Skip to contents

Workflow Setup and Execution

Workflow.Rmd

Typical Package Workflow

This vignette describes how to set up a workflow file and details the different sections of the workflow for the ospsuite.reportingframework package. It serves as a guide for users to effectively utilize the package for processing pharmacokinetic data.

Accessing the Workflow Template

To access the default workflow template provided by the package, you can use the following function:

This function opens the workflow template as a new document in your RStudio environment, allowing you to customize it for your specific needs. For detailed information on what each function in the workflow does, please refer to the help functionality in R.

Access via RStudio Addins

You can also access the workflow template through an RStudio Addin. To use the Addins, simply navigate to the Addins menu in RStudio and select “Open Template Workflow.” This will execute the openWorkflowTemplate() function and open the template in a new document.

Customizing the Workflow Template

By default, the workflow template is loaded from the package’s internal templates. If you wish to customize this template, follow these steps:

  1. Create your own workflow template script and save it with the name template_workflow.R.
  2. Place this file in your designated template directory.
  3. Set the path to your custom template by using the following option:
options(OSPSuite.RF.PathForWorkflowTemplate = "myTemplateDirectory")

After setting this option, calling openWorkflowTemplate() or using the Addins will open your customized template instead of the default one. You can save this option in your “.Rprofile” file (file.path(Sys.getenv("HOME"), ".Rprofile")) to set it automatically.

Project Initialization

The first step in the workflow is to initialize the project. This includes:

  • Loading necessary libraries.
  • Setting the workflow options.
  • Setting up the project directory and configuration files using the project structure of esqlabsR.
  • Initializing the log file.

Data Import

After initialization, the first step should always be data import. The input format for data is CSV files, which can be imported using a dictionary. The imported data types include individual and aggregated time profile data as well as individual and aggregated PK parameter data.

For more information, see Data Import by Dictionary.

Setting Up and Running Simulations Including PK Parameter Calculation

Simulations are set up and run using the esqlabsR package. For more information and detailed documentation, users can visit the esqlabsR Documentation.

The ospsuite.reportingframework package provides additional functionality to:

  • Export random and virtual twin populations (see the Population).
  • Calculate PK Parameters (see the PK Parameters).

Plot and Report Generation

The core functionality of this package lies in plot and report creation. It includes various plotting functions that generate visualizations based on the analyses performed.

Each plot function is designed to create an R Markdown (.Rmd) file, which contains the code and output for the respective plot. This allows for easy documentation and sharing of results.

The package provides a collection of plot functions and interfaces to adjust plots and utilize customized plot functions.

For more information, see the Plot and Report Generation.

Conclusion

This vignette has guided you through the setup and execution of workflows using the OSPSuite Reporting Framework. For further exploration, consult the linked vignettes and documentation.