# Characterisation of OMOP CDM

# 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
--- | ---
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
--- | --- | --- | ---
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/