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")
.
Currently, esqlabsR is available only for Windows system. You can install the package by running:
# {esqlabsR} and its Open Systems Pharmacology Suite's dependencies relies on
# {rClr} (https://github.com/Open-Systems-Pharmacology/rClr) which is not
# available on CRAN.
# Therefore, these must be installed from github using `{remotes}`.
install.packages("remotes")
install.packages("https://github.com/Open-Systems-Pharmacology/rClr/releases/download/v0.9.2/rClr_0.9.2.zip",
repos = NULL,
type = "binary"
)
remotes::install_github("esqLABS/esqlabsR@*release")
Get the latest development version with:
remotes::install_github("esqLABS/esqlabsR")
Note: For projects created for version 3 of esqlabsR
package, install
esqlabsRLegacy
.
# 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)
To get started, first read vignette("esqlabsR")
. Then read more about
the specific topics:
- 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.
{esqlabsR}
relies on the following Open Systems Pharmacology R
packages:
- Follow the OSPS-R coding standards.
- Some additional useful information can be found here.
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.