benchmarks/bench-versus-compare.R

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

compare_versus_others <- function() {
  icd_res <- icd::comorbid_quan_deyo(thousand_pts, return_df = TRUE)
  comorbidity_res <- comorbidity::comorbidity(
    x = thousand_pts, id = "visit_id",
    code = "code", score = "charlson_icd9"
  )
  comorbidity_res$visit_id <- as.character(comorbidity_res$visit_id)
  comorbidity_res <- icd:::binary_to_logical(comorbidity_res)[1:18]
  medicalrisk_res <- medicalrisk::generate_comorbidity_df(
    thousand_pts_mr,
    icd9mapfn = medicalrisk::icd9cm_charlson_quan
  )
  icd_res <- unname(icd_res)
  comorbidity_res <- unname(comorbidity_res)
  medicalrisk_res <- unname(medicalrisk_res)
  identical(icd_res, comorbidity_res)
  identical(icd_res, medicalrisk_res)
  identical(comorbidity_res, medicalrisk_res)
  # oh dear - all three are different
  colSums(icd_res[-1])
  colSums(medicalrisk_res[-1])
  colSums(comorbidity_res[-1])

  # differences are in chronic pulmonary disease (6) and cancer (14)
  icd_res$visit_id[which(icd_res$Pulmonary != comorbidity_res$copd)] # two differences
  icd_res$visit_id[which(icd_res$Cancer != comorbidity_res$canc)] # seven different patients

  icd_res$visit_id[which(icd_res$Pulmonary != medicalrisk_res$chrnlung)] # two differences
  icd_res$visit_id[which(icd_res$Cancer != medicalrisk_res$tumor)] # just one difference

  icd_res$visit_id[which(comorbidity_res$copd != medicalrisk_res$chrnlung)] # agreement
  icd_res$visit_id[which(comorbidity_res$canc != medicalrisk_res$tumor)] # six differ

  # patients "5", "35", "39" appear most
  bad_pts <- thousand_pts[thousand_pts$visit_id %in% c("5", "35", "39"), c("visit_id", "code")]

  pt_39_codes <- bad_pts[bad_pts$visit_id == "39", "code"]
  # look for where chronic lung disease might be hiding
  explain_code(icd:::icd_get_major.icd9(pt_39_codes, short_code = TRUE), warn = FALSE)

  # possible additions Jul 2018:
  #
  # ICD-9 750.87 doesn't exist, but Other specified anomalies of upper
  # alimentary tract is 750.8
  # http://www.icd9data.com/2015/Volume1/740-759/750/750.8.htm


  charlson_cmp_chk <- function(x, y) {
    x2 <- unname(x[2:18])
    y2 <- unname(y[2:18])
    if (is.data.frame(x2)) {
      x2 <- lapply(x2, as.logical)
      y2 <- lapply(y2, as.logical)
    }
    stopifnot(all.equal(x2, y2))
  }

  bad_pt <- data.frame(stringsAsFactors = FALSE, id = 1, icd9cm = "75087")
  charlson_cmp_chk(
    ires <- comorbid_charlson(bad_pt, return_df = TRUE),
    comorbidity::comorbidity(bad_pt, id = "id", code = "icd9cm", score = "charlson_icd9")
  )
  charlson_cmp_chk(
    medicalrisk::generate_comorbidity_df(
      pts_mr,
      icd9mapfn = medicalrisk::icd9cm_charlson_quan
    ),
    ires
  )
  # medicalrisk is outlier
}