cat_trauma: Categorize trauma data

In ablack3/icdpicr: 'ICD' Programs for Injury Categorization in R

Categorize trauma data

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

1. assign a severity (AIS) and ISS body region values to each valid ICD-9 or ICD-10 injury diagnosis code,

2. add variables for maximum severity of each body region,

3. calculate ISS, "New ISS", maximum AIS, and a regression-based mortality prediction,

4. select first 4 e-codes/mechanism codes and categorize major mechanism, minor mechanism, and intent

Usage

cat_trauma(df, dx_pre, icd10, i10_iss_method, calc_method = 1, verbose = FALSE)

Arguments

df	A dataframe in wide format containing ICD-9 and/or 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.)
icd10	Should ICD-10 codes be included? Must be one of: TRUE, FALSE, "cm", or "base". TRUE - ICD-10 codes will be processed by the program FALSE - Any ICD-10 codes in the data will be ignored. "cm" - ICD-10-CM codes will be processed by the program "base" - Basic ICD-10 (international) codes will be processed by the program
i10_iss_method	Method for calculating ISS from ICD-10 codes. Ignored if icd10 = FALSE. Must be one of: "roc_max_NIS" Table derived empirically from National Inpatient Sample (NIS) maximizing area under an ROC curve. For ICD10 codes not in NIS the mapping based on TQIP data will be used as a backup. This option is recommended if the user's data are similar to NIS data. "roc_max_TQIP" Table derived empirically from the Trauma Quality Improvement Program (TQIP) data maximizing area under an ROC curve. For ICD-10 codes not in TQIP the mapping based on NIS data will be used as a backup. This option is recommended if the user's data are similar to TQIP data. "roc_max_NIS_only" Table derived as for "roc_max_NIS", but injury ICD-10 codes not in the NIS dataset will be ignored "roc_max_TQIP_only" Table derived as for "roc_max_TQIP", but injury ICD-10 codes not in the TQIP dataset will be ignored. "gem_max" Table derived by mapping ICD-10-CM to ICD-9-CM using the CMS general equivalence mapping tables and then to AIS and ISS using the ICDPIC table inherited from the Stata version. Mapping conflicts handled by taking the max AIS. "gem_min" Same as "gem_max" except that mapping conflicts are handled by taking the min AIS.
calc_method	ISS calculation method: Method 1 (default) will assign an ISS of 75 if any AIS is 6. Method 2 will change any AIS = 6 to 5 and then calculate ISS normally.
verbose	Should updates be printed to the console? TRUE or FALSE (default). This can be helpful for long running computations.

Details

Data should be in wide format:

ID	dx1	dx2	dx3	etc.
31416	800.1	959.9	E910.9
31417	800.24	410.0

Codes for AIS severity:

• 1 = Minor

• 2 = Moderate

• 3 = Serious

• 4 = Severe

• 5 = Critical

• 6 = Unsurvivable

• 9 = Unknown

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: new injury severity score

• ecode_1-ecode_4: first 4 mechanism/E-Codes (including ICD-10 if requested) found in each row of data

• mechmaj1-mechmaj4: CDC external cause of injury major mechanism for each E-Code captured

• mechmin1-mechmin4: CDC external cause of injury minor mechanism for each E-Code captured

• intent1-intent4: intent for each E-Code captured

• lowmech: lowest CDC external cause of injury major mechanism for all E-Codes captured

• Pmort: The model predicted probability of mortality (only added if using ICD-10 codes with one of the roc_max methods)

Examples

df_in <- read.table(header = TRUE, text = "
    ident    dx1     dx2     dx3
    31416   800.1   959.9   E910.9
    31417   800.24  410.0   NA
")
df_out <- cat_trauma(df_in, "dx", icd10 = FALSE)

ablack3/icdpicr documentation built on March 23, 2022, 10:18 a.m.