getTreatmentPathways: Extracts treatment pathways

In OhdsiReportGenerator: Observational Health Data Sciences and Informatics Report Generator

Extracts treatment pathways

Description

This function extracts results pathways for specified analysis ids and target cohorts

Usage

getTreatmentPathways(
  connectionHandler,
  schema,
  tpTablePrefix = "tp_",
  databaseTable = "database_meta_data",
  age = "all",
  sex = "all",
  indexYear = "all",
  analysisIds = NULL,
  databaseIds = NULL,
  databaseNames = NULL,
  targetIds = NULL
)

Arguments

connectionHandler	A connection handler that connects to the database and extracts sql queries. Create a connection handler via 'ResultModelManager::ConnectionHandler$new()'.
schema	The result database schema (e.g., 'main' for sqlite)
tpTablePrefix	The prefix used for the cohort generator results tables
databaseTable	The name of the table with the database details (default 'database_meta_data')
age	(optional) a string representing an age bucket to restrict (e.g., "0-17", "18-34", "65+")
sex	(optional) A string "male" or "female" to restrict
indexYear	(optional) A string with a four-digit year to restrict
analysisIds	(optional) A vector of analysis ids to restrict to
databaseIds	(optional) A vector of database ids to restrict to
databaseNames	(optional) A vector of database Names to restrict to
targetIds	(optional) A vector of target cohort ids to restrict to

Details

Specify the connectionHandler and the schema

Value

Returns a data.frame with the columns:

• databaseName the name of the database

• databaseId the unique identifier of the database

• analysisId the unique identifier of a treament patterns run

• targetCohortName the target cohort name

• targetCohortId the target cohort unique identifier

• pathway a string representing the progression of events for a target. Use '-' to separate sequential steps and '+' for combination of events at that step

• freq the count of pathway occurance

• age the stratifyed pathways for age

• indexYear the stratifyed pathways for index year

• sex the stratifyed pathways for sex

See Also

Other TreatmentPatterns: getAnalysisCohorts(), getEventDuration()

Examples

conDet <- getExampleConnectionDetails()

connectionHandler <- ResultModelManager::ConnectionHandler$new(conDet)

tp <- getTreatmentPathways(
  connectionHandler = connectionHandler,
  schema = "main"
)

OhdsiReportGenerator documentation built on Nov. 14, 2026, 1:09 a.m.