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Merge pull request #1635 from opensafely/alschaffer-patch-1
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Remove references to cohortextractor and study def
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alschaffer authored Oct 9, 2024
2 parents 54f5d99 + ff362a9 commit fabde52
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2 changes: 1 addition & 1 deletion docs/codelist-creation.md
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Expand Up @@ -107,7 +107,7 @@ Go to the codelist issue in the [codelist repo](https://github.com/opensafely/co
This issue serves as documentation of the choices made that determined the final codelist. The issue can be
re-opened if revisions are required.

## Import the codelist for use in your study definition
## Import the codelist for use in your dataset definition

Once the codelist is in [OpenCodelists](https://www.opencodelists.org), you can retrieve it for use in
your research repo. Follow the [adding codelists to project instructions](codelist-project.md) if you're not sure how to do this.
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4 changes: 2 additions & 2 deletions docs/codelist-intro.md
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Expand Up @@ -19,8 +19,8 @@ that to find all the patients with Type 1 diabetes, you may have to search for
We built a system for building, reviewing and maintaining codelists at
[OpenCodelists](https://www.opencodelists.org/).
We've made an introductory video to help explain OpenCodelists in more detail. Codelists
that are hosted on this website can be used directly in the Study Definition. This means
there is no need to download or alter these codelists in the study definition, and
that are hosted on this website can be used directly in the Dataset Definition. This means
there is no need to download or alter these codelists in the dataset definition, and
they can be reused.

<div class="video-wrapper">
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2 changes: 1 addition & 1 deletion docs/how-to-get-help.md
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Expand Up @@ -66,7 +66,7 @@ To search the OpenSAFELY GitHub organisation for code:
4. Select "Code" to find any matches within previous code (or sometimes "Issues" may help).

It can be helpful to use the option to filter the results by language.
For example, restricting to Python might help you find study definition files.
For example, restricting to Python might help you find dataset definition files.

## Bug reports and feature requests

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2 changes: 1 addition & 1 deletion docs/repositories.md
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Expand Up @@ -74,7 +74,7 @@ This is an important folder, used internally by GitHub, that you can happily ign

By convention, this folder contains:

* Any `study_definition.py` script that defines the study definition
* Any `dataset_definition.py` script that defines the dataset definition
* Analysis scripts in R, Python or Stata

### `codelists/`
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6 changes: 3 additions & 3 deletions docs/workflow.md
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Expand Up @@ -10,10 +10,10 @@ This repo will contain all the code relating to your project, and a history of i
2. **Write a [dataset definition](/ehrql/)** that specifies what data you want to extract from the database:
- specify the patient population (dataset rows) and variables (dataset columns)
- specify the expected distributions of these variables for use in dummy data
- specify (or create) the [codelists](codelist-intro.md) required by the study definition, hosted by [OpenCodelists](https://www.opencodelists.org), and import them to the repo.
- specify (or create) the [codelists](codelist-intro.md) required by the dataset definition, hosted by [OpenCodelists](https://www.opencodelists.org), and import them to the repo.
3. **Generate [dummy data](/ehrql/how-to/dummy-data)** based on the dataset definition, for writing and testing code.
4. **Develop analysis scripts** using the dummy data in R, Stata, or Python. This will include:
- importing and processing the dataset(s) created by the cohort extractor
- importing and processing the dataset(s) created by the dataset definition
- importing any other external files needed for analysis
- generating analysis outputs like tables and figures
- generating log files to debug the scripts when they run on the real data.
Expand All @@ -29,4 +29,4 @@ It is possible to automatically test that the analytical pipeline defined in ste
This pipeline is also [automatically tested](actions-pipelines.md#running-your-code-with-github-actions) against dummy data every time a new version of the study repository is saved ("pushed") to GitHub.

As well as your own Python, R or Stata scripts, other non-standard actions are available.
For example, it's possible to run a matching routine that extracts a matched control population to the population defined in the study definition, without having to extract all candidate matches into a dataset first.
For example, it's possible to run a matching routine that extracts a matched control population to the population defined in the dataset definition, without having to extract all candidate matches into a dataset first.

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