Benchmarking the CodelistGenerator R package

In CodelistGenerator: Identify Relevant Clinical Codes and Evaluate Their Use

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

CDMConnector::requireEunomia("synpuf-1k", "5.3")

To check the performance of the CodelistGenerator package, we can use the benchmarkCodelistGenerator(). This function generates some hypothetical study codelists using various settings and times to check how long these analyses take.

We can start for example by benchmarking our mock data, which uses duckdb.

library(DBI)
library(duckdb)
library(dplyr)
library(CDMConnector)
library(CodelistGenerator)
library(visOmopResults)

# Connect to the database and create the cdm object
con <- dbConnect(duckdb(), 
                      eunomiaDir("synpuf-1k", "5.3"))
cdm <- cdmFromCon(con = con, 
                  cdmName = "Eunomia Synpuf",
                  cdmSchema   = "main",
                  writeSchema = "main", 
                  achillesSchema = "main")

timings <- benchmarkCodelistGenerator(cdm)

visOmopTable(timings,
             hide = c("variable_name", "variable_level", "strata_name", "strata_level"),
             groupColumn = "task")

CodelistGenerator documentation built on Dec. 17, 2025, 5:06 p.m.