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The PEDSnet Data Quality Assessment Toolkit (OMOP CDM)
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Run_DQA.R

ReadMe.md

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", "tictoc", "testthat", "data.table"))

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

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