Database diagnostics"

In PhenotypeR: Assess Study Cohorts Using a Common Data Model

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>", message = FALSE, warning = FALSE,
  fig.width = 7
)

library(CDMConnector)
if (Sys.getenv("EUNOMIA_DATA_FOLDER") == "") Sys.setenv("EUNOMIA_DATA_FOLDER" = tempdir())
if (!dir.exists(Sys.getenv("EUNOMIA_DATA_FOLDER"))) dir.create(Sys.getenv("EUNOMIA_DATA_FOLDER"))
if (!eunomiaIsAvailable()) downloadEunomiaData(datasetName = "synpuf-1k")

Introduction

In this example we're going to be using the Eunomia synthetic data.

library(CDMConnector)
library(CohortConstructor)
library(CodelistGenerator)
library(PhenotypeR)
library(dplyr)
library(ggplot2)

con <- DBI::dbConnect(duckdb::duckdb(), 
                      CDMConnector::eunomiaDir("synpuf-1k", "5.3"))
cdm <- CDMConnector::cdmFromCon(con = con, 
                                cdmName = "Eunomia Synpuf",
                                cdmSchema   = "main",
                                writeSchema = "main", 
                                achillesSchema = "main")

Database diagnostics

We have created our study cohort, but to inform analytic decisions and interpretation of results requires an understanding of the dataset from which it has been derived. The databaseDiagnostics() function will help us better understand a data source.

To run database diagnostics we just need to provide our cdm reference to the function.

db_diagnostics <- databaseDiagnostics(cdm)
db_diagnostics |> glimpse()

From our results we can create a table with a summary of metadata for the data source.

OmopSketch::tableOmopSnapshot(db_diagnostics)

In addition, we also can see a summary of individuals' observation periods. From this we can see if there are individuals with multiple, non-overlapping, observation periods and how long each observation period lasts on average.

OmopSketch::tableObservationPeriod(db_diagnostics)

PhenotypeR documentation built on April 3, 2025, 10:46 p.m.