This function converts the long format of grouped data into a wide format which is fit to other analytical and plotting packages.
groupedDataLongToWide(
dxDataFile,
idColName,
categoryColName,
dateColName,
reDup = TRUE,
numericOrBinary = B,
count = 1,
selectedCaseFile = NULL
)a groupedDT format data frame generated from four strategies of code classification (using unprocessed ICD codes as input is not recommended).
Column name of ID 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.
The wide format data with or without certain diagnostic categories can be marked as binary True/False or numeric diagnosi time counts. Type N or B (character without quotation mark) to specify one of the method. Default is Binary B.
A data frame with the label of case selected or not. Can be generated by selectCases function or a self-defined data frame (as long as the column names and data type are the same as the output of selectCases function, but not recommended). Default is 'NULL'
A new data.table based on classified dxDataFile dataset and converted into a wide format dataset.
The output of this function can be numeric or binary wide format.
# Create a grouped data
ELIX <- icdDxToComorbid(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icd10usingDate = "2015/10/01",
comorbidMethod = elix)
#> 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)
head(ELIX$groupedDT)
#> Short ID ICD Date Comorbidity
#> 1: Z992 A2 Z992 2020-05-22 RENLFAIL
#> 2: Z992 A5 Z992 2020-01-24 RENLFAIL
#> 3: Z992 A8 Z992 2015-10-27 RENLFAIL
#> 4: Z992 A13 Z992 2020-04-26 RENLFAIL
#> 5: Z992 A13 Z992 2025-02-02 RENLFAIL
#> 6: Z992 A15 Z992 2023-05-12 RENLFAIL
# Select case with "Diseases of the urinary system" by level 2 of CCS classification
selectedCaseFile <- selectCases(dxDataFile = sampleDxFile,
idColName = ID,
icdColName = ICD,
dateColName = Date,
icdVerColName = NULL,
icd10usingDate = "2015/10/01",
groupDataType = ccslvl2,
caseCondition = "Diseases of the urinary system",
caseCount = 1)
#> Wrong ICD format: total 9 ICD codes (the number of occurrences is in brackets)
#> c("A0.11 (20)", "E114 (8)", "Z9.90 (6)", "F42 (6)", "001 (5)", "75.52 (4)", "755.2 (3)", "123.45 (3)", "7552 (2)")
#>
#> Wrong ICD version: total 7 ICD codes (the number of occurrences is in brackets)
#> c("V27.0 (18)", "A01.05 (8)", "42761 (7)", "V24.1 (6)", "A0105 (5)", "E03.0 (4)", "650 (4)")
#>
#> Warning: The ICD mentioned above matches to "NA" due to the format or other issues.
#> Warning: "Wrong ICD format" means the ICD has wrong format
#> Warning: "Wrong ICD version" means the ICD classify to wrong ICD version (cause the "icd10usingDate" or other issues)
# Convert the long format of grouped data into a wide binary format with selected case
groupedDataWide <- groupedDataLongToWide(ELIX$groupedDT,
idColName = ID,
categoryColName = Comorbidity,
dateColName = Date,
selectedCaseFile = selectedCaseFile)
groupedDataWide
#> ID ARTH CHRNLUNG DMCX DRUG HRENWORF HTNPREG LIVER LYMPH NEURO OBESE
#> 1: A0 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 2: A1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 3: A10 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 4: A11 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 5: A12 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 6: A13 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 7: A14 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 8: A15 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 9: A16 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 10: A17 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 11: A18 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 12: A2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 13: A3 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 14: A4 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 15: A5 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 16: A6 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 17: A7 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 18: A8 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 19: A9 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 20: B0 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 21: B1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 22: B2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 23: B3 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 24: B4 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 25: C0 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 26: C1 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 27: C2 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 28: C3 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 29: C4 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 30: D0 TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> 31: D1 TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE
#> 32: D2 FALSE FALSE FALSE TRUE FALSE FALSE FALSE TRUE TRUE FALSE
#> 33: D3 FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE TRUE
#> 34: D4 FALSE FALSE TRUE FALSE FALSE TRUE FALSE TRUE FALSE FALSE
#> 35: D5 TRUE TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
#> 36: D6 TRUE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE
#> 37: D7 TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE FALSE FALSE
#> 38: D8 FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE
#> ID ARTH CHRNLUNG DMCX DRUG HRENWORF HTNPREG LIVER LYMPH NEURO OBESE
#> PARA PERIVASC PSYCH RENLFAIL TUMOR ULCER VALVE WGHTLOSS selectedCase
#> 1: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 2: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 3: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 4: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 5: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 6: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 7: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 8: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 9: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 10: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 11: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 12: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 13: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 14: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 15: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 16: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 17: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 18: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 19: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 20: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 21: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 22: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 23: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 24: FALSE FALSE FALSE TRUE FALSE FALSE FALSE FALSE Selected
#> 25: FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE non-Selected
#> 26: FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE non-Selected
#> 27: FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE non-Selected
#> 28: FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE non-Selected
#> 29: FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE non-Selected
#> 30: FALSE FALSE TRUE FALSE FALSE TRUE FALSE FALSE non-Selected
#> 31: FALSE FALSE FALSE FALSE FALSE FALSE FALSE TRUE non-Selected
#> 32: FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE non-Selected
#> 33: FALSE TRUE TRUE FALSE FALSE FALSE FALSE FALSE non-Selected
#> 34: TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE non-Selected
#> 35: FALSE FALSE FALSE FALSE FALSE FALSE TRUE FALSE non-Selected
#> 36: FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE non-Selected
#> 37: FALSE FALSE TRUE FALSE TRUE FALSE FALSE FALSE non-Selected
#> 38: TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE non-Selected
#> PARA PERIVASC PSYCH RENLFAIL TUMOR ULCER VALVE WGHTLOSS selectedCase