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

Obsolete: 'icd9' is replaced by CRAN package 'icd'. Calculate comorbidities, Charlson scores, perform fast and accurate validation, conversion, manipulation, filtering and comparison of ICD-9-CM (clinical modification) codes. ICD-9 codes appear numeric but leading and trailing zeroes, and both decimal and non-decimal "short" format codes exist. The package enables a work flow from raw lists of ICD-9 codes from hospital billing databases to comorbidities. ICD-9 to comorbidity mappings from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included. Any other mapping of codes, such as ICD-10, to comorbidities can be used.

AuthorJack O. Wasey [aut, cre, cph], William Murphy [ctb], R Core Team [ctb, cph]
Date of publication2016-04-15 08:33:09
MaintainerJack O. Wasey <jack@jackwasey.com>
LicenseGPL-3
Version1.3.1
https://github.com/jackwasey/icd9

View on CRAN

Man pages

ahrqComorbid: AHRQ comorbidities

ahrqComorbidAll: AHRQ comorbidities, with HTN, CHF and renal failure subgroups

convert: Convert ICD9 codes between formats and structures.

elixComorbid: Elixhauser comorbidities

elixComorbidNames: Comorbidity names

expandRangeWorker: expand range worker function

factor_: Fast Factor Generation

fastIntToString: fast convert integer vector to character vector

generateSysData: Generate sysdata.rda

icd9AddLeadingZeroes: Add leading zeroes to incomplete ICD codes

icd9Billable: list of annual versions of billable leaf nodes of ICD-9-CM

icd9Chapters: ICD-9-CM chapters

icd9ChaptersToMap: convert the chapter headings to lists of codes

icd9Charlson: Calculate Charlson Comorbidity Index (Charlson Score)

icd9Children: Expand ICD-9 codes to all possible sub-codes

icd9Comorbid: find comorbidities from ICD-9 codes.

icd9ComorbidDfToMat: convert matrix of comorbidities into data frame, preserving...

icd9ComorbidMatToDf: convert matrix of comorbidities into data frame, preserving...

icd9Condense: Condense ICD-9 code by replacing complete families with...

icd9Count: count ICD codes or comorbidities for each patient

icd9DiffComorbid: show the difference between two comorbidity mappings

icd9DropLeadingZeroes: drop zero padding from decimal ICD-9 code.

icd9ExpandMinor: expand decimal part of ICD-9 code to cover all possible...

icd9ExpandRange: take two ICD-9 codes and expand range to include all child...

icd9Explain: explain ICD9 codes

icd9ExtractAlphaNumeric: extract alphabetic, and numeric part of icd9 code prefix

icd9FilterInvalid: Filter ICD-9 codes by invalidity.

icd9FilterPoa: Filters data frame based on present-on-arrival flag

icd9FilterValid: Filter ICD-9 codes by validity.

icd9GetChapters: get ICD-9 Chapters from vector of ICD-9 codes

icd9GetMajor: Get major (three-digit) part of ICD-9 codes

icd9GetValid: invalid subset of decimal or short ICD-9 codes

icd9GuessIsShort: guess whether short or long

icd9Hierarchy: ICD9-CM diagnosis code lookup

icd9InReferenceCode: match ICD9 codes

icd9IsA: test whether elements of vector begin with V, E (or any other...

icd9IsBillable: Determine whether codes are billable leaf-nodes

icd9IsN: do codes belong to numeric, V or E classes?

icd9IsReal: Check whether ICD-9 codes exist

icd9IsValid: check whether ICD-9 codes are syntactically valid

icd9IsValidMapping: validate an icd9 mapping to comorbidities

icd9LongToWide: convert ICD data from long to wide format

icd9-package: Tools for Working with ICD-9 Codes, and Finding Comorbidities

icd9PoaChoices: present-on-admission flags

icd9RandomShort: generate random short-form icd9 E codes

icd9ShortToDecimal: Convert ICD-9 codes between short and decimal forms

icd9Sort: sort short-form icd9 codes

icd9VanWalraven: Calculate van Walraven Elixhauser Score

icd9WideToLong: convert ICD data from wide to long format

logicalToBinary: encode TRUE as 1, and FALSE as 0 (integers)

parseAhrqSas: parse AHRQ data

parseElix: Generate Elixhauser comorbidities

parseIcd9Chapters: Read higher-level ICD-9 structure from a reliable web site

parseLeafDescriptionsAll: get billable codes from all available years

parseLeafDescriptionsVersion: read the ICD-9-CM description data as provided by the Center...

parseQuanDeyoSas: parse original SAS code defining Quan's update of Deyo...

parseRtfFifthDigitRanges: parse a row of RTF source data for ranges to apply fifth...

parseRtfLines: parse a character vector containing RTF strings

parseRtfYear: parse RTF description of entire ICD-9-CM for a specific year

quanDeyoComorbid: Quan adaptation of Deyo/Charlson comorbidities

quanElixComorbid: Quan adaptation of Elixhauser comorbidities

randomShortIcd9: genereate random short icd9 codes

sasDropOtherAssignment: drop superfluous assignment name when the name is already...

sasExtractLetStrings: extract quoted or unquoted SAS string definitions

sasFormatExtract: extract assignments from a SAS FORMAT definition.

sasParseAssignments: get assignments from a character string strings.

stripRtf: Strip RTF

strMultiMatch: return the actual matches from a bracketed regex

vermont_dx: de-identified data from public Vermont source for 2013

zip_single: unzip a single file

Files in this package

icd9
icd9/COPYING
icd9/inst
icd9/inst/COPYING
icd9/inst/COPYRIGHTS
icd9/inst/extdata
icd9/inst/extdata/comformat2012-2013.txt
icd9/inst/extdata/ICD9_E_Charlson.sas
icd9/inst/extdata/ICD9_E_Elixhauser.sas
icd9/inst/extdata/all-covariates.xls
icd9/inst/doc
icd9/inst/doc/introduction.R
icd9/inst/doc/introduction.html
icd9/inst/doc/introduction.Rmd
icd9/inst/include
icd9/inst/include/icd9_RcppExports.h
icd9/inst/include/icd9.h
icd9/tests
icd9/tests/testthat
icd9/tests/testthat/test-icd9.R
icd9/tests/testthat/test-LongToWide.R
icd9/tests/testthat/test-is.R
icd9/tests/testthat/test-sas.R
icd9/tests/testthat/test-openmp.R
icd9/tests/testthat/test-hierarchy.R
icd9/tests/testthat/test-filter.R
icd9/tests/testthat/test-convert.R
icd9/tests/testthat/test-parse.R
icd9/tests/testthat/test-ranges.R
icd9/tests/testthat/test-billable.R
icd9/tests/testthat/test-reshape.R
icd9/tests/testthat/test-valid.R
icd9/tests/testthat/test-score.R
icd9/tests/testthat/test-explain.R
icd9/tests/testthat/helper-base.R
icd9/tests/testthat/test-condense.R
icd9/tests/testthat/test-comorbid-calcs.R
icd9/tests/testthat/test-util.R
icd9/tests/testthat/test-comorbid.R
icd9/tests/test-all.R
icd9/src
icd9/src/convert.cpp
icd9/src/ranges.cpp
icd9/src/cutil.c
icd9/src/config.h.win
icd9/src/ranges.h
icd9/src/config.h.in
icd9/src/is.h
icd9/src/comorbidCommon.cpp
icd9/src/longToWide.cpp
icd9/src/manip.h
icd9/src/comorbid.cpp
icd9/src/util.h
icd9/src/Makevars.in
icd9/src/Makevars.win64
icd9/src/convert.h
icd9/src/local.h
icd9/src/util.cpp
icd9/src/cutil.h
icd9/src/Makevars.win
icd9/src/RcppExports.cpp
icd9/src/manip.cpp
icd9/src/comorbidSetup.cpp
icd9/src/is.cpp
icd9/NAMESPACE
icd9/data
icd9/data/mappingNames.rda
icd9/data/icd9Billable.RData
icd9/data/vermont_dx.RData
icd9/data/icd9ChaptersMajor.RData
icd9/data/quanDeyoComorbid.RData
icd9/data/icd9Hierarchy.RData
icd9/data/quanElixComorbid.RData
icd9/data/icd9ChaptersSub.RData
icd9/data/elixComorbid.RData
icd9/data/ahrqComorbid.RData
icd9/data/icd9Chapters.rda
icd9/R
icd9/R/convert.R icd9/R/explain.R icd9/R/parse-rtf.R icd9/R/manip.R
icd9/R/sysdata.rda
icd9/R/score.R icd9/R/filter.R icd9/R/datadocs.R icd9/R/benchmark.R icd9/R/icd9-package.R icd9/R/valid.R icd9/R/parse-comorbid.R icd9/R/RcppExports.R icd9/R/real.R icd9/R/comorbid.R icd9/R/parse.R icd9/R/condense.R icd9/R/util.R icd9/R/ranges.R icd9/R/sas.R icd9/R/zzz.R
icd9/vignettes
icd9/vignettes/introduction.Rmd
icd9/README.md
icd9/MD5
icd9/build
icd9/build/vignette.rds
icd9/DESCRIPTION
icd9/configure
icd9/man
icd9/man/icd9FilterValid.Rd icd9/man/icd9Charlson.Rd icd9/man/icd9GetValid.Rd icd9/man/icd9Condense.Rd icd9/man/ahrqComorbidAll.Rd icd9/man/icd9ExpandMinor.Rd icd9/man/icd9IsBillable.Rd icd9/man/parseRtfYear.Rd icd9/man/icd9InReferenceCode.Rd icd9/man/quanElixComorbid.Rd icd9/man/parseIcd9Chapters.Rd icd9/man/parseElix.Rd icd9/man/stripRtf.Rd icd9/man/expandRangeWorker.Rd icd9/man/elixComorbid.Rd icd9/man/icd9DiffComorbid.Rd icd9/man/icd9FilterInvalid.Rd icd9/man/parseLeafDescriptionsAll.Rd icd9/man/parseAhrqSas.Rd icd9/man/zip_single.Rd icd9/man/parseRtfFifthDigitRanges.Rd icd9/man/icd9RandomShort.Rd icd9/man/icd9ComorbidDfToMat.Rd icd9/man/icd9ExtractAlphaNumeric.Rd icd9/man/vermont_dx.Rd icd9/man/icd9GuessIsShort.Rd icd9/man/convert.Rd icd9/man/sasFormatExtract.Rd icd9/man/icd9-package.Rd icd9/man/icd9Chapters.Rd icd9/man/icd9IsReal.Rd icd9/man/randomShortIcd9.Rd icd9/man/icd9GetChapters.Rd icd9/man/generateSysData.Rd icd9/man/icd9LongToWide.Rd icd9/man/parseQuanDeyoSas.Rd icd9/man/icd9Children.Rd icd9/man/icd9ExpandRange.Rd icd9/man/elixComorbidNames.Rd icd9/man/parseRtfLines.Rd icd9/man/icd9VanWalraven.Rd icd9/man/sasParseAssignments.Rd icd9/man/sasDropOtherAssignment.Rd icd9/man/icd9WideToLong.Rd icd9/man/strMultiMatch.Rd icd9/man/icd9Billable.Rd icd9/man/logicalToBinary.Rd icd9/man/icd9IsValidMapping.Rd icd9/man/icd9ComorbidMatToDf.Rd icd9/man/icd9ShortToDecimal.Rd icd9/man/icd9IsA.Rd icd9/man/icd9Comorbid.Rd icd9/man/icd9Hierarchy.Rd icd9/man/icd9AddLeadingZeroes.Rd icd9/man/icd9GetMajor.Rd icd9/man/quanDeyoComorbid.Rd icd9/man/fastIntToString.Rd icd9/man/icd9PoaChoices.Rd icd9/man/icd9ChaptersToMap.Rd icd9/man/icd9FilterPoa.Rd icd9/man/ahrqComorbid.Rd icd9/man/icd9IsValid.Rd icd9/man/icd9DropLeadingZeroes.Rd icd9/man/sasExtractLetStrings.Rd icd9/man/factor_.Rd icd9/man/icd9Sort.Rd icd9/man/icd9IsN.Rd icd9/man/icd9Explain.Rd icd9/man/parseLeafDescriptionsVersion.Rd icd9/man/icd9Count.Rd
icd9/configure.win
icd9/cleanup
icd9/.Rinstignore

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