The comorbidities classification (AHRQ, Charlson ,and Elixhauser Comorbidity) for ICD diagnostic codes is a diagnostic categorization scheme that can employ in many types of projects analyzing data on diagnoses.
icdDxToComorbid(
dxDataFile,
idColName,
icdColName,
dateColName,
icdVerColName = NULL,
icd10usingDate = NULL,
comorbidMethod,
isDescription = FALSE
)A data frame object of clinical diagnostic data with at least 3 columns: ID, ICD, and Date. As for date column, the data format should be YYYY/MM/DD or YYYY-MM-DD.
Column name of ID column in dxDataFile. Data type of this argumant should be string without quotation marks.
Column name of ICD column in dxDataFile. Data type of this argumant should be string without quotation marks.
Column name of date column in dxDataFile, and the type of date column should be a date format in R or a string format with date information in YYYY/MM/DD or YYYY-MM-DD. Data type of this argumant should be string without quotation marks.
(Optional) Column name if there is a columns to record ICD-9/10 version used in dxDataFile. In this column, data format should be numeric 9L or 10L to indicate which ICD version is used for each cell. See examples below to get more information.
The date that ICD-10 was started to be used in dxDataFile dataset. The data format should be YYYY/MM/DD or YYYY-MM-DD. Necessary if icdVerColName is null.
Three comorbidity methods: AHRQ, Charlson and Elixhauser Comorbidity. Change it to any of the other possible variables (ahrq,charlson, and elix).
Category name or category description of standard classification methods for ICD diagnostic codes. By default it is set to FALSE (Comorbidity categories).
Three new data.tables. 1) groupedDT: Based on dxDataFile with two new columns for uniform format diagnostic codes and classified categories. 2) summarised_groupedDT: Summarized the groupedDT dataset and sorted by memberID. 3) Error: Potential error codes from standardization step: dxUniform (`icdDxShortToDecimal` and `icdDxDecimalToShort`).
Collapse ICD codes into a smaller number of clinically meaningful categories that are more useful for presenting descriptive statistics than are individual ICD diagnostic codes.
# sample file for example
head(sampleDxFile)
#> ID ICD Date Version
#> 1: A2 Z992 2020-05-22 10
#> 2: A5 Z992 2020-01-24 10
#> 3: A8 Z992 2015-10-27 10
#> 4: A13 Z992 2020-04-26 10
#> 5: A13 Z992 2025-02-02 10
#> 6: A15 Z992 2023-05-12 10
# Group diagnostic codes into charlson comorbidity categories
icdDxToComorbid(sampleDxFile, ID, ICD, Date, icdVerColName = NULL, "2015-10-01", charlson)
#> Wrong ICD format: total 9 ICD codes (the number of occurrences is in brackets)
#> c("A0.11 (20)", "E114 (8)", "Z9.90 (6)", "F42 (6)", "001 (5)", "75.52 (4)", "755.2 (3)", "123.45 (3)", "7552 (2)")
#>
#> Wrong ICD version: total 7 ICD codes (the number of occurrences is in brackets)
#> c("V27.0 (18)", "A01.05 (8)", "42761 (7)", "V24.1 (6)", "A0105 (5)", "E03.0 (4)", "650 (4)")
#>
#> Warning: The ICD mentioned above matches to "NA" due to the format or other issues.
#> Warning: "Wrong ICD format" means the ICD has wrong format
#> Warning: "Wrong ICD version" means the ICD classify to wrong ICD version (cause the "icd10usingDate" or other issues)
#> $groupedDT
#> Short ID ICD Date Comorbidity
#> 1: Z992 A2 Z992 2020-05-22 RD
#> 2: Z992 A5 Z992 2020-01-24 RD
#> 3: Z992 A8 Z992 2015-10-27 RD
#> 4: Z992 A13 Z992 2020-04-26 RD
#> 5: Z992 A13 Z992 2025-02-02 RD
#> ---
#> 296: 650 C2 650 2017-10-10 <NA>
#> 297: 650 D4 650 2022-04-04 <NA>
#> 298: 123.45 C3 123.45 2022-09-28 <NA>
#> 299: 123.45 D8 123.45 2018-06-17 <NA>
#> 300: 123.45 C0 123.45 2017-05-09 <NA>
#>
#> $summarised_groupedDT
#> ID Comorbidity firstCaseDate endCaseDate count period
#> 1: A0 RD 2009-07-25 2013-12-20 5 1609 days
#> 2: A1 RD 2006-11-29 2014-09-24 5 2856 days
#> 3: A10 RD 2007-11-04 2012-07-30 5 1730 days
#> 4: A11 RD 2008-03-09 2011-09-03 5 1273 days
#> 5: A11 DIAB_C 2015-12-16 2015-12-16 1 0 days
#> 6: A12 RD 2006-05-14 2015-06-29 5 3333 days
#> 7: A13 RD 2006-04-29 2025-02-02 5 6854 days
#> 8: A14 RD 2006-11-28 2014-12-21 5 2945 days
#> 9: A15 RD 2007-05-25 2023-05-12 5 5831 days
#> 10: A16 RD 2007-04-15 2014-12-05 5 2791 days
#> 11: A17 RD 2007-02-19 2014-07-03 5 2691 days
#> 12: A18 RD 2007-04-05 2014-03-04 5 2525 days
#> 13: A2 RD 2011-09-20 2020-05-22 5 3167 days
#> 14: A3 RD 2008-07-08 2014-02-24 5 2057 days
#> 15: A4 RD 2006-10-20 2015-03-09 5 3062 days
#> 16: A5 RD 2009-09-10 2020-01-24 5 3788 days
#> 17: A6 RD 2007-10-01 2015-07-12 5 2841 days
#> 18: A7 RD 2007-02-01 2014-08-14 5 2751 days
#> 19: A8 RD 2007-11-22 2015-10-27 5 2896 days
#> 20: A9 RD 2007-03-05 2013-11-09 5 2441 days
#> 21: B0 RD 2015-12-26 2024-02-12 6 2970 days
#> 22: B1 RD 2016-08-08 2024-03-04 6 2765 days
#> 23: B2 RD 2016-03-20 2024-09-20 6 3106 days
#> 24: B3 RD 2019-05-07 2025-05-25 6 2210 days
#> 25: B4 RD 2015-12-02 2025-07-21 6 3519 days
#> 26: C0 CANCER 2015-12-05 2025-02-21 5 3366 days
#> 27: C1 CANCER 2018-02-13 2025-02-20 5 2564 days
#> 28: C2 CANCER 2016-09-09 2024-12-12 5 3016 days
#> 29: C2 DIAB_C 2017-07-08 2017-07-08 1 0 days
#> 30: C3 CANCER 2015-12-06 2021-10-22 4 2147 days
#> 31: C4 CANCER 2017-08-29 2025-09-05 5 2929 days
#> 32: C4 DIAB_C 2015-11-23 2015-11-23 1 0 days
#> 33: D0 PUD 2017-12-24 2017-12-24 1 0 days
#> 34: D0 DIAB_C 2017-01-29 2020-04-04 3 1161 days
#> 35: D1 Rheum 2016-12-06 2016-12-06 1 0 days
#> 36: D1 MSLD 2024-04-04 2024-04-04 1 0 days
#> 37: D2 CANCER 2019-10-13 2019-10-13 1 0 days
#> 38: D3 PVD 2017-11-19 2017-11-19 1 0 days
#> 39: D4 CANCER 2020-03-10 2020-03-10 1 0 days
#> 40: D4 DIAB_C 2019-01-03 2019-01-03 1 0 days
#> 41: D4 CEVD 2020-10-06 2020-10-06 1 0 days
#> 42: D5 CANCER 2021-02-13 2021-02-13 1 0 days
#> 43: D5 Rheum 2022-10-10 2022-10-10 1 0 days
#> 44: D5 COPD 2014-11-15 2014-11-15 1 0 days
#> 45: D5 DIAB_C 2023-07-23 2023-07-23 1 0 days
#> 46: D7 Rheum 2021-12-03 2021-12-03 1 0 days
#> 47: D7 CANCER 2012-07-04 2012-07-04 1 0 days
#> 48: D7 DIAB_C 2021-08-21 2021-08-21 1 0 days
#> 49: D8 PVD 2021-03-18 2021-03-18 1 0 days
#> 50: D8 CANCER 2025-09-10 2025-09-10 1 0 days
#> 51: D8 PARA 2010-09-27 2010-09-27 1 0 days
#> ID Comorbidity firstCaseDate endCaseDate count period
#>
#> $Error
#> ICD count IcdVersionInFile WrongType Suggestion
#> 1: A0.11 20 ICD 10 Wrong format
#> 2: V27.0 18 ICD 10 Wrong version
#> 3: E114 8 ICD 10 Wrong format
#> 4: A01.05 8 ICD 9 Wrong version
#> 5: 42761 7 ICD 10 Wrong version
#> 6: Z9.90 6 ICD 10 Wrong format
#> 7: F42 6 ICD 10 Wrong format
#> 8: V24.1 6 ICD 10 Wrong version
#> 9: A0105 5 ICD 9 Wrong version
#> 10: 001 5 ICD 9 Wrong format 0019
#> 11: 75.52 4 ICD 9 Wrong format
#> 12: E03.0 4 ICD 9 Wrong version
#> 13: 650 4 ICD 10 Wrong version
#> 14: 123.45 3 ICD 10 Wrong format
#> 15: 755.2 3 ICD 9 Wrong format 755.29
#> 16: 7552 2 ICD 9 Wrong format 75529
#>