How to make a data quality report

Edward Palmer

20th September 2019. Updated: 2019-11-22

The primary role of inspectEHR is to process the data inside CC-HIC in such a way as to make it ready to produce a data quality report.

First, install inspectEHR from github, or download the latest release directly.

# If you need inspectEHR
library(devtools)
install_github("CC-HIC/inspectEHR")

You will most likely be working with sqlite as the postgres instance is confined to the UCL IDHS.

library(inspectEHR); library(dbplyr)

# Synthetic database ships with inspectEHR
#db_path <- system.file("testdata/synthetic_db.sqlite3", package = "inspectEHR")
#output_path <- "./2019-09-reports"

Supply the report function with an output folder. Please note, you must have write access to the database for this function to work.

#report(sqlite_file = db_path, output_folder = output_path)

This will perform the following procedures:

1. Episodes will be characterised and verified/validated. This information will be stored inside the database in a new table called episode_verification.

2. Events will be verified/validated. This information will be stored inside the database in a new table called event_verification.

3. Summary information that is necessary for making a data quality report is exported as a .RData file to the output_folder.

4. Plots are pre-drawn and exported to the output_folder.

5. A data quality report is generated and exported to the output_folder.

6. A data quality score is generated and added to the report for each site.

Steps 3 and 4 are necessary as it allows for non identifying information to be exported from a secure location, without any risk of confidential information leak.