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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')

Version

1.1.1

License

LGPL-3

Maintainer

James Craig

Last Published

February 25th, 2025

Functions in Certara.RDarwin (1.1.1)

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

InitialEstimate

Create an object of class InitialEstimate

Create an instance of Observation class.

create_ModelEmax

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

Create a new Covariate object and validate it

Create a new Dosepoint object and validate it

List Unique Omega Names

List Structural Parameters in the currrent PML set

Add Structural parameter into PML models Dosepoints

remove_Observation

Remove Observation from PML models

Modify structural parameter in PML models set

modify_StParmCustom

Modify custom structural parameter in PML spaces

Remove structural parameter from PML models

create_CustomSpace

Create a Custom Space

specify_SimParams

Specify engine parameters for model simulation

Stop pyDarwin Model Search

modify_Observation

Modify Observation class in PML models

pyDarwinOptionsPostprocess

Create pyDarwin Postprocess Options

List Unique Theta Names

ObservationCustom

Create an instance of custom Observation class.

Create an instance of a Structural parameter.

Create an instance of Sigmas class.

modify_Dosepoint

Modify Dosepoint in PML models

specify_EngineParams

Specify engine parameters for model execution

remove_Covariate

Remove Covariate from PML models

Add Covariate into PML models

output.CustomSpace

Output a Custom Space

Modify Omega Parameters in PML Models

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

Run pyDarwin Model Search

Create an Omega instance with validation

add_CustomSpace

Add a Custom Space

Modify Theta Parameters in PML Models

pyDarwinOptionsGA

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

list_Dosepoints

List Dosepoints in the current PML set

pyDarwinOptionsPSO

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

list_Observations

List Observations in the current PML set

pyDarwinOptionsPenalty

Create pyDarwin Penalty Options

write_ModelTemplateTokens

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

create_pyDarwinOptions

Create pyDarwin Options

write_pyDarwinOptions

Write pyDarwin options to a JSON file.

pyDarwinOptionsGridAdapter

Grid Adapter Options for pyDarwin

Create a new Theta instance with validation.

Class initializer for NLME tables

get_ModelTermsToMap

Get Model Terms to Map

list_Covariates

List Covariates in the currrent PML set