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# OpenSAFELY Service Restoration Observatory (SRO) Template
# Pathology Comparators Short Report

This is a template repository for making new OpenSAFELY SRO resarch projects.
This is a repository for work conducted on electronic health records in England via [OpenSAFELY](https://opensafely.org).

# About the OpenSAFELY framework

The OpenSAFELY framework is a secure analytics platform for
electronic health records research in the NHS.
Up to date details of the purpose and any published outputs from this project can be found [on OpenSAFELY](https://jobs.opensafely.org/repo/https%253A%252F%252Fgithub.com%252Fopensafely%252Fpathology-comparators-short-report
).

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](https://opensafely.org).
You can run this project via [Gitpod](https://gitpod.io) in a web browser by clicking on this badge: [![Gitpod ready-to-code](https://img.shields.io/badge/Gitpod-ready--to--code-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/pathology-comparators-short-report)

# OpenSAFELY SRO
# DISCLAIMER
This content has been made public to support the OpenSAFELY [open science and transparency principles](https://www.opensafely.org/about/#contributing-to-best-practice-around-open-science) and to support the sharing of re-usable code for other subsequent users.
However, please note this project may be a work in progress, contain unpublished or unverified work.
Therefore the contents of this repository MUST NOT be considered an accurate or valid representation of the study or its purpose.
This repository may reflect an incomplete or incorrect analysis with no further ongoing work.

The aim of the OpenSAFELY SRO is to describe trends and variation in
clinical activity codes to evaluate NHS service restoration during the
COVID-19 pandemic.
No clinical, policy or safety conclusions must be drawn from the contents of this repository.

Variation in ten key indicators of service disruption can be seen
[in this repo](https://github.com/opensafely/SRO-Measures).
# About the OpenSAFELY framework

This template provides the means to explore variation in any clinical
activity codes of interest.
The OpenSAFELY framework is a Trusted Research Environment (TRE) for electronic
health records research in the NHS, with a focus on public accountability and
research quality.

# How to use this template
Read more at [OpenSAFELY.org](https://opensafely.org).

1. Create a new repository in the OpenSAFELY organisation and select
sro-template as a template.
2. Create or select codelist on [OpenSAFELY Codelists](https://codelists.opensafely.org/).
Instructions on how to do this can be found [in this documentation](https://docs.opensafely.org/en/latest/codelist-creation/)
4. [Add the codelist to your project](https://docs.opensafely.org/en/latest/codelist-project/).
5. Make changes to the study variables in `config.py` in the analysis folder.
6. Update the `--index-date-range` in `project.yaml` to match the dates defined in step 4 in the `generate_study_population` and `generate_study_population_practice_count` actions.
7. This code can then be [run locally](https://docs.opensafely.org/en/latest/actions-pipelines/#running-your-code-locally) using the command `opensafely run run_all`
# Licences
As standard, research projects have a MIT license.
8. For instructions on how to run this code against real data [see this documentation](https://docs.opensafely.org/en/latest/job-server/).


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