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icd9 (version 0.2.1)

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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Monthly Downloads

28

Version

0.2.1

License

GPL-3

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Repository

https://github.com/jackwasey/icd9

Maintainer

Jack O Wasey

Last Published

July 2nd, 2014

Functions in icd9 (0.2.1)

icd9AddLeadingZeroesShort

add leading zeroes to short-form ICD-9 code

icd9ExpandMinor

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

spawnReferenceChildren

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

icd9ExpandRangeDecimal

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

ahrqComorbidAll

AHRQ comorbidities, with HTN, CHF and renal failure subgroups

lookupComorbidities

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

icd9ChildrenShort

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

icd9ExtractAlphaNumeric

extract alphabetic, and numeric part of icd9 code prefix

icd9ValidMapping

validate an icd9 mapping to comorbidities

parseQuanElixhauser

Generate Quan's revised Elixhauser comorbidities

icd9AddLeadingZeroesMajor

zero-pad major part of ICD9 code

quanElixhauserComorbid

Quan adaptation of Elixhauser comorbidities

parseElixhauser

Generate Elixhauser comorbidities

explain ICD9 codes

icd9ShortToParts

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

inverse of %in%

icd9ExpandRangeShort

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

icd9DecimalToShort

convert between icd9 decimal and short formats

icd9ValidNaWarnStop

stop, warn, replace invalid with NA or continue

create range of icd9 major parts

check whether any ICD-9 code is syntactically valid

icd9PartsRecompose

recompose major and minor parts into icd9 codes

icd9Comorbidities

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

icd9ChildrenDecimal

generate all child codes for given decimal ICD9 codes

getInvalidDecimalIcd9

invalid subset of decimal or short ICD-9 codes

icd9DecimalToParts

icd9DecimalToParts

parseQuanDeyoSas

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

sasExtractLetStrings

extract quoted or unquoted SAS string definitions

AHRQ comorbidities

icd9CondenseShort

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

sasDropOtherAssignment

drop superfluous assignment name when the name is already defined.

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

icd9DropZeroFromDecimal

drop zero padding from decimal ICD-9 code.

elixhauserComorbid

Elixhauser comorbidities

sasParseAssignments

get assignments from a character string strings.

icd9ShortToDecimal

icd9ShortToDecimal

icd9ValidDecimal

check whether decimal icd9 codes are valid

validate a major part

icd9AddLeadingZeroesDecimal

pad decimal ICD-9 codes with leading zeroes

logicalToBinary

encode TRUE as 1, and FALSE as 0

parse AHRQ data

stopIfInvalidIcd9

warn or stop with invalid ICD-9 codes

return the actual matches from a bracketed regex

quanDeyoComorbid

Quan adaptation of Deyo/Charlson comorbidities

strip whitespace from ends of each string in given character vector

icd9CondenseToExplainShort

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

appendZeroToNine

append zero to nine

sort short-form icd9 codes

sasFormatExtract

extract assignments from a SAS FORMAT definition.

saveSourceTreeData

save data in source tree

strip all whitespace

check whether character vector represents all numeric values

validate ICD-9 short form code

asNumericNoWarn

convert factor or vector to numeric without warnings

ICD9-CM diagnosis code lookup

icd9InReferenceCode

match ICD9 codes

icd9SubsequentMinors

determine preceding or subsequent post-decimal parts of ICD9 codes

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

benchmark and profile major functions with larger data sets

icd9WarnStopMessage

warn or stop with message based on switch

asCharacterNoWarn

convert factor or vector to character without warnings