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Extracts treatment pathways

Source: R/TreatmentPatternsQueries.R
getTreatmentPathways.Rd

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

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

Details

Specify the connectionHandler and the schema

See also

Other TreatmentPatterns: getAnalysisCohorts(), getEventDuration()

Examples

conDet <- getExampleConnectionDetails()

connectionHandler <- ResultModelManager::ConnectionHandler$new(conDet)
#> Connecting using SQLite driver

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