Modularising code and adding measures framework #3
+105
−99
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Creating a separate module will make it easier to share this code across different dataset definitions that we might be working on for this project. This also fixes the path to themethylphenidate_codelist, before the path was pointing to the same NHSD Primary Care Refset for ADHD.
The main change here is to take out looping through the years, there is another framework in ehrQL, measures, that does this for us. I also switched the naming of patient attributes to have the prefix has (instead of had), we often use this naming convention for our studies. To shorten the code I also removed some of the variables that were only used to define the population and explicitly mention them only inside the define_population function.
This is using the ehrQL measures framework to run the same query for multiple time intervals. I tried to match your original 7 years, although I'd recommend to reduce this to 3 years for the first run to keep the run times short.
|
All the changes looks good |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
The initial code looked like a great start! Here the main changes I tried to implement in this PR.
Some other things I noticed or added:
Currently you're only looking at whether someone has a coded ADHD event. There is also Attention Deficit Hyperactivity Disorder in remission Codelist that you could look at. For example, rule 2 of the
LDOB091indicator (see Learning Disabilities data 2019-2020 business rules version 3.0) is defined as:I removed your analysis script
report.pyfor now as I wasnt sure the content was still needed. We can explore in our next session what analysis would be good to run as a first testI categoried age into age bands so that this can be used as a
group_byin the measures for the prevalence following this example in our docs.My main aim with these changes was to make it easier for us to execute code in the secure environment soon and also to introduce ehrQL concepts you hadn't used before. See what you think and let's discuss later this week.