R/m4_meta.R

In hdshea/MIMIC4db: Package for building, loading and referencing the Google BigQuery verion of the MIMIC-IV

#' Encapsulated meta data for MIMIC IV tables
#'
#' The function returns a tibble with the table name, MIMIC module and a description (all descriptive data are
#' referenced from the [MIMIC-IV website](https://mimic.mit.edu/docs/iv/)).
#'
#' @return a tibble containing meta data concerning MIMIC IV tables.
#' @export
#'
#' @examples
#' core <- m4_meta_data()
#' core <- core[core$module == "mimic_core", ]
#' for (i in 1:length(core)) {
#'   cat(stringr::str_c(
#'     "select * from physionet-data.",
#'     core[i, "module"],
#'     ".",
#'     core[i, "table"],
#'     "\n"
#'   ))
#' }
m4_meta_data <- function() {
  tibble::tribble(
    ~table, ~module, ~description,
    "admissions", "mimic_core", "The admissions table defines all hospitalizations in the database. Hospitalizations are assigned a unique random integer known as the hadm_id.",
    "patients", "mimic_core", "Information that is consistent for the lifetime of a patient is stored in this table.",
    "transfers", "mimic_core", "Physical locations for patients throughout their hospital stay.",
    "d_hcpcs", "mimic_hosp", "Dimension table for hcpcsevents; provides a description of CPT codes.",
    "d_icd_diagnoses", "mimic_hosp", "Dimension table for diagnoses_icd; provides a description of ICD-9/ICD-10 billed diagnoses.",
    "d_icd_procedures", "mimic_hosp", "Dimension table for procedures_icd; provides a description of ICD-9/ICD-10 billed procedures.",
    "d_labitems", "mimic_hosp", "Dimension table for labevents; provides a description of all lab items.",
    "diagnoses_icd", "mimic_hosp", "Billed ICD-9/ICD-10 diagnoses for hospitalizations.",
    "drgcodes", "mimic_hosp", "Billed DRG codes for hospitalizations.",
    "emar", "mimic_hosp", "The Electronic Medicine Administration Record (eMAR); barcode scanning of medications at the time of administration.",
    "emar_detail", "mimic_hosp", "Supplementary information for electronic administrations recorded in emar.",
    "hcpcsevents", "mimic_hosp", "Billed events occurring during the hospitalization. Includes CPT codes.",
    "labevents", "mimic_hosp", "Laboratory measurements sourced from patient derived specimens.",
    "microbiologyevents", "mimic_hosp", "Microbiology cultures.",
    "pharmacy", "mimic_hosp", "Formulary, dosing, and other information for prescribed medications.",
    "poe", "mimic_hosp", "Orders made by providers relating to patient care.",
    "poe_detail", "mimic_hosp", "Supplementary information for orders made by providers in the hospital.",
    "prescriptions", "mimic_hosp", "Prescribed medications.",
    "procedures_icd", "mimic_hosp", "Billed procedures for patients during their hospital stay.",
    "services", "mimic_hosp", "The hospital service(s) which cared for the patient during their hospitalization.",
    "d_items", "mimic_icu", "Dimension table describing itemid. Defines concepts recorded in the events table in the ICU module.",
    "chartevents", "mimic_icu", "Charted items occurring during the ICU stay. Contains the majority of information documented in the ICU.",
    "datetimeevents", "mimic_icu", "Documented information which is in a date format (e.g. date of last dialysis).",
    "icustays", "mimic_icu", "Tracking information for ICU stays including adminission and discharge times.",
    "inputevents", "mimic_icu", "Information documented regarding continuous infusions or intermittent administrations.",
    "outputevents", "mimic_icu", "Information regarding patient outputs including urine, drainage, and so on.",
    "procedureevents", "mimic_icu", "Procedures documented during the ICU stay (e.g. ventilation), though not necessarily conducted within the ICU (e.g. x-ray imaging)."
  )
}

#' Encapsulated descriptive data for services
#'
#' The function returns a tibble with descriptive data from services including service code, detailed description and
#' short description.
#'
#' @return a tibble containing descriptive data for services.
#' @export
#'
#' @examples
#' neuro <- m4_service_decsriptions()
#' neuro <- neuro[startsWith(neuro$short_description, "Neurologic"), ]
#' neuro[, c("service", "short_description")]
m4_service_decsriptions <- function() {
  tibble::tribble(
    ~service, ~description,
    "CMED", "Cardiac Medical - for non-surgical cardiac related admissions",
    "CSURG", "Cardiac Surgery - for surgical cardiac admissions",
    "DENT", "Dental - for dental/jaw related admissions",
    "ENT", "Ear, nose, and throat - conditions primarily affecting these areas",
    "GU", "Genitourinary - reproductive organs/urinary system",
    "GYN", "Gynecological - female reproductive systems and breasts",
    "MED", "Medical - general service for internal medicine",
    "NB", "Newborn - infants born at the hospital",
    "NBB", "Newborn baby - infants born at the hospital",
    "NMED", "Neurologic Medical - non-surgical, relating to the brain",
    "NSURG", "Neurologic Surgical - surgical, relating to the brain",
    "OBS", "Obstetrics - conerned with childbirth and the care of women giving birth",
    "ORTHO", "Orthopaedic - surgical, relating to the musculoskeletal system",
    "OMED", "Orthopaedic medicine - non-surgical, relating to musculoskeletal system",
    "PSURG", "Plastic - restortation/reconstruction of the human body (including cosmetic or aesthetic)",
    "PSYCH", "Psychiatric - mental disorders relating to mood, behaviour, cognition, or perceptions",
    "SURG", "Surgical - general surgical service not classified elsewhere",
    "TRAUM", "Trauma - injury or damage caused by physical harm from an external source",
    "TSURG", "Thoracic Surgical - surgery on the thorax, located between the neck and the abdomen",
    "VSURG", "Vascular Surgical - surgery relating to the circulatory system"
  ) %>%
    dplyr::mutate(short_description = stringr::str_split(description, " - ", simplify = TRUE)[, 1])
}