Package {ofhsyn}

Type: Package
Title: Synthetic Our Future Health Data Generator
Version: 0.1.1
Author: Hannah Nicholls [aut, cre]
Maintainer: Hannah Nicholls <h.l.nicholls@qmul.ac.uk>
Description: Generates synthetic Our Future Health cohort datasets for method development, including participant, questionnaire, clinic measurements, outpatient, inpatient, emergency, mortality, primary care medication, and geography outputs. Supports reproducible generation with configurable cohort size and user-defined International Classification of Diseases, Tenth Revision (ICD-10), Office of Population Censuses and Surveys Classification of Interventions and Procedures, version 4 (OPCS-4), and British National Formulary (BNF) code pools.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.2
Depends: R (≥ 4.2.0)
Imports: methods, utils, stats
Suggests: testthat (≥ 3.0.0), knitr, rmarkdown
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2026-06-04 15:10:53 UTC; btx925
Repository: CRAN
Date/Publication: 2026-06-09 15:40:08 UTC

Reference Class for OFH Cohort Generation

Description

Reference class API for configuring and running synthetic cohort generation.

Usage

OFHCohortSynthesizer

Details

Create an instance with OFHCohortSynthesizer$new(...) and run generation via $run_all(n = ...).

Value

A ReferenceClass generator object. Use OFHCohortSynthesizer$new(...) to create an instance. Instance methods return the instance invisibly for chaining where applicable, and $run_all() returns a named list of data frames when return_objects = TRUE (otherwise invisible NULL).

Examples

syn <- OFHCohortSynthesizer$new(project_root = ".", seed = 123)
out <- syn$run_all(n = 100, save_csv = FALSE, return_objects = TRUE)

Generate Synthetic OFH Cohort Datasets

Description

Generate linked synthetic health datasets for a configurable cohort.

Usage

generate_ofh_cohort(
  n = 5000,
  seed = 42,
  icd10 = NULL,
  icd10_file = NULL,
  opcs4 = NULL,
  opcs4_file = NULL,
  bnf_codes = NULL,
  bnf_codes_file = NULL,
  proportions = NULL,
  record_multipliers = NULL,
  code_config = NULL,
  save_csv = TRUE,
  return_objects = TRUE,
  output_dir = NULL
)

Arguments

n

Total synthetic cohort size.

seed

Random seed.

icd10

Optional named character vector of ICD-10 descriptions.

icd10_file

Optional path to a TXT/CSV file containing ICD-10 code and description pairs. TXT format should be tab-separated with code and description columns. CSV format should provide code and description columns.

opcs4

Optional named character vector of OPCS-4 descriptions.

opcs4_file

Optional path to a TXT/CSV file containing OPCS-4 code and description pairs. TXT format should be tab-separated with code and description columns. CSV format should provide code and description columns.

bnf_codes

Optional BNF input for primary care meds. Can be either a character vector of BNF codes or a data frame with columns for code, name, and formulation (optional strength).

bnf_codes_file

Optional path to a TXT/CSV file for BNF input. TXT supports one BNF code per line. CSV supports either code-only or structured medication rows containing code, name, and formulation (optional strength).

proportions

Optional named list of dataset-level coverage proportions. Names should match names(ofh_default_proportions()).

record_multipliers

Optional named list of multipliers for multi-record datasets. Names should match names(ofh_default_record_multipliers()).

code_config

Optional nested list overriding field-level code generation probabilities and pools. Structure should follow ofh_default_code_config().

save_csv

Whether to write CSV outputs to disk.

return_objects

Whether to return generated data frames as an R object.

output_dir

Output directory when save_csv = TRUE.

Value

Named list of generated data frames when return_objects = TRUE; otherwise invisible NULL.

Acknowledgement

We extend our thanks to GitHub user @icallumwebb for contributing a bug fix that improved custom code handling.

Examples

out <- generate_ofh_cohort(n = 200, seed = 123, save_csv = FALSE, return_objects = TRUE)
names(out)

Standalone Synthetic Generation Primitives

Description

Utility functions for generating participant populations and event-level synthetic records.

Usage

generate_ofh_population(n = 1000, seed = 123)

add_inpatient_events(
  data,
  events_per_person = 5,
  icd10_codes = c("I210", "I500", "I639", "E110", "J440"),
  opcs4_codes = c("K401", "K451", "K561", "M011", "E033"),
  seed = 123
)

synthesize_drug_exposure(
  data,
  drug_list = c("0212000B0", "0601023A0"),
  seed = 123,
  mean_items_per_person = 2
)

Arguments

data

Input data frame containing a pid column.

n

Number of participants.

seed

Random seed.

events_per_person

Mean events per participant.

icd10_codes

ICD-10 code pool.

opcs4_codes

OPCS-4 code pool.

drug_list

Medication code pool.

mean_items_per_person

Mean prescription items per participant.

Value

Return value depends on the function called:

generate_ofh_population()

Data frame with one row per participant and columns including pid, sex, and birth_year.

add_inpatient_events()

Data frame of synthetic inpatient events with columns pid, admidate, icd10, and opcs4.

synthesize_drug_exposure()

Data frame of synthetic primary-care medication records with participant IDs and prescribing/dispensing fields (for example prescribedbnfcode, paidbnfcode).

Configuration Helpers for OFH Generation

Description

Helper functions that return default settings and compose full generation configuration lists.

Usage

ofh_default_proportions()
ofh_default_record_multipliers()
ofh_default_code_config()
ofh_build_config(
  n = 5000,
  proportions = ofh_default_proportions(),
  record_multipliers = ofh_default_record_multipliers(),
  code_config = list()
)

Arguments

n

Total cohort size.

proportions

Dataset proportions list.

record_multipliers

Record multiplier list for event datasets.

code_config

Optional code configuration overrides.

Value

Return value depends on the function called:

ofh_default_proportions()

Named numeric list of dataset proportions in [0, 1].

ofh_default_record_multipliers()

Named numeric list of multipliers for multi-record datasets.

ofh_default_code_config()

Nested named list containing default code pools, weights, and generation controls by dataset.

ofh_build_config()

Named list with total_pid_count (integer), datasets (nested list of dataset sizing settings), and code_config (merged code configuration list).