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Add cancer diagnoses by topography (site only, ignoring morphology)

Source: R/add_diagnoses_and_operations.R
add_cancer_without_morphology.Rd

Flags cancer from the Swedish Cancer Register by topography (tumour site) only, ignoring morphology/histology. Use this when the phenotype is site-level – "any breast cancer", "any endometrial cancer" – which is the granularity ICD-10 and the patient register encode cancer at. Morphology / histology (cell type, behaviour) is out of scope for this function.

Usage

add_cancer_without_morphology(skeleton, dataset, id_name, codes = list())

Arguments

skeleton

The skeleton data.table created by create_skeleton()

dataset

Cancer register data.table containing icdo10 and/or icdo3 columns and an indatum date column.

id_name

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

codes

Named list of topography (C-code) patterns. Names become column names in the skeleton; values are character vectors of code prefixes. Matching is prefix-only via startsWith(); "!"-prefixed patterns act as row-level vetoes. See add_diagnoses for the full pattern-syntax description.

Value

The skeleton data.table is modified by reference; one boolean column per pattern, TRUE when the cancer topography code is present.

Details

Searches BOTH ICD-O topography columns and unions the result, giving complete coverage:

  • icdo10 – ICD-O/2 topography, populated back to register start (the complete column).

  • icdo3 – ICD-O/3 topography, populated from ~2000 onward.

Despite its name, icdo10 is not "ICD-O edition 10" (ICD-O has only editions 1-3). It is Socialstyrelsen's (confusingly named) column for ICD-O/2 topography, whose codes ARE the ICD-10 neoplasm site codes (e.g. C50 = breast). That is why ICD-10 cancer patterns match it – and why it must not be mistaken for a stray ICD-O column and dropped.

Note: in-situ tumours carry the malignant topography code (in-situ breast is C50 + morphology /2, never D05), so a C50 pattern here captures both invasive and in-situ breast.

See also

add_diagnoses for ICD-10 patient-register codes, make_lowercase_names for data preprocessing

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

Examples

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.
skeleton <- create_skeleton(fake_person_ids[1:10], "2020-01-01", "2020-12-31")
cancer_codes <- list("breast" = c("C50"), "endometrial" = c("C54", "C55"))
add_cancer_without_morphology(skeleton, fake_diagnoses, "lopnr", cancer_codes)