Vignette explaining model

[athowes]

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

• A summary of the maths in Park et al. https://athowes.github.io/cfa-notes/delay-dist-math
• Issue 48: Ebola vignette #52 the Ebola vignette scoped to include spatial structure -- will be an example of playing with the model structure

[seabbs]

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]

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]

Yes makes sense