OmopSketch (version 1.0.0)

summariseClinicalRecords: Summarise an omop table from a cdm object

Description

You will obtain information related to the number of records, number of subjects, whether the records are in observation, number of present domains, number of present concepts, missing data and inconsistencies in start date and end date.

Usage

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

Value

A summarised_result object with the results.

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.

recordsPerPerson

Generates summary statistics for the number of records per person. Set to NULL if no summary statistics are required.

conceptSummary

Logical. If TRUE, includes summaries of concept-level information, including:

• Domain ID of standard concepts.

• Type concept ID.

• Standard vs non-standard concepts.

• Source vocabulary usage.

missingData

Logical. If TRUE, includes a summary of missing data for relevant fields.

quality

Logical. If TRUE, performs basic data quality checks, including:

• Percentage of records within the observation period.

• Number of records with end date before start date.

• Number of records with start date before the person's birth date.

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)).

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.

inObservation

Deprecated. Use quality = TRUE instead.

standardConcept

Deprecated. Use conceptSummary = TRUE instead.

sourceVocabulary

Deprecated. Use conceptSummary = TRUE instead.

domainId

Deprecated. Use conceptSummary = TRUE instead.

typeConcept

Deprecated. Use conceptSummary = TRUE instead.

Examples

# \donttest{
library(OmopSketch)
library(omock)

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

result <- summariseClinicalRecords(
  cdm = cdm,
  omopTableName = "condition_occurrence",
  recordsPerPerson = c("mean", "sd"),
  quality = TRUE,
  conceptSummary = TRUE,
  missingData = TRUE
)

tableClinicalRecords(result = result)

cdmDisconnect(cdm = cdm)
# }