devtools::load_all()
#> ℹ Loading esqlabsR
#> Loading required package: ospsuite
#> 
#> Loading required package: rClr
#> 
#> Loading the dynamic library for Microsoft .NET runtime...
#> Loaded Common Language Runtime version 4.0.30319.42000

# Create a project
p <- testProject()

# Project Overview
p
#> 
#> ── Project Configuration ───────────────────────────────────────────────────────
#>   • Project Configuration:
#>   'inst/extdata/examples/TestProject/ProjectConfiguration.xlsx'
#>   • Model folder: 'inst/extdata/examples/TestProject/Models/Simulations'
#>   • Configurations folder: 'inst/extdata/examples/TestProject/Configurations'
#>   • Model Parameters:
#>   'inst/extdata/examples/TestProject/Configurations/ModelParameters.xlsx'
#>   • Individuals:
#>   'inst/extdata/examples/TestProject/Configurations/Individuals.xlsx'
#>   • Populations:
#>   'inst/extdata/examples/TestProject/Configurations/Populations.xlsx'
#>   • PopulationsCSV:
#>   'inst/extdata/examples/TestProject/Configurations/PopulationsCSV'
#>   • Scenarios:
#>   'inst/extdata/examples/TestProject/Configurations/Scenarios.xlsx'
#>   • Applications:
#>   'inst/extdata/examples/TestProject/Configurations/Applications.xlsx'
#>   • Plots: 'inst/extdata/examples/TestProject/Configurations/Plots.xlsx'
#>   • Data folder: 'inst/extdata/examples/TestProject/Data'
#>   • Data file:
#>   'inst/extdata/examples/TestProject/Data/TestProject_TimeValuesData.xlsx'
#>   • Data importer configuration:
#>   'inst/extdata/examples/TestProject/Data/esqlabs_dataImporter_configuration.xml'
#>   • Compound Properties File:
#>   • Output folder: 'inst/extdata/examples/TestProject/Results'
#> 
#> ── Configurations ──────────────────────────────────────────────────────────────
#>   • Scenarios: 5
#>   • Models: 1
#>   • Model Parameters: 3
#>   • Individuals: 1
#> 
#> ── Scenarios ───────────────────────────────────────────────────────────────────
#>   • ✅ TestScenario
#>   • ✅ TestScenario2
#>   • ✅ PopulationScenario
#>   • ✅ PopulationScenarioFromCSV
#>   • ✅ TestScenario_missingParam
#> 
#> ── Simulation Results ──────────────────────────────────────────────────────────
#> No Simulation Results available.

# Explore configurations
p$configurations
#> 
#> ── Configurations ──────────────────────────────────────────────────────────────
#> • Scenarios:
#>   • TestScenario
#>   • TestScenario2
#>   • PopulationScenario
#>   • PopulationScenarioFromCSV
#>   • TestScenario_missingParam
#> • Models:
#>   • Aciclovir.pkml
#> • Model Parameters:
#>   • Global
#>   • MissingParam
#>   • Aciclovir
#> • Individuals:
#>   • Indiv1
#> • Applications:
#>   • Aciclovir_iv_250mg

p$configurations$scenarios$TestScenario
#> $id
#> [1] "TestScenario"
#> 
#> $individual
#> [1] "Indiv1"
#> 
#> $population
#> [1] NA
#> 
#> $populationFromCSV
#> [1] NA
#> 
#> $modelParameters
#> [1] "Global"
#> 
#> $applications
#> [1] "Aciclovir_iv_250mg"
#> 
#> $time
#> [1] "0, 24, 60"
#> 
#> $timeUnit
#> [1] "h"
#> 
#> $steadyState
#> [1] FALSE
#> 
#> $steadyStateTime
#> [1] NA
#> 
#> $steadyStateTimeUnit
#> [1] NA
#> 
#> $model
#> [1] "Aciclovir.pkml"
#> 
#> $outputPaths
#> [1] NA

# Modify configurations
p$configurations$modelParameters$Global$`EHC continuous fraction`$value
#> [1] 1
p$configurations$modelParameters$Global$`EHC continuous fraction`$value <- 0.5
p$configurations$scenarios$TestScenario$modelParameters <- c("Global", "Aciclovir")

# Explore scenarios
p$scenarios$TestScenario$configuration$modelParameters
#> $Global
#> $Global$`EHC continuous fraction`
#> $containerPath
#> [1] "Organism|Liver"
#> 
#> $parameterName
#> [1] "EHC continuous fraction"
#> 
#> $value
#> [1] 0.5
#> 
#> $units
#> [1] ""
#> 
#> 
#> 
#> $Aciclovir
#> $Aciclovir$Lipophilicity
#> $containerPath
#> [1] "Aciclovir"
#> 
#> $parameterName
#> [1] "Lipophilicity"
#> 
#> $value
#> [1] -0.1
#> 
#> $units
#> [1] "Log Units"

# Select which scenarios to run (all active by default)
p$selectScenarios("TestScenario")


# Check the scenarios status
p$scenarios
#> $TestScenario
#> • Status: ✅ active
#> • Type: individual
#> • simulateSteadyTime:
#> • Configurations:
#>   • Model: Aciclovir.pkml
#>   • Model Parameters:
#>     • Global
#>     • Aciclovir
#>   • Individual: Indiv1
#>   • Applications:
#>     • Aciclovir_iv_250mg
#> 
#> $TestScenario2
#> • Status: ⏸ inactive
#> • Type: individual
#> • simulateSteadyTime:
#> • Configurations:
#>   • Model: Aciclovir.pkml
#>   • Model Parameters:
#>     • Global
#>   • Individual: Indiv1
#>   • Applications:
#>     • Aciclovir_iv_250mg
#> 
#> $PopulationScenario
#> • Status: ⏸ inactive
#> • Type: population
#> • simulateSteadyTime:
#> • Configurations:
#>   • Model: Aciclovir.pkml
#>   • Model Parameters:
#>     • Global
#>   • Individual: Indiv1
#>   • Applications:
#>     • Aciclovir_iv_250mg
#> 
#> $PopulationScenarioFromCSV
#> • Status: ⏸ inactive
#> • Type: population
#> • simulateSteadyTime:
#> • Configurations:
#>   • Model: Aciclovir.pkml
#>   • Model Parameters:
#>     • Global
#>   • Individual: Indiv1
#>   • Applications:
#>     • Aciclovir_iv_250mg
#> 
#> $TestScenario_missingParam
#> • Status: ⏸ inactive
#> • Type: individual
#> • simulateSteadyTime:
#> • Configurations:
#>   • Model: Aciclovir.pkml
#>   • Model Parameters:
#>   • Individual: Indiv1
#>   • Applications:
#>     • Aciclovir_iv_250mg

# Run the scenarios
p$runScenarios()
#> Loading Scenarios ■■■■■■■ 20% | ETA: 20s
## This will load and run the scenarios but this can be done in two separated manual steps
# p$loadScenarios()
# modify scenarios
# p$runScenarios()

# Access simulation results
p$simulationResults
#> $TestScenario
#> SimulationResults: 
#>    Number of individuals: 1