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


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Documentation for package ‘icd9’ version 1.1

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A C E I P Q misc

icd9-package tools for working with ICD-9 codes, and finding comorbidities

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ahrqComorbid AHRQ comorbidities
ahrqComorbidAll AHRQ comorbidities, with HTN, CHF and renal failure subgroups
ahrqComorbidNames Comorbidity names
ahrqComorbidNamesAbbrev Comorbidity names
ahrqComorbidNamesHtn Comorbidity names
ahrqComorbidNamesHtnAbbrev Comorbidity names

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charlsonComorbidNames Comorbidity names
charlsonComorbidNamesAbbrev Comorbidity names
convert work around Rcpp issue https://github.com/RcppCore/Rcpp/issues/272

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elixComorbid Elixhauser comorbidities
elixComorbidNames Comorbidity names
elixComorbidNamesAbbrev Comorbidity names
elixComorbidNamesHtn Comorbidity names
elixComorbidNamesHtnAbbrev Comorbidity names

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icd9 tools for working with ICD-9 codes, and finding comorbidities
icd9Chapters ICD-9-CM chapters
icd9chapters ICD-9-CM chapters
icd9ChaptersMajor ICD-9-CM chapters
icd9ChaptersSub ICD-9-CM chapters
icd9Charlson Calculate Charlson Comorbidity Index (Charlson Score)
icd9Charlson.data.frame Calculate Charlson Comorbidity Index (Charlson Score)
icd9CharlsonComorbid Calculate Charlson Comorbidity Index (Charlson Score)
icd9Children Expand ICD-9 codes to all possible sub-codes
icd9ChildrenDecimal Expand ICD-9 codes to all possible sub-codes
icd9ChildrenShort Expand ICD-9 codes to all possible sub-codes
icd9ComorbidDfToMat convert matrix of comorbidities into data frame, preserving visitId information
icd9ComorbidMatToDf convert matrix of comorbidities into data frame, preserving visitId information
icd9Condense Condense ICD-9 code by replacing complete families with parent codes
icd9CondenseDecimal Condense ICD-9 code by replacing complete families with parent codes
icd9CondenseShort Condense ICD-9 code by replacing complete families with parent codes
icd9CondenseToMajor Condense ICD-9 code by replacing complete families with parent codes
icd9CondenseToMajorDecimal Condense ICD-9 code by replacing complete families with parent codes
icd9CondenseToMajorShort Condense ICD-9 code by replacing complete families with parent codes
icd9Count count ICD codes or comorbidities for each patient
icd9CountComorbidBin count ICD codes or comorbidities for each patient
icd9CountWide count ICD codes or comorbidities for each patient
icd9DecimalToParts work around Rcpp issue https://github.com/RcppCore/Rcpp/issues/272
icd9DecimalToShort work around Rcpp issue https://github.com/RcppCore/Rcpp/issues/272
icd9DiffComorbid show the difference between two comorbidity mappings
icd9ExpandRange take two ICD-9 codes and expand range to include all child codes
icd9ExpandRangeDecimal take two ICD-9 codes and expand range to include all child codes
icd9ExpandRangeMajor take two ICD-9 codes and expand range to include all child codes
icd9ExpandRangeShort take two ICD-9 codes and expand range to include all child codes
icd9Explain explain ICD9 codes
icd9Explain.character explain ICD9 codes
icd9Explain.factor explain ICD9 codes
icd9Explain.list explain ICD9 codes
icd9Explain.numeric explain ICD9 codes
icd9ExplainDecimal explain ICD9 codes
icd9ExplainShort explain ICD9 codes
icd9FilterInvalid Filter ICD-9 codes by invalidity.
icd9FilterPoa Filters data frame based on present-on-arrival flag
icd9FilterPoaNo Filters data frame based on present-on-arrival flag
icd9FilterPoaNotNo Filters data frame based on present-on-arrival flag
icd9FilterPoaNotYes Filters data frame based on present-on-arrival flag
icd9FilterPoaYes Filters data frame based on present-on-arrival flag
icd9FilterValid Filter ICD-9 codes by validity.
icd9GetInvalid invalid subset of decimal or short ICD-9 codes
icd9GetInvalidDecimal invalid subset of decimal or short ICD-9 codes
icd9GetInvalidMappingDecimal validate an icd9 mapping to comorbidities
icd9GetInvalidMappingShort validate an icd9 mapping to comorbidities
icd9GetInvalidShort invalid subset of decimal or short ICD-9 codes
icd9GetMajor work around Rcpp issue https://github.com/RcppCore/Rcpp/issues/272
icd9GetReal Check whether ICD-9 codes exist
icd9GetRealDecimal Check whether ICD-9 codes exist
icd9GetRealShort Check whether ICD-9 codes exist
icd9GetValid invalid subset of decimal or short ICD-9 codes
icd9GetValidDecimal invalid subset of decimal or short ICD-9 codes
icd9GetValidShort invalid subset of decimal or short ICD-9 codes
icd9Hierarchy ICD9-CM diagnosis code lookup
icd9Is are the given codes numeric, V or E type?
icd9IsE are the given codes numeric, V or E type?
icd9IsN are the given codes numeric, V or E type?
icd9IsReal Check whether ICD-9 codes exist
icd9IsRealDecimal Check whether ICD-9 codes exist
icd9IsRealShort Check whether ICD-9 codes exist
icd9IsV are the given codes numeric, V or E type?
icd9IsValid check whether ICD-9 codes are syntactically valid
icd9IsValidDecimal check whether ICD-9 codes are syntactically valid
icd9IsValidMajor check whether ICD-9 codes are syntactically valid
icd9IsValidMapping validate an icd9 mapping to comorbidities
icd9IsValidMappingDecimal validate an icd9 mapping to comorbidities
icd9IsValidMappingShort validate an icd9 mapping to comorbidities
icd9IsValidShort check whether ICD-9 codes are syntactically valid
icd9IsValidShortE check whether ICD-9 codes are syntactically valid
icd9IsValidShortN check whether ICD-9 codes are syntactically valid
icd9IsValidShortV check whether ICD-9 codes are syntactically valid
icd9LongToWide convert ICD data from long to wide format
icd9MajMinToCode work around Rcpp issue https://github.com/RcppCore/Rcpp/issues/272
icd9MajMinToDecimal work around Rcpp issue https://github.com/RcppCore/Rcpp/issues/272
icd9MajMinToParts work around Rcpp issue https://github.com/RcppCore/Rcpp/issues/272
icd9MajMinToShort work around Rcpp issue https://github.com/RcppCore/Rcpp/issues/272
icd9PartsToDecimal work around Rcpp issue https://github.com/RcppCore/Rcpp/issues/272
icd9PartsToShort work around Rcpp issue https://github.com/RcppCore/Rcpp/issues/272
icd9PoaChoices present-on-admission flags
icd9ShortToDecimal work around Rcpp issue https://github.com/RcppCore/Rcpp/issues/272
icd9ShortToParts work around Rcpp issue https://github.com/RcppCore/Rcpp/issues/272
icd9Sort sort short-form icd9 codes
icd9SortDecimal sort short-form icd9 codes
icd9SortShort sort short-form icd9 codes
icd9Valid check whether ICD-9 codes are syntactically valid
icd9ValidDecimal check whether ICD-9 codes are syntactically valid
icd9ValidShort check whether ICD-9 codes are syntactically valid
icd9WideToLong convert ICD data from wide to long format

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package-icd9 tools for working with ICD-9 codes, and finding comorbidities

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quanDeyoComorbid Quan adaptation of Deyo/Charlson comorbidities
quanElixComorbid Quan adaptation of Elixhauser comorbidities
quanElixComorbidNames Comorbidity names
quanElixComorbidNamesAbbrev Comorbidity names
quanElixComorbidNamesHtn Comorbidity names
quanElixComorbidNamesHtnAbbrev Comorbidity names

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%i9d% take two ICD-9 codes and expand range to include all child codes
%i9da% take two ICD-9 codes and expand range to include all child codes
%i9mj% take two ICD-9 codes and expand range to include all child codes
%i9s% take two ICD-9 codes and expand range to include all child codes
%i9sa% take two ICD-9 codes and expand range to include all child codes