icdpicr: ICDPICR
In ablack3/icdpicr: 'ICD' Programs for Injury Categorization in R
icdpicr R Documentation
ICDPICR
Description
International Classification of Diseases Programs for Injury Categorization.
The ICDPICR package is an adaptation of the ICDPIC package originally written for Stata.
The original ICDPIC is a collection of Stata programs for injury categorization
and is available as a Stata download or online at https://ideas.repec.org/c/boc/bocode/s457028.html
Version
ICDPICR Version 0.1.0 was adapted from the ICDPIC Version 3.0 Stata program,
especially to accommodate both ICD-9 and ICD-10 diagnosis codes. Some of the
functionality of the original Stata program was reduced in the interest of providing updates for
only the most useful elements of the original ICDPIC program, and some of this functionality
has been restored along with other features in the current ICDPICR Version 1.0.
ICDPICR is open source and all code is availble at https://github.com/ablack3/icdpicr.
Documentation can be found online at https://ablack3.github.io/icdpicr/.
Description
ICDPICR (International Classification of Diseases Programs for Injury Categorization in R)
is an R package currently consisting of a single function "cat_trauma" that performs
the same task that the "trauma" program does in the Stata version of ICDPIC.
The intention of these programs is to provide inexpensive methods for translating International
Classification of Diseases (ICD) diagnosis codes into standard injury
categories and/or scores.
The authors would appreciate suggestions or corrections from any user of the software.
Bug reports or feature requests may be submitted at https://github.com/ablack3/icdpicr/issues.
Publications of studies in which these programs or tables are used should cite the authors.
Methods
For each valid ICD-9-CM or ICD-10-CM injury diagnosis, ICDPICR is programmed to generate an approximate AIS
and body region, using the original AIS anatomic classification (as modified by Baker and colleagues) into
six body regions: Head and neck, face, chest, abdomen and pelvic contents, extremities and pelvic bones, and
general. In addition, each code referring to a mechanism of injury is categorized as recommended or
proposed by the CDC. For each injured person, ICDPICR determines the maximal AIS in each body region
and overall, an Injury Severity Score (RISS), a regression-based prediction of mortality, and CDC mechanism/intent categories.
Mapping of ICD-9-CM E-codes to CDC mechanism categories simply involved translation of the programming
code from Stata into R, using essentially the same table. Mapping of ICD-10-CM codes to mechanism categories was
based on a similar table published by the CDC.
The National Trauma Data Standard used by the ACS Trauma Quality Improvement Project (TQIP)
considers valid ICD-10-CM injury codes to be those in the
ranges S00-S99, T07, T14, T20-T28, and T30-32. ICDPICR recognizes only these codes in the calculation
of injury severity from ICD-10-CM, and also requires that the codes have a decimal point in the fourth position
and the letter "A", "B", or "C" in the eighth position (indicating an initial encounter).
Mapping of ICD-10-CM codes to AIS severity may be performed in several ways, as described below.
"ROCmax" mapping method for ICD-10-CM codes or basic ICD-10 codes:
The ROCmax option in ICDPICR Version 1.0 allows the user to choose either TQIP or
National Inpatient Survey (NIS) as the reference database. Ridge regression is used to
estimate the independent effect of each injury diagnosis on mortality. If one of the ROCmax
options is chosen, a prediction of mortality for each subject (Pmort) is provided directly from
the regression, as well as an estimated Injury Severity Score (ISS). As in the earlier Stata
version of ICDPIC, a "New Injury Severity Score" (NISS) is now also calculated for all options.
"GEM" mapping method for ICD-10-CM codes:
ICD-10-CM codes are first mapped to ICD-9-CM codes using the General Equivalency Mapping (GEM)
tables provided by the Centers for Medicare and Medicaid Services (CMS), and then those ICD-9-CM
codes are mapped to AIS using the table inherited from the Stata version of ICDPIC.
The user is given the option to ignore ICD-10-CM codes if desired. Otherwise, if the GEM maps an
ICD-10-CM code to two or more ICD-9-CM codes associated with different severities, the user
is given the option whether to assign the greater or lesser of these severities
("GEMmax" or "GEMmin"). When the GEM maps an ICD-10-CM code to two or more ICD-9-CM codes
associated with different AIS body regions, the verbal description of the ICD-10-CM code in the
GEM table is used to assign a body region.
A GEM mapping method is necessary when injuries have been coded with ICD-9-CM codes only,
and may be preferable when they have been coded with a mix of ICD-9-CM and ICD-10-CM.
For any of the mapping methods in ICDPICR, the maximum AIS Severity for each AIS body region
(MXAISBR1 ... MXAISBR6 in the output) is 0 if there are no valid injury codes for that body region. It is
recorded as "missing" if there are valid codes for that body region, but their severity cannot be determined.
Otherwise, it is the maximum known severity (1 through 6) for that body region. Maximum AIS Severity
(MAXAIS in the output data) is the maximum of (MXAISBR1 ... MXAISBR6); MAXAIS will thus be 0 if there is no
diagnosis code associated with an AIS severity.
Injury Severity Score (RISS) is calculated according to the classic description of Baker and colleagues,
namely the sum of the squares of the three largest elements of (MXAISBR1 ... MXAISBR6). The user can choose
whether to assign RISS=75 when any injury is assigned a severity of 6, or to reassign a severity of 5 to
these injuries and calculate RISS as above. The first option, RISS = 75 when any severity = 6, is the default
in ICDPICR, since by definition an AIS severity of 6 should denote an injury that is uniformly fatal and
thus should rarely be found in hospital data.
Functions
cat_trauma provides various classifications and characterizations of trauma
based on ICD-9 or ICD-10 injury diagnosis codes. Details can be found in the help file for cat_trauma.
ablack3/icdpicr documentation built on March 23, 2022, 10:18 a.m.
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ICDPICR
Description
International Classification of Diseases Programs for Injury Categorization. The ICDPICR package is an adaptation of the ICDPIC package originally written for Stata. The original ICDPIC is a collection of Stata programs for injury categorization and is available as a Stata download or online at https://ideas.repec.org/c/boc/bocode/s457028.html
Version
ICDPICR Version 0.1.0 was adapted from the ICDPIC Version 3.0 Stata program, especially to accommodate both ICD-9 and ICD-10 diagnosis codes. Some of the functionality of the original Stata program was reduced in the interest of providing updates for only the most useful elements of the original ICDPIC program, and some of this functionality has been restored along with other features in the current ICDPICR Version 1.0. ICDPICR is open source and all code is availble at https://github.com/ablack3/icdpicr. Documentation can be found online at https://ablack3.github.io/icdpicr/.
Description
ICDPICR (International Classification of Diseases Programs for Injury Categorization in R) is an R package currently consisting of a single function "cat_trauma" that performs the same task that the "trauma" program does in the Stata version of ICDPIC. The intention of these programs is to provide inexpensive methods for translating International Classification of Diseases (ICD) diagnosis codes into standard injury categories and/or scores. The authors would appreciate suggestions or corrections from any user of the software. Bug reports or feature requests may be submitted at https://github.com/ablack3/icdpicr/issues. Publications of studies in which these programs or tables are used should cite the authors.
Methods
For each valid ICD-9-CM or ICD-10-CM injury diagnosis, ICDPICR is programmed to generate an approximate AIS and body region, using the original AIS anatomic classification (as modified by Baker and colleagues) into six body regions: Head and neck, face, chest, abdomen and pelvic contents, extremities and pelvic bones, and general. In addition, each code referring to a mechanism of injury is categorized as recommended or proposed by the CDC. For each injured person, ICDPICR determines the maximal AIS in each body region and overall, an Injury Severity Score (RISS), a regression-based prediction of mortality, and CDC mechanism/intent categories.
Mapping of ICD-9-CM E-codes to CDC mechanism categories simply involved translation of the programming code from Stata into R, using essentially the same table. Mapping of ICD-10-CM codes to mechanism categories was based on a similar table published by the CDC.
The National Trauma Data Standard used by the ACS Trauma Quality Improvement Project (TQIP) considers valid ICD-10-CM injury codes to be those in the ranges S00-S99, T07, T14, T20-T28, and T30-32. ICDPICR recognizes only these codes in the calculation of injury severity from ICD-10-CM, and also requires that the codes have a decimal point in the fourth position and the letter "A", "B", or "C" in the eighth position (indicating an initial encounter). Mapping of ICD-10-CM codes to AIS severity may be performed in several ways, as described below.
"ROCmax" mapping method for ICD-10-CM codes or basic ICD-10 codes: The ROCmax option in ICDPICR Version 1.0 allows the user to choose either TQIP or National Inpatient Survey (NIS) as the reference database. Ridge regression is used to estimate the independent effect of each injury diagnosis on mortality. If one of the ROCmax options is chosen, a prediction of mortality for each subject (Pmort) is provided directly from the regression, as well as an estimated Injury Severity Score (ISS). As in the earlier Stata version of ICDPIC, a "New Injury Severity Score" (NISS) is now also calculated for all options.
"GEM" mapping method for ICD-10-CM codes: ICD-10-CM codes are first mapped to ICD-9-CM codes using the General Equivalency Mapping (GEM) tables provided by the Centers for Medicare and Medicaid Services (CMS), and then those ICD-9-CM codes are mapped to AIS using the table inherited from the Stata version of ICDPIC. The user is given the option to ignore ICD-10-CM codes if desired. Otherwise, if the GEM maps an ICD-10-CM code to two or more ICD-9-CM codes associated with different severities, the user is given the option whether to assign the greater or lesser of these severities ("GEMmax" or "GEMmin"). When the GEM maps an ICD-10-CM code to two or more ICD-9-CM codes associated with different AIS body regions, the verbal description of the ICD-10-CM code in the GEM table is used to assign a body region.
A GEM mapping method is necessary when injuries have been coded with ICD-9-CM codes only, and may be preferable when they have been coded with a mix of ICD-9-CM and ICD-10-CM.
For any of the mapping methods in ICDPICR, the maximum AIS Severity for each AIS body region (MXAISBR1 ... MXAISBR6 in the output) is 0 if there are no valid injury codes for that body region. It is recorded as "missing" if there are valid codes for that body region, but their severity cannot be determined. Otherwise, it is the maximum known severity (1 through 6) for that body region. Maximum AIS Severity (MAXAIS in the output data) is the maximum of (MXAISBR1 ... MXAISBR6); MAXAIS will thus be 0 if there is no diagnosis code associated with an AIS severity.
Injury Severity Score (RISS) is calculated according to the classic description of Baker and colleagues, namely the sum of the squares of the three largest elements of (MXAISBR1 ... MXAISBR6). The user can choose whether to assign RISS=75 when any injury is assigned a severity of 6, or to reassign a severity of 5 to these injuries and calculate RISS as above. The first option, RISS = 75 when any severity = 6, is the default in ICDPICR, since by definition an AIS severity of 6 should denote an injury that is uniformly fatal and thus should rarely be found in hospital data.
Functions
cat_trauma provides various classifications and characterizations of trauma based on ICD-9 or ICD-10 injury diagnosis codes. Details can be found in the help file for cat_trauma.
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