esqlabsR

The {esqlabsR} package facilitates and standardizes the modeling and simulation of physiologically based kinetic (PBK) and quantitative systems pharmacology/toxicology (QSP/T) models implemented in the Open Systems Pharmacology Software (OSPS).

The {esqlabsR} package is designed for PBK modelers who use the OSPS suite. By using this package, you can streamline your modeling and simulation (M&S) workflow and ensure standardized and reproducible practices.

The package provides functions to:

• Design, import and run Simulations,
• Generate standardized plots and other reporting materials,
• Interact with the OSPS features using simple Excel files.

To get started with the esqlabsR package, please follow the Get Started tutorial.

Installation

Pre-requisites

• For Windows
• For Linux

Install the package

You can install the package by running:

install.packages("pak")
pak::pak("esqLABS/esqlabsR@*release")

Get the latest development version with:

pak::pak("esqLABS/esqlabsR")

Note: For projects created for version 3 of esqlabsR package, install esqlabsRLegacy.

Usage

You can start with the “Get Started” vignette: vignette("esqlabsR"). Below is a simple example of how to work with the package:

# load esqlabsR
library(esqlabsR)

# Load excel-based configuration
my_project_configuration <-
  createProjectConfiguration(example_ProjectConfiguration())


# Setup simulation scenarios
my_scenarios <-
  createScenarios(
    readScenarioConfigurationFromExcel( # Read scenarios from excel file
      scenarioNames = "TestScenario", # Import the scenario defined as "TestScenario"
      # in the excel file
      projectConfiguration = my_project_configuration
    )
  )

# Run simulations
my_simulation <- runScenarios(
  scenarios = my_scenarios
)

# Initialize a `DataCombined` object to store simulation results
my_datacombined <- DataCombined$new()

my_datacombined$addSimulationResults(my_simulation$TestScenario$results,
  names = "Simulated",
  groups = "Aciclovir"
)

# Plot simulation results
plotIndividualTimeProfile(my_datacombined)

Learn More

You can find more information on specific topics in dedicated vignettes:

• Start with vignette("esqlabsR-workflow-overview") to learn about the esqlabsR’s streamlined workflow.
• vignette("esqlabsR-project-structure") details the structure and purpose of each component file and directory of an esqlabsR project.
• vignette("esqlabsR-design-scenarios") explains how you can design your own simulations only using excel files.
• vignette("esqlabsR-run-simulations") describes all you need to know to run your customized simulations.
• vignette("esqlabsR-plot-results") explains how to generate visualizations from simulations.

Related Work

{esqlabsR} relies on the following Open Systems Pharmacology R packages:

• rSharp
• ospsuite.utils
• tlf
• ospsuite

Contributing

• Follow the OSPS-R coding standards.
• Our contribution guide can be found here.

Code of Conduct

Please note that the esqlabsR project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.