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 read the vignette("esqlabsR").

Installation

Pre-requisites

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 <-
  createDefaultProjectConfiguration(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:

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.

esqLABS / esqlabsR

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