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# 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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