categorize_simple: Categorize codes according to a mapping
In icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes

Description Usage Arguments Details Examples

This is the function which prepares the input data for the categorization, and forms the core of the package, along with the C++ matrix code. This is pure data manipulation and generalizable beyond medical data.

categorize_simple(
  x,
  map,
  id_name,
  code_name,
  return_df = FALSE,
  return_binary = FALSE,
  restore_id_order = TRUE,
  preserve_id_type = FALSE,
  comorbid_fun = comorbid_mat_mul_wide,
  ...
)

`x`	Data frame containing a column for an 'id' and a column for a code, e.g., an ICD-10 code.
`map`	named list containing vectors of ICD-9 codes. E.g. the AHRQ ICD-9 comorbidities, contains `list(OBESE = c("2780", "27800", "27801", "27803", "V8554", "79391", "64910", "64911", "64912", "64913", "64914", "V8530", "V8531", "V8532", "V8533", "V8534", "V8535", "V8536", "V8537", "V8538", "V8539", "V8541", "V8542", "V8543", "V8544", "V8545" ), DEPRESS = c("3004", "30112", "3090", "3091", "311"))` amongst other longer groups.
`id_name`	The name of the `data.frame` field which is the unique identifier.
`code_name`	String with name(s) of column(s) containing the codes.
`return_df`	single logical value, if `TRUE`, return 'tidy' data, i.e., the result is a data frame with the first column being the `visit_id`, and the second being the count. If `visit_id` was a factor or named differently in the input, this is preserved.
`return_binary`	Logical value, if `TRUE`, the output will be in 0s and 1s instead of `TRUE` and `FALSE`.
`restore_id_order`	Logical value, if `TRUE`, the default, the order of the visit IDs will match the order of visit IDs first encountered in the input data. This takes a third of the time in calculations on data with tens of millions of rows, so, if the visit IDs will be discarded when summarizing data, this can be set to `FALSE` for a big speed-up.
`preserve_id_type`	Single logical value, if `TRUE`, the visit ID column will be converted back to its original type. The default of `FALSE` means only `factors` and `character` types are restored in the returned data frame. For matrices, the row names are necessarily stored as character vectors.
`comorbid_fun`	function i.e. the function symbol (not character string) to be called to do the comorbidity calculation
`...`	arguments passed on to other functions

The roadmap for icd includes the optimized categorization component being packaged independently, and the comorbidity package taking on the front-end for doing ICD-code-based comorbidities. This is in discussion.

u <- uranium_pathology
m <- icd10_map_ahrq
u$icd10 <- decimal_to_short(u$icd10)
j <- icd:::categorize_simple(u, m, id_name = "case", code_name = "icd10")