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Update readme #115

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Update readme #115

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b988db4
provide more details on what can be found on OpenSAFELY.org
LFISHER7 Apr 3, 2024
562756d
signpost the repo contents
LFISHER7 Apr 3, 2024
c6cf38c
Placeholder for codespaces instructions
LFISHER7 Apr 3, 2024
2b4dd14
Update the disclaimer
LFISHER7 Apr 3, 2024
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33 changes: 28 additions & 5 deletions README.md
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# ${GITHUB_REPOSITORY_NAME}
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This needs instructions for an analyst on what to do once they clone the template

E.g. When you first clone you should change {github-reposiroy-name} to x
You may want to link to other information about your project for example if you have standalone website
Once your study is published it is a good idea to update the repo with DOI for your paper so interested readrs can read more

Suggest these are written in italics - and first bit of advice is. Once you have tweaked the information you should delete the instructions in italics


[View on OpenSAFELY](https://jobs.opensafely.org/repo/https%253A%252F%252Fgithub.com%252Fopensafely%252F${GITHUB_REPOSITORY_NAME})
This is a repository for work conducted on electronic health records in England via [OpenSAFELY](https://opensafely.org).

Details of the purpose and any published outputs from this project can be found at the link above.
Up to date details of this project can be found by
[viewing this project on OpenSAFELY](https://jobs.opensafely.org/repo/https%253A%252F%252Fgithub.com%252Fopensafely%252F${GITHUB_REPOSITORY_NAME}). This includes:

* The project purpose
* Logs for all analyses run against real patient data
* Published outputs
* Links to any related reports/papers

# Contents

* Analysis code can be found in the [analysis folder](./analysis/).
* If you are interested in how we defined our variables and study population, take a look at the [dataset definition](analysis/dataset_definition.py); this is written in `python`, but non-programmers should be able to understand what is going on there.
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is non-programmers bit still true with ehrQL?

The ones I have found looked a bit harder than cohort extractor to understand

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It probably is - we may want to test that at some point!

* Codelists used to define these variables can be found in the [codelists folder](./codelists/).
* The project pipeline is specified in [`project.yaml`](./project.yaml).
* The [logs](./logs/) and [outputs](./outputs/) folders are empty. These are populated when a study is run on OpenSAFELY. Logs and published outputs for analyses run against real patient data are available on OpenSAFELY via the link above.

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I think it would be helpful to add details of which branch the final analysis for a publication was run on as this isn't always 'main' and is sometimes unclear from the jobs site

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I agree....not sure it fits well in a template such as this? How would you add it?

# Running this repository against dummy data

[//]: # (TODO: Add instructions for codespaces)

For your interest — to evaluate the code only, without any use of any actual patient data — you can execute the code for this project against randomly generated dummy patient data via....

# DISCLAIMER

This repository contains technical content. It is not a research publication. It 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 of the OpenSAFELY platform.
This repository must be interpreted in context: it may reflect the final codebase for a published project; or it may be an incomplete project; or have other shortcomings to be expected of a technical working document shared during development of the work. Therefore the contents of this repository may not be an accurate or valid representation of the study or its purpose. For this, you should view the project on OpenSAFELY using the link provided above.

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 content has ONLY 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.
No clinical, policy or safety conclusions must be drawn from the contents of this repository.


# About the OpenSAFELY framework

The OpenSAFELY framework is a Trusted Research Environment (TRE) for electronic
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