addPathwaySettings: Add set of pathway settings.

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

Add set of pathway settings.

Description

Add set of pathway settings.

Usage

addPathwaySettings(
  studyName = "name_unknown",
  targetCohortId,
  eventCohortIds,
  includeTreatments = "startDate",
  periodPriorToIndex = 0,
  minEraDuration = 0,
  splitEventCohorts = "",
  splitTime = 30,
  eraCollapseSize = 30,
  combinationWindow = 30,
  minPostCombinationDuration = 30,
  filterTreatments = "First",
  maxPathLength = 5,
  minCellCount = 5,
  minCellMethod = "Remove",
  groupCombinations = 10,
  addNoPaths = FALSE
)

Arguments

studyName	Name identifying the set of study parameters.
targetCohortId	Target cohort ID of current study settings.
eventCohortIds	Event cohort IDs of current study settings.
includeTreatments	Include treatments starting ('startDate') or ending ('endDate') after target cohort start date
periodPriorToIndex	Number of days prior to the index date of the target cohort that event cohorts are allowed to start
minEraDuration	Minimum time an event era should last to be included in analysis
splitEventCohorts	Specify event cohort to split in acute (< X days) and therapy (>= X days)
splitTime	Specify number of days (X) at which each of the split event cohorts should be split in acute and therapy
eraCollapseSize	Window of time between which two eras of the same event cohort are collapsed into one era
combinationWindow	Window of time two event cohorts need to overlap to be considered a combination treatment
minPostCombinationDuration	Minimum time an event era before or after a generated combination treatment should last to be included in analysis
filterTreatments	Select first occurrence of ("First") / changes between ("Changes') / all event cohorts ("All")
maxPathLength	Maximum number of steps included in treatment pathway (max 5)
minCellCount	Minimum number of persons with a specific treatment pathway for the pathway to be included in analysis
minCellMethod	Select to completely remove / sequentially adjust (by removing last step as often as necessary) treatment pathways below minCellCount
groupCombinations	Select to group all non-fixed combinations in one category 'other’ in the sunburst plot
addNoPaths	Select to include untreated persons without treatment pathway in the sunburst plot

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