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(CohortConstructor)

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")

cdm$injuries <- conceptCohort(cdm = cdm,
  conceptSet = list(
    "ankle_sprain" = 81151L,
    "ankle_fracture" = 4059173L,
    "forearm_fracture" = 4278672L,
    "hip_fracture" = 4230399L
  ),
  name = "injuries")

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$injuries)

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.
Person table: Summarises the person table by using summarisePerson(). This provides demographic information including sex, race, ethnicity, year/month/day of birth distributions, and location/provider/care site information.
Clinical Records: The diagnostics will detect which domains appears to the codelist associated to your cohort (i.e., Drug), and use summariseClinicalRecords() to summarise the clinical table associated (i.e., “drug_exposure”).

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)

Snapshot of the cdm Eunomia Synpuf
	Database name
	Eunomia Synpuf
	Diagnostic
	databaseDiagnostics
Estimate	Phenotyper version
Estimate	0.3.9000
General
Snapshot date	2026-01-20
Person count	1,000
Vocabulary version	v5.0 06-AUG-21
Cdm
Source name	Synpuf
Version	5.3
Holder name	ohdsi
Release date	2018-03-15
Description
Documentation reference
Observation period
N	1,000
Start date	2008-01-01
End date	2010-12-31
Cdm source
Type	duckdb
Package	CDMConnector
Write schema	main

Observation Periods

tableObservationPeriod(db_diagnostics)

Summary of observation_period table
				CDM name
				Eunomia Synpuf
				Diagnostic
				databaseDiagnostics
Observation period ordinal	Variable name	Variable level	Estimate name	Phenotyper version
Observation period ordinal	Variable name	Variable level	Estimate name	0.3.9000
all	Number records	–	N	1,048
	Number subjects	–	N	1,000
	Subjects not in person table	–	N (%)	0 (0.00%)
	Records per person	–	Mean (SD)	1.05 (0.21)
			Median [Q25 - Q75]	1 [1 - 1]
			Range [min to max]	[1 to 2]
	Duration in days	–	Mean (SD)	979.71 (262.79)
			Median [Q25 - Q75]	1,096 [1,096 - 1,096]
			Range [min to max]	[1 to 1,096]
	Days to next observation period	–	Mean (SD)	172.17 (108.35)
			Median [Q25 - Q75]	138 [93 - 254]
			Range [min to max]	[32 to 366]
	Type concept id	Period while enrolled in insurance	N (%)	1,048 (100.00%)
	Start date before birth date	–	N (%)	0 (0.00%)
	End date before start date	–	N (%)	0 (0.00%)
	Column name	Observation period end date	N missing data (%)	0 (0.00%)
		Observation period id	N missing data (%)	0 (0.00%)
			N zeros (%)	0 (0.00%)
		Observation period start date	N missing data (%)	0 (0.00%)
		Period type concept id	N missing data (%)	0 (0.00%)
			N zeros (%)	0 (0.00%)
		Person id	N missing data (%)	0 (0.00%)
			N zeros (%)	1 (0.10%)
1st	Number subjects	–	N	1,000
	Duration in days	–	Mean (SD)	994.16 (257.95)
			Median [Q25 - Q75]	1,096 [1,096 - 1,096]
			Range [min to max]	[1 to 1,096]
	Days to next observation period	–	Mean (SD)	172.17 (108.35)
			Median [Q25 - Q75]	138 [93 - 254]
			Range [min to max]	[32 to 366]
2nd	Number subjects	–	N	48
	Duration in days	–	Mean (SD)	678.60 (164.50)
			Median [Q25 - Q75]	730 [730 - 730]
			Range [min to max]	[31 to 730]
	Days to next observation period	–	Mean (SD)	–
			Median [Q25 - Q75]	–
			Range [min to max]	–

Person Table

tablePerson(db_diagnostics)

Summary of person table
			CDM name
			Eunomia Synpuf
			Diagnostic
			databaseDiagnostics
Variable name	Variable level	Estimate name	Phenotyper version
Variable name	Variable level	Estimate name	0.3.9000
Number subjects	–	N	1,000
Number subjects not in observation	–	N (%)	0 (0.00%)
Sex	Female	N (%)	498 (49.80%)
	Male	N (%)	502 (50.20%)
	None	N (%)	0 (0.00%)
Sex source	Female	N (%)	498 (49.80%)
	Male	N (%)	502 (50.20%)
Race	Black or African American	N (%)	114 (11.40%)
	No matching concept	N (%)	67 (6.70%)
	White	N (%)	819 (81.90%)
Race source	Black	N (%)	114 (11.40%)
	Hispanic	N (%)	17 (1.70%)
	Others	N (%)	50 (5.00%)
	White	N (%)	819 (81.90%)
Ethnicity	Hispanic or Latino	N (%)	17 (1.70%)
	No matching concept	N (%)	50 (5.00%)
	Not Hispanic or Latino	N (%)	933 (93.30%)
Ethnicity source	Hispanic or Latino	N (%)	17 (1.70%)
	Not Hispanic or Latino	N (%)	933 (93.30%)
	Others	N (%)	50 (5.00%)
Year of birth	–	Missing (%)	0 (0.00%)
		Median [Q25 - Q75]	1,935 [1,928 - 1,942]
		90% Range [Q05 to Q95]	1,919 to 1,962
		Range [min to max]	1,909 to 1,983
Month of birth	–	Missing (%)	0 (0.00%)
		Median [Q25 - Q75]	7 [3 - 10]
		90% Range [Q05 to Q95]	1 to 12
		Range [min to max]	1 to 12
Day of birth	–	Missing (%)	0 (0.00%)
		Median [Q25 - Q75]	1 [1 - 1]
		90% Range [Q05 to Q95]	1 to 1
		Range [min to max]	1 to 1
Location	–	Missing (%)	0 (0.00%)
		Zero count (%)	1 (0.10%)
		Distinct values	626
Provider	–	Missing (%)	1,000 (100.00%)
		Zero count (%)	0 (0.00%)
		Distinct values	1
Care site	–	Missing (%)	1,000 (100.00%)
		Zero count (%)	0 (0.00%)
		Distinct values	1

Clinical Records

tableClinicalRecords(db_diagnostics)

Summary of condition_occurrence table
			Database name
			Eunomia Synpuf
			Diagnostic
			databaseDiagnostics
Variable name	Variable level	Estimate name	Phenotyper version
Variable name	Variable level	Estimate name	0.3.9000
condition_occurrence
Number records	–	N	160,322
Number subjects	–	N (%)	836 (100.00%)
Subjects not in person table	–	N (%)	0 (0.00%)
Records per person	–	Mean (SD)	191.77 (148.24)
		Median [Q25 - Q75]	160 [76 - 278]
		Range [min to max]	[1 to 765]
In observation	Yes	N (%)	160,322 (100.00%)
Domain	Condition	N (%)	159,651 (99.58%)
	Observation	N (%)	666 (0.42%)
	Procedure	N (%)	5 (0.00%)
Source vocabulary	Icd9cm	N (%)	160,322 (100.00%)
Standard concept	S	N (%)	153,665 (95.85%)
	–	N (%)	6,657 (4.15%)
Type concept id	Carrier claim detail - 10th position	N (%)	308 (0.19%)
	Carrier claim detail - 11th position	N (%)	210 (0.13%)
	Carrier claim detail - 12th position	N (%)	170 (0.11%)
	Carrier claim detail - 13th position	N (%)	122 (0.08%)
	Carrier claim detail - 1st position	N (%)	34,738 (21.67%)
	Carrier claim detail - 2nd position	N (%)	14,405 (8.99%)
	Carrier claim detail - 3rd position	N (%)	7,484 (4.67%)
	Carrier claim detail - 4th position	N (%)	4,235 (2.64%)
	Carrier claim detail - 5th position	N (%)	2,598 (1.62%)
	Carrier claim detail - 6th position	N (%)	1,595 (0.99%)
	Carrier claim detail - 7th position	N (%)	876 (0.55%)
	Carrier claim detail - 8th position	N (%)	599 (0.37%)
	Carrier claim detail - 9th position	N (%)	420 (0.26%)
	Carrier claim header - 1st position	N (%)	34,477 (21.50%)
	Carrier claim header - 2nd position	N (%)	19,670 (12.27%)
	Carrier claim header - 3rd position	N (%)	11,387 (7.10%)
	Carrier claim header - 4th position	N (%)	6,436 (4.01%)
	Carrier claim header - 5th position	N (%)	828 (0.52%)
	Carrier claim header - 6th position	N (%)	468 (0.29%)
	Carrier claim header - 7th position	N (%)	238 (0.15%)
	Carrier claim header - 8th position	N (%)	177 (0.11%)
	Inpatient header - 10th position	N (%)	31 (0.02%)
	Inpatient header - 11th position	N (%)	476 (0.30%)
	Inpatient header - 1st position	N (%)	515 (0.32%)
	Inpatient header - 2nd position	N (%)	491 (0.31%)
	Inpatient header - 3rd position	N (%)	490 (0.31%)
	Inpatient header - 4th position	N (%)	466 (0.29%)
	Inpatient header - 5th position	N (%)	450 (0.28%)
	Inpatient header - 6th position	N (%)	424 (0.26%)
	Inpatient header - 7th position	N (%)	397 (0.25%)
	Inpatient header - 8th position	N (%)	371 (0.23%)
	Inpatient header - 9th position	N (%)	335 (0.21%)
	Outpatient header - 10th position	N (%)	8 (0.00%)
	Outpatient header - 11th position	N (%)	1,225 (0.76%)
	Outpatient header - 1st position	N (%)	4,977 (3.10%)
	Outpatient header - 2nd position	N (%)	3,161 (1.97%)
	Outpatient header - 3rd position	N (%)	2,004 (1.25%)
	Outpatient header - 4th position	N (%)	1,202 (0.75%)
	Outpatient header - 5th position	N (%)	715 (0.45%)
	Outpatient header - 6th position	N (%)	460 (0.29%)
	Outpatient header - 7th position	N (%)	315 (0.20%)
	Outpatient header - 8th position	N (%)	213 (0.13%)
	Outpatient header - 9th position	N (%)	155 (0.10%)
Start date before birth date	–	N (%)	0 (0.00%)
End date before start date	–	N (%)	0 (0.00%)
Column name	Condition concept id	N missing data (%)	0 (0.00%)
		N zeros (%)	0 (0.00%)
	Condition end date	N missing data (%)	0 (0.00%)
	Condition end datetime	N missing data (%)	160,322 (100.00%)
	Condition occurrence id	N missing data (%)	0 (0.00%)
		N zeros (%)	1 (0.00%)
	Condition source concept id	N missing data (%)	0 (0.00%)
		N zeros (%)	0 (0.00%)
	Condition source value	N missing data (%)	0 (0.00%)
	Condition start date	N missing data (%)	0 (0.00%)
	Condition start datetime	N missing data (%)	160,322 (100.00%)
	Condition status concept id	N missing data (%)	160,322 (100.00%)
		N zeros (%)	0 (0.00%)
	Condition status source value	N missing data (%)	160,322 (100.00%)
	Condition type concept id	N missing data (%)	0 (0.00%)
		N zeros (%)	0 (0.00%)
	Person id	N missing data (%)	0 (0.00%)
		N zeros (%)	191 (0.12%)
	Provider id	N missing data (%)	0 (0.00%)
		N zeros (%)	73,682 (45.96%)
	Stop reason	N missing data (%)	160,322 (100.00%)
	Visit detail id	N missing data (%)	160,322 (100.00%)
		N zeros (%)	0 (0.00%)
	Visit occurrence id	N missing data (%)	0 (0.00%)
		N zeros (%)	10 (0.01%)