epidm (version 1.0.6)

inpatient_codes: Inpatient Codes cleanup

Description

When HES/SUS ICD/OPCS codes are provided in wide format you may want to clean them up into long for easier analysis. This function helps by reshaping long as a separate table. Ensuring they're separate allows you to retain source data, and aggregate appropriately later.

Usage

inpatient_codes(
  x,
  field_strings,
  patient_id_vars,
  type = c("icd9", "icd10", "opcs"),
  .forceCopy = FALSE
)

Value

a separate table with codes and id in long form

Arguments

x

a data.frame or data.table containing inpatient data

field_strings

a vector or string containing the regex for the the columns

patient_id_vars

a vector containing colnames used to identify a patient episode or spell

type

a string to denote if the codes are diagnostic or procedural

.forceCopy

Logical (default FALSE). If FALSE, the input is converted to a data.table and modified by reference. If TRUE, the input must already be a data.table, and the function will create an explicit copy to avoid modifying the original object.

Examples

# Example inpatient dataset
inpatient_test <- data.frame(
  id = c(1053L, 5487L, 8180L),
  spell_id = c("dwPDw", "iSpUq", "qpgk5"),
  primary_diagnosis_code = c("K602", "U071-", "I501"),
  procedure_code = c("H201", "H251", NA),
  procedure_date = as.Date(c("2023-01-01", "2023-01-04", NA))
)

# ICD-10 cleaning example
inpatient_codes(
  x = inpatient_test,
  field_strings = "diagnosis",
  patient_id_vars = c("id", "spell_id"),
  type = "icd10"
)

# OPCS cleaning example
inpatient_codes(
  x = inpatient_test,
  field_strings = c("procedure_code", "procedure_date"),
  patient_id_vars = c("id", "spell_id"),
  type = "opcs"
)