tests/testthat/helper-icd10.R

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

message("loading helper-icd10.R")
one_icd10_pt <- icd_long_data(
  visit = c("a"),
  icd = as.icd10("I2609"),
  date = as.Date(c("2011-01-01"))
)
icd10_each_quan_elix_cmb <- icd:::icd10cm(c(
  "I42.6",
  "I44.39",
  "Z95.3",
  "I27.81",
  "K55.8",
  "I10", # I10.x in Quan et al, but I10 is a lead node in ICD-10-CM
  "I13.11", # htncx
  "G82.50", # paralysis
  "R56.00",
  "J45.998", # pulm
  "E13.11", # DM, Quan is less specific, without wildcard
  "E13.359", # DMcx
  "E00.0",
  "N19", # N19.x in Quan, yet N19 is leaf node in CM
  "B18.9", # liver
  "K26.9", # PUD
  # B22 not defined in ICD-10-CM, B20 covers all HIV, but Quan uses B20-22,24
  "B22",
  "C82.28",
  "C77.9",
  "C00.8",
  "M31.31",
  "D69.41",
  "E66.09",
  "E42",
  "E86.1",
  "D50.0",
  "D50.8",
  "F10.959",
  "F11.988",
  "F29",
  "F31.31"
))
icd10_each_ahrq_cmb <- icd:::icd10cm(c(
  "I50.9", # CHF I42.6 not in AHRQ, but in Quan Elix
  "Z95.3",
  "I27.81",
  "K55.8",
  "I10", # I10.x in Quan et al, but I10 is a lead node in ICD-10-CM
  "O11.9", # htncx, use pregnancy HTN, so I don't also get CHF, renal or DM
  "G82.50", # paralysis
  "R56.00",
  "J45.998", # pulm
  "E13.11", # DM, Quan is less specific, without wildcard
  "E13.359", # DMcx
  "E00.0",
  "N19", # N19.x in Quan, yet N19 is leaf node in CM
  "B18.2", # liver http://www.icd10data.com/ICD10CM/Codes/A00-B99/B15-B19/B18-
  "K26.9", # PUD
  # B22 not defined in ICD-10-CM, B20 covers all HIV, but Quan uses B20-22,24
  "B20", # HIV or AIDS
  "C82.28",
  "C77.9",
  "C00.8",
  "M08.979", # arth/rheum M31.31 in Quan but not AHRQ,
  "D69.41",
  "E66.09",
  "E42",
  "E86.1",
  "D50.0",
  "D50.8",
  "F10.959",
  "F11.988",
  "F29",
  "F43.21"
)) # depression F31.31 not in AHRQ, but appears in Quan Elix
icd10_all_quan_elix <- data.frame(
  pt_id = 1:31,
  icd10_code = icd10_each_quan_elix_cmb,
  stringsAsFactors = FALSE
)
icd10_all_quan_elix_one_pt <- data.frame(
  pt_id = rep(1, 31),
  icd10_code = icd10_each_quan_elix_cmb
)

icd10_all_ahrq <- data.frame(
  pt_id = 1:30,
  icd10_code = icd10_each_ahrq_cmb,
  stringsAsFactors = FALSE
)
icd10_all_ahrq_one_pt <- data.frame(
  pt_id = rep(1, 30),
  icd10_code = icd10_each_ahrq_cmb
)

icd10_tricky <- icd:::icd10cm(
  c(
    "V97.33XD", "W51.XXXA", "V00.01XD", "Y93.D", "Z99.89", "Y92.146",
    "S10.87XA", "W55.41XA", "W61.62XD", "Z63.1", "Y93.D", "V91.07XD",
    "W55.29XA", "V95.43XS", "W61.12XA", "R46.1"
  )
)
n <- 500
set.seed(1441)
random_short_icd10_codes <-
  sample(unlist(icd10_map_elix), replace = TRUE, size = n)
random_icd10_pts <- data.frame(
  visit_id = sample(seq(1, np), replace = TRUE, size = n),
  icd10 = random_short_icd10_codes,
  poa = as.factor(sample(
    x = c("Y", "N", "n", "n", "y", "X", "E", "", NA),
    replace = TRUE, size = n
  ))
)