R/manip.R

In jackwasey/icd9: Tools for Working with ICD-9 Codes, and Finding Comorbidities

# Copyright (C) 2014 - 2015  Jack O. Wasey
#
# This file is part of icd9.
#
# icd9 is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# icd9 is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with icd9. If not, see <http:#www.gnu.org/licenses/>.

#' @title extract alphabetic, and numeric part of icd9 code prefix
#' @description removes whitespace and separates V or E if present.
#' @template icd9-any
#' @return vector or matrix, with first item of each row (or whole vector)
#'   containing V, E or "". The second part contains the numeric parts of the
#'   code, which may include a decimal point.
#' @keywords internal manip
icd9ExtractAlphaNumeric <- function(icd9) {
  assertFactorOrCharacter(icd9)
  # generate list, then flip into a matrix with a row for each code, and the
  # alpha part in first column, and numeric part in the second
  t(
    vapply(
      strMultiMatch(pattern = "([VvEe]?)([[:digit:].]+)",
                    text = as.character(icd9), dropEmpty = FALSE),
      function(x) matrix(data = x[1:2], nrow = 1, ncol = 2),
      FUN.VALUE = rep(NA_character_, times = 2)
    )
  )
}

#' @title drop zero padding from decimal ICD-9 code.
#' @description decimal form ICD-9 codes are not ambiguous if the leading zeroes
#'   are dropped. Some short-form ICD-9 codes would not be ambiguous, e.g. "1"
#'   but many would be problematic. This is the inverse of
#'   \code{icd9AddLeadingZeroesDecimal}.
#'
#'   Invalid codes have no guaranteed result, and may give NA, or a (possibly
#'   valid) code in repsonse.
#' @template icd9-any
#' @return character vector of ICD-9 codes with extra zeroes dropped from major
#'   part
#' @family ICD-9 convert
#' @keywords internal manip
icd9DropLeadingZeroes <- function(icd9, isShort) {
  assertFactorOrCharacter(icd9)
  assertFlag(isShort)
  if (isShort) return(
    icd9DropLeadingZeroesShort(icd9Short = icd9))
  icd9DropLeadingZeroesDecimal(icd9Decimal = icd9)
}

#' @rdname icd9DropLeadingZeroes
#' @template icd9-decimal
icd9DropLeadingZeroesDecimal <- function(icd9Decimal) {
  assertFactorOrCharacter(icd9Decimal)
  out <- vapply(
    X = strMultiMatch(
      pattern = "[[:space:]]*([EeVv]?)(0*)([\\.[:digit:]]+)[[:space:]]*",
      text = icd9Decimal),
    FUN = function(x) if (length(x) > 0) sprintf("%s%s", x[1], x[3]) else NA_character_,
    FUN.VALUE = character(1)
  )
  out
}

#' @rdname icd9DropLeadingZeroes
#' @template icd9-short
icd9DropLeadingZeroesShort <- function(icd9Short) {
  assertFactorOrCharacter(icd9Short)
  parts <- icd9ShortToParts(icd9Short = icd9Short, minorEmpty = "")
  # very important: only drop the zero in V codes if the minor part is empty.
  areEmpty <- parts[["minor"]] == ""

  icd9Short[areEmpty] <- icd9DropLeadingZeroesMajor(parts[areEmpty, "major"])
  icd9Short
}

#' @rdname icd9DropLeadingZeroes
icd9DropLeadingZeroesMajor <- function(major) {
  # (valid) E codes don't ever have leading zeroes
  # major can legitimately be an integer
  major <- trim(major) # my trim loses encoding, but this shouldn't matter
  isV <- icd9IsV(major) # not checking validity, necessarily, just quick check
  isN <- icd9IsValidMajorN(major)
  major[isV] <- sub(pattern = "^([Vv])0([[:digit:]]{1})$",
                    replacement = "\\1\\2",
                    x = major[isV])
  #just replace the FIRST string of zeros everything else is passed through
  major[isN] <- sub(pattern = "^[[:space:]]*0{1,2}",
                    replacement = "",
                    x = major[isN])
  major
}