2 Introduction
- 2.1 Create a mock cdm
3 Snapshot
4 Clinical tables characterisation
5 Observation period characterisation
- 5.1 Subjects in observation
- 5.2 Observation periods

2 Introduction

In this vignette, we explore how OmopSketch functions can serve as a valuable tool for characterising databases containing electronic health records mapped to the OMOP Common Data Model.

2.1 Create a mock cdm

Let’s see an example of its functionalities. To start with, we will load essential packages and create a mock cdm using the mockOmopSketch() database.

library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(DBI)
library(duckdb)
library(OmopSketch)


# Connect to Eunomia database
con <- DBI::dbConnect(duckdb::duckdb(), CDMConnector::eunomiaDir())
cdm <- CDMConnector::cdmFromCon(
  con = con, cdmSchema = "main", writeSchema = "main", cdmName = "Eunomia"
)

cdm
#> 
#> ── # OMOP CDM reference (duckdb) of Eunomia ────────────────────────────────────
#> • omop tables: person, observation_period, visit_occurrence, visit_detail,
#> condition_occurrence, drug_exposure, procedure_occurrence, device_exposure,
#> measurement, observation, death, note, note_nlp, specimen, fact_relationship,
#> location, care_site, provider, payer_plan_period, cost, drug_era, dose_era,
#> condition_era, metadata, cdm_source, concept, vocabulary, domain,
#> concept_class, concept_relationship, relationship, concept_synonym,
#> concept_ancestor, source_to_concept_map, drug_strength
#> • cohort tables: -
#> • achilles tables: -
#> • other tables: -

3 Snapshot

Let’s start by using the summariseOmopSnapshot() function to summarise the available metadata of the cdm_reference object, including the vocabulary version and the time span covered by the observation_period table

snapshot <- summariseOmopSnapshot(cdm)
snapshot |>
  tableOmopSnapshot()

Estimate	Database name
Estimate	Eunomia
General
Snapshot date	2025-04-14
Person count	2,694
Vocabulary version	v5.0 18-JAN-19
Observation period
N	5,343
Start date	1908-09-22
End date	2019-07-03
Cdm
Source name	Synthea synthetic health database
Version	v5.3.1
Holder name	OHDSI Community
Release date	2019-05-25
Description	SyntheaTM is a Synthetic Patient Population Simulator. The goal is to output synthetic, realistic (but not real), patient data and associated health records in a variety of formats.
Documentation reference	https://synthetichealth.github.io/synthea/
Source type	duckdb

4 Clinical tables characterisation

Next, we define the tables of interest, specify the study period, and determine whether to stratify the analysis by sex, age groups, or time intervals.

tableName <- c(
  "observation_period", "visit_occurrence", "condition_occurrence", "drug_exposure", "procedure_occurrence",
  "device_exposure", "measurement", "observation", "death"
)

dateRange <- as.Date(c("2012-01-01", NA))

sex <- TRUE

ageGroup <- list(c(0, 59), c(60, Inf))

interval <- "years"

4.1 Missing values

We can now use the summariseMissingData() function to assess the presence of missing values in the tables.

result_missingData <- summariseMissingData(cdm,
  omopTableName = tableName,
  sex = sex,
  ageGroup = ageGroup,
  interval = interval,
  dateRange = dateRange
)
result_missingData |> glimpse()
#> Rows: 26,726
#> Columns: 13
#> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
#> $ cdm_name         <chr> "Eunomia", "Eunomia", "Eunomia", "Eunomia", "Eunomia"…
#> $ group_name       <chr> "omop_table", "omop_table", "omop_table", "omop_table…
#> $ group_level      <chr> "observation_period", "observation_period", "observat…
#> $ strata_name      <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ strata_level     <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ variable_name    <chr> "observation_period_id", "observation_period_id", "ob…
#> $ variable_level   <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
#> $ estimate_name    <chr> "na_count", "na_percentage", "zero_count", "zero_perc…
#> $ estimate_type    <chr> "integer", "percentage", "integer", "percentage", "in…
#> $ estimate_value   <chr> "NA", "NA", "NA", "NA", "NA", "NA", "NA", "NA", "NA",…
#> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…

4.2 Clinical tables overview

The function sumamriseClinicalRecords() provides key insights into the clinical tables content, including the number of records, number of subjects, portion of records in observation, and the number of distinct domains and concepts.

result_clinicalRecords <- summariseClinicalRecords(cdm,
  omopTableName = tableName,
  sex = sex,
  ageGroup = ageGroup,
  dateRange = dateRange
)
#> ℹ Adding variables of interest to observation_period.
#> ℹ Summarising records per person in observation_period.
#> ℹ Summarising observation_period: `in_observation` and `type_concept`.
#> ℹ Adding variables of interest to visit_occurrence.
#> ℹ Summarising records per person in visit_occurrence.
#> ℹ Summarising visit_occurrence: `in_observation`, `standard_concept`,
#>   `source_vocabulary`, `domain_id`, and `type_concept`.
#> ℹ Adding variables of interest to condition_occurrence.
#> ℹ Summarising records per person in condition_occurrence.
#> ℹ Summarising condition_occurrence: `in_observation`, `standard_concept`,
#>   `source_vocabulary`, `domain_id`, and `type_concept`.
#> ℹ Adding variables of interest to drug_exposure.
#> ℹ Summarising records per person in drug_exposure.
#> ℹ Summarising drug_exposure: `in_observation`, `standard_concept`,
#>   `source_vocabulary`, `domain_id`, and `type_concept`.
#> ℹ Adding variables of interest to procedure_occurrence.
#> ℹ Summarising records per person in procedure_occurrence.
#> ℹ Summarising procedure_occurrence: `in_observation`, `standard_concept`,
#>   `source_vocabulary`, `domain_id`, and `type_concept`.
#> ℹ Adding variables of interest to measurement.
#> ℹ Summarising records per person in measurement.
#> ℹ Summarising measurement: `in_observation`, `standard_concept`,
#>   `source_vocabulary`, `domain_id`, and `type_concept`.
#> ℹ Adding variables of interest to observation.
#> ℹ Summarising records per person in observation.
#> ℹ Summarising observation: `in_observation`, `standard_concept`,
#>   `source_vocabulary`, `domain_id`, and `type_concept`.
result_clinicalRecords |> tableClinicalRecords()

Variable name	Variable level	Estimate name	Database name
Variable name	Variable level	Estimate name	Eunomia
condition_occurrence; overall; overall
Domain	Condition	N (%)	7,234 (100.00%)
In observation	No	N (%)	445 (6.15%)
	Yes	N (%)	6,789 (93.85%)
Number records	-	N	7,234.00
Number subjects	-	N (%)	2,372 (88.05%)
Records per person	-	Mean (SD)	2.69 (1.89)
		max	12.00
		median	2.00
		min	0.00
		q25	1.00
		q75	4.00
Source vocabulary	Icd10cm	N (%)	89 (1.23%)
	No matching concept	N (%)	4 (0.06%)
	Snomed	N (%)	7,141 (98.71%)
Standard concept	S	N (%)	7,234 (100.00%)
Type concept id	Ehr encounter diagnosis	N (%)	7,234 (100.00%)
condition_occurrence; 0 to 59; overall
Domain	Condition	N (%)	4,960 (100.00%)
In observation	No	N (%)	318 (6.41%)
	Yes	N (%)	4,642 (93.59%)
Number records	-	N	4,960.00
Number subjects	-	N (%)	1,643 (60.99%)
Records per person	-	Mean (SD)	1.84 (2.04)
		max	12.00
		median	1.00
		min	0.00
		q25	0.00
		q75	3.00
Source vocabulary	Icd10cm	N (%)	89 (1.79%)
	No matching concept	N (%)	2 (0.04%)
	Snomed	N (%)	4,869 (98.17%)
Standard concept	S	N (%)	4,960 (100.00%)
Type concept id	Ehr encounter diagnosis	N (%)	4,960 (100.00%)
condition_occurrence; 60 or above; overall
Domain	Condition	N (%)	2,274 (100.00%)
In observation	No	N (%)	127 (5.58%)
	Yes	N (%)	2,147 (94.42%)
Number records	-	N	2,274.00
Number subjects	-	N (%)	880 (76.59%)
Records per person	-	Mean (SD)	1.98 (1.72)
		max	9.00
		median	2.00
		min	0.00
		q25	1.00
		q75	3.00
Source vocabulary	No matching concept	N (%)	2 (0.09%)
	Snomed	N (%)	2,272 (99.91%)
Standard concept	S	N (%)	2,274 (100.00%)
Type concept id	Ehr encounter diagnosis	N (%)	2,274 (100.00%)
condition_occurrence; overall; Female
Domain	Condition	N (%)	3,712 (100.00%)
In observation	No	N (%)	224 (6.03%)
	Yes	N (%)	3,488 (93.97%)
Number records	-	N	3,712.00
Number subjects	-	N (%)	1,203 (87.62%)
Records per person	-	Mean (SD)	2.70 (1.88)
		max	10.00
		median	3.00
		min	0.00
		q25	1.00
		q75	4.00
Source vocabulary	Icd10cm	N (%)	42 (1.13%)
	No matching concept	N (%)	1 (0.03%)
	Snomed	N (%)	3,669 (98.84%)
Standard concept	S	N (%)	3,712 (100.00%)
Type concept id	Ehr encounter diagnosis	N (%)	3,712 (100.00%)
condition_occurrence; overall; Male
Domain	Condition	N (%)	3,522 (100.00%)
In observation	No	N (%)	221 (6.27%)
	Yes	N (%)	3,301 (93.73%)
Number records	-	N	3,522.00
Number subjects	-	N (%)	1,169 (88.49%)
Records per person	-	Mean (SD)	2.67 (1.90)
		max	12.00
		median	2.00
		min	0.00
		q25	1.00
		q75	4.00
Source vocabulary	Icd10cm	N (%)	47 (1.33%)
	No matching concept	N (%)	3 (0.09%)
	Snomed	N (%)	3,472 (98.58%)
Standard concept	S	N (%)	3,522 (100.00%)
Type concept id	Ehr encounter diagnosis	N (%)	3,522 (100.00%)
condition_occurrence; 0 to 59; Female
Domain	Condition	N (%)	2,569 (100.00%)
In observation	No	N (%)	160 (6.23%)
	Yes	N (%)	2,409 (93.77%)
Number records	-	N	2,569.00
Number subjects	-	N (%)	843 (61.40%)
Records per person	-	Mean (SD)	1.87 (2.02)
		max	10.00
		median	1.00
		min	0.00
		q25	0.00
		q75	3.00
Source vocabulary	Icd10cm	N (%)	42 (1.63%)
	Snomed	N (%)	2,527 (98.37%)
Standard concept	S	N (%)	2,569 (100.00%)
Type concept id	Ehr encounter diagnosis	N (%)	2,569 (100.00%)
condition_occurrence; 0 to 59; Male
Domain	Condition	N (%)	2,391 (100.00%)
In observation	No	N (%)	158 (6.61%)
	Yes	N (%)	2,233 (93.39%)
Number records	-	N	2,391.00
Number subjects	-	N (%)	800 (60.56%)
Records per person	-	Mean (SD)	1.81 (2.05)
		max	12.00
		median	1.00
		min	0.00
		q25	0.00
		q75	3.00
Source vocabulary	Icd10cm	N (%)	47 (1.97%)
	No matching concept	N (%)	2 (0.08%)
	Snomed	N (%)	2,342 (97.95%)
Standard concept	S	N (%)	2,391 (100.00%)
Type concept id	Ehr encounter diagnosis	N (%)	2,391 (100.00%)
condition_occurrence; 60 or above; Female
Domain	Condition	N (%)	1,143 (100.00%)
In observation	No	N (%)	64 (5.60%)
	Yes	N (%)	1,079 (94.40%)
Number records	-	N	1,143.00
Number subjects	-	N (%)	436 (75.30%)
Records per person	-	Mean (SD)	1.97 (1.76)
		max	9.00
		median	2.00
		min	0.00
		q25	1.00
		q75	3.00
Source vocabulary	No matching concept	N (%)	1 (0.09%)
	Snomed	N (%)	1,142 (99.91%)
Standard concept	S	N (%)	1,143 (100.00%)
Type concept id	Ehr encounter diagnosis	N (%)	1,143 (100.00%)
condition_occurrence; 60 or above; Male
Domain	Condition	N (%)	1,131 (100.00%)
In observation	No	N (%)	63 (5.57%)
	Yes	N (%)	1,068 (94.43%)
Number records	-	N	1,131.00
Number subjects	-	N (%)	444 (77.89%)
Records per person	-	Mean (SD)	1.98 (1.67)
		max	9.00
		median	2.00
		min	0.00
		q25	1.00
		q75	3.00
Source vocabulary	No matching concept	N (%)	1 (0.09%)
	Snomed	N (%)	1,130 (99.91%)
Standard concept	S	N (%)	1,131 (100.00%)
Type concept id	Ehr encounter diagnosis	N (%)	1,131 (100.00%)
drug_exposure; overall; overall
Domain	Drug	N (%)	8,899 (100.00%)
In observation	No	N (%)	247 (2.78%)
	Yes	N (%)	8,652 (97.22%)
Number records	-	N	8,899.00
Number subjects	-	N (%)	2,446 (90.79%)
Records per person	-	Mean (SD)	3.30 (2.03)
		max	16.00
		median	3.00
		min	0.00
		q25	2.00
		q75	4.00
Source vocabulary	Cvx	N (%)	4,475 (50.29%)
	Ndc	N (%)	495 (5.56%)
	No matching concept	N (%)	4 (0.04%)
	Rxnorm	N (%)	3,925 (44.11%)
Standard concept	S	N (%)	8,899 (100.00%)
Type concept id	Dispensed in outpatient office	N (%)	4,475 (50.29%)
	Prescription written	N (%)	4,424 (49.71%)
drug_exposure; 0 to 59; overall
Domain	Drug	N (%)	5,949 (100.00%)
In observation	No	N (%)	186 (3.13%)
	Yes	N (%)	5,763 (96.87%)
Number records	-	N	5,949.00
Number subjects	-	N (%)	1,617 (60.02%)
Records per person	-	Mean (SD)	2.21 (2.27)
		max	16.00
		median	2.00
		min	0.00
		q25	0.00
		q75	4.00
Source vocabulary	Cvx	N (%)	3,120 (52.45%)
	Ndc	N (%)	495 (8.32%)
	No matching concept	N (%)	2 (0.03%)
	Rxnorm	N (%)	2,332 (39.20%)
Standard concept	S	N (%)	5,949 (100.00%)
Type concept id	Dispensed in outpatient office	N (%)	3,120 (52.45%)
	Prescription written	N (%)	2,829 (47.55%)
drug_exposure; 60 or above; overall
Domain	Drug	N (%)	2,950 (100.00%)
In observation	No	N (%)	61 (2.07%)
	Yes	N (%)	2,889 (97.93%)
Number records	-	N	2,950.00
Number subjects	-	N (%)	955 (83.12%)
Records per person	-	Mean (SD)	2.57 (2.10)
		max	14.00
		median	2.00
		min	0.00
		q25	1.00
		q75	4.00
Source vocabulary	Cvx	N (%)	1,355 (45.93%)
	No matching concept	N (%)	2 (0.07%)
	Rxnorm	N (%)	1,593 (54.00%)
Standard concept	S	N (%)	2,950 (100.00%)
Type concept id	Dispensed in outpatient office	N (%)	1,355 (45.93%)
	Prescription written	N (%)	1,595 (54.07%)
drug_exposure; overall; Female
Domain	Drug	N (%)	4,495 (100.00%)
In observation	No	N (%)	121 (2.69%)
	Yes	N (%)	4,374 (97.31%)
Number records	-	N	4,495.00
Number subjects	-	N (%)	1,241 (90.39%)
Records per person	-	Mean (SD)	3.27 (2.03)
		max	16.00
		median	3.00
		min	0.00
		q25	2.00
		q75	4.00
Source vocabulary	Cvx	N (%)	2,290 (50.95%)
	Ndc	N (%)	266 (5.92%)
	No matching concept	N (%)	2 (0.04%)
	Rxnorm	N (%)	1,937 (43.09%)
Standard concept	S	N (%)	4,495 (100.00%)
Type concept id	Dispensed in outpatient office	N (%)	2,290 (50.95%)
	Prescription written	N (%)	2,205 (49.05%)
drug_exposure; overall; Male
Domain	Drug	N (%)	4,404 (100.00%)
In observation	No	N (%)	126 (2.86%)
	Yes	N (%)	4,278 (97.14%)
Number records	-	N	4,404.00
Number subjects	-	N (%)	1,205 (91.22%)
Records per person	-	Mean (SD)	3.33 (2.03)
		max	14.00
		median	3.00
		min	0.00
		q25	2.00
		q75	5.00
Source vocabulary	Cvx	N (%)	2,185 (49.61%)
	Ndc	N (%)	229 (5.20%)
	No matching concept	N (%)	2 (0.05%)
	Rxnorm	N (%)	1,988 (45.14%)
Standard concept	S	N (%)	4,404 (100.00%)
Type concept id	Dispensed in outpatient office	N (%)	2,185 (49.61%)
	Prescription written	N (%)	2,219 (50.39%)
drug_exposure; 0 to 59; Female
Domain	Drug	N (%)	3,120 (100.00%)
In observation	No	N (%)	93 (2.98%)
	Yes	N (%)	3,027 (97.02%)
Number records	-	N	3,120.00
Number subjects	-	N (%)	823 (59.94%)
Records per person	-	Mean (SD)	2.27 (2.32)
		max	16.00
		median	2.00
		min	0.00
		q25	0.00
		q75	4.00
Source vocabulary	Cvx	N (%)	1,620 (51.92%)
	Ndc	N (%)	266 (8.53%)
	No matching concept	N (%)	1 (0.03%)
	Rxnorm	N (%)	1,233 (39.52%)
Standard concept	S	N (%)	3,120 (100.00%)
Type concept id	Dispensed in outpatient office	N (%)	1,620 (51.92%)
	Prescription written	N (%)	1,500 (48.08%)
drug_exposure; 0 to 59; Male
Domain	Drug	N (%)	2,829 (100.00%)
In observation	No	N (%)	93 (3.29%)
	Yes	N (%)	2,736 (96.71%)
Number records	-	N	2,829.00
Number subjects	-	N (%)	794 (60.11%)
Records per person	-	Mean (SD)	2.14 (2.22)
		max	12.00
		median	2.00
		min	0.00
		q25	0.00
		q75	4.00
Source vocabulary	Cvx	N (%)	1,500 (53.02%)
	Ndc	N (%)	229 (8.09%)
	No matching concept	N (%)	1 (0.04%)
	Rxnorm	N (%)	1,099 (38.85%)
Standard concept	S	N (%)	2,829 (100.00%)
Type concept id	Dispensed in outpatient office	N (%)	1,500 (53.02%)
	Prescription written	N (%)	1,329 (46.98%)
drug_exposure; 60 or above; Female
Domain	Drug	N (%)	1,375 (100.00%)
In observation	No	N (%)	28 (2.04%)
	Yes	N (%)	1,347 (97.96%)
Number records	-	N	1,375.00
Number subjects	-	N (%)	476 (82.21%)
Records per person	-	Mean (SD)	2.37 (1.98)
		max	14.00
		median	2.00
		min	0.00
		q25	1.00
		q75	4.00
Source vocabulary	Cvx	N (%)	670 (48.73%)
	No matching concept	N (%)	1 (0.07%)
	Rxnorm	N (%)	704 (51.20%)
Standard concept	S	N (%)	1,375 (100.00%)
Type concept id	Dispensed in outpatient office	N (%)	670 (48.73%)
	Prescription written	N (%)	705 (51.27%)
drug_exposure; 60 or above; Male
Domain	Drug	N (%)	1,575 (100.00%)
In observation	No	N (%)	33 (2.10%)
	Yes	N (%)	1,542 (97.90%)
Number records	-	N	1,575.00
Number subjects	-	N (%)	479 (84.04%)
Records per person	-	Mean (SD)	2.76 (2.20)
		max	13.00
		median	2.50
		min	0.00
		q25	1.00
		q75	4.00
Source vocabulary	Cvx	N (%)	685 (43.49%)
	No matching concept	N (%)	1 (0.06%)
	Rxnorm	N (%)	889 (56.44%)
Standard concept	S	N (%)	1,575 (100.00%)
Type concept id	Dispensed in outpatient office	N (%)	685 (43.49%)
	Prescription written	N (%)	890 (56.51%)
measurement; overall; overall
Domain	Measurement	N (%)	4,335 (100.00%)
In observation	Yes	N (%)	4,335 (100.00%)
Number records	-	N	4,335.00
Number subjects	-	N (%)	1,453 (53.93%)
Records per person	-	Mean (SD)	1.61 (3.82)
		max	65.00
		median	1.00
		min	0.00
		q25	0.00
		q75	2.00
Source vocabulary	Loinc	N (%)	2,899 (66.87%)
	Snomed	N (%)	1,436 (33.13%)
Standard concept	S	N (%)	4,335 (100.00%)
Type concept id	Test ordered through ehr	N (%)	4,335 (100.00%)
measurement; 0 to 59; overall
Domain	Measurement	N (%)	2,492 (100.00%)
In observation	Yes	N (%)	2,492 (100.00%)
Number records	-	N	2,492.00
Number subjects	-	N (%)	941 (34.93%)
Records per person	-	Mean (SD)	0.92 (2.61)
		max	52.00
		median	0.00
		min	0.00
		q25	0.00
		q75	1.00
Source vocabulary	Loinc	N (%)	1,623 (65.13%)
	Snomed	N (%)	869 (34.87%)
Standard concept	S	N (%)	2,492 (100.00%)
Type concept id	Test ordered through ehr	N (%)	2,492 (100.00%)
measurement; 60 or above; overall
Domain	Measurement	N (%)	1,843 (100.00%)
In observation	Yes	N (%)	1,843 (100.00%)
Number records	-	N	1,843.00
Number subjects	-	N (%)	567 (49.35%)
Records per person	-	Mean (SD)	1.60 (4.06)
		max	63.00
		median	0.00
		min	0.00
		q25	0.00
		q75	1.00
Source vocabulary	Loinc	N (%)	1,276 (69.23%)
	Snomed	N (%)	567 (30.77%)
Standard concept	S	N (%)	1,843 (100.00%)
Type concept id	Test ordered through ehr	N (%)	1,843 (100.00%)
measurement; overall; Female
Domain	Measurement	N (%)	2,352 (100.00%)
In observation	Yes	N (%)	2,352 (100.00%)
Number records	-	N	2,352.00
Number subjects	-	N (%)	760 (55.35%)
Records per person	-	Mean (SD)	1.71 (3.90)
		max	63.00
		median	1.00
		min	0.00
		q25	0.00
		q75	2.00
Source vocabulary	Loinc	N (%)	1,558 (66.24%)
	Snomed	N (%)	794 (33.76%)
Standard concept	S	N (%)	2,352 (100.00%)
Type concept id	Test ordered through ehr	N (%)	2,352 (100.00%)
measurement; overall; Male
Domain	Measurement	N (%)	1,983 (100.00%)
In observation	Yes	N (%)	1,983 (100.00%)
Number records	-	N	1,983.00
Number subjects	-	N (%)	693 (52.46%)
Records per person	-	Mean (SD)	1.50 (3.74)
		max	65.00
		median	1.00
		min	0.00
		q25	0.00
		q75	2.00
Source vocabulary	Loinc	N (%)	1,341 (67.62%)
	Snomed	N (%)	642 (32.38%)
Standard concept	S	N (%)	1,983 (100.00%)
Type concept id	Test ordered through ehr	N (%)	1,983 (100.00%)
measurement; 0 to 59; Female
Domain	Measurement	N (%)	1,323 (100.00%)
In observation	Yes	N (%)	1,323 (100.00%)
Number records	-	N	1,323.00
Number subjects	-	N (%)	499 (36.34%)
Records per person	-	Mean (SD)	0.96 (2.44)
		max	32.00
		median	0.00
		min	0.00
		q25	0.00
		q75	1.00
Source vocabulary	Loinc	N (%)	850 (64.25%)
	Snomed	N (%)	473 (35.75%)
Standard concept	S	N (%)	1,323 (100.00%)
Type concept id	Test ordered through ehr	N (%)	1,323 (100.00%)
measurement; 0 to 59; Male
Domain	Measurement	N (%)	1,169 (100.00%)
In observation	Yes	N (%)	1,169 (100.00%)
Number records	-	N	1,169.00
Number subjects	-	N (%)	442 (33.46%)
Records per person	-	Mean (SD)	0.88 (2.77)
		max	52.00
		median	0.00
		min	0.00
		q25	0.00
		q75	1.00
Source vocabulary	Loinc	N (%)	773 (66.12%)
	Snomed	N (%)	396 (33.88%)
Standard concept	S	N (%)	1,169 (100.00%)
Type concept id	Test ordered through ehr	N (%)	1,169 (100.00%)
measurement; 60 or above; Female
Domain	Measurement	N (%)	1,029 (100.00%)
In observation	Yes	N (%)	1,029 (100.00%)
Number records	-	N	1,029.00
Number subjects	-	N (%)	294 (50.78%)
Records per person	-	Mean (SD)	1.78 (4.59)
		max	63.00
		median	1.00
		min	0.00
		q25	0.00
		q75	2.00
Source vocabulary	Loinc	N (%)	708 (68.80%)
	Snomed	N (%)	321 (31.20%)
Standard concept	S	N (%)	1,029 (100.00%)
Type concept id	Test ordered through ehr	N (%)	1,029 (100.00%)
measurement; 60 or above; Male
Domain	Measurement	N (%)	814 (100.00%)
In observation	Yes	N (%)	814 (100.00%)
Number records	-	N	814.00
Number subjects	-	N (%)	273 (47.89%)
Records per person	-	Mean (SD)	1.43 (3.45)
		max	36.00
		median	0.00
		min	0.00
		q25	0.00
		q75	1.00
Source vocabulary	Loinc	N (%)	568 (69.78%)
	Snomed	N (%)	246 (30.22%)
Standard concept	S	N (%)	814 (100.00%)
Type concept id	Test ordered through ehr	N (%)	814 (100.00%)
observation; overall; overall
Domain	Observation	N (%)	56 (100.00%)
In observation	Yes	N (%)	56 (100.00%)
Number records	-	N	56.00
Number subjects	-	N (%)	55 (2.04%)
Records per person	-	Mean (SD)	0.02 (0.15)
		max	2.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	Snomed	N (%)	56 (100.00%)
Standard concept	S	N (%)	56 (100.00%)
Type concept id	Problem list from ehr	N (%)	56 (100.00%)
observation; 0 to 59; overall
Domain	Observation	N (%)	31 (100.00%)
In observation	Yes	N (%)	31 (100.00%)
Number records	-	N	31.00
Number subjects	-	N (%)	31 (1.15%)
Records per person	-	Mean (SD)	0.01 (0.11)
		max	1.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	Snomed	N (%)	31 (100.00%)
Standard concept	S	N (%)	31 (100.00%)
Type concept id	Problem list from ehr	N (%)	31 (100.00%)
observation; 60 or above; overall
Domain	Observation	N (%)	25 (100.00%)
In observation	Yes	N (%)	25 (100.00%)
Number records	-	N	25.00
Number subjects	-	N (%)	24 (2.09%)
Records per person	-	Mean (SD)	0.02 (0.15)
		max	2.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	Snomed	N (%)	25 (100.00%)
Standard concept	S	N (%)	25 (100.00%)
Type concept id	Problem list from ehr	N (%)	25 (100.00%)
observation; overall; Female
Domain	Observation	N (%)	21 (100.00%)
In observation	Yes	N (%)	21 (100.00%)
Number records	-	N	21.00
Number subjects	-	N (%)	20 (1.46%)
Records per person	-	Mean (SD)	0.02 (0.13)
		max	2.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	Snomed	N (%)	21 (100.00%)
Standard concept	S	N (%)	21 (100.00%)
Type concept id	Problem list from ehr	N (%)	21 (100.00%)
observation; overall; Male
Domain	Observation	N (%)	35 (100.00%)
In observation	Yes	N (%)	35 (100.00%)
Number records	-	N	35.00
Number subjects	-	N (%)	35 (2.65%)
Records per person	-	Mean (SD)	0.03 (0.16)
		max	1.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	Snomed	N (%)	35 (100.00%)
Standard concept	S	N (%)	35 (100.00%)
Type concept id	Problem list from ehr	N (%)	35 (100.00%)
observation; 0 to 59; Female
Domain	Observation	N (%)	12 (100.00%)
In observation	Yes	N (%)	12 (100.00%)
Number records	-	N	12.00
Number subjects	-	N (%)	12 (0.87%)
Records per person	-	Mean (SD)	0.01 (0.09)
		max	1.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	Snomed	N (%)	12 (100.00%)
Standard concept	S	N (%)	12 (100.00%)
Type concept id	Problem list from ehr	N (%)	12 (100.00%)
observation; 0 to 59; Male
Domain	Observation	N (%)	19 (100.00%)
In observation	Yes	N (%)	19 (100.00%)
Number records	-	N	19.00
Number subjects	-	N (%)	19 (1.44%)
Records per person	-	Mean (SD)	0.01 (0.12)
		max	1.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	Snomed	N (%)	19 (100.00%)
Standard concept	S	N (%)	19 (100.00%)
Type concept id	Problem list from ehr	N (%)	19 (100.00%)
observation; 60 or above; Female
Domain	Observation	N (%)	9 (100.00%)
In observation	Yes	N (%)	9 (100.00%)
Number records	-	N	9.00
Number subjects	-	N (%)	8 (1.38%)
Records per person	-	Mean (SD)	0.02 (0.14)
		max	2.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	Snomed	N (%)	9 (100.00%)
Standard concept	S	N (%)	9 (100.00%)
Type concept id	Problem list from ehr	N (%)	9 (100.00%)
observation; 60 or above; Male
Domain	Observation	N (%)	16 (100.00%)
In observation	Yes	N (%)	16 (100.00%)
Number records	-	N	16.00
Number subjects	-	N (%)	16 (2.81%)
Records per person	-	Mean (SD)	0.03 (0.17)
		max	1.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	Snomed	N (%)	16 (100.00%)
Standard concept	S	N (%)	16 (100.00%)
Type concept id	Problem list from ehr	N (%)	16 (100.00%)
procedure_occurrence; overall; overall
Domain	Procedure	N (%)	2,807 (100.00%)
In observation	No	N (%)	6 (0.21%)
	Yes	N (%)	2,801 (99.79%)
Number records	-	N	2,807.00
Number subjects	-	N (%)	969 (35.97%)
Records per person	-	Mean (SD)	1.04 (2.53)
		max	58.00
		median	0.00
		min	0.00
		q25	0.00
		q75	1.00
Source vocabulary	Snomed	N (%)	2,807 (100.00%)
Standard concept	S	N (%)	2,807 (100.00%)
Type concept id	Ehr order list entry	N (%)	2,807 (100.00%)
procedure_occurrence; 0 to 59; overall
Domain	Procedure	N (%)	1,162 (100.00%)
In observation	No	N (%)	2 (0.17%)
	Yes	N (%)	1,160 (99.83%)
Number records	-	N	1,162.00
Number subjects	-	N (%)	543 (20.16%)
Records per person	-	Mean (SD)	0.43 (1.78)
		max	58.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	Snomed	N (%)	1,162 (100.00%)
Standard concept	S	N (%)	1,162 (100.00%)
Type concept id	Ehr order list entry	N (%)	1,162 (100.00%)
procedure_occurrence; 60 or above; overall
Domain	Procedure	N (%)	1,645 (100.00%)
In observation	No	N (%)	4 (0.24%)
	Yes	N (%)	1,641 (99.76%)
Number records	-	N	1,645.00
Number subjects	-	N (%)	460 (40.03%)
Records per person	-	Mean (SD)	1.43 (2.66)
		max	17.00
		median	0.00
		min	0.00
		q25	0.00
		q75	2.00
Source vocabulary	Snomed	N (%)	1,645 (100.00%)
Standard concept	S	N (%)	1,645 (100.00%)
Type concept id	Ehr order list entry	N (%)	1,645 (100.00%)
procedure_occurrence; overall; Female
Domain	Procedure	N (%)	1,377 (100.00%)
In observation	No	N (%)	2 (0.15%)
	Yes	N (%)	1,375 (99.85%)
Number records	-	N	1,377.00
Number subjects	-	N (%)	476 (34.67%)
Records per person	-	Mean (SD)	1.00 (2.32)
		max	37.00
		median	0.00
		min	0.00
		q25	0.00
		q75	1.00
Source vocabulary	Snomed	N (%)	1,377 (100.00%)
Standard concept	S	N (%)	1,377 (100.00%)
Type concept id	Ehr order list entry	N (%)	1,377 (100.00%)
procedure_occurrence; overall; Male
Domain	Procedure	N (%)	1,430 (100.00%)
In observation	No	N (%)	4 (0.28%)
	Yes	N (%)	1,426 (99.72%)
Number records	-	N	1,430.00
Number subjects	-	N (%)	493 (37.32%)
Records per person	-	Mean (SD)	1.08 (2.72)
		max	58.00
		median	0.00
		min	0.00
		q25	0.00
		q75	1.00
Source vocabulary	Snomed	N (%)	1,430 (100.00%)
Standard concept	S	N (%)	1,430 (100.00%)
Type concept id	Ehr order list entry	N (%)	1,430 (100.00%)
procedure_occurrence; 0 to 59; Female
Domain	Procedure	N (%)	580 (100.00%)
In observation	Yes	N (%)	580 (100.00%)
Number records	-	N	580.00
Number subjects	-	N (%)	268 (19.52%)
Records per person	-	Mean (SD)	0.42 (1.55)
		max	37.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	Snomed	N (%)	580 (100.00%)
Standard concept	S	N (%)	580 (100.00%)
Type concept id	Ehr order list entry	N (%)	580 (100.00%)
procedure_occurrence; 0 to 59; Male
Domain	Procedure	N (%)	582 (100.00%)
In observation	No	N (%)	2 (0.34%)
	Yes	N (%)	580 (99.66%)
Number records	-	N	582.00
Number subjects	-	N (%)	275 (20.82%)
Records per person	-	Mean (SD)	0.44 (2.00)
		max	58.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	Snomed	N (%)	582 (100.00%)
Standard concept	S	N (%)	582 (100.00%)
Type concept id	Ehr order list entry	N (%)	582 (100.00%)
procedure_occurrence; 60 or above; Female
Domain	Procedure	N (%)	797 (100.00%)
In observation	No	N (%)	2 (0.25%)
	Yes	N (%)	795 (99.75%)
Number records	-	N	797.00
Number subjects	-	N (%)	225 (38.86%)
Records per person	-	Mean (SD)	1.38 (2.58)
		max	16.00
		median	0.00
		min	0.00
		q25	0.00
		q75	2.00
Source vocabulary	Snomed	N (%)	797 (100.00%)
Standard concept	S	N (%)	797 (100.00%)
Type concept id	Ehr order list entry	N (%)	797 (100.00%)
procedure_occurrence; 60 or above; Male
Domain	Procedure	N (%)	848 (100.00%)
In observation	No	N (%)	2 (0.24%)
	Yes	N (%)	846 (99.76%)
Number records	-	N	848.00
Number subjects	-	N (%)	235 (41.23%)
Records per person	-	Mean (SD)	1.49 (2.74)
		max	17.00
		median	0.00
		min	0.00
		q25	0.00
		q75	2.00
Source vocabulary	Snomed	N (%)	848 (100.00%)
Standard concept	S	N (%)	848 (100.00%)
Type concept id	Ehr order list entry	N (%)	848 (100.00%)
visit_occurrence; overall; overall
Domain	Visit	N (%)	163 (100.00%)
In observation	Yes	N (%)	163 (100.00%)
Number records	-	N	163.00
Number subjects	-	N (%)	160 (5.94%)
Records per person	-	Mean (SD)	0.06 (0.24)
		max	2.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	None	N (%)	163 (100.00%)
Standard concept	S	N (%)	163 (100.00%)
Type concept id	Visit derived from encounter on claim	N (%)	163 (100.00%)
visit_occurrence; 0 to 59; overall
Domain	Visit	N (%)	131 (100.00%)
In observation	Yes	N (%)	131 (100.00%)
Number records	-	N	131.00
Number subjects	-	N (%)	130 (4.83%)
Records per person	-	Mean (SD)	0.05 (0.22)
		max	2.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	None	N (%)	131 (100.00%)
Standard concept	S	N (%)	131 (100.00%)
Type concept id	Visit derived from encounter on claim	N (%)	131 (100.00%)
visit_occurrence; 60 or above; overall
Domain	Visit	N (%)	32 (100.00%)
In observation	Yes	N (%)	32 (100.00%)
Number records	-	N	32.00
Number subjects	-	N (%)	30 (2.61%)
Records per person	-	Mean (SD)	0.03 (0.17)
		max	2.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	None	N (%)	32 (100.00%)
Standard concept	S	N (%)	32 (100.00%)
Type concept id	Visit derived from encounter on claim	N (%)	32 (100.00%)
visit_occurrence; overall; Female
Domain	Visit	N (%)	85 (100.00%)
In observation	Yes	N (%)	85 (100.00%)
Number records	-	N	85.00
Number subjects	-	N (%)	83 (6.05%)
Records per person	-	Mean (SD)	0.06 (0.25)
		max	2.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	None	N (%)	85 (100.00%)
Standard concept	S	N (%)	85 (100.00%)
Type concept id	Visit derived from encounter on claim	N (%)	85 (100.00%)
visit_occurrence; overall; Male
Domain	Visit	N (%)	78 (100.00%)
In observation	Yes	N (%)	78 (100.00%)
Number records	-	N	78.00
Number subjects	-	N (%)	77 (5.83%)
Records per person	-	Mean (SD)	0.06 (0.24)
		max	2.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	None	N (%)	78 (100.00%)
Standard concept	S	N (%)	78 (100.00%)
Type concept id	Visit derived from encounter on claim	N (%)	78 (100.00%)
visit_occurrence; 0 to 59; Female
Domain	Visit	N (%)	67 (100.00%)
In observation	Yes	N (%)	67 (100.00%)
Number records	-	N	67.00
Number subjects	-	N (%)	66 (4.81%)
Records per person	-	Mean (SD)	0.05 (0.22)
		max	2.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	None	N (%)	67 (100.00%)
Standard concept	S	N (%)	67 (100.00%)
Type concept id	Visit derived from encounter on claim	N (%)	67 (100.00%)
visit_occurrence; 0 to 59; Male
Domain	Visit	N (%)	64 (100.00%)
In observation	Yes	N (%)	64 (100.00%)
Number records	-	N	64.00
Number subjects	-	N (%)	64 (4.84%)
Records per person	-	Mean (SD)	0.05 (0.21)
		max	1.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	None	N (%)	64 (100.00%)
Standard concept	S	N (%)	64 (100.00%)
Type concept id	Visit derived from encounter on claim	N (%)	64 (100.00%)
visit_occurrence; 60 or above; Female
Domain	Visit	N (%)	18 (100.00%)
In observation	Yes	N (%)	18 (100.00%)
Number records	-	N	18.00
Number subjects	-	N (%)	17 (2.94%)
Records per person	-	Mean (SD)	0.03 (0.18)
		max	2.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	None	N (%)	18 (100.00%)
Standard concept	S	N (%)	18 (100.00%)
Type concept id	Visit derived from encounter on claim	N (%)	18 (100.00%)
visit_occurrence; 60 or above; Male
Domain	Visit	N (%)	14 (100.00%)
In observation	Yes	N (%)	14 (100.00%)
Number records	-	N	14.00
Number subjects	-	N (%)	13 (2.28%)
Records per person	-	Mean (SD)	0.02 (0.17)
		max	2.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
Source vocabulary	None	N (%)	14 (100.00%)
Standard concept	S	N (%)	14 (100.00%)
Type concept id	Visit derived from encounter on claim	N (%)	14 (100.00%)
observation_period; overall; overall
Number records	-	N	0.00
Number subjects	-	N (%)	0 (0.00%)
Records per person	-	Mean (SD)	0.00 (0.00)
		max	0.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
observation_period; 0 to 59; overall
Number records	-	N	0.00
Number subjects	-	N (%)	0 (0.00%)
Records per person	-	Mean (SD)	0.00 (0.00)
		max	0.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
observation_period; 60 or above; overall
Number records	-	N	0.00
Number subjects	-	N (%)	0 (0.00%)
Records per person	-	Mean (SD)	0.00 (0.00)
		max	0.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
observation_period; overall; Female
Number records	-	N	0.00
Number subjects	-	N (%)	0 (0.00%)
Records per person	-	Mean (SD)	0.00 (0.00)
		max	0.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
observation_period; overall; Male
Number records	-	N	0.00
Number subjects	-	N (%)	0 (0.00%)
Records per person	-	Mean (SD)	0.00 (0.00)
		max	0.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
observation_period; 0 to 59; Female
Number records	-	N	0.00
Number subjects	-	N (%)	0 (0.00%)
Records per person	-	Mean (SD)	0.00 (0.00)
		max	0.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
observation_period; 0 to 59; Male
Number records	-	N	0.00
Number subjects	-	N (%)	0 (0.00%)
Records per person	-	Mean (SD)	0.00 (0.00)
		max	0.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
observation_period; 60 or above; Female
Number records	-	N	0.00
Number subjects	-	N (%)	0 (0.00%)
Records per person	-	Mean (SD)	0.00 (0.00)
		max	0.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00
observation_period; 60 or above; Male
Number records	-	N	0.00
Number subjects	-	N (%)	0 (0.00%)
Records per person	-	Mean (SD)	0.00 (0.00)
		max	0.00
		median	0.00
		min	0.00
		q25	0.00
		q75	0.00

4.3 Records in observation

We can retrieve the number of records in observation for each table using the summariseRecordCount() function.

result_recordCounts <- summariseRecordCount(cdm,
  tableName,
  sex = sex,
  ageGroup = ageGroup,
  interval = interval,
  dateRange = dateRange
)
result_recordCounts |>
  filter(group_level %in% c("drug_exposure", "condition_occurrence")) |>
  plotRecordCount(
    colour = "omop_table",
    facet = c("sex", "age_group")
  )

4.4 Concept id counts

We can then use the summariseConceptIdCounts() function to compute the record counts for each concept_id present in the analysed OMOP tables.

result_conceptIdCount <- OmopSketch::summariseConceptIdCounts(cdm,
  omopTableName = tableName,
  sex = sex,
  ageGroup = ageGroup,
  interval = interval,
  dateRange = dateRange
)
result_conceptIdCount |> glimpse()
#> Rows: 10,614
#> Columns: 13
#> $ result_id        <int> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,…
#> $ cdm_name         <chr> "Eunomia", "Eunomia", "Eunomia", "Eunomia", "Eunomia"…
#> $ group_name       <chr> "omop_table", "omop_table", "omop_table", "omop_table…
#> $ group_level      <chr> "visit_occurrence", "visit_occurrence", "visit_occurr…
#> $ strata_name      <chr> "overall", "age_group", "age_group", "sex", "sex", "o…
#> $ strata_level     <chr> "overall", "0 to 59", "60 or above", "Female", "Male"…
#> $ variable_name    <chr> "Inpatient Visit", "Inpatient Visit", "Inpatient Visi…
#> $ variable_level   <chr> "9201", "9201", "9201", "9201", "9201", "9201", "9201…
#> $ estimate_name    <chr> "count_records", "count_records", "count_records", "c…
#> $ estimate_type    <chr> "integer", "integer", "integer", "integer", "integer"…
#> $ estimate_value   <chr> "163", "131", "32", "85", "78", "30", "23", "19", "19…
#> $ additional_name  <chr> "overall", "overall", "overall", "overall", "overall"…
#> $ additional_level <chr> "overall", "overall", "overall", "overall", "overall"…

5 Observation period characterisation

OmopSketch can also provide an overview of the observation_period table.

5.1 Subjects in observation

The summariseInObservation() function calculates the number of subjects and the distribution of person-days in observation across specific time intervals.


result_inObservation <-summariseInObservation(cdm$observation_period,
                                              output = c("record","person-days"),
                                              interval = interval,
                                              sex = sex,
                                              ageGroup = ageGroup,
                                              dateRange = dateRange) 

result_inObservation |>    
  filter(variable_name == "Number person-days") |>
  plotInObservation(colour = "sex", 
                    facet = "age_group")
#> `result_id` is not present in result.
#> `result_id` is not present in result.



result_inObservation |>
  filter(variable_name == "Number person-days") |>
  plotInObservation(
    colour = "sex",
    facet = "age_group"
  )
#> `result_id` is not present in result.
#> `result_id` is not present in result.

5.2 Observation periods

From the observation_table, we can extract information on the duration of observation periods, the time until the next observation period, and the number of subjects in each ordinal observation period (1st, 2nd, etc.). This can be done using the summariseObservationPeriod() function.

result_observationPeriod <- summariseObservationPeriod(cdm$observation_period,
  sex = sex,
  ageGroup = ageGroup,
  dateRange = dateRange
)

result_observationPeriod |>
  plotObservationPeriod(
    variableName = "Duration in days",
    plotType = "boxplot",
    colour = "sex",
    facet = "age_group"
  )

Finally, disconnect from the cdm

PatientProfiles::mockDisconnect(cdm = cdm)

The results of the characterisation using OmopSketch can be further explored through the ShinyApp at https://dpa-pde-oxford.shinyapps.io/OmopSketch-vignette/

Characterisation of OMOP CDM