R/databaseDiagnostics.R

In PhenotypeR: Assess Study Cohorts Using a Common Data Model

#' Database diagnostics
#'
#' @description
#' phenotypeR diagnostics on the cdm object.
#'
#' Diagnostics include:
#' * Summarise a cdm_reference object, creating a snapshot with the metadata of the cdm_reference object.
#' * Summarise the observation period table getting some overall statistics in a summarised_result object.
#'
#' @param cdm CDM reference
#'
#' @return A summarised result
#' @export
#'
#' @examples
#' \donttest{
#' library(PhenotypeR)
#'
#' cdm <- mockPhenotypeR()
#'
#' result <- databaseDiagnostics(cdm)
#'
#' CDMConnector::cdmDisconnect(cdm = cdm)
#' }
databaseDiagnostics <- function(cdm){

results <- list()
results[["snap"]] <- OmopSketch::summariseOmopSnapshot(cdm)
results[["obs_period"]] <- OmopSketch::summariseObservationPeriod(cdm$observation_period)
results <- results |>
  vctrs::list_drop_empty() |>
  omopgenerics::bind() |>
  omopgenerics::newSummarisedResult()

results

}