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OpenSAFELY Anticoagulant Switching Research

This is the code and configuration for our paper, 'OpenSAFELY: impact of national guidance on switching from warfarin to direct oral anticoagulants (DOACs) in early phase of COVID-19 pandemic in England' which is published in BMJ OpenHeart here

  • The published version of our paper is here.
  • The main analysis is in a notebook here, including charts and tables, with additional more detailed outputs here. This was carried out in the very early stages of OpenSAFELY development during the pandemic and uses a deprecated method for accessing OpenSafely data involving SQL. See below for further details.
  • An additional notebook assessing the associated prescribing costs is here.
  • Raw model outputs from the "factors associated with switching" analysis, including charts, crosstabs, etc, are here
  • If you are interested in how we defined our code lists, look in the codelists folder and all codelists are available on OpenCodelists for re-use.
  • If you are interested in how we defined our variables (for the "factors associated" analysis), take a look at the study definition; this is written in python, but non-programmers should be able to understand what is going on there
  • Developers and epidemiologists interested in the code should review DEVELOPERS.md.
  • The preprint version of our paper is archived here.

How to view notebooks

Notebooks live in the notebooks/ folder (with an ipynb extension). You can most easily view them on nbviewer, if looking at them in Github does not work.

To do development work, you'll need to set up a local jupyter server and git repository - see notes below.

Getting started re-running these notebooks

This project uses reproducible, cross-platform analysis notebook, using Docker. It also includes:

  • configuration for jupytext, to support easier code review
  • cross-platform startup scripts
  • best practice folder structure and documentation

Loading SQL credentials when running notebooks

The main notebook here is fed from live SQL connection to either the dummy or real data held on OpenSAFELY. This could previously be run in dummy data, by launching the notebook using command py run.py in Windows, but the dummy data connection is no longer available. For developers re-running this within OpenSAFELY, you need to create a local file environ.txt in your local drive with SQL server details/credentials as follows: DBCONN="DRIVER={ODBC Driver 17 for SQL Server};SERVER=[servername];DATABASE=[dbname];UID=[your_UID];PWD=[your_pw]" (do not keep the square brackets). Add --env-file <path>/environ.txt to the docker run command (replacing <path> with the location of the environ.txt file.

The credentials are loaded into notebooks as follows:

dbconn = os.environ.get('DBCONN', None).strip('"')
def closing_connection(dbconn):
    cnxn = pyodbc.connect(dbconn)
    try:
        yield cnxn
    finally:
        cnxn.close()

About the OpenSAFELY framework

The OpenSAFELY framework is a new secure analytics platform for electronic health records research in the NHS.

Instead of requesting access for slices of patient data and transporting them elsewhere for analysis, the framework supports developing analytics against dummy data, and then running against the real data within the same infrastructure that the data is stored. Read more at OpenSAFELY.org.

The framework is under fast, active development to support rapid analytics relating to COVID19; we're currently seeking funding to make it easier for outside collaborators to work with our system. You can read our current roadmap here.