{esqlabsR} What ?

{esqlabsR} Why ?

• Simple functions to design, run and save simulations,
• Interact with the OSPS features using Excel files,
• Generate standardized plots automatically.

{esqlabsR} Where ?

• Code repository: github.com/esqLABS/esqlabsR

• Documentation: esqlabs.github.io/esqlabsR/

• Get Started: esqlabs.github.io/esqlabsR/dev/

{esqlabsR} How ?

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")

{esqlabsR} How ?

Project Structure

library(esqlabsR)
init_project()

init_project() will create the expected simulation project’s folder structure.

Project Structure

Each one of these folders contains a series of .xlsx files with specific purpose.

my_project
├── ProjectConfiguration.xlsx
├── Data
├── Models
├── Parameters
│   ├── ApplicationParameters.xlsx
│   ├── Individuals.xlsx
│   ├── ModelParameters.xlsx
│   ├── Plots.xlsx
│   ├── PopulationParameters.xlsx
│   ├── Populations
│   │   └── PopulationScenario_population.csv
│   └── Scenarios.xlsx
└── Results
├── Figures
└── SimulationResults

Project Structure

Project’s files are linked by the ProjectConfiguration.xlsx file.

my_project
├── ProjectConfiguration.xlsx
├── Data
├── Models
├── Parameters
│   ├── ApplicationParameters.xlsx
│   ├── Individuals.xlsx
│   ├── ModelParameters.xlsx
│   ├── Plots.xlsx
│   ├── PopulationParameters.xlsx
│   ├── Populations
│   │   └── PopulationScenario_population.csv
│   └── Scenarios.xlsx
└── Results
├── Figures
└── SimulationResults

Project Structure

Everything is already configured !

ProjectConfiguration

• targets ProjectConfiguration.xlsx file,
• creates a ProjectConfiguration object,
• Needed for all next steps !

my_project_configuration <- 
  createDefaultProjectConfiguration(path = "path/to/ProjectConfiguration.xlsx")

ProjectConfiguration

my_project_configuration

ProjectConfiguration: 
Project Configuration File: TestProject/Code/projectConfiguration.xlsx 
Model folder: TestProject/Models/Simulations 
Parameters folder: TestProject/Parameters 
Parameters file name: TestProject/Parameters/ModelParameters.xlsx 
Individual parameters file name: TestProject/Parameters/Individuals.xlsx 
...

Scenarios

Simulations are defined by Scenarios.

Scenarios parameterization

• Model
• Model parameters
• Application protocol
• Time range
• Individual characteristics
• Population
• …

Parameters files

Read Scenarios

my_scenarios <- createScenarios(
  readScenarioConfigurationFromExcel(
    scenarioNames = "TestScenario",
    projectConfiguration = my_project_configuration
  )
)

Scenarios Recap

my_scenarios

ScenarioConfiguration: 
   Model file name: Aciclovir.pkml 
   Scenario name: TestScenario 
   Parameters sheets: Global 
   Individual Id: Indiv1 
   Population Id: 
   Read population from csv file: FALSE 
   Application protocol: Aciclovir_iv_250mg 
   Simulation time intervals: 
     Interval: 1 
       Start: 0 
       End: 24 
       Resolution: 60 
   Simulation time intervals unit: h 
   Simulate steady-state: FALSE 
   Steady-state time: 1000 

Run Simulations

myScenarioResults <- runScenarios(my_scenarios)

OSPS plotting functions

Simulation results are compatible with {ospsuite} plotting workflow.

my_datacombined <- DataCombined$new()

my_datacombined$addSimulationResults(myScenarioResults$TestScenario$results,
  names = "Simulated",
  groups = "Aciclovir"
)

OSPS plotting functions

plotIndividualTimeProfile(my_datacombined)

New in 5.0.0

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