summariseClinicalRecords: Summarise an omop table from a cdm object. You will obtain...

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

Summarise an omop table from a cdm object. You will obtain information related to the number of records, number of subjects, whether the records are in observation, number of present domains and number of present concepts.

Description

Summarise an omop table from a cdm object. You will obtain information related to the number of records, number of subjects, whether the records are in observation, number of present domains and number of present concepts.

Usage

summariseClinicalRecords(
  cdm,
  omopTableName,
  recordsPerPerson = c("mean", "sd", "median", "q25", "q75", "min", "max"),
  inObservation = TRUE,
  standardConcept = TRUE,
  sourceVocabulary = TRUE,
  domainId = TRUE,
  typeConcept = TRUE,
  sex = FALSE,
  ageGroup = NULL,
  dateRange = NULL
)

Arguments

cdm	A cdm_reference object.
omopTableName	A character vector of the names of the tables to summarise in the cdm object.
recordsPerPerson	Generates summary statistics for the number of records per person. Set to NULL if no summary statistics are required.
inObservation	Boolean variable. Whether to include the percentage of records in observation.
standardConcept	Boolean variable. Whether to summarise standard concept information.
sourceVocabulary	Boolean variable. Whether to summarise source vocabulary information.
domainId	Boolean variable. Whether to summarise domain id of standard concept id information.
typeConcept	Boolean variable. Whether to summarise type concept id field information.
sex	Boolean variable. Whether to stratify by sex (TRUE) or not (FALSE).
ageGroup	A list of age groups to stratify results by.
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.

Value

A summarised_result object.

Examples

cdm <- mockOmopSketch()

summarisedResult <- summariseClinicalRecords(
  cdm = cdm,
  omopTableName = "condition_occurrence",
  recordsPerPerson = c("mean", "sd"),
  inObservation = TRUE,
  standardConcept = TRUE,
  sourceVocabulary = TRUE,
  domainId = TRUE,
  typeConcept = TRUE
)

summarisedResult

PatientProfiles::mockDisconnect(cdm = cdm)

OmopSketch documentation built on June 8, 2025, 1:36 p.m.