| Title: | International Classifcation of Diseases (ICD) Data |
| Version: | 1.0 |
| Description: | Data from the United States Center for Medicare and Medicaid Services (CMS) is included in this package. There are ICD-9 and ICD-10 diagnostic and procedure codes, and lists of the chapter and sub-chapter headings and the ranges of ICD codes they encompass. There are also two sample datasets. These data are used by the 'icd' package for finding comorbidities. |
| Depends: | R (≥ 3.0.0) |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| LazyData: | true |
| LazyDataCompression: | xz |
| RoxygenNote: | 6.0.1 |
| Imports: | utils |
| Suggests: | testthat, icd |
| NeedsCompilation: | no |
| Packaged: | 2018-05-23 14:03:02 UTC; waseyj |
| Author: | Jack O. Wasey [aut, cre, cph] |
| Maintainer: | Jack O. Wasey <jack@jackwasey.com> |
| Repository: | CRAN |
| Date/Publication: | 2018-05-23 22:06:33 UTC |
icd.data: International Classifcation of Diseases (ICD) Data
Description
Data from the United States Center for Medicare and Medicaid Services (CMS) is included in this package. There are ICD-9 and ICD-10 diagnostic and procedure codes, and lists of the chapter and sub-chapter headings and the ranges of ICD codes they encompass. There are also two sample datasets. These data are used by the 'icd' package for finding comorbidities.
Author(s)
Jack O. Wasey jack@jackwasey.com
Assign all the data in the package to the calling environment
Description
Used by icd to load all the data into its environment. This should not
be needed by most users, who can simply refer to the data objects normally
after calling library(icd.data).
Usage
assign_icd_data(env = parent.frame())
Examples
## Not run:
assign_icd_data()
# but really all most users need to do is:
library(icd.data)
# then refer to the data in the package in the normal way:
print(icd10_chapters)
## End(Not run)
ICD-10 chapters
Description
The WHO ICD-10 scheme chapters. The chapter level is the highest in the hierarchy, each chapter containing sets of codes which span multiple three-digit 'major' codes, and in some cases also span codes across two alphabetic initial characters. E.g. Chapter I spans A00 to B99.
Details
2017 ICD-10-CM does not have any U codes (codes for special purposes). U00-U49 - Provisional assignment of new diseases of uncertain etiology or emergency use U82-U85 - Resistance to antimicrobial and anti-neoplastic drugs
Format: list with chapter names stored in list names, each with two element named character vector with start and end codes.
Source
http://apps.who.int/classifications/icd10/browse/2016/en
AHRQ ICD-10-PCS categories
Description
The AHRQ has categorized each of the ICD-10-PCS (Procedure Codes) into one of
four groups: minor diagnostic, minor therapeutic, major diagnostic or major
therapeutic. This mapping can be used to get the type(s) of procedure(s)
performed on a patient from a data.frame of patients and associated
procedure codes in 'long' format. See the ICD-10 vignette for an example.
See Also
https://www.hcup-us.ahrq.gov/toolssoftware/procedureicd10/procedure_icd10.jsp
ICD-10-CM Procedure Codes
Description
ICD-10-PCS is the annually-updated set of procedure codes designed by 3M for the US CMS. There is no directory of WHO ICD procedure codes.
Details
Format: A named list of data frames. The elements of the list are named by
the year, e.g., "2018". Each data frame contains two character
columns, the first, named code is the procedure code; the second,
named desc, has the description.
See Also
https://www.cms.gov/Medicare/Coding/ICD10/downloads/pcs_refman.pdf
ICD-10 sub-chapters
Description
The WHO ICD-10 scheme sub-chapters. N.b. there may be WHO vs CM differences:
please file bug if noted. In the XML definition of ICD-10-CM there are
some intermediate hierarchical levels, e.g. for neoplasms. Sub-chapter here
is defined as the lowest-level grouping of three-digit codes, e.g. C00-C14
"Malignant neoplasms of lip, oral cavity and pharynx", not C00-C96 "Malignant
neoplasms" which itself is a subset of the chapter C00-D49 "Neoplasms"
Details
Format: list with sub-chapter or major names stored in list names, each with two element named character vector with start and end codes.
Source
http://apps.who.int/classifications/icd10/browse/2016/en
ICD-10-CM
Description
The public domain modified ICD-10 classification as published in the public
domain by the US CDC. Currently this has a slightly different structure to
icd9cm_hierarchy because the published data helpfully has a
leaf flag indicating whether a code is a billable leaf node, or
a code higher in the hierarchy which nevertheless will have a description.
Details
There are annual revisions to this data. Currently, the 2016 edition is included.
Format: data frame, with columns for code, leaf status (0 or 1), short and long descriptions.
Source
http://www.cdc.gov/nchs/icd/icd10cm.htm
ICD-9 chapters
Description
icd9_chapters, icd9_chapters_sub and icd9_majors contain
mappings from the higher level descriptions of ICD-9 codes to the ranges of
ICD-9 codes they describe. Helpful in summarizing codes or grouping for
human-readable output. These can easily be converted to a co-morbidity
mapping, as shown in the vignette.
Details
001-139 Infectious And Parasitic Diseases
140-239 Neoplasms
240-279 Endocrine, Nutritional And Metabolic Diseases, And Immunity Disorders
280-289 Diseases Of The Blood And Blood-Forming Organs
290-319 Mental Disorders
320-389 Diseases Of The Nervous System And Sense Organs
390-459 Diseases Of The Circulatory System
460-519 Diseases Of The Respiratory System
520-579 Diseases Of The Digestive System
580-629 Diseases Of The Genitourinary System
-
630-679 Complications Of Pregnancy, Childbirth, And The Puerperium
-
680-709 Diseases Of The Skin And Subcutaneous Tissue
710-739 Diseases Of The Musculoskeletal System And Connective Tissue
740-759 Congenital Anomalies
760-779 Certain Conditions Originating In The Perinatal Period
780-799 Symptoms, Signs, And Ill-Defined Conditions
-
800-999 Injury And Poisoning
V01-V91 Supplementary Classification Of Factors Influencing Health Status And Contact With Health Services
-
E000-E999 Supplementary Classification Of External Causes Of Injury And Poisoning
Format: list with chapter/sub-chapter or major names stored in list names, each with two element named character vector with start and end codes.
Source
http://www.cms.gov/Medicare/Coding/ICD9ProviderDiagnosticCodes/codes.html
list of annual versions of billable leaf nodes of ICD-9-CM
Description
These are derived from the CMS published updates, with versions 23 to 32
currently available going back to 2004/5. The source files back to version 27
have short and long descriptions. The short descriptions are in ASCII with no
special characters, whereas the long descriptions contain accented characters
which seem to be interpreted as Unicode, latin-1 or cp1252.
This all done during package creation, but can be repeated by package users,
including pulling the data from the web pages directly. Despite my best
efforts, current locale can give different results, but this packaged data is
correct, with some UTF-8 encoded strings.
Details
Format: list of data frames. Each list item is named by the version as a
string, e.g. "32". The constituent data frames have columns icd9,
shortDesc, and longDesc.
Source
http://www.cms.gov/Medicare/Coding/ICD9ProviderDiagnosticCodes/codes.html
Latest ICD-9-CM diagnosis codes, in flat data.frame format
Description
Short-form ICD-9 codes with short and long descriptions, and description of each hierarchy level containing each code.
Details
Format: data frame
Source
http://wonder.cdc.gov/wonder/sci_data/codes/icd9/type_txt/icd9cm.asp
Rich text descriptions here: http://www.cdc.gov/nchs/icd/icd9cm.htm http://www.cms.gov/Medicare/Coding/ICD9ProviderDiagnosticCodes/codes.html This page has versions 23 to 32 (2005 to 2014). At present, only the 2014 data is included in this package.
http://wonder.cdc.gov/wonder/sci_data/codes/icd9/type_txt/icd9abb.asp
http://wonder.cdc.gov/wonder/sci_data/codes/icd9/type_txt/icd9cm.asp
http://wonder.cdc.gov/wonder/sci_data/codes/icd9/type_txt/icdcm.asp
http://wonder.cdc.gov/wonder/sci_data/codes/icd9/type_txt/icd9abb.asp
List the data in this package
Description
List the data in this package
Usage
ls_icd_data()
Examples
## Not run:
ls_icd_data()
## End(Not run)
United States Transuranium & Uranium Registries
Description
an ICD-10 data set (not ICD-10-CM) with mortality from the United States Transuranium & Uranium Registries, published in the public domain.
Source
https://ustur.wsu.edu/about-us/
Hospital discharge data from Vermont
Description
Anonymous data from public Vermont source for 2013
Details
Conditions of Release Release of public use data is subject to the following conditions, which the requestor agrees to upon accepting copies of the data:
1. The data may not be used in any manner that attempts to or does identify, directly or indirectly, any individual patient or physician.
2. The requestor agrees to incorporate the following, or a substantially similar, disclaimer in all reports or publications that include public use data: "Hospital discharge data for use in this study were supplied by the Vermont Association of Hospitals and Health Systems-Network Services Organization (VAHHS-NSO) and the Vermont Department of Banking, Insurance, Securities and Health Care Administration (BISHCA). All analyses, interpretations or conclusions based on these data are solely that of [the requestor]. VAHHS-NSO and BISHCA disclaim responsibility for any such analyses, interpretations or conclusions. In addition, as the data have been edited and processed by VAHHS-NSO, BISHCA assumes no responsibility for errors in the data due to coding or processing"
Format: CSV original, minimally processed into R data frame.
Author(s)
Vermont Division of Health Care Administration