R/icd9-package.R

In 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/>.

#' @details
#'   \describe{
#'
#'   \item{Comorbidities}{ \code{\link{icd9Comorbid}} determines co-morbidities
#'   for a set of patients with one or more ICD-9 codes each.
#'   \code{\link{icd9Charlson}} calculates Charlson score (Comorbidity Index).
#'
#'   \itemize{
#'
#'   \item AHRQ comorbidity mapping is provided, and a function to read the raw
#'   SAS code from AHRQ into R data structures. The pre-processed data is
#'   available by lazy-loading in \code{\link{ahrqComorbid}}. AHRQ releases new
#'   mappings annually.
#'
#'   \item Quan revised both Deyo/Charlson and Elixhauser ICD-9 to comorbidity
#'   mappings. These are presented as: \code{link{quanDeyoComorbid}} (which is
#'   also derived from the original SAS code used in his publication, referenced
#'   in the data documentation), and \code{\link{quanElixComorbid}} which was
#'   transcribed directly from the same paper.
#'
#'   \item The original Elixhauser mapping is provided, with codes transcribed
#'   from the original publication. See \code{\link{elixComorbid}}.
#'
#'   } }
#'
#'   \item{Validation}{\code{\link{icd9IsValid}} checks whether ICD-9 codes are
#'   syntactically valid (although not necessarily genuine ICD-9 diagnoses). In
#'   contrast, \code{\link{icd9IsReal}} checks whether ICD-9 codes correspond to
#'   diagnoses in the current ICD-9-CM definition from CMS.}
#'
#'   \item{Conversion}{ There are many functions to convert ICD-9 codes or their
#'   components between different formats and structures. The most commonly used
#'   are:  \code{\link{icd9DecimalToShort}}, \code{\link{icd9ShortToDecimal}} to
#'   convert, e.g., 002.3 to 0023 and back again. See \link{convert} for other
#'   options.}
#'
#'   \item{Manipulation}{You can find children of a higher-level ICD-9 code with
#'   \code{\link{icd9Children}} and find a common parent to a set of children
#'   (or arbitrary list of ICD-9 codes) with \code{\link{icd9Condense}}.
#'   \code{\link{icd9Sort}} sorts in hierarchical, then numerical order, so
#'   100.0 comes before 100.00, for example. \code{\link{icd9WideToLong}} and
#'   \code{\link{icd9LongToWide}} convert the two most common data structures
#'   containing patient disease data. This is more sophisticated than standard R
#'   or Hadleyverse reshaping.}
#'
#'   \item{Explanation, or decoding}{Use \code{\link{icd9Explain}} to convert a
#'   list of codes into human-readable descriptions. This function can
#'   optionally reduce the codes to a their top-level groups if all the child
#'   members of a group are present. \code{\link{icd9DiffComorbid}} allows
#'   summary of the differences between comorbidity mappings, e.g. to find what
#'   has changed from year-to-year or between revisions by different authors.
#'   \code{\link{icd9Hierarchy}} is a \code{data.frame} containing the full
#'   ICD-9 classification for each diagnosis. \code{\link{icd9Chapters}}
#'   contains definitions of chapters, sub-chapters and three-digit groups.}
#'
#'   }
#'
"_PACKAGE"
#' @docType package
#' @name icd9-package
#' @aliases icd9 package-icd9
#' @author Jack O. Wasey \email{jack@@jackwasey.com}
#' @keywords misc utilities
#' @references
#' \url{http://www.hcup-us.ahrq.gov/toolssoftware/comorbidity/comorbidity.jsp}
#' @seealso rClinicalCodes comorbidities
#' @concept icd9 ICD-9 comorbidity comorbidities
#' @useDynLib icd9
#' @import Rcpp
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