Data Quality Assessment in PEDSnet

Objective

This toolkit has been designed for conducting data quality assessments on clinical datasets modeled using the OMOP common data model. The toolkit includes a wide variety of data quality checks and a GitHub-based issue reporting mechanism. The toolkit is being routinely used by the PEDSnet CDRN.

Contents

• Data: the data quality catalog of checks, summaries of previous data cycle, and acceptable valuesets for various fields.
• Doc: documentation and set up instruction for the program
• Infrastructure: constants and internal helper functions
• Library: contains data quality checks and utility functions
• Main: single and multi-variable data quality scripts
• Resources: configuration file
• Tools: scripts for GitHub-based feedback generation

Required Downloads

JDK

Java version 5

If using OSX, download here

Note: version 5 must be installed, even if a higher version of Java is installed

R

R version 3.1.x or above, 64-bit (Comprehensive R Archive Network)

R Packages

install.packages(c("DBI","yaml","ggplot2","RJDBC","devtools","futile.logger","plyr","dplyr","dbplyr","lubridate"))

install.packages("RPostgres")
library(devtools)
install_github("ohdsi/SqlRender")
install_github("ohdsi/DatabaseConnector")
install_github("baileych/ohdsi-argos")

• Minimum Versions Required:
  • R: 3.2
  • DBI: 0.7
  • dplyr: 0.7
  • dbplyr: 1.2
  • readr: 1.1
  • rlang: 0.1.4
  • stringr: 1.2
• The RPostgres package is not required if PostgreSQL is not the target database type
• For Oracle users, the ROracle package should be installed

For troubleshooting with install_github("ohdsi/SqlRender"), please see here.

Note: if previously installed, run update.packages() to get the latest version of each library