Function for creating dataset which can be used as input for Cohort2Trajectory package

Function for creating dataset which can be used as input for Cohort2Trajectory package

Usage

createC2TInput(
  data,
  cdm,
  targetCohortId = "target",
  complementaryMappingTable = NULL
)

Arguments

data

Data list object

cdm

Connection to database (CDMConnector)

targetCohortId

Target cohort id

complementaryMappingTable

Mapping table for mapping concept_ids if present

Examples

if (FALSE) { # \dontrun{
  data <- readRDS("./snapshots/CohortContrastDataSnapshot.rds")
  user <- Sys.getenv("DB_USERNAME")
  pw <- Sys.getenv("DB_PASSWORD")
  server <- stringr::str_c(Sys.getenv("DB_HOST"), "/", Sys.getenv("DB_NAME"))
  port <- Sys.getenv("DB_PORT")

  cdmSchema <-
    Sys.getenv("OHDSI_CDM")
  cdmVocabSchema <-
    Sys.getenv("OHDSI_VOCAB")
  cdmResultsSchema <-
    Sys.getenv("OHDSI_RESULTS")
  writeSchema <-
    Sys.getenv("OHDSI_WRITE")
  writePrefix <- "cc_"

  db = DBI::dbConnect(
    RPostgres::Postgres(),
    dbname = Sys.getenv("DB_NAME"),
    host = Sys.getenv("DB_HOST"),
    user = Sys.getenv("DB_USERNAME"),
    password = Sys.getenv("DB_PASSWORD"),
    port = port
  )

  cdm <- CDMConnector::cdmFromCon(
    con = db,
    cdmSchema = cdmSchema,
    achillesSchema = cdmResultsSchema,
    writeSchema = list(schema = writeSchema, prefix = writePrefix)
  )

  data = createC2TInput(data, cdm)
} # }