From b988db41349a4a69efe446978834e58c931da252 Mon Sep 17 00:00:00 2001 From: Louis Fisher Date: Wed, 3 Apr 2024 11:15:18 +0100 Subject: [PATCH 1/4] provide more details on what can be found on OpenSAFELY.org --- README.md | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index db682a6..71377bf 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,14 @@ # ${GITHUB_REPOSITORY_NAME} -[View on OpenSAFELY](https://jobs.opensafely.org/repo/https%253A%252F%252Fgithub.com%252Fopensafely%252F${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 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. From 562756d52749c81f43176b737a4be7c5bf428cd6 Mon Sep 17 00:00:00 2001 From: Louis Fisher Date: Wed, 3 Apr 2024 11:15:59 +0100 Subject: [PATCH 2/4] signpost the repo contents --- README.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/README.md b/README.md index 71377bf..536782a 100644 --- a/README.md +++ b/README.md @@ -10,6 +10,16 @@ Up to date details of this project can be found by * 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. +* 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. + + + 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. From c6cf38cb3755d2fdf02caba5cdad6e4c9ed3e61e Mon Sep 17 00:00:00 2001 From: Louis Fisher Date: Wed, 3 Apr 2024 11:21:11 +0100 Subject: [PATCH 3/4] Placeholder for codespaces instructions --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 536782a..fe1aee2 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,11 @@ Up to date details of this project can be found by * 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. +# 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.... 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. From 2b4dd1429df40cd70cd9713d5ddb2ed19ba35a7e Mon Sep 17 00:00:00 2001 From: Louis Fisher Date: Wed, 3 Apr 2024 11:25:08 +0100 Subject: [PATCH 4/4] Update the disclaimer - Give it a title - Remove "ONLY". from the reason for making public. That's not the sole reason. - The repository may or may not be a valid representation of the study --- README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index fe1aee2..fc5d281 100644 --- a/README.md +++ b/README.md @@ -24,11 +24,14 @@ Up to date details of this project can be found by 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.... -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. +# 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. + 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