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README.Rmd
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README.Rmd
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---
output:
github_document:
df_print: "kable"
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
message = FALSE,
warning = FALSE
)
library(tidyr)
library(dplyr)
```
# esqlabsR <a href="https://esqlabs.github.io/esqlabsR/"><img src="man/figures/logo.png" align="right" height="139" alt="esqlabsR website" /></a>
<!-- badges: start -->
[](https://github.com/esqlabs/esqlabsR/actions/workflows/main-workflow.yaml)
[](https://app.codecov.io/gh/esqlabs/esqlabsR?branch=main)
<!-- badges: end -->
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](https://www.open-systems-pharmacology.org/) (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
Currently, esqlabsR is available only for Windows system. You can install the package by running:
```{r, eval=FALSE}
install.packages("pak")
pak::pak("esqLABS/esqlabsR@*release")
```
Get the latest development version with:
```{r, eval=FALSE}
pak::pak("esqLABS/esqlabsR")
```
Note: For projects created for version 3 of `esqlabsR` package, install [`esqlabsRLegacy`](https://github.com/esqLABS/esqlabsRLegacy).
## Usage
```{r, include=FALSE}
showtext::showtext_opts(dpi = 300)
```
```{r, out.width="80%", fig.align="center", fig.width=5, fig.asp=0.618, dpi=300}
# 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
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.
## Related Work
`{esqlabsR}` relies on the following Open Systems Pharmacology R packages:
- [rSharp](https://github.com/Open-Systems-Pharmacology/rSharp/)
- [ospsuite.utils](https://github.com/Open-Systems-Pharmacology/OSPSuite.RUtils)
- [tlf](https://github.com/Open-Systems-Pharmacology/TLF-Library)
- [ospsuite](https://github.com/Open-Systems-Pharmacology/OSPSuite-R)
- [ospsuite.parameteridentification](https://github.com/Open-Systems-Pharmacology/OSPSuite.ParameterIdentification)
## Contributing
- Follow the OSPS-R [coding standards](https://dev.open-systems-pharmacology.org/r-development-resources/coding_standards_r).
- Our contribution guide can be found [here](https://dev.open-systems-pharmacology.org/r-development-resources/collaboration_guide).
## Code of Conduct
Please note that the esqlabsR project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.