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icd9 (version 0.3)

tools for working with ICD-9 codes, and finding comorbidities

Description

This package allows accurate manipulation, validation and comparison of ICD-9-CM (clinical modification) codes. Although ICD-9 codes appear numeric, this is not the case, since trailing zeroes, and a mixture of decimal and non-decimal "short" format codes exist. Tools to map ICD-9 codes to co-morbidities are also provided, with mappings from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included.

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Version

Monthly Downloads

28

Version

0.3

License

GPL-3

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Repository

https://github.com/jackwasey/icd9

Maintainer

Jack O Wasey

Last Published

July 7th, 2014

Functions in icd9 (0.3)

icd9AddLeadingZeroes

pad decimal ICD-9 codes with leading zeroes

icd9ValidDecimal

check whether decimal icd9 codes are valid

check whether character vector represents all numeric values

tools for working with ICD-9 codes, and finding comorbidities

asCharacterNoWarn

convert factor or vector to character without warnings

icd9ExpandRangeDecimal

expand range of ICD-9 decimal codes to all possible intermediate and sub-codes

validate a major part

icd9ExtractAlphaNumeric

extract alphabetic, and numeric part of icd9 code prefix

appendZeroToNine

append zero to nine

ahrqComorbidAll

AHRQ comorbidities, with HTN, CHF and renal failure subgroups

icd9ExpandRangeMajor

create range of icd9 major parts

icd9ValidMapping

validate an icd9 mapping to comorbidities

spawnReferenceChildren

spawn reference codes into all possible lower-level codes (and memoise)

icd9DecimalToMajor

extract major part from decimal ICD-9 code

icd9DecimalToParts

icd9DecimalToParts

icd9InvalidDecimal

invalid subset of decimal or short ICD-9 codes

parseQuanElixhauser

Generate Quan's revised Elixhauser comorbidities

icd9ChapterShort

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

icd9DropLeadingZeroes

drop zero padding from decimal ICD-9 code.

icd9ChildrenShort

expand 5 character form 'short' ICD9 to all possible sub codes

icd9InReferenceCode

match ICD9 codes

ICD-9-CM chapters

sasFormatExtract

extract assignments from a SAS FORMAT definition.

read file from zip at URL

quanElixhauserComorbid

Quan adaptation of Elixhauser comorbidities

icd9ParentMinor

get parent of an ICD-9 code

icd9ValidNaWarnStop

stop, warn, replace invalid with NA or continue

stopIfInvalidIcd9

warn or stop with invalid ICD-9 codes

inverse of %in%

icd9ChildrenDecimal

generate all child codes for given decimal ICD9 codes

AHRQ comorbidities

icd9ExpandMinor

expand decimal part of ICD-9 code to cover all possible sub-codes

sasDropOtherAssignment

drop superfluous assignment name when the name is already defined.

icd9PartsRecompose

recompose major and minor parts into icd9 codes

icd9ExpandRangeShort

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

parseElixhauser

Generate Elixhauser comorbidities

icd9ShortToDecimal

icd9ShortToDecimal

parse AHRQ data

benchmark and profile major functions with larger data sets

icd9WarnStopMessage

warn or stop with message based on switch

icd9DecimalToShort

convert between icd9 decimal and short formats

strip all whitespace

icd9Comorbidities

merge comorbidities with icd9 codes per visitId (or other identity)

read the ICD-9-CM description data as provided by the Center for Medicaid Services.

asNumericNoWarn

convert factor or vector to numeric without warnings

saveSourceTreeData

save data in source tree

strip whitespace from ends of each string in given character vector

is the given code V or E type?

icd9ShortToParts

extract major and minor parts of a decimal ICD-9 code

sasExtractLetStrings

extract quoted or unquoted SAS string definitions

elixhauserComorbid

Elixhauser comorbidities

logicalToBinary

encode TRUE as 1, and FALSE as 0

icd9CondenseToExplainShort

condense list of short ICD-9 code into minimal set of parent codes which have descriptions.

sort short-form icd9 codes

describe ICD-9 codes, guess whether short or long

icd9SubsequentMinors

determine preceding or subsequent post-decimal parts of ICD9 codes

validate ICD-9 short form code

lookupComorbidities

lookup pre-calculated co-morbidities for given list of visit IDs

explain ICD9 codes

return the actual matches from a bracketed regex

parseIcd9Chapters

parse list of top-level ICD-9 chapters from canonical data from CDC.

sasParseAssignments

get assignments from a character string strings.

parseQuanDeyoSas

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

icd9InvalidActions

invalid actions, default is first item

icd9ShortToMajor

extract major part from short ICD-9 code

check whether any ICD-9 code is syntactically valid

icd9CondenseShort

condense list of short ICD-9 code into minimal set of parent codes

quanDeyoComorbid

Quan adaptation of Deyo/Charlson comorbidities

ICD9-CM diagnosis code lookup