R/data.R

In billdenney/Rsdtm: Study Data Tabulation Model (SDTM) import, export, and management assistance

#' A data.frame with 4 columns and one row per valid SDTM version/IG/IG version
#' combination
#' 
#' @format
#' \describe{
#'   \item{SDTM}{The SDTM version}
#'   \item{IG_NAME}{The implementation guide (IG) name being used}
#'   \item{IG_VERSION}{The implemetation guide (IG) version}
#'   \item{archived}{The SDTM version/IG pair has been archived (and should not
#'     be used for current studies)}
#' }
"valid_versions"

#' The current SDTM terminology
#' 
#' SDTM terminology is used for reserved words and lists of codes that can be
#' used for values in the SDTM standard.  The version date from the download is
#' available via \code{attr(sdtm_terminology, "version")}.
#' 
#' The description of the columns draw from
#' \url{https://evs.nci.nih.gov/ftp1/CDISC/SDTM/SDTM CDISC ReadMe.doc}, and
#' the column names are modified slightly to work better in R.
#' 
#' @format
#' \describe{
#'   \item{code}{Unique numeric code randomly generated by NCI Thesaurus (NCIt) and assigned to individual CDISC controlled terms.}
#'   \item{codelist_code}{Unique numeric code randomly generated by NCI Thesaurus (NCIt) and assigned to the SDTM parent codelist names. This code is repeated for each controlled term (aka permissible value) belonging to a codelist. **NOTE - light blue highlighting is used to identify the beginning of a new SDTM codelist and its applicable term set.}
#'   \item{codelist_extensible_yes_no}{Defines if controlled terms may be added to the codelist. New terms may be added to existing codelist values when the codelist has "Yes" in Column C as long as the terms are not duplicates or synonyms of existing terms. The expectation is that sponsors will use the published controlled terminology as a standard baseline and codelists defined as "extensible" (or "Yes") may have terms added by the sponsor internally.  For codelists with "No" in Column C sponsor organizations may not add to the published lists. Suggestions for new terms may be requested through the New Term Request Page.}
#'   \item{codelist_name}{Contains the descriptive name of the codelist. As with the Codelist Code, the Codelist Name is repeated for each controlled term belonging to a codelist.}
#'   \item{CDISC_submission_value}{IMPORTANT COLUMN: Currently this is the specific value expected for submissions. Each value corresponds to a SDTM Codelist Name as indicated by light blue shading.}
#'   \item{CDISC_synonym}{This identifies the applicable synonyms for the CDISC Submission Value in Column E. These terms should not be submitted, but are included for collection and mapping purposes.**NOTE - this is especially important in instances where a Test name or Parameter Test name contains a corresponding Test Code or Parameter Test Code.}
#'   \item{CDISC_definition}{This identifies the CDISC definition for a particular term. In many cases an existing NCI definition has been used. The source for a definition is noted in parentheses (e.g. NCI, CDISC glossary).}
#'   \item{NCI_preferred_term}{This identifies the NCI preferred name for a term as identified in NCIt. **NOTE - This column designates the human readable, fully specified preferred term corresponding to the NCI c-code, and is especially helpful for searching NCIt to get the entire concept with links to all instances of the term.}
#' }
"sdtm_terminology"