Type: Package
Title: Synthetic Hybrid Electronic Health Records Dataset Generator with COVID/CT Research Views
Version: 0.1.0
Maintainer: Dennis Boadu <doboadu@st.ug.edu.gh>
Description: Tools to generate synthetic electronic health records including patients, encounters, vitals, labs, medications, procedures, and allergies, with optional COVID-19-focused and computed tomography (CT)-research views, and export them to comma separated values ('CSV'), 'SQLite', and 'Excel' formats for researchers and developers.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (≥ 4.1.0)
Imports: dplyr, tidyr, tibble, lubridate, jsonlite, openxlsx, DBI, RSQLite, magrittr
Suggests: knitr, rmarkdown
RoxygenNote: 7.3.3
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2025-12-16 21:34:38 UTC; dennisboadu
Author: Dennis Boadu [aut, cre], Isaac Osei [aut], Justice Appati [aut]
Repository: CRAN
Date/Publication: 2025-12-19 21:00:09 UTC

Export a hybrid EHR dataset to disk

Description

Export a hybrid EHR dataset to disk

Usage

export_hybrid_ehr_dataset(dataset, output_dir, verbose = TRUE)

Arguments

dataset

A list as returned by generate_hybrid_ehr_dataset().

output_dir

Directory to write files into.

verbose

Logical; if TRUE, print messages.

Value

The output directory (invisibly).

High-level wrapper to generate and export a hybrid EHR dataset

Description

High-level wrapper to generate and export a hybrid EHR dataset

Usage

generate_hybrid_ehr(
  n_patients = 500,
  n_sites = 3,
  covid_focused = TRUE,
  include_ct_links = FALSE,
  output_dir,
  seed = NULL,
  verbose = TRUE
)

Arguments

n_patients

Number of unique patients.

n_sites

Number of sites/hospitals to simulate.

covid_focused

Logical; if TRUE, use COVID-era encounter and lab patterns.

include_ct_links

Logical; if TRUE, add CT timing variables and a CT severity score in the CT research view.

output_dir

Directory for exported files.

seed

Optional integer used to set the random seed for reproducibility.

verbose

Logical; if TRUE, print progress messages to the console.

Value

A list with:

dataset

The in-memory dataset list (as from generate_hybrid_ehr_dataset).

output_dir

The output directory path where files were written.

A list containing:

dataset

Generated dataset object

output_dir

Path to exported files

Examples


ehr <- generate_hybrid_ehr_dataset(
  n_patients = 10,
  seed = 123,
  verbose = FALSE
)

export_hybrid_ehr_dataset(
  ehr,
  output_dir = tempdir(),
  verbose = FALSE
)

Generate synthetic hybrid EHR tables

Description

Generate synthetic hybrid EHR tables

Usage

generate_hybrid_ehr_dataset(
  n_patients = 500,
  n_sites = 3,
  covid_focused = TRUE,
  include_ct_links = FALSE,
  seed = NULL,
  verbose = TRUE
)

Arguments

n_patients

Number of unique patients.

n_sites

Number of sites/hospitals to simulate.

covid_focused

Logical; if TRUE, use COVID-era encounter and lab patterns.

include_ct_links

Logical; if TRUE, add CT timing variables and a CT severity score in the CT research view.

seed

Optional integer used to set the random seed for reproducibility.

verbose

Logical; if TRUE, print progress messages to the console.

Value

A list with elements:

tables

Named list of core EHR tables (patients, encounters, vitals, labs, medications, procedures, allergies).

research

Named list with ct_research_view (if covid_focused) and ml_flat_view (aggregated ML-ready table).

metadata

List of high-level generation settings and table metadata.

Examples

ehr <- generate_hybrid_ehr_dataset(
  n_patients = 10,
  n_sites = 2,
  covid_focused = TRUE,
  include_ct_links = FALSE,
  seed = 123,
  verbose = FALSE
)

names(ehr$tables)
head(ehr$tables$patients)