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icd9 (version 0.5)

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

Description

This package allows accurate manipulation, conversion, 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

0.5

License

GPL-3

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Repository

https://github.com/jackwasey/icd9

Maintainer

Jack O Wasey

Last Published

July 21st, 2014

Functions in icd9 (0.5)

sort short-form icd9 codes

icd9GuessIsShort

guess whether short or long

parse AHRQ data

icd9PartsRecompose

recompose major and minor parts into icd9 codes

icd9DecimalToShort

convert between icd9 decimal and short formats

icd9Comorbidities

find comorbidities from ICD-9 codes.

icd9ChildrenDecimal

generate all child codes for given decimal ICD9 codes

validate a major part

icd9InvalidDecimal

invalid subset of decimal or short ICD-9 codes

ICD-9-CM chapters

ICD9-CM diagnosis code lookup

icd9WarnStopMessage

warn or stop with message based on switch

Does ICD-9 code exist

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

icd9ChaptersToMap

convert the chapter headings to lists of codes

return the actual matches from a bracketed regex

AHRQ comorbidities

logicalToBinary

encode TRUE as 1, and FALSE as 0

icd9ParentMinor

get parent of an ICD-9 code

icd9CondenseToMajor

condense list of short ICD-9 code into minimal set of major-part-only codes

strip whitespace from ends of each string in given character vector

parseIcd9Chapters

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

saveSourceTreeData

save data in source tree

sasFormatExtract

extract assignments from a SAS FORMAT definition.

asNumericNoWarn

convert factor or vector to numeric without warnings

icd9GetChapters

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

check whether character vector represents all numeric values

asCharacterNoWarn

convert factor or vector to character without warnings

quanElixhauserComorbid

Quan adaptation of Elixhauser comorbidities

quanDeyoComorbid

Quan adaptation of Deyo/Charlson comorbidities

icd9ValidDecimal

check whether decimal icd9 codes are valid

benchmark and profile major functions with larger data sets

icd9SubsequentMinors

determine preceding or subsequent post-decimal parts of ICD9 codes

icd9ExpandRangeMajor

create range of icd9 major parts

elixhauserComorbid

Elixhauser comorbidities

filters data frame based on present-on-arrival flag

icd9ExpandRangeShort

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

icd9DropLeadingZeroes

drop zero padding from decimal ICD-9 code.

icd9ParseAndSaveMappings

parse all known mappings and save to development tree

inverse of %in%

icd9DecimalToParts

convert decimal-form ICD-9 code to major and minor parts

icd9AddLeadingZeroes

pad decimal ICD-9 codes with leading zeroes

icd9ShortToDecimal

convert short-form ICD-9 code to decimal form

appendZeroToNine

append zero to nine

check whether any ICD-9 code is syntactically valid

extract major part from short or decimal ICD-9 code

stopIfInvalidIcd9

warn or stop with invalid ICD-9 codes

elixhauserComorbidNames

Comorbidity names

ahrqComorbidAll

AHRQ comorbidities, with HTN, CHF and renal failure subgroups

sasParseAssignments

get assignments from a character string strings.

icd9ExpandMinor

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

icd9ExpandRangeDecimal

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

icd9ValidMapping

validate an icd9 mapping to comorbidities

icd9CondenseToExplain

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

spawnReferenceChildren

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

explain ICD9 codes

icd9ExtractAlphaNumeric

extract alphabetic, and numeric part of icd9 code prefix

strip all whitespace

sasDropOtherAssignment

drop superfluous assignment name when the name is already defined.

parseElixhauser

Generate Elixhauser comorbidities

parseQuanElixhauser

Generate Quan's revised Elixhauser comorbidities

parseIcd9Descriptions

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

present-on-admission flags

validate ICD-9 short form code

read file from zip at URL

icd9InvalidActions

invalid actions, default is first item

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

icd9ValidNaWarnStop

stop, warn, replace invalid with NA or continue

parseQuanDeyoSas

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

icd9InReferenceCode

match ICD9 codes

icd9ChildrenShort

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