ICD flagging function — icd_morb

This function serves to add flags to an input data set (morbidity at this stage) pursuant to ICD codes. Flags can be added for general categories based on pre-established ICD codes (e.g., any mental health contact, any substance-related contact, any alcohol/tobacco-related contact etc.) or add a custom set of ICD codes. The file with these pre-established ICD codes are saved as an .RData file and are trivial to change.

Usage

icd_morb_flag(
  data,
  dobmap = NULL,
  flag_category,
  flag_other_varname,
  diag_type,
  diag_type_custom_vars = NULL,
  diag_type_custom_params,
  under_age = FALSE,
  age = 18,
  person_summary = FALSE,
  id_var = "rootnum",
  morb_date_var = "subadm",
  dobmap_dob_var = "dob",
  dobmap_other_vars = NULL
)

Arguments

data: Input dataset (morbidity).
dobmap: DOBmap file corresponding to input dataset.
flag_category: Type of flag to generate. Takes values from reference file (e.g., MH_morb, Sub_morb, etc.) or "Other" for custom ICD specification and flagging.
flag_other_varname: Flag variable name (specified only When flag_category == "Other"). Input as character string.
diag_type: Diagnosis type. Select from "principal diagnosis", (all) "additional diagnoses", "external cause of injury", "custom".
diag_type_custom_vars: Variables to search across when diag_type == "custom".
diag_type_custom_params: Search parameters to search across when diag_type == "custom". Must be a list where the keys are the variable names and values are the inputs to WAACHShelp::val_filt. Can also be a list of lists where multiple ICD can be searched across for a single variable. See examples for specification.
under_age: Return additional variables corresponding to when participant was strictly under age y.o.. Uses DOBmap DOB and subadm morbidity admission date. Variables have suffix "_under{age}".
age: Numeric. Age (years) to consider for the under_age variable (default 18).
person_summary: Summarise results at a person-level.
id_var: Joining (ID) variable consistent between data and dobmap. Default rootnum.
morb_date_var: Hospital morbidity date variable in data. Default "subadm".
dobmap_dob_var: Date of birth (DOB) variable in dobmap. Default "dob".
dobmap_other_vars: Other variables to carry across from DOBmap file when joining to data. Default NULL. Can be a vector of strings.

Value

Flagged dataframe.

Details

For more details, see the vignette.

Examples

if (FALSE) { # \dontrun{
# Example 1: Basic use
## Create any mental health or substance-related morbidity flag, "MH_morb"
## Searches "principal diagnosis", "additional diagnoses", "external cause of injury".
## Create additional flag for whether admission occurred when under 18 years of age
icd_morb_flag(
  data = morb,
  dobmap = dob,
  flag_category = "MH_morb",
  under_age = T,
  age = 18,
  dobmap_other_vars = c("xyz123", "abc456") # Also join `xyz123`, `abc456` from DOBmap
  )

# Example 2: Basic use
## Create any substance-related morbidity flag, "Sub_morb"
icd_morb_flag(data = morb,
              flag_category = "Sub_morb" # Create any MH contact flag
              )

# Example 3: Search  *principal diagnosis* and *first additional diagnosis*
# for a custom set of ICD codes
## Call this variable "test_var"
icd_morb_flag(data = morb,
              flag_category = "Other",
              diag_type = "custom",
              diag_type_custom_vars = c("diagnosis", "ediag20"),
              diag_type_custom_params = list("diagnosis" = list("letter" = "F",
                                                                "lower" = 0,
                                                                "upper" = 99.9999),
                                             "ediag20" = list("letter" = "",
                                                              "lower" = 0,
                                                              "upper" = 99.9999)),
              flag_other_varname = "test_var"
              )

# Example 4:
# Search only across primary diagnosis and
# (all) additional diagnosis fields for a custom set of ICD codes.
## Call this variable "test_var2"
icd_morb_flag(data = morb,
              flag_category = "Other",
              diag_type = c("principal diagnosis", "additional diagnoses"),
              diag_type_custom_params = list("principal diagnosis" = list("letter" = "F",
                                                                          "lower" = 0,
                                                                          "upper" = 99.9999),
                                             "additional diagnoses" = list("letter" = "",
                                                                           "lower" = 0,
                                                                           "upper" = 99.9999)),
              flag_other_varname = "test_var2"
              )

# Example 5: Search across (all) additional diagnosis fields and another random field, `dagger`
## Call this variable "test_var3"
icd_morb_flag(data = morb,
              flag_category = "Other",
              diag_type = c("custom", "additional diagnoses"),
              diag_type_custom_vars = "dagger",
              diag_type_custom_params = list("dagger" = list("letter" = "F",
                                                             "lower" = 0,
                                                             "upper" = 99.9999)),
              flag_other_varname = "test_var3"
              )

# Example 6: Searching across multiple ICD code types within a variable
## Call this variable "test_var4" -- replicating MH_morb flag
icd_morb_flag(data = morb,
              flag_category = "Other",
              diag_type = c("additional diagnoses",
                            "additional diagnoses",
                            "external cause of injury"),
              flag_other_varname = "test_var3",
              diag_type_custom_params =
              list("principal diagnosis" = list(list("letter" = "F",
                                                     "lower" = 0,
                                                     "upper" = 99.9999),
                                                list("letter" = "",
                                                     "lower" = 290,
                                                     "upper" = 319.9999)),
                    "additional diagnoses" = list(list("letter" = "F",
                                                       "lower" = 0,
                                                       "upper" = 99.9999),
                                                  list("letter" = "",
                                                       "lower" = 290,
                                                       "upper" = 319.9999)),
                    "external cause of injury" = list(list("letter" = "E",
                                                           "lower" = 950,
                                                           "upper" = 959.9999),
                                                      list("letter" = "X",
                                                           "lower" = 60,
                                                           "upper" = 84.9999))))
} # }