Calculate comorbidities, Charlson scores, perform fast and accurate validation, conversion, manipulation, filtering and comparison of ICD-9 and ICD-10 codes. Common ambiguities and code formats are handled. This package enables a work flow from raw lists of ICD codes in hospital billing databases to comorbidities. ICD-9 and ICD-10 comorbidity mappings from Quan (Deyo and Elixhauser versions), Elixhauser and AHRQ included. This package replaces 'icd9', which should be uninstalled.
icd_comorbid
determines comorbidities for a set of patients with one or more ICD-9 codes
each. icd_charlson calculates Charlson score (Comorbidity
Index). If you already calculated the comorbidities, you can use
icd_charlson_from_comorbid.
AHRQ comorbidity mapping is provided, and a function to read the raw
SAS code from AHRQ into R data structures. The data is available by
lazy-loading in icd9_map_ahrq. AHRQ releases new mappings
annually.
Quan revised both Deyo/Charlson and Elixhauser ICD-9 to comorbidity
mappings. These are presented as: icd9_map_quan_deyo (which is
also derived from the original SAS code used in his publication, referenced
in the data documentation), icd10_map_quan_deyo,
icd9_map_quan_elix, and icd10_map_quan_elix
which was transcribed directly from the same paper.
The original Elixhauser mapping is provided, with codes transcribed
from the original publication. See icd9_map_elix.
icd_is_valid checks whether ICD-9 codes are
syntactically valid (although not necessarily genuine ICD-9 diagnoses). In
contrast, icd_is_defined 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: icd_decimal_to_short,
icd_short_to_decimal 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
icd_children and find a common parent to a set of children
(or arbitrary list of ICD-9 codes) with icd_condense.
icd_sort sorts in hierarchical, then numerical order, so
100.0 comes before 100.00, for example. icd_wide_to_long and
icd_long_to_wide convert the two most common data structures
containing patient disease data. This is more sophisticated and tailored to
the problem than base reshaping or extension packages, although these could
no doubt be used.
Use icd_explain 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. icd_diff_comorbid 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.
icd9cm_hierarchy is a data.frame containing the full
ICD-9 classification for each diagnosis. icd9_chapters
contains definitions of chapters, sub-chapters and three-digit groups.
http://www.hcup-us.ahrq.gov/toolssoftware/comorbidity/comorbidity.jsp
Useful links: