uk_patient_id: Patient ID record grouping

In alexbhatt/epidm: UK Epidemiological Data Management

Patient ID record grouping

Description

Groups patient records from multiple isolates with a single integer patientID by grouping patient identifiers.

Grouping is based on the following stages:

1. matching nhs number and date of birth

2. Hospital number & Date of Birth

3. NHS number & Hospital Number

4. NHS number & Name

5. Hospital number & Name

6. Sex & Date of Birth & Surname

7. Sex & Date of Birth & Fuzzy Name

8. Sex & Year and Month of Birth & Fuzzy Name

9. Postcode & Name

10. Name Swaps (when first and last name are the wrong way around)

Identifiers are copied over where they are missing or invalid to the grouped records.

Usage

uk_patient_id(
  data,
  id = list(nhs_number = "nhs_number", hospital_number = "patient_hospital_number",
    date_of_birth = "date_of_birth", sex_mfu = "sex", forename = "forename", surname =
    "surname", postcode = "postcode"),
  .useStages = c(1:11),
  .sortOrder,
  .keepValidNHS = FALSE,
  .forceCopy = FALSE
)

Arguments

data	a data.frame or data.table containing the patient data
id	a named list to provide the column names with identifiers, quoted nhs_number the patient NHS number hospital_number the patient Hospital numbers also known as the local patient identifier date_of_birth the patient date of birth sex_mfu the patient sex or gender field as Male/Female/Unknown forename the patient forename surname the patient surname postcode the patient postcode
.useStages	optional, default 1:11; set to 1 if you wish patient ID to be assigned cases with the same DOB and NHS number, set to 2 if you wish patient ID to be assigned to cases with the same hospital number (HOS) and DOB, set to 3 if you wish patient ID to be assigned cases with the same NHS and HOS number, set to 4 if you wish patient ID to be assigned cases with the same NHS number and surname, set to 5 if you wish patient ID to be assigned cases with the same hospital number and surname, set to 6 if you wish patient ID to be assigned cases with the same DOB and surname, set to 7 if you wish patient ID to be assigned cases with the same sex and full name, set to 8 if you wish patient ID to be assigned cases with the same sex, DOB and fuzzy name, set to 9 if you wish patient ID to be assigned cases with the same DOB and fuzzy name, set to 10 if you wish patient ID to be assigned cases with the same name and postcode, set to 11 if you wish patient ID to be assigned cases with the same first name or second name in changing order and date of birth.
.sortOrder	optional; a column as a character to allow a sorting order on the id generation
.keepValidNHS	optional, default FALSE; set TRUE if you wish to retain the column with the NHS checksum result stored as a BOOLEAN
.forceCopy	optional, default FALSE; TRUE will force data.table to take a copy instead of editing the data without reference

Value

A dataframe with one new variable:

id

a unique patient id

valid_nhs

if retained using argument .keepValidNHS=TRUE, a BOOLEAN containing the result of the NHS checksum validation

Examples

uk_patient_id(
 data = head(epidm::lab_data),
 id = list(
   nhs_number = 'nhs_number',
   hospital_number = 'local_patient_identifier',
   date_of_birth = 'patient_birth_date',
   sex_mfu = 'sex',
   forename = 'forename',
   surname = 'surname'
   postcode = 'postcode'
 ),
 .sortOrder = 'specimen_date',
 .forceCopy = TRUE
)[]

alexbhatt/epidm documentation built on Aug. 21, 2024, 8:25 a.m.