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Vignette explaining model #64

Closed
Tracked by #206
athowes opened this issue May 28, 2024 · 9 comments · Fixed by #514
Closed
Tracked by #206

Vignette explaining model #64

athowes opened this issue May 28, 2024 · 9 comments · Fixed by #514
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@parksw3
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documentation Improvements or additions to documentation enhancement New feature or request medium Nice to have for next release

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@athowes
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athowes commented May 28, 2024

Goal

This issue is for creation of a vignette going into greater detail about the model latent_truncation_censoring_adjusted_delay.

Context

The epidist package focuses on a particular statistical model. How the model works is quite complex, and likely to be challenging to understand. However, better understanding of the model is likely to lead to better use of the package. Furthermore, there is scope for the model structure to be altered in specific ways within the remit of epidst by using brms formula interface. Users looking to make use of this functionality will likely need some kind of tutorial, and will particularly benefit from a good understanding of the model structure and implementation.

Required features

  • An .Rmd explaining the latent_truncation_censoring_adjusted_delay statistical model
  • To include:
    • Its generative form
    • An explanation of how it accounts for censoring and right truncation
    • How it is implemented in the package
    • What the extra arguments of the function do, if you'd like to change them
    • Which parts of the arguments we would imagine you might want to change and the potential use-cases
    • The limitations of the model (ways it's not ideal)

Related documents
@athowes athowes added documentation Improvements or additions to documentation enhancement New feature or request labels May 28, 2024
@athowes athowes self-assigned this May 28, 2024
@seabbs
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seabbs commented May 28, 2024 •
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Yes good idea. I see this as part of scoping documentation (i.e do now/soon) vs help for a user (i.e do later/never).

Which parts of the arguments we would imagine you might want to change and the potential use-cases
The limitations of the model (ways it's not ideal)

These parts of the exercise seem particularly useful from a design perspective.

A summary of the maths in Park et al

There is also a description in the Ward et al. paper that Park et a. cites but I find the former easier to follow/more correct

@athowes athowes mentioned this issue May 28, 2024
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@athowes
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athowes commented May 31, 2024

At the moment I think working this is a priority for me as I'm finding I'm blocked on things like "implement different delay distribution" and "implement stratified (space/sex) example" by my limited understanding of the model. I am also finding this to be important scoping documentation as Sam suggests, including for things like post-processing. More broadly I think it's quite important for me to understand where we are with brms, how much we can rely on it, how fragile it is, ...

@seabbs
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seabbs commented May 31, 2024

Yes makes sense

@athowes athowes mentioned this issue Jul 30, 2024
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@athowes athowes added the medium Nice to have for next release label Aug 8, 2024
@athowes athowes removed their assignment Aug 8, 2024
@athowes athowes mentioned this issue Sep 16, 2024
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@athowes
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athowes commented Oct 1, 2024

Closed branch #330 and tentatively assigned to @parksw3 for 1-2 weeks.

@athowes
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athowes commented Oct 21, 2024

@parksw3 do you think this is something you'll have a chance to have a go at this week?

@parksw3
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parksw3 commented Oct 21, 2024

Yes, I'll look at it today. Sorry for the delay. Had to prepare a presentation for today and didn't get a chance to get to this.

@parksw3
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parksw3 commented Oct 22, 2024

I've made some progress. Wasn't sure if I should make a pull request yet or not so commenting here for now. Let's discuss tomorrow and will do more work. I also realized that we don't need latent variables for the secondary events and not sure how none of us noticed this earlier????

@seabbs
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seabbs commented Oct 22, 2024

Nice. Could throw up a draft PR for @athowes to take a gander at.

I also realized that we don't need latent variables for the secondary events and not sure how none of us noticed this earlier????

LOL. I feel like we noticed the distribution didn't matter and then took no further action...

@seabbs
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seabbs commented Oct 22, 2024

@SamuelBrand1 fancy acting as a notation reviewer for this as @parksw3 did on your write up?

@athowes athowes mentioned this issue Oct 22, 2024
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@parksw3 parksw3 mentioned this issue Jan 28, 2025
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seabbs added a commit that referenced this issue Feb 18, 2025
@parksw3 @seabbs
Issue #64: Add vignette explaining models (#514)
f5eead1 
* vignette in a new branch

* tweak

* Add a news entry

* add some fluff text, grammar, linting

* remove commented out text

* Update model.Rmd

* run precommit locally

* Update model.Rmd

* Update model.Rmd

* Update lint-changed-files.yaml

---------

Co-authored-by: Sam Abbott <[email protected]>
Co-authored-by: Sam Abbott <[email protected]>
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