Database diagnostics

Introduction

In this example we’re going to be using the Eunomia synthetic data.

library(CDMConnector)
library(OmopSketch)
library(PhenotypeR)
library(dplyr)
library(ggplot2)

con <- DBI::dbConnect(duckdb::duckdb(), 
                      CDMConnector::eunomiaDir("synpuf-1k", "5.3"))
cdm <- CDMConnector::cdmFromCon(con = con, 
                                cdmName = "Eunomia Synpuf",
                                cdmSchema   = "main",
                                writeSchema = "main", 
                                achillesSchema = "main")

Database diagnostics

Although we may have created our study cohort, to inform analytic decisions and interpretation of results requires an understanding of the dataset from which it has been derived. The databaseDiagnostics() function will help us better understand a data source.

To run database diagnostics we just need to provide our cdm reference to the function.

db_diagnostics <- databaseDiagnostics(cdm)

Database diagnostics builds on OmopSketch package to perform the following analyses:

• Snapshot: Summarises the meta data of a CDM object by using summariseOmopSnapshot()
• Observation periods: Summarises the observation period table by using summariseObservationPeriod(). This will allow us to see if there are individuals with multiple, non-overlapping, observation periods and how long each observation period lasts on average.

The output is a summarised result object.

Visualise the results

We can use OmopSketch package functions to visualise the results obtained.

Snapshot

tableOmopSnapshot(db_diagnostics)

Estimate	Database name
	Eunomia Synpuf
General
Snapshot date	2025-07-22
Person count	1,000
Vocabulary version	v5.0 06-AUG-21
Observation period
N	1,048
Start date	2008-01-01
End date	2010-12-31
Cdm
Source name	Synpuf
Version	v5.3.1
Holder name	ohdsi
Release date	2018-03-15
Description
Documentation reference
Source type	duckdb

Observation periods

tableObservationPeriod(db_diagnostics)

Observation period ordinal	Variable name	Estimate name	CDM name
			Eunomia Synpuf
all	Number records	N	1,048
	Number subjects	N	1,000
	Records per person	mean (sd)	1.05 (0.21)
		median [Q25 - Q75]	1 [1 - 1]
	Duration in days	mean (sd)	979.71 (262.79)
		median [Q25 - Q75]	1,096 [1,096 - 1,096]
	Days to next observation period	mean (sd)	172.17 (108.35)
		median [Q25 - Q75]	138 [93 - 254]
1st	Number subjects	N	1,000
	Duration in days	mean (sd)	994.16 (257.95)
		median [Q25 - Q75]	1,096 [1,096 - 1,096]
	Days to next observation period	mean (sd)	172.17 (108.35)
		median [Q25 - Q75]	138 [93 - 254]
2nd	Number subjects	N	48
	Duration in days	mean (sd)	678.60 (164.50)
		median [Q25 - Q75]	730 [730 - 730]
	Days to next observation period	mean (sd)	-
		median [Q25 - Q75]	-