Extraction of CPRD additional clinical data using R [version 1; peer review: awaiting peer review]

Abstract

The Clinical Practice Research Datalink is a nation-wide database of primary healthcare data records in England (UK) linked to several health services. A visit to a health practitioner can result in the digital storing of diagnostic and prescription therapeutic information. Access to patient primary care and linked service data depends on the research in mind; however, typically several flat files that describe patient interactions with a health practitioner are delivered. Some of these files will describe additional data such as the result of medical tests and patient lifestyles, denoted collectively into entity values. This data is used to supplement the medical notes recorded by a general practitioner. We have made available a set of R scripts that reads the clinical flat files, additional clinical flat files and entity values, and returns patient clinical data linked with the requested additional data. We have also included medcode descriptions associated with several entities along with instruction of how to extend the code for additional entities. The code is free to download under the MIT license: https://github.com/acnash/CPRD_Additional_Clinical