| Type: | Package |
| Title: | Categorize Injury Diagnosis Codes |
| Version: | 2.1.0 |
| Description: | Functions read a dataframe containing one or more International Classification of Diseases Tenth Revision codes per subject. They return original data with injury categorizations and severity scores added. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 7.2.3 |
| Depends: | R (≥ 2.10) |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| Imports: | dplyr, stringr, tidyr |
| NeedsCompilation: | no |
| Packaged: | 2025-09-02 11:21:06 UTC; davideugeneclark |
| Author: | David Clark [aut, cre], Adam Black [aut] |
| Maintainer: | David Clark <david.clark@tufts.edu> |
| Repository: | CRAN |
| Date/Publication: | 2025-09-08 18:40:23 UTC |
Categorize trauma data and calculate scores
Description
This function adds Abbreviated Injury Scores (AIS), Injury Severity Scores (ISS), and other descriptors of injury to a dataframe. For each observation this function will
assign a severity (AIS) and ISS body region values to each valid ICD-10 injury diagnosis code,
add variables for maximum severity of each body region,
calculate ISS, "New ISS", maximum AIS, and regression-based mortality predictions,
select the first 4 mechanism (external cause) codes and categorize mechanism and intent following CDC guidelines
Usage
cat_trauma2(df, dx_pre, messages = TRUE)
Arguments
df |
A dataframe in wide format containing ICD-10 diagnosis codes with a common column name prefix. Diagnosis codes should be character strings and may have a decimal or not. |
dx_pre |
Prefix for diagnosis code column names (example: dx1, dx2, etc.) |
messages |
Should the program report completion of each step? Must be TRUE or FALSE (default).
|
Details
Data should be in wide format, as in the example below:
Value
A dataframe identical to the dataframe passed to the function with the following additional variables added:
sev_1-sev_n: AIS severity for diagnosis codes 1..n
issbr_1-issbr_n: ISS body region for diagnosis codes 1..n
mxaisbr1-mxaisbr6: maximum AIS severity for each of the 6 ISS body regions
maxais: maximum AIS severity over all ISS body regions
riss: computed injury severity score
niss: computed "new injury severity score"
PmortTQP: TQP model predicted probability of mortality
PmortNIS: NIS model predicted probability of mortality
mechcode_1-mechcode_4: first 4 mechanism codes found in each row of data
mech_1-mech_4: CDC external cause of injury major mechanism for each mechanism code captured
intent_1-intent_4: intent for each mechanism code captured
Examples
df_in <- read.table(header = TRUE, text = "
ident dx1 dx2 dx3
31416 S32110A S3251 NA
31417 S72141A T07XXXA D62
")
df_out <- cat_trauma2(df_in, "dx", TRUE)
Categorize ICD-10 injury diagnosis codes similar to the "Barell Matrix" used for ICD-9
Description
This function categorizes ICD-10 diagnosis codes according to the table given in Hedegaard H, Johnson RL, Garnett MF, Thomas KE. The 2020 International Classification of Diseases, 10th Revision, Clinical Modification injury diagnosis framework for categorizing injuries by body region and nature of injury. Nat Health Stat Reports 2020;150:1-26, and (if option selected) predicts mortality for each subject as described in Clark DE, Ahmad S. Estimating injury severity using the Barell matrix. Inj Prev 2006;12:111-116.
Usage
framework(df, dx_pre, severity = FALSE, messages = FALSE)
Arguments
df |
A dataframe in wide format containing ICD-10 diagnosis codes with a common column name prefix. Diagnosis codes should be character strings and may have a decimal or not. |
dx_pre |
Prefix for diagnosis code column names (example: dx1, dx2, etc.) |
severity |
Should the program calculate a severity score? Must be TRUE or FALSE (default).
|
messages |
Should the program report completion of each step? Must be TRUE or FALSE (default).
|
Details
Data should be in wide format, as in the example below:
Value
A dataframe identical to the dataframe passed to the function with the following additional variables added:
cell_1-cell_n: Cell assigned for diagnosis codes 1..n
PsCell_1-PsCell_n: Survival in TQP and NIS for patients with a diagnosis in this cell
bPSmin: The minimum of PsCell_1-PsCell_n for this subject
Examples
df_in <- read.table(header = TRUE, text = "
ident dx1 dx2 dx3
31416 S32110A S3251 NA
31417 S72141A T07XXXA D62
")
df_out <- framework(df_in, "dx", TRUE, FALSE)
Table i10_map_frame
Description
A dataset containing ICD-10 diagnosis codes and their properties for assignment to the CDC Framework.
Usage
i10_map_frame
Format
A data frame with 20,499 rows and 5 variables:
- dx
A valid ICD-10 diagnosis code.
- cell
The corresponding cell in the CDC Framework.
- PmCell
The observed mortality for subjects with a diagnosis in this cell.
- PsCell
The observed survival for subjects with a diagnosis in this cell.
- version
The most recent date when this dataset was revised. Encoded vyymmdd.
...
Table i10_map_iciss
Description
A dataset containing ICD-10 diagnosis codes and their properties for calculation of several versions of the ICD Injury Severity Score (ICISS).
Usage
i10_map_iciss
Format
A data frame with 20,551 rows and 12 variables:
- dx
A valid ICD-10 diagnosis code.
- digits1234
The 4-digit version of dx.
- tot_int
The number of cases in international data from which the observed survival was calculated.
- dsp_int
The observed survival in international data for subjects with this diagnosis.
- dsp_int_c
Same as above, but NA if tot_int < 5.
- tot_TQP
The number of cases in TQP data from which the observed survival was calculated.
- dsp_TQP
The observed survival in TQP data for subjects with this diagnosis.
- dsp_TQP_c
Same as above, but NA if tot_TQP < 5.
- tot_NIS
The number of cases in NIS data from which the observed survival was calculated.
- dsp_NIS
The observed survival in NIS data for subjects with this diagnosis.
- dsp_NIS_c
Same as above, but NA if tot_NIS < 5.
- Version
The most recent date when this dataset was revised. Encoded vyymmdd.
...
Table i10_map_mech
Description
A dataset containing ICD-10 diagnosis codes and their properties for determination of injury mechanism.
Usage
i10_map_mech
Format
A data frame with 8,117 rows and 5 variables:
- dx
A valid ICD-10 diagnosis code.
- mechmaj
The CDC major mechanism category.
- intent
The CDC intent category.
- mechmin
The CDC minor mechanism category, if any.
- version
The most recent date when this dataset was revised. Encoded vyymmdd.
...
Table i10_map_sev
Description
A dataset containing ICD-10 diagnosis codes and their properties for determination of ISS and other injury severity scores.
Usage
i10_map_sev
Format
A data frame with 20,551 rows and 8 variables:
- dx
A valid ICD-10 diagnosis code.
- severity
The associated Abbreviated Injury Score for this diagnosis.
- issbr
The associated ISS body region for this diagnosis.
- TQIPeffect
The coefficient for this diagnosis in the TQP regression model.
- TQIPint
The intercept in the TQP regression model.
- NISeffect
The coefficient for this diagnosis in the NIS regression model.
- NISint
The intercept in the TQP regression model.
- version
The most recent date when this dataset was revised. Encoded vyymmdd.
...
Compute International Classification of Diseases-Based Injury Severity Score (ICISS)
Description
This function adds Diagnosis-specific Survival Probabilities (DSP) to a dataframe, based on the table provided by Gedeborg and colleagues (J Trauma Acute Care Surgery 2014) and also TQP and NIS. ICD-10-CM codes longer than four digits are treated as if they were four-digit ICD-10 codes as published by the World Health Organization. Thus, an ICD-10-CM code like S00552A is considered the same as S005. For each observation this function will
assign a severity (DSP) to each valid ICD-10 injury diagnosis code,
calculate one version of ICISS as the product of these DSP, and
calculate another version of ICISS as the minimum of these DSP.
It repeats the above using international data, TQP, and NIS as reference data.
Usage
iciss(df, dx_pre, conservative = TRUE, messages = TRUE)
Arguments
df |
A dataframe in wide format containing ICD-10 diagnosis codes with a common column name prefix. Diagnosis codes should be character strings and may have a decimal or not. |
dx_pre |
Prefix for diagnosis code column names (example: dx1, dx2, etc.) |
conservative |
Should the program exclude DSP based on fewer than 5 observations? Must be TRUE (default) or FALSE.
|
messages |
Should the program report completion of each step? Must be TRUE or FALSE (default).
|
Details
Data should be in wide format, as in the example below
Value
A dataframe identical to the dataframe passed to the function with the following additional variables added:
dsp_int1-dsp_intn: DSP for diagnosis codes 1..n, from international data
dsp_TQP1-dsp_TQPn: DSP for diagnosis codes 1..n, from TQP data
dsp_TQP1-dsp_NISn: DSP for diagnosis codes 1..n, from NIS data
PS_int_prod: ICISS calculated as the product of dsp_int1-dsp_intn
PS_int_min: ICISS calculated as the minimum of dsp_int1-dsp_intn
PS_TQP_prod: ICISS calculated as the product of dsp_TQP1-dsp_TQPn
PS_TQP_min: ICISS calculated as the minimum of dsp_TQP1-dsp_TQPn
PS_NIS_prod: ICISS calculated as the product of dsp_NIS1-dsp_NISn
PS_NIS_min: ICISS calculated as the minimum of dsp_NIS1-dsp_NISn
Examples
df_in <- read.table(header = TRUE, text = "
ident dx1 dx2 dx3
31416 S32110A S3251 NA
31417 S72141A T07XXXA D62
")
df_out <- iciss(df_in, "dx", TRUE, FALSE)
Test Data
Description
A dataset containing a sample of trauma registry data for use in examples and tests.
Usage
testdata
Format
A data frame with 20,000 rows and 13 variables:
- temp_id
A sequential number to identify individual subjects.
- died
A binary indicator variable for death. 1 = died. 0 = survived.
- I10_DX1
1st ICD-10-CM injury code recorded on an encounter.
- I10_DX2
2nd ICD-10-CM injury code recorded on an encounter.
- I10_DX3
3rd ICD-10-CM injury code recorded on an encounter.
- I10_DX4
4th ICD-10-CM injury code recorded on an encounter.
- I10_DX5
5th ICD-10-CM injury code recorded on an encounter.
- I10_DX6
6th ICD-10-CM injury code recorded on an encounter.
- I10_DX7
7th ICD-10-CM injury code recorded on an encounter.
- I10_DX8
8th ICD-10-CM injury code recorded on an encounter.
- I10_DX9
9th ICD-10-CM injury code recorded on an encounter.
- I10_DX10
10th ICD-10-CM injury code recorded on an encounter.
- Version
The most recent date when this dataset was revised. Encoded vyymmdd.
...