createCohorts: This function will create the target and event cohorts...

In mi-erasmusmc/AsthmaCOPDTreatmentPatterns: A package to analyse real-world treatment patterns for patients with asthma, COPD and Asthma-COPD Overlap.

This function will create the target and event cohorts following the definitions included in this package .

Description

This function will create the target and event cohorts following the definitions included in this package .

Usage

createCohorts(
  connection,
  connectionDetails,
  cdmDatabaseSchema,
  cohortDatabaseSchema,
  vocabularyDatabaseSchema = cdmDatabaseSchema,
  cohortTable,
  outputFolder,
  loadCohorts = FALSE,
  baseUrl = "...",
  generateCohorts = TRUE,
  detailedCount = TRUE,
  minCellCount,
  flowChart = TRUE
)

Arguments

connection	Connection to database server.
connectionDetails	An object of type connectionDetails as created using the createConnectionDetails function in the DatabaseConnector package.
cdmDatabaseSchema	Schema name where your patient-level data resides. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
cohortDatabaseSchema	Schema name where intermediate data can be stored. You will need to have write priviliges in this schema. Note that for SQL Server, this should include both the database and schema name, for example 'cdm_data.dbo'.
cohortTable	The name of the table that will be created in the work database schema. This table will hold the target and event cohorts used in this study.
outputFolder	Name of local folder to place results; make sure to use forward slashes (/).
loadCohorts	Setting to load cohorts from ATLAS.
baseUrl	The base URL for the WebApi instance, for example: "http://server.org:80/WebAPI". Note, there is no trailing '/'. If trailing '/' is used, you may receive an error.
generateCohorts	Setting to extract specified target/event cohorts from database.
detailedCount	Setting to count which specific concepts occur in database.
minCellCount	Minimum number of persons with a specific treatment pathway for the pathway to be included in analysis.
flowChart	Setting to return numbers for flowchart with inclusion/exclusion criteria.

mi-erasmusmc/AsthmaCOPDTreatmentPatterns documentation built on Feb. 25, 2024, 2:34 p.m.