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Add ICD-O-3 oncology codes to skeleton

Source: R/add_diagnoses_and_operations.R
add_icdo3s.Rd

Searches for specific ICD-O-3 (International Classification of Diseases for Oncology, 3rd edition) codes in Swedish cancer registry data and adds corresponding boolean variables to the skeleton. ICD-O-3 is used to classify malignant neoplasms (cancers) by histological type (morphology) and anatomical site (topography).

Usage

add_icdo3s(skeleton, dataset, id_name, codes = list(), icdo3s = NULL)

Arguments

skeleton

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

dataset

A data.table containing cancer registry data with ICD-O-3 codes. Must have columns for person ID, date variables, and ICD-O-3 code column (icdo3)

id_name

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

codes

Named list of ICD-O-3 code patterns to search for. Names become variable names in skeleton.

icdo3s

Deprecated. Use codes instead. ICD-O-3 codes combine morphology (4 digits + behavior code) and topography (C codes). Examples of pattern matching:

  • "^8140" - Adenocarcinoma, NOS (morphology code)

  • "^C50" - Breast cancer (topography code)

  • "8500/3" - Infiltrating duct carcinoma (morphology with behavior)

Value

The skeleton data.table is modified by reference with ICD-O-3 variables added. New boolean variables are created for each ICD-O-3 pattern, TRUE when code is present.

See also

create_skeleton for creating the skeleton structure, add_diagnoses for ICD-10 diagnosis codes, add_operations for surgical procedure codes, make_lowercase_names for data preprocessing

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

Examples

# Load fake data
data("fake_person_ids", package = "swereg")
data("fake_diagnoses", package = "swereg")
swereg::make_lowercase_names(fake_diagnoses, date_columns = "indatum")
#> Found additional date columns not in date_columns: utdatum. Consider adding them for automatic date parsing.

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

# Add ICD-O-3 codes for specific cancer types
cancer_codes <- list(
  "adenocarcinoma" = c("^8140"),
  "breast_cancer" = c("^C50")
)
add_icdo3s(skeleton, fake_diagnoses, "lopnr", cancer_codes)