icd9 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,
Elixhauser and AHRQ included. * icd9Validicd9ValidDecimal,
icd9ValidShort and related functions
(icd9ValidDecimalN, icd9ValidDecimalV,
icd9ValidDecimalE, icd9ValidShortN,
icd9ValidShortV), icd9ValidShortE) check
whether given ICD-9 codes are syntactically valid (although not necessarily
genuine ICD-9 codes) * icd9Comorbidities determines
co-morbidities for a set of patients with one or more ICD-9 codes each.
* Functions to convert vectors (not lists) of ICD-9 codes include:
icd9DecimalToShort, icd9ShortToDecimal.
icd9ShortToParts and icd9DecimalToParts split a
vector of ICD-9 codes into the 'major' part (before decimal point), and
'minor' part (after decimal). The inverse operations are
icd9PartsToShort and icd9PartsToDecimal.
* Several functions interpret or generate ranges of ICD-9 codes. ICD-9
codes in publications are often specified in ranges, and this requires
careful interpretation to avoid including overly broad intermediate codes
that might appear in a simple numerical range. See the test suite for some
example cases. icd9ChildrenDecimal and
icd9ChildrenShort generate the full range of child ICD-9
codes. The reverse operation is icd9CondenseShort, which
takes a mass of codes and finds the smallest set of parent codes with any
of the original codes, which exactly describes the original set.
icd9CondenseToExplainShort) does the same as
icd9CondenseShort, but only finds parents which have a
human-readable name. Many top-level codes, e.g. "391" are not themselves
defined, but have description for their children. %i9mj%
creates a range of icd9 major codes, whereas %i9s%
(icd9ExpandRangeShort) and %i9d%
(icd9ExpandRangeDecimal) create correct ranges of short and
decimal ICD-9 codes, respectively. The only limitation is that E code
ranges are not implemented (not ever seen in the wild by the author).
* icd9SortShort sorts in heirarchical, then numerical order,
so 100.0 comes before 100.00, for example.
* AHRQ comorbidity mapping is provided, and a function to read the raw SAS
code from AHRQ into R data structures. The pre-processed data is available
by lazy-loading in ahrqComorbid. AHRQ releases new mappings
annually.
* Quan revised both Deyo/Charlson and Elixhauser ICD-9 to comorbidity
mappings. These are presented as: link{quanDeyoComorbid} (which is
also derived from the original SAS code used in his publication, referenced
in the data documentation), and quanElixhauserComorbid which
was transcribed directly from the same paper.
* The original Elixhauser mapping is provided, with codes transcribed from the original publication.
* parseAhrqSas interprets an SAS format file, returning R
data, intended currently only for the FORMAT code provided by AHRQ for
comorbidities.