Benchmarking the CodelistGenerator R package

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.

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")

CDM name	Dbms	N person	N concepts	Estimate name	Estimate value
Getting drug ingredient codes (acetaminophen, codeine, adalimumab)
Eunomia Synpuf	duckdb	1,000	6,224,227	time_taken_minutes	0.01
Getting atc codes (atc 1st level, 1 name of interest)
Eunomia Synpuf	duckdb	1,000	6,224,227	time_taken_minutes	0.02
Getting candidate codes for dementia, excluding `child`, within all domains, and all options set to true
Eunomia Synpuf	duckdb	1,000	6,224,227	time_taken_minutes	0.04

Need mirroring services?
Contact our team at info@vpspulse.com.

Mirror powered by VPSpulse

Infrastructure sponsored by VPSPulse & Secure Payments by ArionPay.

VPSPulse Mirrors

Benchmarking the CodelistGenerator R package