Skip to contents

Add surgical operation data to skeleton

Source: R/add_diagnoses_and_operations.R
add_operations.Rd

Searches for specific surgical operation codes in Swedish hospital registry data and adds corresponding boolean variables to the skeleton. Includes predefined operation codes relevant to gender-affirming procedures.

Usage

add_operations(
  skeleton,
  dataset,
  id_name,
  codes = list(op_afab_mastectomy = c("HAC10", "HAC20", "HAC99", "HAC15"),
    op_afab_breast_reconst_and_other_breast_ops = c("HAD20", "HAD30", "HAD35", "HAD99",
    "HAE99"), op_afab_penis_test_prosth = c("KFH50", "KGV30", "KGW96", "KGH96"),
    op_afab_internal_genital = c("LCD00", "LCD01", "LCD04", "LCD10", "LCD11", "LCD96",
    "LCD97"), op_afab_colpectomy = c("LED00"),
    op_amab_breast_reconst_and_other_breast_ops = c("HAD00", "HAD10", "HAD99", "HAE00",
    "HAE20", "HAE99"), op_amab_reconst_vag = c("LEE10", "LEE40", "LEE96", 
     "LFE10",
    "LFE96"), op_amab_penis_amp = c("KGC10"), op_amab_larynx = c("DQD40")),
  ops = NULL
)

Arguments

skeleton

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

dataset

A data.table containing hospital registry data with operation codes. Must have columns for person ID, date variables, and operation codes (op1, op2, etc.)

id_name

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

codes

Named list of operation 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 (the same matcher is shared between add_diagnoses, add_operations, add_cods, add_icdo3s, add_snomed3s and add_snomedo10s).

Default includes comprehensive gender-affirming surgery codes:

  • Mastectomy procedures (HAC10, HAC20, etc.)

  • Breast reconstruction (HAD20, HAD30, etc.)

  • Genital operations (various KFH, KGV, LCD, LED, LEE codes)

  • Larynx operations (DQD40)

ops

Deprecated. Use codes instead.

Value

The skeleton data.table is modified by reference with operation variables added. New boolean variables are created for each operation pattern, TRUE when operation 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_cods(), add_diagnoses(), add_icdo3s(), add_onetime(), add_quality_registry(), 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 operations (using default gender-affirming surgery codes)
add_operations(skeleton, fake_diagnoses, "lopnr")

# Or specify custom operation codes
custom_ops <- list("mastectomy" = c("HAC10", "HAC20"))
add_operations(skeleton, fake_diagnoses, "lopnr", custom_ops)