Package 'PatientGenerator'

Title: Generator of Synthetic Patient Data for the OMOP Common Data Model
Description: Tools to generate synthetic patient-level test datasets in the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). Includes a chat-driven generator backed by large language models and an interactive 'shiny' designer for editing CDM test sets.
Authors: Cesar Barboza [aut, cre] (ORCID: <https://orcid.org/0009-0002-4453-3071>), Ger Inberg [aut] (ORCID: <https://orcid.org/0000-0001-8993-8748>), Adam Black [aut] (ORCID: <https://orcid.org/0000-0001-5576-8701>)
Maintainer: Cesar Barboza <[email protected]>
License: Apache License (>= 2)
Version: 0.1.4
Built: 2026-06-08 08:11:35 UTC
Source: https://github.com/ohdsi/patientgenerator

Help Index

availableModels() If the API key is valid in the system, returns available models to the user from the LLM provider.

Description

OpenAI is the only one currently supported.

Usage

availableModels()

Value

A string list with the id of a vailable models.

Concept search Shiny module

Description

Reusable UI and server for searching the vocabulary (Hecate) and selecting a concept. Shows a button that opens a modal with text input, search button, and results in a DT table. Optional callback when a concept is selected.

Usage

conceptSearchUI(id, buttonLabel = "Concept search")

conceptSearchServer(id, onConceptSelected = NULL, placeholderText = "")

Arguments

id

Module namespace id.
buttonLabel

Label for the trigger button (default "Concept search").
onConceptSelected

Optional function of one argument conceptId called when user selects a concept; modal is closed after.
placeholderText

Character string used as placeholder text in the search input field.

Functions

  • conceptSearchUI(): UI for the concept search: a single button that opens the search modal.

  • conceptSearchServer(): Server for the concept search modal (text input, search, DT, close).

Useful to list available datasets in the testCases folder

Description

Useful to list available datasets in the testCases folder

Usage

getTestSets(path = NULL)

Arguments

path

Optional directory containing JSON test sets. If NULL, the package resolves a default path with testthat integration.

Value

A list()

Create a Hecate API client

Description

Create a Hecate API client

Usage

hecateClient(baseUrl = NULL, timeoutMs = NULL, apiKey = NULL)

Arguments

baseUrl

Base URL of the Hecate API (default from config).
timeoutMs

Timeout in milliseconds (default from config).
apiKey

Optional API key for authorization (default from config).

Value

A client object with class hecate_client.

Search Hecate concepts and return results as a data frame

Description

Search Hecate concepts and return results as a data frame

Usage

hecateSearch(
  query,
  vocabularyId = NULL,
  standardConcept = NULL,
  domainId = NULL,
  conceptClassId = NULL,
  limit = 20,
  client = hecateClient()
)

Arguments

query

Character(1); search query (required).
vocabularyId

Character(1) or NULL; optional vocabulary filter (comma-separated).
standardConcept

Character(1) or NULL; e.g. "S" (Standard), "C" (Classification).
domainId

Character(1) or NULL; optional domain filter (comma-separated).
conceptClassId

Character(1) or NULL; optional concept class filter.
limit

Integer(1); max results (default 20, max 150).
client

Hecate client (default hecateClient()).

Value

Data frame of search results, or NULL if an error occurred (API error or bad response shape).

Examples

## Not run: 
# Simple search
df <- hecateSearch("diabetes")

# Search with filters
df <- hecateSearch("hypertension", domainId = "Condition", limit = 10)

## End(Not run)

Null coalescing operator

Description

Null coalescing operator

Usage

x %||% y

Arguments

x

First value (any type).
y

Fallback value when x is NULL.

Value

x if not NULL, otherwise y.

patientChat() generates synthetic patients in the OMOP-CDM using an LLM API.

Description

Requires an OPEN_AI_KEY in ~/.Renviron. After that just sent a prompt and save() the results. The JSON file can be used as an OMOP-CDM patient test set.

Details

Accepts a prompt as input. Produces a test set using a structured JSON schema. Utilizes tools such as CodelistGenerator or Hecate to look up concept IDs. Accepts subsequent prompts to modify existing test sets that the LLM uses as context.

This class allows testing patient sets created by the LLM, prompt engineering, integration of search tools and functionality, and creating a set of patients to test analytical packages.

Value

A JSON response that includes: the natural language answer from the LLM and a JSON with test set patients in accordance to the provided schema.

Public fields

chat

An ellmer chat instance

json_schema_path

JSON schema to output structured results

response

Ouput from the LLM

codelist

A codelist with details to search for concepts ids

Methods

Public methods

Method new()

Create a new chat to create JSON test sets for OMOP-CDM.

Usage
patientChat$new(
  system_prompt = NULL,
  model = "gpt-5.4",
  jsonSchemaPath = NULL,
  echo = c("none", "output", "all"),
  codelist_data = NULL
)
Arguments
system_prompt

Initial system prompt to impose behaviour to the LLM

model

Such as "gpt-5.3". For a complete list, call patientChat$availableModels()

jsonSchemaPath

The JSON schema to structure output from LLM

echo

How the output will be displayed in the console

codelist_data

A codelist with details to search for concepts ids

Returns

A new Person object.

Method prompt()

Prompt to request data from LLM API

Usage
patientChat$prompt(prompt)
Arguments
prompt

A query in character.

Method json_response()

Output in JSON format

Usage
patientChat$json_response()

Method output()

Returns the chat object

Usage
patientChat$output()

Method retrieveCodelist()

Retrieves and filters data from codelist_data

Usage
patientChat$retrieveCodelist(concept_label = "Stage 1", domain = "Measurement")
Arguments
concept_label

Filters the concept_name in the codelist with details

domain

Filters the domain in the codelist with details.

Method save()

Saves the JSON test set to disk.

Usage
patientChat$save(name = "patient-chat-test", path = NULL)
Arguments
name

Name of the file

path

To save the file. If NULL, the package first tries testthat::test_path("testCases"), then checks options(PatientGenerator.testSetDir = "..."), and finally falls back to the package user data directory.

Method availableModels()

Retrieves available models from the LLM API.

Usage
patientChat$availableModels()

Method clone()

The objects of this class are cloneable with this method.

Usage
patientChat$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Examples

## Not run: 
generator <- patientChat$new()
generator$prompt("Give me 5 patients")
generator$save("my_test")

## End(Not run)

patientChatNaive() is a grapper for the ellmer package to send prompts and send the output test set to an LLM. Requires a valid API key.

Description

Priorities: - Accepts a prompt as an input. - Produces a test set in accordance to the provided JSON schema. - Utilizes tools such as CodelistGenerator or Hecate to look up for functions. - Accepts a subsequent prompt with a test set that the LLM has to use as a context

One function for this tasks allow us to: - Test the test sets created by the LLM. - Test prompt engineering. - Test integration of tools functionality. - Allow us to create fast a small set of patients to test analytical packages.

Usage

patientChatNaive(
  prompt = "### Give me a sample of five patients",
  model = "gpt-5.2",
  jsonSchemaPath = NULL
)

Arguments

prompt

A prompt to the LLM, in character or JSON response.
model

The model used by the LLM. Currently only OpenAI models are accepted.
jsonSchemaPath

Path to a JSON schema used to structure the response.

Value

A JSON response that includes: the natural language answer from the LLM and a JSON with test set patients in accordance to the provided schema.

patientDesigner() is a visual interface based on D3 to construct test datasets for the OMOP-CDM

Description

patientDesigner() is a visual interface based on D3 to construct test datasets for the OMOP-CDM

Usage

patientDesigner(path = NULL)

Arguments

path

Optional folder containing JSON test sets. If NULL, default path resolution keeps testthat integration.

Value

A Shiny app