R/HLA_typing_synthetic_LIS-data.R

In immunogenetr: A Comprehensive Toolkit for Clinical HLA Informatics

#' Synthetic clinical-laboratory HLA typing table (HistoTrac "Patient" layout).
#'
#' A larger, deliberately messy synthetic data set patterned on a real
#' laboratory information system "Patient" table, with one individual per row.
#' It is intended as realistic development and test data for
#' \code{\link{HLA_columns_to_GLstring}} and related functions: the typing
#' columns exercise the full range of wild-caught notation, including serologic
#' values with and without a leading "w" (e.g. \code{"w4"}, \code{"4"}),
#' leading zeros (\code{"06"}), bare-asterisk molecular shorthand
#' (\code{"*17"}), colon-delimited molecular alleles (\code{"02:01"}), blanks,
#' and \code{NA}s. Both serologic (\code{A1Cd:dq2cd}) and molecular
#' (\code{mA1Cd:mDPB12cd}) typings are present for the HLA-A, B, Bw, C, DRB1,
#' DRB3/4/5, DQB1, DQA1, DPB1 and DPA1 loci.
#'
#' Note that the molecular (\code{m...}) columns deliberately contain a
#' \emph{mix} of true molecular values (e.g. \code{"31:01"}) and serologic
#' values (e.g. \code{"w6"}): the source laboratory historically recorded
#' serologic typing in the molecular columns, so this captures that real-world
#' mixed-nomenclature-within-a-column case.
#'
#' All identifiers, names and dates are synthetic.
#'
#' @docType data
#'
#' @usage data(HLA_typing_synthetic_LIS)
#'
#' @format
#' A tibble with 63 rows and 53 columns:
#' \describe{
#'   \item{PatientId, UNOSId, HospitalID, PhysicianID}{Synthetic record identifiers.}
#'   \item{firstnm, lastnm, DOB}{Synthetic demographics (donors carry their donor ID in \code{firstnm}).}
#'   \item{categoryCd, RaceCd, GenderCd, ABOCd, PatientTypeCd, StatusCd}{Synthetic categorical fields.}
#'   \item{A1Cd:dq2cd}{Serologic HLA typing (A, B, Bw, Cw, DR, DRw, DQ), as character.}
#'   \item{mA1Cd:mDPB12cd}{Molecular HLA typing (A, B, C, DRB1, DRB3/4/5, DQA1, DQB1, DPA1, DPB1), as character.}
#'   \item{UNOSCPRAAmt}{Synthetic calculated PRA value.}
#'   \item{UnacceptAntigenTxt, ModerateRiskAntibodyTxt, UNOSUnacceptAntigenTxt}{Synthetic antibody text fields.}
#' }
#'
#' @keywords datasets
#'
#' @source Synthetic data from Nicholas K. Brown, patterned on a clinical
#'   laboratory information system.
#'
"HLA_typing_synthetic_LIS"