1. Initialize a Project

Initialize the Project Structure

Project Structure can be initialized by calling the function init_project().

library(esqlabsR)

init_project()

This will create a set of directories and files that match the expected project’s structure.

#> /home/runner/work/_temp/Library/esqlabsR/extdata/examples/TestProject
#> ├── Code
#> │   ├── DoNotSource
#> │   ├── InputCode
#> │   ├── Scenarios
#> │   └── utils
#> ├── Data
#> │   ├── Digitized Figures
#> │   ├── PKML
#> │   ├── TestProject_TimeValuesData.xlsx
#> │   └── esqlabs_dataImporter_configuration.xml
#> ├── Models
#> │   ├── PKML
#> │   ├── Simulations
#> │   │   └── Aciclovir.pkml
#> │   └── Snapshots
#> ├── Parameters
#> │   ├── ApplicationParameters.xlsx
#> │   ├── Individuals.xlsx
#> │   ├── ModelParameters.xlsx
#> │   ├── Plots.xlsx
#> │   ├── PopulationParameters.xlsx
#> │   ├── Populations
#> │   │   └── TestPopulation.csv
#> │   └── Scenarios.xlsx
#> ├── ProjectConfiguration.xlsx
#> └── Results
#>     ├── All plots.png
#>     ├── Figures
#>     └── SimulationResults

Create a ProjectConfiguration

The ProjectConfiguration stores the paths to the model-, data-, and other files and directories. It will be used at several steps in esqlabsR workflows so it needs to be created before performing any simulations.

By printing the ProjectConfiguration, we can see the locations of all files used in the workflows:

my_project_configuration <- createDefaultProjectConfiguration(path = example_ProjectConfiguration())

Now that the project structure is initialized and the ProjectConfiguration is created, read vignette("esqlabsR-design-scenarios") to continue the process. To learn more about ProjectConfiguration, read the following sections.

Details

Change ProjectConfiguration from R

If required, you can change the location of one of the files or folders using relative or absolute paths

# change the location of the output folder
projectConfiguration$outputFolder <- "../anotherOutputFolder"

# change the location of the model parameters file
projectConfiguration$modelParametersFile <- "absolute/path/to/anotherModelParameters.xlsx"

About ProjectConfiguration.xlsx

The ProjectConfiguration.xlsx file will be used by esqlabsR to generate a ProjectConfiguration object which is the central piece of a project. It should be located in the root folder of the project.

This file defines where all the necessary files are stored in the project folder. All the path specified in the Value column should be relative to the ProjectConfiguration.xlsx location.

All these directories and files have a specific purpose and template and are describe in next sections.