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Add cause of death data to skeleton

Source: R/add_diagnoses_and_operations.R
add_cods.Rd

Searches for specific ICD-10 cause of death codes in Swedish death registry data and adds corresponding boolean variables to the skeleton. Can search in underlying cause of death, multiple causes, or both.

Usage

add_cods(
  skeleton,
  dataset,
  id_name,
  cod_type = "both",
  codes = list(icd10_F64_0 = c("F640"), icd10_F64_89 = c("F6489"), icd10_F64_089 =
    c("F640", "F648", "F649")),
  cods = NULL
)

Arguments

skeleton

A data.table containing the main skeleton structure created by create_skeleton

dataset

A data.table containing death registry data with cause of death codes. Must have columns for person ID, death date (dodsdat), and cause codes (ulorsak, morsak variables)

id_name

Character string specifying the name of the ID variable in the dataset

cod_type

Character string specifying which cause types to search:

  • "both" (default) - Search in both underlying (ulorsak) and multiple (morsak) causes

  • "underlying" - Search only in underlying cause of death (ulorsak)

  • "multiple" - Search only in multiple/contributing causes (morsak variables)

codes

Named list of ICD-10 code patterns. Names become column names in the skeleton; values are character vectors of code prefixes.

Matching is **prefix-only** via startsWith(). A pattern like "I21" matches "I21", "I210", "I219", etc. This is not regex – characters such as ^, $, *, [A-Z] are taken literally and will not match anything.

Prefixing a pattern with "!" turns it into a *row-level veto*: any source row whose code matches the (un-prefixed) pattern is masked out and does not contribute. The veto is applied per source row across all scanned columns (e.g. ulorsak + morsak*), and is reset between code names. Important: the veto operates on the raw source row, not on the (id, isoyearweek) bucket – if a person has both a vetoed code and a non-vetoed code in the same week, the non-vetoed code still triggers TRUE for that week.

Examples:

  • c("I21", "I22") – any acute MI code.

  • c("I", "!I21", "!I22") – any chapter-I code except acute MI.

cods

Deprecated alias for codes. If supplied, a warning is issued and the value is used as codes.

Value

The skeleton data.table is modified by reference with cause of death variables added. New boolean variables are created for each cause pattern, TRUE when cause is present.

See also

create_skeleton for creating the skeleton structure, add_diagnoses for diagnosis codes, add_rx for prescription data, make_lowercase_names for data preprocessing

Other data_integration: add_annual(), add_diagnoses(), add_icdo3s(), add_onetime(), add_operations(), add_quality_registry(), add_rx(), add_snomed3s(), add_snomedo10s()

Examples

# Load fake data
data("fake_person_ids", package = "swereg")
data("fake_cod", package = "swereg")
swereg::make_lowercase_names(fake_cod, date_columns = "dodsdat")

# Create skeleton
skeleton <- create_skeleton(fake_person_ids[1:10], "2020-01-01", "2020-12-31")

# Add cause of death data
cod_patterns <- list(
  "cardiovascular_death" = c("I21", "I22"),
  "external_causes" = c("X60", "X70")
)
add_cods(skeleton, fake_cod, "lopnr", "both", cod_patterns)