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Add SNOMED-CT version 3 codes to skeleton

Source: R/add_diagnoses_and_operations.R
add_snomed3s.Rd

Searches for specific SNOMED-CT (Systematized Nomenclature of Medicine - Clinical Terms) version 3 codes in Swedish hospital registry data and adds corresponding boolean variables to the skeleton. SNOMED-CT v3 provides standardized clinical terminology for procedures, findings, and diagnoses used in Swedish healthcare records.

Usage

add_snomed3s(skeleton, dataset, id_name, codes = list(), snomed3s = NULL)

Arguments

skeleton

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

dataset

A data.table containing hospital registry data with SNOMED-CT v3 codes. Must have columns for person ID, date variables, and SNOMED-CT v3 code column (snomed3)

id_name

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

codes

Named list of SNOMED-CT v3 code patterns to search for. Names become variable names in skeleton.

snomed3s

Deprecated. Use codes instead. SNOMED-CT codes are hierarchical and can be matched using pattern matching. Examples of pattern matching:

  • "^80146002" - Appendectomy procedure

  • "^44054006" - Diabetes mellitus type 2

  • Use regex patterns to match code families or hierarchies

Value

The skeleton data.table is modified by reference with SNOMED-CT v3 variables added. New boolean variables are created for each SNOMED-CT pattern, TRUE when code is present.

See also

create_skeleton for creating the skeleton structure, add_diagnoses for ICD-10 diagnosis codes, add_snomedo10s for SNOMED-CT version 10 codes, make_lowercase_names for data preprocessing

Other data_integration: add_annual(), add_cods(), add_diagnoses(), add_icdo3s(), add_onetime(), add_operations(), add_rx(), 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 SNOMED-CT v3 codes for specific clinical concepts
snomed_codes <- list(
  "appendectomy" = c("^80146002"),
  "diabetes_t2" = c("^44054006")
)
add_snomed3s(skeleton, fake_diagnoses, "lopnr", snomed_codes)