executeTreatmentPatterns: This is the main function which runs all parts of the...

In mi-erasmusmc/TreatmentPatterns: A package to analyse real-world treatment patterns of a study population of interest

This is the main function which runs all parts of the treatment pathways analysis. The following tasks are performed sequentially: 1) Create target/event cohorts of interest, 2) Optional, only for OMOP-CDM data: Perform baseline characterization of study/target population, 3) Construct treatment pathways, 4) Generate output (sunburst plots, Sankey diagrams and more), 5) Launch shiny application to visualize the results.

Description

This is the main function which runs all parts of the treatment pathways analysis. The following tasks are performed sequentially: 1) Create target/event cohorts of interest, 2) Optional, only for OMOP-CDM data: Perform baseline characterization of study/target population, 3) Construct treatment pathways, 4) Generate output (sunburst plots, Sankey diagrams and more), 5) Launch shiny application to visualize the results.

Usage

executeTreatmentPatterns(
  dataSettings,
  cohortSettings,
  characterizationSettings = NULL,
  pathwaySettings,
  saveSettings,
  runCreateCohorts = TRUE,
  runCohortCharacterization = TRUE,
  runConstructPathways = TRUE,
  runGenerateOutput = TRUE,
  launchShiny = TRUE
)

Arguments

dataSettings	Settings object as created by createDataSettings().
cohortSettings	Settings object as created by createCohortSettings().
characterizationSettings	Optional, only for OMOP-CDM data: Settings object as created by createCharcterizationSettings().
pathwaySettings	Settings object as created by createPathwaySettings().
saveSettings	Settings object as created by createSaveSettings().
runCreateCohorts	Setting to run 1) createCohorts().
runCohortCharacterization	Optional, only for OMOP-CDM data: Setting to run 2) cohortCharacterization().
runConstructPathways	Setting to run 3) constructPathways().
runGenerateOutput	Setting to run 4) generateOutput().
launchShiny	Setting to run 5) launchResultsExplorer().

mi-erasmusmc/TreatmentPatterns documentation built on July 1, 2023, 9:20 p.m.