Calculate comorbidities, and perform fast and accurate validation, conversion, manipulation, filtering and comparison of ICD-9-CM (clinical modification) codes. ICD-9 codes appear numeric but leading and trailing zeroes, and both decimal and non-decimal "short" format codes exist. The package enables a work flow from raw lists of ICD-9 codes from hospital billing databases to comorbidities. ICD-9 to comorbidity mappings from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included.
icd9Comorbid determines co-morbidities
for a set of patients with one or more ICD-9 codes each.
icd9Charlson calculates Charlson score (Comorbidity Index).
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 quanElixComorbid which was
transcribed directly from the same paper.
The original Elixhauser mapping is provided, with codes transcribed
from the original publication. See elixComorbid.
icd9IsValid checks whether ICD-9 codes are
syntactically valid (although not necessarily genuine ICD-9 diagnoses). In
contrast, icd9IsReal checks whether ICD-9 codes correspond to
diagnoses in the current ICD-9-CM definition from CMS.
There are many functions to convert ICD-9 codes or their
components between different formats and structures. The most commonly used
are: icd9DecimalToShort, icd9ShortToDecimal to
convert, e.g., 002.3 to 0023 and back again. See convert for other
options.
You can find children of a higher-level ICD-9 code with
icd9Children and find a common parent to a set of children
(or arbitrary list of ICD-9 codes) with icd9Condense.
icd9Sort sorts in hierarchical, then numerical order, so
100.0 comes before 100.00, for example. icd9WideToLong and
icd9LongToWide convert the two most common data structures
containing patient disease data. This is more sophisticated than standard R
or Hadleyverse reshaping.
Use icd9Explain to convert a
list of codes into human-readable descriptions. This function can
optionally reduce the codes to a their top-level groups if all the child
members of a group are present. icd9DiffComorbid allows
summary of the differences between comorbidity mappings, e.g. to find what
has changed from year-to-year or between revisions by different authors.
icd9Hierarchy is a data.frame containing the full
ICD-9 classification for each diagnosis. icd9Chapters
contains definitions of chapters, sub-chapters and three-digit groups.
http://www.hcup-us.ahrq.gov/toolssoftware/comorbidity/comorbidity.jsp
rClinicalCodes comorbidities