadd_StParm
Create a new Covariate object and validate itCovariate
Create a Custom Space (PML Model) from Codecreate_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
Create an Expression objectExpression
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
Generate NLME Model Template from JSON Specificationoutput_NLMETemplate
Output a Custom Spaceoutput.CustomSpace
Create options for the Genetic Algorithm (GA) in pyDarwin.pyDarwinOptionsGA
Grid Adapter Options for pyDarwinpyDarwinOptionsGridAdapter
Create Options for the pyDarwin MOGA BlockpyDarwinOptionsMOGA
Create pyDarwin Penalty OptionspyDarwinOptionsPenalty
Create pyDarwin Postprocess OptionspyDarwinOptionsPostprocess
Create options for the Particle Swarm Optimization (PSO) in pyDarwin.pyDarwinOptionsPSO
Reconnect, Monitor, and Retrieve Results from a Remote pyDarwin Jobreconnect_pyDarwinJob
Remove Covariate from PML modelsremove_Covariate
Remove Observation from PML modelsremove_Observation
Remove structural parameter from PML modelsremove_StParm
Run pyDarwin Model Searchrun_pyDarwin
Run pyDarwin on a Remote Host via SSHrun_pyDarwinRemote
Create an instance of Sigmas class.Sigmas
Specify Engine Parameters for NLME Model Executionspecify_EngineParams
Specify Engine Parameters for Model Simulationspecify_SimParams
Stop pyDarwin Model Searchstop_pyDarwin
Stop a Remote pyDarwin Jobstop_pyDarwinRemote
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