R/generate_mappings.R

In jackwasey/icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes

# nocov start

#' Generate Elixhauser comorbidities
#'
#' This function uses the \code{\%i9d\%} operator, so cannot be done as an R
#' file in the \code{data} directory. The data is documented in
#' \code{datadocs.R}.
#' @template parse-template
#' @keywords internal
#' @noRd
icd9_generate_map_elix <- function(save_pkg_data = TRUE) {
  icd9_map_elix <- list(
    chf = c(
      "398.91", "402.11", "402.91", "404.11", "404.13", "404.91",
      "404.93", "428.0" %i9da% "428.9"
    ),
    arrhythmia = c(
      "426.1", "426.11", "426.13", "426.2" %i9da% "426.53",
      "426.6" %i9da% "426.89", "427.0", "427.2", "427.31",
      "427.60", "427.9", "785", "V45.0", "V53.3"
    ),
    valve = c(
      "93.20" %i9da% "93.24", "394.0" %i9da% "397.1",
      "424.0" %i9da% "424.91", "746.3" %i9da% "746.6",
      "V42.2", "V43.3"
    ),
    pulm.circ = c("416.0" %i9da% "416.9", " 417.9"),
    pvd = c(
      "440.0" %i9da% "440.9", "441.2", "441.4", "441.7", "441.9",
      "443.1" %i9da% "443.9", "447.1", "557.1", "557.9", "V43.4"
    ),
    htn = c("401.1", "401.9"),
    htncx = c(
      "402.10", "402.90", "404.10", "404.90", "405.11", "405.19",
      "405.91", "405.99"
    ),
    paralysis = c("342.0" %i9da% "342.12", "342.9" %i9da% "344.9"),
    neuro.other = c(
      "331.9", "332.0", "333.4", "333.5", "334.0" %i9da% "335.9",
      "340", "341.1" %i9da% "341.9", "345.00" %i9da% "345.11",
      "345.40" %i9da% "345.51", "345.80" %i9da% "345.91", "348.1",
      "348.3", "780.3", "784.3"
    ),
    chronic.pulm = c(
      "490" %i9da% "492.8", "493.00" %i9da% "493.91", "494",
      "495.0" %i9da% "505", "506.4"
    ),
    dm.uncomp = c("250.00" %i9da% "250.33"),
    dm.comp = c("250.40" %i9da% "250.73", "250.90" %i9da% "250.93"),
    hypothyroid = c("243" %i9da% "244.2", "244.8", "244.9"),
    renal = c(
      "403.11", "403.91", "404.12", "404.92", "585", "586", "V42.0",
      "V45.1", "V56.0", "V56.8"
    ),
    liver = c(
      "70.32", "70.33", "70.54", "456.0", "456.1", "456.20", "456.21",
      "571.0", "571.2", "571.3", "571.40" %i9da% "571.49", "571.5",
      "571.6", "571.8", "571.9", "572.3", "572.8", "V42.7"
    ),
    pud = c(
      "531.70", "531.90", "532.70", "532.90", "533.70", "533.90",
      "534.70", "534.90", "V12.71"
    ),
    hiv = c("42" %i9da% "44.9"),
    lymphoma = c(
      "200.00" %i9da% "202.38", "202.50" %i9da% "203.01",
      "203.8" %i9da% "203.81", "238.6", "273.3", "V10.71", "V10.72",
      "V10.79"
    ),
    mets = c("196.0" %i9da% "199.1"),
    solid.tumor = c(
      "140.0" %i9da% "172.9", "174.0" %i9da% "175.9",
      "179" %i9da% "195.8", "V10.00" %i9da% "V10.9"
    ),
    rheum = c(
      "701.0", "710.0" %i9da% "710.9", "714.0" %i9da% "714.9",
      "720.0" %i9da% "720.9", "725"
    ),
    coag = c("286.0" %i9da% "286.9", "287.1", "287.3" %i9da% "287.5"),
    obesity = c("278.0"),
    wt.loss = c("260" %i9da% "263.9"),
    lytes = c("276.0" %i9da% "276.9"),
    anemia.loss = c("280.0"),
    anemia.def = c("280.1" %i9da% "281.9", "285.9"),
    etoh = c(
      "291.1", "291.2", "291.5", "291.8", "291.9",
      "303.90" %i9da% "303.93", "305.00" %i9da% "305.03", "V11.3"
    ),
    drugs = c(
      "292.0", "292.82" %i9da% "292.89", "292.9",
      "304.00" %i9da% "304.93", "305.20" %i9da% "305.93"
    ),
    psychoses = c("295.00" %i9da% "298.9", "299.10" %i9da% "299.11"),
    depression = c("300.4", "301.12", "309.0", "309.1", "311")
  )
  icd9_map_elix <- lapply(icd9_map_elix, decimal_to_short.icd9)
  icd9_map_elix <- lapply(
    icd9_map_elix,
    children.icd9,
    short_code = TRUE, defined = FALSE
  )
  names(icd9_map_elix) <- icd::names_elix_htn_abbrev
  icd9_map_elix <- as.comorbidity_map(icd9_map_elix)
  if (save_pkg_data) {
    .save_in_data_dir(icd9_map_elix)
  }
  invisible(icd9_map_elix)
}

#' @rdname icd9_generate_map_elix
#' @keywords internal
#' @noRd
icd10_generate_map_elix <- function(save_pkg_data = TRUE) {
  icd10_map_elix <- list(
    chf = c(
      "I099", "I110", "I130", "I132", "I255", "I420", "I425", "I426",
      "I427", "I428", "I429",
      "I43", "I50", "P290"
    ),
    arrhythmia = c(
      "I441", "I442", "I443", "I456", "I459", "I47", "I48", "I49",
      "R000", "R001",
      "R008", "T821", "Z450", "Z950"
    ),
    valve = c(
      "A520", "I05", "I06", "I07", "I08", "I091", "I098", "I34", "I35",
      "I36", "I37", "I38",
      "I39", "Q230", "Q231", "Q232", "Q233", "Z952", "Z953", "Z954"
    ),
    pulm.circ = c("I26", "I27", "I280", "I288", "I289"),
    pvd = c(
      "I70", "I71", "I731", "I738", "I739", "I771", "I790", "I792",
      "K551", "K558", "K559",
      "Z958", "Z959"
    ),
    htn = c("I10"),
    htncx = c("I11", "I12", "I13", "I15"),
    paralysis = c(
      "G041", "G114", "G801", "G802", "G81", "G82", "G830", "G831",
      "G832", "G833",
      "G834", "G839"
    ),
    neuro.other = c(
      "G10", "G11", "G12", "G13", "G20", "G21", "G22", "G254",
      "G255", "G312", "G318",
      "G319", "G32", "G35", "G36", "G37", "G40", "G41", "G931",
      "G934", "R470", "R56"
    ),
    chronic.pulm = c(
      "I278", "I279", "J40", "J41", "J42", "J43", "J44", "J45",
      "J46", "J47", "J60",
      "J61", "J62", "J63", "J64", "J65", "J66", "J67", "J684",
      "J701", "J703"
    ),
    dm.uncomp = c(
      "E100", "E101", "E109", "E110", "E111", "E119", "E120",
      "E121", "E129", "E130",
      "E131", "E139", "E140", "E141", "E149"
    ),
    dm.comp = c(
      "E102", "E103", "E104", "E105", "E106", "E107", "E108", "E112",
      "E113", "E114",
      "E115", "E116", "E117", "E118", "E122", "E123", "E124", "E125",
      "E126", "E127",
      "E128", "E132", "E133", "E134", "E135", "E136", "E137", "E138",
      "E142", "E143",
      "E144", "E145", "E146", "E147", "E148"
    ),
    hypothyroid = c("E00", "E01", "E02", "E03", "E890"),
    renal = c(
      "I120", "I131", "N18", "N19", "N250", "Z490", "Z491", "Z492",
      "Z940", "Z992"
    ),
    liver = c(
      "B18", "I85", "I864", "I982", "K70", "K711", "K713", "K714",
      "K715", "K717", "K72",
      "K73", "K74", "K760", "K762", "K763", "K764", "K765", "K766",
      "K767", "K768", "K769",
      "Z944"
    ),
    pud = c("K257", "K259", "K267", "K269", "K277", "K279", "K287", "K289"),
    hiv = c("B20", "B21", "B22", "B24"),
    lymphoma = c(
      "C81", "C82", "C83", "C84", "C85", "C88", "C96", "C900",
      "C902"
    ),
    mets = c("C77", "C78", "C79", "C80"),
    solid.tumor = c(
      "C00", "C01", "C02", "C03", "C04", "C05", "C06", "C07",
      "C08", "C09", "C10",
      "C11", "C12", "C13", "C14", "C15", "C16", "C17", "C18",
      "C19", "C20", "C21",
      "C22", "C23", "C24", "C25", "C26", "C30", "C31", "C32",
      "C33", "C34", "C37",
      "C38", "C39", "C40", "C41", "C43", "C45", "C46", "C47",
      "C48", "C49", "C50",
      "C51", "C52", "C53", "C54", "C55", "C56", "C57", "C58",
      "C60", "C61", "C62",
      "C63", "C64", "C65", "C66", "C67", "C68", "C69", "C70",
      "C71", "C72", "C73",
      "C74", "C75", "C76", "C97"
    ),
    rheum = c(
      "L940", "L941", "L943", "M05", "M06", "M08", "M120", "M123",
      "M30", "M310", "M311",
      "M312", "M313", "M32", "M33", "M34", "M35", "M45", "M461", "M468",
      "M469"
    ),
    coag = c(
      "D65", "D66", "D67", "D68", "D691", "D693", "D694", "D695",
      "D696"
    ),
    obesity = c("E66"),
    wt.loss = c("E40", "E41", "E42", "E43", "E44", "E45", "E46", "R634", "R64"),
    lytes = c("E222", "E86", "E87"),
    anemia.loss = c("D500"),
    anemia.def = c("D508", "D509", "D51", "D52", "D53"),
    etoh = c(
      "F10", "E52", "G621", "I426", "K292", "K700", "K703", "K709",
      "T51", "Z502", "Z714",
      "Z721"
    ),
    drugs = c(
      "F11", "F12", "F13", "F14", "F15", "F16", "F18", "F19", "Z715",
      "Z722"
    ),
    psychoses = c(
      "F20", "F22", "F23", "F24", "F25", "F28", "F29", "F302",
      "F312", "F315"
    ),
    depression = c(
      "F204", "F313", "F314", "F315", "F32", "F33", "F341",
      "F412", "F432"
    )
  )
  names(icd10_map_elix) <- icd::names_elix_htn_abbrev
  icd10_map_elix <- .apply_over_icd10who_vers(icd10_map_elix)
  icd10_map_elix <- .apply_over_icd10cm_vers(icd10_map_elix)
  .msg("applied ICD-10-CM and WHO versions")
  icd10_map_elix <- lapply(icd10_map_elix, as.short_diag)
  .msg("applied as.short_diag")
  icd10_map_elix <- lapply(icd10_map_elix, as.icd10)
  .msg("applied as.icd10")
  icd10_map_elix <- as.comorbidity_map(icd10_map_elix)
  if (save_pkg_data) {
    .save_in_data_dir(icd10_map_elix)
  }
  invisible(icd10_map_elix)
}

#' Generate Quan's revised Elixhauser comorbidities
#'
#' Generate Quan's revised Elixhauser comorbidities, expanded out
#'   to include all possible ICD-9 codes.
#' @template parse-template
#' @keywords internal
#' @noRd
icd9_generate_map_quan_elix <- function(save_pkg_data = TRUE) {
  icd9_map_quan_elix <- list(
    chf = c(
      "398.91", "402.01", "402.11", "402.91", "404.01", "404.03",
      "404.11", "404.13", "404.91", "404.93", "425.4" %i9da% "425.9",
      "428"
    ),
    arrhythmia = c(
      "426.0", "426.13", "426.7", "426.9", "426.10", "426.12",
      "427.0" %i9da% "427.4", "427.6" %i9da% "427.9", "785.0",
      "996.01", "996.04", "V45.0", "V53.3"
    ),
    valve = c(
      "93.2", "394" %i9da% "397", "424", "746.3" %i9da% "746.6",
      "V42.2", "V43.3"
    ),
    pulm.circ = c("415.0", "415.1", "416", "417.0", "417.8", "417.9"),
    pvd = c(
      "093.0", "437.3", "440", "441", "443.1" %i9da% "443.9", "447.1",
      "557.1", "557.9", "V43.4"
    ),
    htn = c("401"),
    htncx = c("402" %i9da% "405"),
    paralysis = c("334.1", "342", "343", "344.0" %i9da% "344.6", "344.9"),
    neuro.other = c(
      "331.9", "332.0", "332.1", "333.4", "333.5", "333.92",
      "334", "335", "336.2", "340", "341", "345", "348.1",
      "348.3", "780.3", "784.3"
    ),
    chronic.pulm = c(
      "416.8", "416.9", "490" %i9da% "505", "506.4", "508.1",
      "508.8"
    ),
    dm.uncomp = c("250.0" %i9da% "250.3"),
    dm.comp = c("250.4" %i9da% "250.9"),
    hypothyroid = c("240.9", "243", "244", "246.1", "246.8"),
    renal = c(
      "403.01", "403.11", "403.91", "404.02", "404.03", "404.12",
      "404.13", "404.92", "404.93", "585", "586", "588.0", "V42.0",
      "V45.1", "V56"
    ),
    liver = c(
      "70.22", "70.23", "70.32", "70.33", "70.44", "70.54", "70.6",
      "70.9", "456.0" %i9da% "456.2", "570", "571",
      "572.2" %i9da% "572.8", "573.3", "573.4", "573.8", "573.9",
      "V42.7"
    ),
    pud = c(
      "531.7", "531.9", "532.7", "532.9", "533.7", "533.9", "534.7",
      "534.9"
    ),
    hiv = c("42" %i9da% "44"),
    lymphoma = c("200" %i9da% "202", "203.0", "238.6"),
    mets = c("196" %i9da% "199"),
    solid.tumor = c("140" %i9da% "172", "174" %i9da% "195"),
    rheum = c(
      "446", "701.0", "710.0" %i9da% "710.4", "710.8", "710.9", "711.2",
      "714", "719.3", "720", "725", "728.5", "728.89", "729.30"
    ),
    coag = c("286", "287.1", "287.3" %i9da% "287.5"),
    obesity = c("278.0"),
    wt.loss = c("260" %i9da% "263", "783.2", "799.4"),
    lytes = c("253.6", "276"),
    anemia.loss = c("280.0"),
    anemia.def = c("280.1" %i9da% "280.9", "281"),
    etoh = c(
      "265.2", "291.1" %i9da% "291.3", "291.5" %i9da% "291.9", "303.0",
      "303.9", "305.0", "357.5", "425.5", "535.3",
      "571.0" %i9da% "571.3", "980", "V11.3"
    ),
    drugs = c("292", "304", "305.2" %i9da% "305.9", "V65.42"),
    psychoses = c(
      "293.8", "295", "296.04", "296.14", "296.44", "296.54", "297",
      "298"
    ),
    depression = c("296.2", "296.3", "296.5", "300.4", "309", "311")
  )
  icd9_map_quan_elix <- lapply(
    icd9_map_quan_elix,
    function(x) decimal_to_short.icd9(x)
  )
  icd9_map_quan_elix <- lapply(
    icd9_map_quan_elix,
    children.icd9,
    short_code = TRUE, defined = FALSE
  )
  names(icd9_map_quan_elix) <- icd::names_quan_elix_htn_abbrev
  icd9_map_quan_elix <- as.comorbidity_map(icd9_map_quan_elix)
  if (save_pkg_data) {
    .save_in_data_dir(icd9_map_quan_elix)
  }
  invisible(icd9_map_quan_elix)
}

#' generate ICD-10 Quan Elixhauser mapping
#'
#' Started with Quan's SAS code (in raw data directory of source tree):
# ` \code{grep %STR\(.*[[:digit:]] ICD10_Elixhauser.sas}
#
#' @template parse-template
#' @keywords internal
#' @noRd
icd10_generate_map_quan_elix <- function(save_pkg_data = TRUE) {
  quan_elix_raw <- list(
    c(
      "I099", "I110", "I130", "I132", "I255", "I420", "I425", "I426", "I427",
      "I428", "I429", "I43", "I50", "P290"
    ),
    c(
      "I441", "I442", "I443", "I456", "I459", "I47", "I48", "I49", "R000",
      "R001", "R008", "T821", "Z450", "Z950"
    ),
    c(
      "A520", "I05", "I06", "I07", "I08", "I091", "I098", "I34", "I35", "I36",
      "I37", "I38", "I39", "Q230", "Q231",
      "Q232", "Q233", "Z952", "Z953", "Z954"
    ),
    c("I26", "I27", "I280", "I288", "I289"),
    c(
      "I70", "I71", "I731", "I738", "I739", "I771", "I790", "I792", "K551",
      "K558", "K559", "Z958", "Z959"
    ),
    c("I10"),
    c("I11", "I12", "I13", "I15"),
    c(
      "G041", "G114", "G801", "G802", "G81", "G82", "G830", "G831", "G832",
      "G833", "G834", "G839"
    ),
    c(
      "G10", "G11", "G12", "G13", "G20", "G21", "G22", "G254", "G255", "G312",
      "G318", "G319", "G32", "G35", "G36",
      "G37", "G40", "G41", "G931", "G934", "R470", "R56"
    ),
    c(
      "I278", "I279", "J40", "J41", "J42", "J43", "J44", "J45", "J46", "J47",
      "J60", "J61", "J62", "J63", "J64", "J65",
      "J66", "J67", "J684", "J701", "J703"
    ),
    c(
      "E100", "E101", "E109", "E110", "E111", "E119", "E120", "E121", "E129",
      "E130", "E131", "E139", "E140", "E141",
      "E149"
    ),
    c(
      "E102", "E103", "E104", "E105", "E106", "E107", "E108", "E112", "E113",
      "E114", "E115", "E116", "E117", "E118",
      "E122", "E123", "E124", "E125", "E126", "E127", "E128", "E132", "E133",
      "E134", "E135", "E136", "E137", "E138",
      "E142", "E143", "E144", "E145", "E146", "E147", "E148"
    ),
    c("E00", "E01", "E02", "E03", "E890"),
    c(
      "I120", "I131", "N18", "N19", "N250", "Z490", "Z491", "Z492", "Z940",
      "Z992"
    ),
    c(
      "B18", "I85", "I864", "I982", "K70", "K711", "K713", "K714", "K715",
      "K717", "K72", "K73", "K74", "K760", "K762",
      "K763", "K764", "K765", "K766", "K767", "K768", "K769", "Z944"
    ),
    c("K257", "K259", "K267", "K269", "K277", "K279", "K287", "K289"),
    c("B20", "B21", "B22", "B24"),
    c("C81", "C82", "C83", "C84", "C85", "C88", "C96", "C900", "C902"),
    c("C77", "C78", "C79", "C80"),
    # tumor
    c(
      "C00", "C01", "C02", "C03", "C04", "C05", "C06", "C07", "C08", "C09",
      "C10", "C11", "C12", "C13", "C14", "C15",
      "C16", "C17", "C18", "C19", "C20", "C21", "C22", "C23", "C24", "C25",
      "C26", "C30", "C31", "C32", "C33", "C34",
      "C37", "C38",
      "C39", "C40", "C41", "C43", "C45", "C46", "C47", "C48", "C49", "C50",
      "C51", "C52", "C53", "C54", "C55", "C56",
      "C57", "C58", "C60", "C61", "C62", "C63", "C64", "C65", "C66", "C67",
      "C68", "C69", "C70", "C71", "C72", "C73",
      "C74", "C75", "C76", "C97"
    ),
    c(
      "L940", "L941", "L943", "M05", "M06", "M08", "M120", "M123", "M30",
      "M310", "M311", "M312", "M313", "M32", "M33",
      "M34", "M35", "M45", "M461", "M468", "M469"
    ),
    c("D65", "D66", "D67", "D68", "D691", "D693", "D694", "D695", "D696"),
    c("E66"),
    c("E40", "E41", "E42", "E43", "E44", "E45", "E46", "R634", "R64"),
    c("E222", "E86", "E87"),
    c("D500"),
    c("D508", "D509", "D51", "D52", "D53"),
    c(
      "F10", "E52", "G621", "I426", "K292", "K700",
      "K703", "K709", "T51", "Z502", "Z714", "Z721"
    ),
    drugs = c(
      "F11", "F12", "F13", "F14", "F15", "F16",
      "F18", "F19", "Z715", "Z722"
    ),
    c("F20", "F22", "F23", "F24", "F25", "F28", "F29", "F302", "F312", "F315"),
    c("F204", "F313", "F314", "F315", "F32", "F33", "F341", "F412", "F432")
  )
  # there are 31 items in the list: hypertension is typically combined into one
  # category, whereas diabetes is kept as two categories
  names(quan_elix_raw) <- icd::names_elix_htn_abbrev

  # this expansion will only be for 'defined' codes (currently the most
  # up-to-date canonical CMS ICD-10-CM list). Will ultimately need to generalize
  # this.

  # this function accounts for the fact that some Quan Elixhauser ICD-10 codes
  # are not in fact defined in ICD-10-CM, and currently generation of ICD-10
  # children is limited to 'defined' ones, but only as defined in ICD-10-CM, not
  # ICD-10 in general.
  #
  # It does appear that there are numerous codes in the Quan Elixhauser scheme
  # which are not present (?anymore) in the ICD-10-CM 2016 list. In particular,
  # see C43 in Tumor.
  icd10_map_quan_elix <- .apply_over_icd10cm_vers(quan_elix_raw)
  icd10_map_quan_elix <- .apply_over_icd10who_vers(icd10_map_quan_elix)
  icd10_map_quan_elix <- lapply(icd10_map_quan_elix, as.short_diag)
  icd10_map_quan_elix <- lapply(icd10_map_quan_elix, as.icd10)
  icd10_map_quan_elix <- as.comorbidity_map(icd10_map_quan_elix)
  if (save_pkg_data) {
    .save_in_data_dir(icd10_map_quan_elix)
  }
  invisible(icd10_map_quan_elix)
}

#' Generate Quan mapping for Charlson categories of ICD-10 codes
#'
#' Based on Quan's SAS lists, transcribed by wmurphyrd
#' @template parse-template
#' @keywords internal
#' @noRd
icd10_generate_map_quan_deyo <- function(save_pkg_data = TRUE) {
  quan_charl_raw <- list(
    mi = c("I21", "I22", "I252"),
    chf = c(
      "I43", "I50", "I099", "I110", "I130", "I132",
      "I255", "I420", "I425", "I426", "I427", "I428", "I429", "P290"
    ),
    pvd = c(
      "I70", "I71", "I731", "I738", "I739", "I771",
      "I790", "I792", "K551", "K558", "K559", "Z958", "Z959"
    ),
    cvd = c(
      "G45", "G46", "I60", "I61", "I62", "I63", "I64", "I65", "I66",
      "I67", "I68", "I69", "H340"
    ),
    dementica = c("F00", "F01", "F02", "F03", "G30", "F051", "G311"),
    copd = c(
      "J40", "J41", "J42", "J43", "J44", "J45", "J46", "J47",
      "J60", "J61", "J62", "J63", "J64", "J65", "J66", "J67",
      "I278", "I279", "J684", "J701", "J703"
    ),
    rheum = c(
      "M05", "M32", "M33", "M34", "M06",
      "M315", "M351", "M353", "M360"
    ),
    ulcer = c("K25", "K26", "K27", "K28"),
    liver_m = c(
      "B18", "K73", "K74", "K700", "K701", "K702", "K703", "K709",
      "K717", "K713", "K714", "K715", "K760", "K762", "K763",
      "K764", "K768", "K769", "Z944"
    ),
    dm_s = c(
      "E100", "E101", "E106", "E108", "E109",
      "E110", "E111", "E116", "E118", "E119",
      "E120", "E121", "E126", "E128", "E129",
      "E130", "E131", "E136", "E138", "E139",
      "E140", "E141", "E146", "E148", "E149"
    ),
    dm_cx = c(
      "E102", "E103", "E104", "E105", "E107",
      "E112", "E113", "E114", "E115", "E117",
      "E122", "E123", "E124", "E125", "E127",
      "E132", "E133", "E134", "E135", "E137",
      "E142", "E143", "E144", "E145", "E147"
    ),
    para = c(
      "G81", "G82", "G041", "G114", "G801", "G802",
      "G830", "G831", "G832", "G833", "G834", "G839"
    ),
    renal = c(
      "N18", "N19", "N052", "N053", "N054", "N055", "N056", "N057",
      "N250", "I120", "I131", "N032", "N033", "N034", "N035", "N036",
      "N037", "Z490", "Z491", "Z492", "Z940", "Z992"
    ),
    cancer = c(
      "C00", "C01", "C02", "C03", "C04", "C05", "C06", "C07",
      "C08", "C09", "C10", "C11", "C12", "C13", "C14", "C15", "C16",
      "C17", "C18", "C19", "C20", "C21", "C22", "C23", "C24", "C25",
      "C26", "C30", "C31", "C32", "C33", "C34", "C37", "C38", "C39",
      "C40", "C41", "C43", "C45", "C46", "C47", "C48", "C49",
      "C50", "C51", "C52", "C53", "C54", "C55", "C56", "C57", "C58",
      "C60", "C61", "C62", "C63", "C64", "C65", "C66", "C67", "C68",
      "C69", "C70", "C71", "C72", "C73", "C74", "C75", "C76",
      # not in the original non-ICD-10-CM, but clearly appropriate:
      "C7A", "C7B",
      # mets is recorded separately
      "C81", "C82", "C83", "C84", "C85", "C88",
      "C90", "C91", "C92", "C93", "C94", "C95", "C96", "C97"
    ),
    liver_s = c(
      "K704", "K711", "K721", "K729", "K765", "K766", "K767", "I850",
      "I859", "I864", "I982"
    ),
    mets = c("C77", "C78", "C79", "C80"),
    hiv = c("B20", "B21", "B22", "B24")
  )
  names(quan_charl_raw) <- icd::names_charlson_abbrev
  # this expansion will only be for 'defined' codes (currently the most
  # up-to-date canonical CMS ICD-10-CM list). Will ultimately need to generalize
  # this.

  # note that the children is actually an ICD-10-CM function. This needs
  # addressing. I already know that doing string matching is way too slow for
  # millions of rows, so some compromise of an exhaustive list of WHO/ICD-10-CM
  # children will likely be needed. Maybe generating a huge structure is still
  # worth it, even for ICD-10-CM, because I do end up cutting it back down to
  # size based on the input data before comorbidity matching.
  icd10_map_quan_deyo <- .apply_over_icd10cm_vers(quan_charl_raw)
  icd10_map_quan_deyo <- .apply_over_icd10who_vers(icd10_map_quan_deyo)
  icd10_map_quan_deyo <- lapply(icd10_map_quan_deyo, as.short_diag)
  icd10_map_quan_deyo <- lapply(icd10_map_quan_deyo, as.icd10)
  icd10_map_quan_deyo <- as.comorbidity_map(icd10_map_quan_deyo)
  icd10_map_charlson <- icd10_map_quan_deyo
  # It does appear that there are numerous codes in the Quan Elixhauser scheme
  # which are not present (?anymore) in the ICD-10-CM 2016 list.
  if (save_pkg_data) {
    .save_in_data_dir(icd10_map_quan_deyo)
    .save_in_data_dir(icd10_map_charlson)
  }
  invisible(icd10_map_quan_deyo)
}
# nocov end

.apply_over_ver_worker <- function(x, inner_fun, ...) {
  y <- inner_fun(x, short_code = TRUE, ...)
  unclass(c(x, y))
}

.apply_over_ver_updater <- function(out, upd) {
  for (cmb in seq_along(out)) {
    only_prev <- setdiff(out[[cmb]], upd[[cmb]])
    only_this <- setdiff(upd[[cmb]], out[[cmb]])
    if (length(only_prev)) {
      message("Only in previous for item ", cmb)
      print(only_prev)
      stop("Not going to make a map smaller without manual review.")
    }
    if (length(only_this)) {
      .dbg("Found new items for ", cmb)
      .dbg(only_this, print = TRUE)
    }
    out[[cmb]] <- sort(union(out[[cmb]], upd[[cmb]]))
  }
  out
}

.apply_over_icd10cm_vers <- function(raw) {
  out <- raw
  for (yr in 2014:2019) {
    .msg("Applying ICD-10-CM year: ", yr)
    with_icd10cm_version(
      as.character(yr),
      code = {
        upd <- sapply(out,
          FUN = .apply_over_ver_worker,
          inner_fun = children_defined.icd10cm,
          simplify = FALSE,
          USE.NAMES = TRUE
        )
        out <- .apply_over_ver_updater(out, upd)
      }
    ) # end of with active version
  } # end year loop
  out
}

#' Augment map with codes that have ever appeared in available WHO versions of ICD-10
#' @examples
#' # Codes have been added and removed since 2008
#' \dontrun{
#' setdiff(icd10who2016$code, icd10who2008fr$code)
#' setdiff(icd10who2008fr$code, icd10who2016$code)
#' }
#' @keywords internal
#' @noRd
.apply_over_icd10who_vers <- function(raw) {
  out <- raw
  for (who_ver in c("icd10who2016", "icd10who2008fr")) {
    .msg("Working on ", who_ver)
    upd <- sapply(out,
      FUN = .apply_over_ver_worker,
      inner_fun = children_defined.icd10who,
      who_ver = who_ver,
      simplify = FALSE,
      USE.NAMES = TRUE
    )
    .apply_over_ver_updater(out, upd)
  }
  out
}