summariseConceptIdCounts: Summarise concept use in patient-level data

In OmopSketch: Characterise Tables of an OMOP Common Data Model Instance

Summarise concept use in patient-level data

Description

Only concepts recorded during observation period are counted.

Usage

summariseConceptIdCounts(
  cdm,
  omopTableName,
  countBy = "record",
  interval = "overall",
  sex = FALSE,
  ageGroup = NULL,
  inObservation = FALSE,
  sample = NULL,
  dateRange = NULL,
  year = lifecycle::deprecated()
)

Arguments

cdm	A cdm_reference object. Use CDMConnector to create a reference to a database or omock to create a reference to synthetic data.
omopTableName	A character vector of the names of the tables to summarise in the cdm object. Run clinicalTables() to check the available options.
countBy	Either "record" for record-level counts or "person" for person-level counts.
interval	Time interval to stratify by. It can either be "years", "quarters", "months" or "overall".
sex	Logical; whether to stratify results by sex (TRUE) or not (FALSE).
ageGroup	A list of age groups to stratify the results by. Each element represents a specific age range. You can give them specific names, e.g. ageGroup = list(children = c(0, 17), adult = c(18, Inf)).
inObservation	Logical. If TRUE, the results are stratified to indicate whether each record occurs within an observation period.
sample	Either an integer or a character string. If an integer (n > 0), the function will first sample n distinct person_ids from the person table and then subset the input tables to those subjects. If a character string, it must be the name of a cohort in the cdm; in this case, the input tables are subset to subjects (subject_id) belonging to that cohort. Use NULL to disable subsetting (default value).
dateRange	A vector of two dates defining the desired study period. Only the start_date column of the OMOP table is checked to ensure it falls within this range. If dateRange is NULL, no restriction is applied.
year	deprecated.

Value

A summarised_result object with the results.

Examples

library(OmopSketch)
library(omock)

cdm <- mockCdmFromDataset(datasetName = "GiBleed", source = "duckdb")

result <- summariseConceptIdCounts(
  cdm = cdm,
  omopTableName = "condition_occurrence",
  countBy = c("record", "person"),
  sex = TRUE
)

tableConceptIdCounts(result = result)

cdmDisconnect(cdm = cdm)

OmopSketch documentation built on Aug. 27, 2026, 5:07 p.m.