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RDarwin

Overview

RDarwin is an R package designed to facilitate the usage of pyDarwin with the Certara NLME pharmacometric modeling engine from the R command line. The Python package, pyDarwin, is a powerful tool for using machine learning algorithms for model selection.

RDarwin defines a structure for NLME-pyDarwin usage by providing a set of R functions that can be used to specify search options across observation, dosepoints, structural parameters, fixed effects (thetas), random effects (omegas), and covariate effects. Additionally, users may execute a pyDarwin search directly from R using the function run_pyDarwin() (supports both NLME and NONMEM modeling engines).

Installation

install.packages("Certara.RDarwin", 
  repos = c("https://certara.jfrog.io/artifactory/certara-cran-release-public/", 
  "https://cloud.r-project.org"), method = "libcurl")

*Note: Additional installation of pyDarwin and Certara's NLME-Engine used by RsNLME is required. * Request NLME-Engine.

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Version

Install

install.packages('Certara.RDarwin')

Monthly Downloads

128

Version

1.2.0

License

LGPL-3

Maintainer

James Craig

Last Published

December 1st, 2025

Functions in Certara.RDarwin (1.2.0)

Get the list of objects describing the PML models by set of PD parameters

Add Multiple Model Spaces to a PMLModels Object

Add Structural parameter into PML models Dosepoints

create_CustomSpace

Create a Custom Space (PML Model) from Code

Add Covariate into PML models

Add Dosepoint in PML models

add_CustomSpace

Add a Custom Space to a PMLModels Object

Create a new Theta instance with validation.

Get the list of objects describing the PML models by set of PK parameters

create_ModelEmax

Get the list of objects describing the PML models by set of Emax parameters

get_ModelTermsToMap

Get Model Terms to Map

create_pyDarwinOptions

Create pyDarwin Options

List Unique Omega Names

list_Observations

List Observations in the current PML set

modify_Dosepoint

Modify Dosepoint in PML models

modify_Observation

Modify Observation class in PML models

List Structural Parameters in the currrent PML set

List Unique Theta Names

list_Covariates

List Covariates in the currrent PML set

list_Dosepoints

List Dosepoints in the current PML set

output_NLMETemplate

Generate NLME Model Template from JSON Specification

pyDarwinOptionsMOGA

Create Options for the pyDarwin MOGA Block

Modify structural parameter in PML models set

output.CustomSpace

Output a Custom Space

Modify Omega Parameters in PML Models

pyDarwinOptionsGridAdapter

Grid Adapter Options for pyDarwin

pyDarwinOptionsGA

Create options for the Genetic Algorithm (GA) in pyDarwin.

Modify Theta Parameters in PML Models

pyDarwinOptionsPSO

Create options for the Particle Swarm Optimization (PSO) in pyDarwin.

modify_StParmCustom

Modify custom structural parameter in PML spaces

pyDarwinOptionsPostprocess

Create pyDarwin Postprocess Options

remove_Covariate

Remove Covariate from PML models

run_pyDarwinRemote

Run pyDarwin on a Remote Host via SSH

specify_SimParams

Specify Engine Parameters for Model Simulation

Run pyDarwin Model Search

reconnect_pyDarwinJob

Reconnect, Monitor, and Retrieve Results from a Remote pyDarwin Job

specify_EngineParams

Specify Engine Parameters for NLME Model Execution

remove_Observation

Remove Observation from PML models

Remove structural parameter from PML models

pyDarwinOptionsPenalty

Create pyDarwin Penalty Options

stop_pyDarwinRemote

Stop a Remote pyDarwin Job

Stop pyDarwin Model Search

write_pyDarwinOptions

Write pyDarwin options to a JSON file.

write_ModelTemplateTokens

Prints NLME metamodel template file and token json file using given options, filepaths and data

Create an Expression object

InitialEstimate

Create an object of class InitialEstimate

Create an Omega instance with validation

Create an instance of Sigmas class.

Create a new Covariate object and validate it

Create a new Dosepoint object and validate it

Create an instance of Observation class.

ObservationCustom

Create an instance of custom Observation class.

Create an instance of a Structural parameter.

Class initializer for NLME tables