R/dms_codeset_tbl.R

In RollieParrish/ccdm: R functions for the Core Clinical Data Model (CCDM)

#' Create a tbl pointer to the Clinical Analytics CODESET data
#'
#' @param conn a DBI-compliant connection object. recommend using the 'connect_cdw()` function
#'
#' @return a tbl with codeset data
#'
#' @importFrom dplyr tbl
#' @importFrom dbplyr in_schema
#' @importFrom dplyr select
#' @importFrom dplyr inner_join
#' @importFrom dplyr starts_with
#'
#' @export
#'
#' @examples

#' \dontrun{
#' conn <- connect_cdw()
#'
#' ccdm_tbl(conn)
#'
#' dms_codeset_tbl(conn)
#'
#' disconnect_cdw(conn)
#'}


dms_codeset_tbl <- function(conn) {

    # Todo: check that there's a valid connection

    cs_name <- dplyr::tbl(conn, dbplyr::in_schema("CLINICAL_ANALYTICS_PROD.REF", "CODESET_NAME"))
    cs_code <- dplyr::tbl(conn, dbplyr::in_schema("CLINICAL_ANALYTICS_PROD.REF", "CODESET_CODE"))
    cs_attribute <- dplyr::tbl(conn, dbplyr::in_schema("CLINICAL_ANALYTICS_PROD.REF", "CODESET_CODE_ATTRIBUTE"))

    #cs_name <- dplyr::tbl(conn, DBI::Id(database = "CLINICAL_ANALYTICS_PROD", schema = "REF", table = "CODESET_NAME"))
    #cs_code <- dplyr::tbl(conn, DBI::Id(database = "CLINICAL_ANALYTICS_PROD", schema = "REF", table = "CODESET_CODE"))
    #cs_attribute <- dplyr::tbl(conn, DBI::Id(database = "CLINICAL_ANALYTICS_PROD", schema = "REF", table = "CODESET_CODE_ATTRIBUTE"))

   codeset_tbl <-
       cs_name %>%
       dplyr::inner_join(cs_code, by = c("CODESET_NAME_KEY" = "CODESET_NAME_KEY"), suffix = c(".name", ".code")) %>%
       dplyr::select(-dplyr::starts_with("INSERT_DTS"), -dplyr::starts_with("UPDATE_DTS"))

   codeset_tbl

}